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PBS Professional User's Guide

1. PBS O HOME Value of HOME from submission environment PBS O HOST The host name on which the qsub command was executed PBS O LANG Value of LANG from submission environment PBS _O LOGNAME Value of LOGNAME from submission environment PBS O MAIL Value of MAIL from submission environment PBS O PATH Value of PATH from submission environment PBS O QUEUE The original queue name to which the job was submitted 160 Appendix A PBS Environment Variables Table 23 PBS Environment Variables Variable Meaning PBS O SHELL Value of SHELL from submission environment PBS _O_ SYSTEM The operating system name where qsub was executed PBS O TZ Value of TZ from submission environment PBS _O WORKDIR The absolute path of directory where gsub was executed PBS QUEUE The name of the queue from which the job is executed PBS TASKNUM The task process number for the job on this node TMPDIR The job specific temporary directory for this job PBS Professional 7 User s Guide Appendix B Converting From NQS to PBS 161 For those converting to PBS from NQS or NQE PBS includes a utility called nqgs2pbs which converts an existing NQS job script so that it will work with PBS In fact the resulting script will be valid to both NQS and PBS The existing script is copied and PBS directives PBS are inserted prior to each NQS directive either OQSUB or
2. W stagein Documents and Settings user inputfile unix host a b file will copy the input file a b file from unix host over to Documents and Settings user inputfile on the Windows host before the job is sent to that host Important If you re staging in or staging out a directory to the Windows host the destination pathname must be an existing directory 8 6 2 Stage in Failure When stage in fails the job is placed in a 30 minute wait to allow the user time to fix the problem Typically this is a missing file or a network outage Email is sent to the job owner when the problem is detected Once the problem has been resolved the job owner or the Operator may remove the wait by resetting the time after which the job is eligible to be run via the a option to qalter 8 7 The pbsdsh Command The pbsdsh command allows you to distribute and execute a task on each of the nodes assigned to your job pbsdsh uses the PBS Task Manager API see tm 3 to distribute the program on the allocated nodes Important The pbsdsh command is not available under Windows Usage of the pbsdsh command is 118 Chapter 8 Advanced PBS Features pbsdsh c N The available options are C n N o s v program args The program is spawned on the first N nodes allocated If the value of N is greater than the number of nodes it will wrap around running multiple copies on the nodes This option is mutually exclusive w
3. paraman Array Array Range Array Index qstat Array Array Range Array Index qdel Array amp Array Range where Array Index Array REMAINING Array REMAINING qalter Array erroneous erroneous qorder Array erroneous erroneous qmove Array amp erroneous erroneous Array QUEUED qhold Array amp erroneous erroneous Array QUEUED qrls Array amp erroneous erroneous Array QUEUED qrerun Array RUNNING amp Array Range where Array Index Array DONE Array RUNNING qrun erroneous Array Range where Array Index Array QUEUED tracejob erroneous erroneous Array Index qsig Array RUNNING Array Range where Array Index Atrray RUNNING qmsg erroneous erroneous erroneous PBS Professional 7 145 User s Guide 9 7 2 qstat Status of a Job Array The qstat command is used to query the status of a Job Array The default output is to list the Job Array in a single line showing the Job Array Identifier Options can be combined To show the state of all running subjobs use t r To show the state only of subjobs not job arrays use t J Table 21 Job Array and Subjob Options to qstat Option Result t Shows state of job array object and subjobs Will also show state of jobs J Shows state only of job arrays p Prints the default display with column for Percentage Completed For a job array this is the number of subjobs completed or deleted divided by the total number of subjob
4. The process of stopping a running executing job and putting it back into the queued Q state This includes placing the job as close as possible to its former position in that queue If a PBS job can be terminated and its execution restarted from the beginning without harmful side effects the job is rerunnable This process refers to moving a file or files to the execution host prior to the PBS job beginning execution This process refers to moving a file or files off of the execution host after the PBS job completes execution Each system user is identified by a unique character string the user name and by a unique number the user id Task is a POSIX session started by MOM on behalf of a job Privilege to access system resources and services is typically established by the user id which is a numeric identifier uniquely assigned to each user see User 14 Chapter 2 Concepts and Terms Job Array A collection of jobs submitted under a single job id These jobs can be modified queried and displayed as a set PBS Professional 7 15 User s Guide Chapter 3 Getting Started With PBS This chapter introduces the user to the Portable Batch System PBS It describes new user level features in this release explains the different user interfaces introduces the concept of a PBS job and shows how to set up your environment for running batch jobs with PBS 3 1 New Features in PBS Professional 7 PBS Prof
5. qrls h u 54 qstat a 54 Queue Jobname Sess NDS 54 south barry workq engine If you attempted to release a hold on a job which is not on hold the request will be ignored If you use the qr 1s command to release a hold on a job that had been previously running and subsequently checkpointed the hold will be released and the job will return to the queued Q state and be eligible to be scheduled to run when resources come avail able To hold or release a job using xpbs first select the job s of interest then click the hold or release button 7 3 Deleting Jobs PBS provides the qde1 command for deleting jobs from the system The qde1 command deletes jobs in the order in which their job identifiers are presented to the command A job that has been deleted is no longer subject to management by PBS A batch job may be deleted by its owner a PBS operator or a PBS administrator Example qdel 51 qdel 1234 server PBS Professional 7 103 User s Guide Job array identifiers must be enclosed in double quotes To delete a job using xpbs first select the job s of interest then click the delete button 7 4 Sending Messages to Jobs To send a message to a job is to write a message string into one or more output files of the job Typically this is done to leave an informative message in the output of the job Such messages can be written using the qmsg command Important A message can only be sent to running jobs
6. 133 User s Guide By optional we mean that the customer may acquire a copy of PBS Professional with the standard security and authentication module replaced with the KRB5 module To use a forwardable renewable Kerberos V5 TGT specify the W cred krb5 option to qsub This will cause gsub to check the user s credential cache for a valid forward able renewable TGT which it will send to the Server and then eventually to the execution MOM While it s at the Server and the MOM this TGT will be periodically refreshed until either the job finishes or the maximum refresh time on the TGT is exceeded whichever comes first If the maximum refresh time on the TGT is exceeded no KRBS services will be available to the job even though it will continue to run 134 Chapter 8 Advanced PBS Features PBS Professional 7 135 User s Guide Chapter 9 Job Arrays This chapter describes job arrays and their use A job array represents a collection of jobs which only differ by a single index parameter The purpose of a job array is twofold It offers the user a mechanism for grouping related work making it possible to submit query modify and display the set as a single unit Second it offers a way to possibly improve performance because the batch system can use certain known aspects of the col lection for speedup 9 1 Definitions Subjob Individual entity within a job array e g 1234 7 where 1234 is the job array itself and 7 is t
7. The o path and e path options to qsub allows you to specify the name of the files to which the standard output stdout and the standard error stderr file streams should be written The path argument is of the form hostname path name where hostname is the name of a host to which the file will be returned and path_name is the path name on that host You may specify relative or absolute paths If you specify only a file name it is assumed to be relative to your home directory The following examples illus trate these various options PBS o u userl myOutputFile PBS e u userl myErrorFile PBS Professional 7 47 User s Guide myOutputFile my job u user1l myOutputFile my job myWorkstation u userl myOutputFile my job myErrorFile my _ job u userl myErrorFile my job myWorkstation u userl myErrorFile my job Note that if the PBS client commands are used on a Windows host then special characters like spaces backslashes and colons can be used in command line arguments such as for specifying pathnames as well as drive letter specifications The following are allowed qsub o temp my out job scr qsub e host e Documents and Settings user Desktop output The error output of the above job is to be copied onto the e drive on host using the path Documents and Settings user Desktop output The quote marks are required when arguments to qsub contain spaces 4 10 3 Exporting environment
8. The usage syntax of the qmsg command is qmsg E O message string job identifier Example qmsg O output file message 54 qmsg O output file message 1234 server Job array identifiers must be enclosed in double quotes The E option writes the message into the error file of the specified job s The O option writes the message into the output file of the specified job s If neither option is specified the message will be written to the error file of the job The first operand message string is the message to be written If the string contains blanks the string must be quoted If the final character of the string is not a newline a newline character will be added when written to the job s file All remaining operands are job identifiers which specify the jobs to receive the message string For example qmsg E hello to my error e file 55 qmsg O hello to my output o file 55 qmsg this too will go to my error e file 55 To send a message to a job using xpbs first select the job s of interest then click the 104 Chapter 7 Working With PBS Jobs msg button Doing so will launch the Send Message to Job dialog box From this window you may enter the message you wish to send and indicate whether it should be written to the standard output or the standard error file of the job Click the Send Message button to complete the process 7 5 Sending Signals to Jobs The qsig com
9. in resource requests and job placement See the qsub 1B qalter 1B and pbs_rsub 1B manual pages 3 2 7 The qstat Command The exec host attribute displayed via qstat will be expanded to show the allocated resources on each node 3 2 8 Warning About Conversion from nodespec When a nodespec is converted into a select statement the job will have the environment variables NCPUS and OMP NUM THREADS set to the value of ncpus in the first piece of the nodespec This may produce incompatibilities with prior versions when a complex node specification using different values of ncpus and ppn in different pieces is converted For detailed information on conversion from 1 nodes nodespec to 1 select and 1 place see the PBS Professional User s Guide 3 2 9 Node Grouping Changes If the complex wide node grouping feature is enabled i e the server attribute node_group_ enable True then jobs that request place scatter or place free will be grouped within a node group If however the job requests placement other than scatter chunks will be allocated as if place scatter were specified and a message entered into the scheduler s log If a job requests grouping by a resource i e place group resource then the chunks are placed as requested and complex wide node grouping is ignored If scatter is not also requested the scheduler will log a message If a job is to use node grouping but the required number of nodes is not defined in any one g
10. s Guide 66 99 e notify when the reservation period ends 66 99 c notify when the reservation is confirmed Specifies the list of users to whom the Server will attempt to send a mail message whenever the reservation transitions to one of the mail states specified in the m option Default reservation s owner Specifies a comma separated list of entries of the form user host Entries on this list are used by the Server in conjunc tion with an ordered set of rules to associate a user name with the reservation Specifies a comma separated list of entries of the form group host names Entries on this list are used by the Server in conjunction with an ordered set of rules to associate a group name with the reservation Specifies a comma separated list of entries of the form user host These are the users who are allowed or denied permission to submit jobs to the queue associated with this reservation This list becomes the acl_users attribute for the reservation s queue Specifies a comma separated list of entries of the form group_name Entries on this list help control the enqueu ing of jobs into the reservation s queue Jobs owned by members belonging to these groups are either allowed or denied entry into the queue Any group on the list is to be interpreted in the con text of the Server s host not the context of the host from which qsub was submitted This list
11. If the month portion MM is not specified it defaults to the current month provided that the specified day DD is in the future Otherwise the month will be set to next month Similar comments apply to the two other optional left hand components Specifies the reservation end time See the R flag for a description of the datetime string If start time and duration are the only times specified the end time value is calculated Specifies reservation duration Timestring can either be expressed in seconds of walltime or it can be expressed as a colon delimited timestring e g HH MM SS or MM SS If the start time and end time are the only times specified this dura tion time is calculated Specifies the destination server to which to submit the reserva tion The default server is used if this option is not specified Specifies whether mail is sent to user_list and when The argu ment mail point is a string It can be either n for no mail or a string composed of any combination of a b e or c efault is ac Must be enclo i u u Default is ac Must b losed in double quotes 66 99 n do not send mail 66 99 a notify if the reservation is terminated for any reason b notify when the reservation period begins M mail list u user list g group list U auth user list G auth group list H auth host list PBS Professional 7 121 User
12. To move jobs between queues or between Servers using xpbs select the job s of inter est and then click the move button Doing so will launch the Move Job dialog box from which you can select the queue and or Server to which you want the job s moved The qmove command can only be used with job array objects not with subjobs or ranges Job arrays can only be moved from one server to another if they are in the Q H or W states and only if there are no running subjobs The state of the job array object is pre served in the move The job array will run to completion on the new server As with jobs a qstat on the server from which the job array was moved will not show the job array A qstat on the job array object will be redirected to the new server Note The subjob accounting records will be split between the two servers 7 8 Converting a Job into a Reservation Job The pbs_rsub command can be used to convert a normal job into a reservation job that will run as soon as possible PBS creates a reservation queue and a reservation and moves the job into the queue Other jobs can also be moved into that queue via qmove 1B or submitted to that queue via qsub 1B The format for converting a normal job into a reservation job is pbs_rsub 1 walltime time W qmove job_ identifier 108 Chapter 7 Working With PBS Jobs Example pbs_rsub W qmove 54 pbs_rsub W qmove 1234 server The R and E options to pb
13. and name it newjob the user could type 32 Chapter 4 Submitting a PBS Job qsub N newjob my_job 4 2 1 2 Submitting a Simple Job Jobs can also be submitted without specifying values for attributes The simplest way to submit a job is to type qsub myjobscript lt ret gt Here the user has simply told PBS to run myapplication 4 2 1 3 Jobs Without a Job Script It is possible to submit a job to PBS without first creating a job script file If you run the qsub command with the resource requests on the command line and then press enter without naming a job file PBS will read input from the keyboard This is often referred to as a here document You can direct qsub to stop reading input and submit the job by typing on a line by itself a control d UNIX or control z then enter Win dows Note that under UNIX if you enter a control c while qsub is reading input qsub will terminate the process and the job will not be submitted Under Windows however often the control c sequence will depending on the command prompt used cause qsub to submit the job to PBS In such case a control break sequence will usually terminate the gsub command qsub lt ret gt directives tasks ctrI D 4 3 Requesting Resources Resources are used in a new way They can be requested as job wide resources or in chunks A chunk is a set of resources that are allocated as a unit to a job A chunk is also the smallest set of
14. done S Queue 1235 host ArrayExample userl 40 B workgq 1235 1 host ArrayExample userl 100 X workq 1235 2 host ArrayExample userl 100 X workq 1235 3 host ArrayExample userl R workgq 1235 4 host ArrayExample userl R workgq 1235 5 host ArrayExample userl Q workg 1236 host JobExample userl Q workgq Now if we wait until only the last subjob is still running qstat rt host Req d Req d Elap Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time 1235 5 host userl workq ArrayExamp 3048 1 R 00 00 1236 host userl workq JobExample 3042 SH 1 R 00 00 qstat Jrt host Req d Req d Elap Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time 1235 5 host userl workq ArrayExamp 048 1 R 00 01 148 Chapter 9 Job Arrays 9 7 3 qdel Deleting a Job Array The qdel command will take a job array identifier subjob identifier or job array range The indicated object s are deleted including any currently running subjobs Running subjobs are treated like running jobs Subjobs not running will be deleted and never run 9 7 4 qalter Altering a Job Array The qalter command can only be used on a job array object not on subjobs or ranges Job array attributes are the same as for jobs 9 7 5 qorder Ordering Job Arrays in the Queue The gorder command can only be used with job array objects not on subjobs or ranges This will change the queue order of the job array in association with othe
15. it is necessary to process the PBS_NODEFILE to eliminate duplicate entries 10 2 MPI Jobs with PBS For most implementations of the Message Passing Interface MPI you would use the mpirun command to launch your application For example here is a sample PBS script for an MPI job PBS 1 select arch linux mpirun np 32 machinefile PBS NODEFILE a out 10 2 1 MPICH Jobs With PBS For users of PBS with MPICH on Linux the mpirun command has been changed slightly The syntax and arguments are the same except for one option which should not be set by the user machinefile file PBS supplies the machinefile If the user tries to specify it PBS will print a warning that it is replacing the machinefile PBS Professional 7 155 User s Guide PBS 1 select arch linux mpirun a out Under Windows the localroot option to MPICH s mpirun command may be needed in order to allow the job s processes to run more efficiently 10 2 2 MPI Jobs Using AIX POE For PBS users of AIX machines running IBM s Parallel Operating Environment or POE the poe command has been changed slightly The syntax and arguments are the same except for the following procs option If this is not set the number of task processes is set by PBS If the user sets this value to a number higher than that set by PBS PBS prints a warning that it is assigning multiple processes per pro cessor hostfile option PBS supplies the hos
16. limit of 2 If a select directive is supplied and the corresponding job limits are not specified then job limits are created from the directive for each consumable resource For example qsub lselect 2 ncpus 3 mem 4gb arch linux will have the following job limits set ncpus 6 and mem 8gb 4 4 Placing Jobs on Nodes PBS Professional 7 37 User s Guide The place statement controls how the job is placed on the nodes from which resources may be allocated for the job It may be used with or without the select statement The place statement has this form place modifier modifier where modifier is any combination of group excl and or one of free pack scatter Table 3 Placement Modifiers Modifier Meaning free Place job on any node pack All chunks will be taken from one host exclusive Only this job uses the allocable subunits chosen scatter Only one chunk will be taken from any node group Chunks will be grouped according to a resource name The resource name request will look like this place group resource_name Grouping by resource name will override node_group_ key 4 5 How PBS Parses a Job Script The qsub command scans the lines of the script file for directives Scanning will continue until the first executable line that is a line that is not blank not a directive line nor a line whose first non white space character is If directives occur on subsequent lines they
17. the direction of travel is local file t remote host remote file Note that all relative paths are relative to the user s home directory on the respective hosts The following example shows how to stage in a file named grid dat located in the directory u user1 of the computer called server The staged in file is requested to be placed relative to the users home directory under the name of dat1 Note that the example uses UNIX style path separators PBS W stagein datl server u user1 grid dat Note that under Windows special characters such as spaces backslashes colons and drive letter specifications are valid pathnames For example the following will stage in the grid dat file at hostB to a local file dat1 on drive C qsub W stagein C temp dat1 hostB grid dat In Windows the stagein and stageout string must be contained in double quotes when using array_index Example of a stagein qsub W stagein foo array_index host 3 C WINNT Temp foo array_index J 1 5 stage script 116 Chapter 8 Advanced PBS Features Example of a stageout qsub W stageout C WINNT Temp foo array_index vmwhost 3 0 pbsuser31 foo array_index out J 1 5 stage script PBS uses rcp or scp or cp if the remote host is the local host to perform the transfer Hence stage in and stage out are just a Ju rcp r remote _host remote_file local_ rcp r local file remote_host r
18. will be ignored A line in the script file will be processed as a directive to qsub if and only if the string of characters starting with the first non white space character on the line and of the same length as the directive prefix matches the directive prefix i e PBS The remainder of the directive line consists of the options to gsub in the same syntax as they appear on the command line The option character is to be preceded with the character 38 Chapter 4 Submitting a PBS Job If an option is present in both a directive and on the command line that option and its argument if any will be ignored in the directive The command line takes precedence If an option is present in a directive and not on the command line that option and its argu ment if any will be taken from there 4 6 A Sample PBS Job Let s look at an example PBS job in detail UNIX Windows bin sh PBS 1 walltime 1 00 00 PBS 1 walltime 1 00 00 PBS 1 select mem 400mb PBS j oe PBS 1 select mem 400mb PBS j oe date t _application te t date my_ application date 6 Cl amp D NHN e f On line one in the example above Windows does not show a shell directive The default on Windows is the batch command language Also note that it is possible under both Win dows and UNIX to specify to PBS the scripting language to use to interpret the job script see the S opt
19. 7 User s Guide Table of Contents PRGIAGCE sediscsssscxicnnsdcesucnsiapsctsssuesoanaecssounaiudacinsicessendvusaetaipentes Vii Acknowledgements sscccssccscssecsssecsscscesscssssecssescesees ix 1 Introduction eessesssessosseeseescoesoesoesooesoesoeseossoessessossossse 1 Book organization sessseeseesessseessessrsssessessresresseese 1 What is PBS Professional ccccsceesseceteeeeeeeeees 2 History Of PBS arenlar a a nieces 3 About the PBS Team civsccusvisneie wi gunna yeas 4 About Altair Engineering ee ceceeeeeseeeseeeeeees 4 Why Use PBS oati RO E 4 2 Concepts and Terms se ssesssesssocssoossoossssssssesssosssosseo 7 PBS Components sessseesseeseeessoersooessssessessseesseessoos 8 Defining PBS Concepts and Terms c eeeee 10 3 Getting Started With PBS se sseosseoesoossoossossssossssee 15 New Features in PBS Professional 7 006 15 Major Changes sesessesessessssseessessrssresseessesressresse 16 Using PBS onean a E a 19 PBS Interfaces scsisnisiatr entada aa 20 User s PBS Environment c cccccesseeeeeeeseeeteees 22 Usernames Under PBS i cus nivieaurnt eatin 22 Setting Up Your UNIX Linux Environment 22 Setting Up Your Windows Environment 24 Environment Variables 2 cscs sectitioccedatssacdlesidzicess 26 Temporary Scratch Space TMPDIR eee 27 4 Submitting a PBS JOb seoesooesosesssesssess
20. 7 65 User s Guide e double clicking an entry usually activates some action that uses the selected entry as a parameter An entry widget is brought into focus with a left click To manipulate this widget simply type in the text value Use of arrow keys and mouse selection of text for deletion over write copying and pasting with sole use of mouse buttons are permitted This widget has a scrollbar for horizontally scanning a long text entry string A matrix of entry boxes is usually shown as several rows of entry widgets where a number of entries called fields can be found per row The matrix is accompanied by up down arrow buttons for paging through the rows of data and each group of fields gets one scrollbar for horizontally scanning long entry strings Moving from field to field can be done using the lt Tab gt move forward lt Cntrl f gt move forward or lt Cntrl b gt move backward keys A spinbox is a combination of an entry widget and a horizontal scrollbar The entry widget will only accept values that fall within a defined list of valid values and incrementing through the valid values is done by clicking on the up down arrows A button is a rectangular region appearing either raised or pressed that invokes an action when clicked with the left mouse button When the button appears pressed then hitting the lt RETURN gt key will automatically select the button A text region is an editor like widget This widget is
21. Altering a Job Array 148 Altix 156 Ames Research Center ix API vii 5 9 11 117 array 59 array_id 59 array_index 59 115 array indices remaining 60 array_indices_submitted 60 array_state_count 60 Attribute account string 54 defined 11 ncpus 156 priority 6 50 rerunnable 13 49 attributes modifying 97 B Batch job 20 processing 12 batch job 12 block 110 Boolean Resources 17 Bourne 30 C Changing PBS Pro 5 4 163 User s Guide order of jobs 105 Checking status of jobs 79 of queues 83 of server 82 checkpoint 57 Checkpointing interval 51 job arrays 151 SGI MPI 157 checkpointing 101 CLI 20 Cluster 10 Command line interface 20 Commands 8 comment 59 88 Common User Environ ment 6 Complex 10 12 Computational Grid Sup port 5 Conversion from nodespec 18 Cpusets 156 cred 132 credential 133 164 Index Cross System Scheduling 6 CSA 126 csh 23 ctime 60 D DCE 132 Deleting Job Array 148 job array range 148 subjob 148 Deleting a Job Array 148 Deleting Jobs 102 depend 57 dependencies job arrays 151 Deprecations 19 Destination defined 12 identifier 12 specifing 46 Directive 12 directive 20 27 37 38 74 116 117 129 161 Directives 30 directives 29 Display nodes assigned to job 87 non running jobs 86 queue limits 88 running jobs 86 size in gigabytes 87 size in megawords 87 user specific jobs 86 Distributed clustering 5 workload management 7 E egroup 60
22. Array Services the session id is insufficient to track which processes belong to the job Where a different identifier is required it is recorded in this attribute If set it will also be recorded in the end of job accounting record For Irix 6 x running Array Services the alt_id attribute is set to the Array Session Handle ASH assigned to the job boolean true if applied to a job array string applies to subjob job array identifier for given subjob string applies to subjob index number of given subjob 60 Chapter 4 Submitting a PBS Job array _indices_ remaining array indices submitted array state co unt time time exec_host egroup euser hashname interactive Job Owner Job st m tate time string applies to job array list of indices of subjobs still queued Range or list of ranges string applies to job array complete list of indices of subjobs given at submission time Given as a range string applies to job array lists number of subjobs in each state The time that the job was created The time that the job became eligible to run i e in a queued state while residing in an execution queue If the job is running this is set to the name of the host or hosts on which the job is executing The format of the string is node N C where node is the name of a node N is pro cess or task slot on that node and C is the number of CP
23. Holding a job delaying execution The h option specifies that a user hold be applied to the job at submission time The job will be submitted then placed in a hold state The job will remain ineligible to run until the hold is released For details on releasing a held job see Holding and Releasing Jobs on page 100 4 10 13 Specifying job checkpoint interval The c interval option defines the interval in minutes at which the job will be checkpointed if this capability is provided by the operating system i e under SGI IRIX and Cray Unicos If the job executes upon a host which does not support checkpointing this option will be ignored The interval argument is specified as n Nocheckpointing is to be performed s Checkpointing is to be performed only when the Server executing the job is shutdown c Checkpointing is to be performed at the default minimum time for the Server executing the job c minutes Checkpointing is to be performed at an interval of minutes which is the integer number of minutes of CPU time used by the job This value must be greater than zero u Checkpointing is unspecified thus resulting in the same behavior as 6699 S If c is not specified the checkpoint attribute is set to the value u 52 Chapter 4 Submitting a PBS Job an Checkpointing is not supported for job arrays 4 10 14 Specifying Job User ID PBS requires that a user s name be consistent
24. account name associated with the job Account Name checkpoint attribute Checkpoint time the job is eligible for queueing execution Queue Time resources requested by the job Resources prior ity attached to the job Priority and whether or not the job is rerunnable Rerunnable The selection criteria can be modified by clicking on any of the appropriate command but tons to bring up a selection box The criteria command buttons are accompanied by a Select Jobs button which when clicked will update the contents of the Jobs listbox based on the new selection criteria Note that only jobs that meet all the selected criteria will be displayed 70 Chapter 5 Using the xpbs GUI Finally to the right of the Jobs panel are the following command buttons for operating on selected job s detail modify delete hold release signal msg move order run rerun provides information about selected job s This functionality can also be achieved by double clicking on a Jobs listbox entry for modifying attributes of the selected job s for deleting the selected job s for placing some type of hold on selected job s for releasing held job s for sending signals to selected job s that are running for writing a message into the output streams of selected job s for moving selected job s into some specified destination for exchanging order of two selected jobs in a queue for running selected job s admin only fo
25. available when all valid subjobs have completed The individual exit status of a completed subjob is passed to the epilogue and is available in the E accounting log record of that subjob See Job Array Exit Status on page 151 8 2 Changing UNIX Job umask The W umask nnn option to qsub allows you to specify on UNIX systems what umask PBS should use when creating and or copying your stdout and stderr files and any other files you direct PBS to transfer on your behalf Important This feature does not apply to Windows The following example illustrates how to set your umask to 022 i e to have files created with write permission for owner only rw r r qsub W umask 022 my_job PBS W umask 022 8 3 Requesting qsub Wait for Job Completion The W block true option to qsub allows you to specify that you want qsub to wait for the job to complete i e block and report the exit value of the job If job sub mission fails no special processing will take place If the job is successfully submitted qsub will block until the job terminates or an error occurs If qsub receives one of the signals STGHUP SIGINT or SIGTERM it will print a mes sage and then exit with the exit status 2 If the job is deleted before running to completion or an internal PBS error occurs an error message describing the situation will be printed to this error stream and qsub will exit with an exit status of 3 Signals STGQUIT a
26. becomes the acl groups list for the reservation s queue Specifies a comma separated list of entries of the form hostname These entries help control the enqueuing of jobs into the reservation s queue by allowing denying jobs submit ted from these hosts This list becomes the acl hosts list for the reservation s queue 122 Chapter 8 Advanced PBS Features N reservation name Declares a name for the reservation The name specified may be up to 15 characters in length It must consist of printable non white space characters with the first character alphabetic l resource_list Specifies a list of resources required for the reservation These resources will be used for the limits on the queue that s dynami cally created to service the reservation The aggregate amount of resources for currently running jobs from this queue will not exceed these resource limits In addition the queue inherits the value of any resource limit set on the Server if the reservation request itself is silent about that resource I seconds Interactive mode is specified if the submitter wants to wait for an answer to the request The pbs_rsub command will block up to the number of seconds specified while waiting for the scheduler to either confirm or deny the reservation request A negative number of seconds may be specified and is interpreted to mean if the confirm deny decision isn t made in the number of seconds specified automatica
27. brought into focus with a left click To manipulate this widget simply type in the text Use of arrow keys backspace delete key mouse selection of text for deletion or overwrite and copying and pasting with sole use of mouse buttons are permitted This widget has a scrollbar for vertically scanning a long entry 5 3 Introducing the xpbs Main Display The main window or display of xpbs is comprised of five collapsible subwindows or panels Each panel contains specific information Top to bottom these panels are the Menu Bar Hosts panel Queues panel Jobs panel and the Info panel 5 3 1 xpbs Menu Bar The Menu Bar is composed of a row of command buttons that signal some action with a click of the left mouse button The buttons are 66 Chapter 5 Using the xpbs GUI Manual Update forces an update of the information on hosts queues and jobs Auto Update sets an automatic update of information every user specified number of minutes Track Job for periodically checking for returned output files of jobs Preferences for setting parameters such as the list of Server host s to query Help contains some help information About gives general information about the xpbs GUI Close for exiting xpbs plus saving the current setup information PBS Professional 7 67 User s Guide 5 3 2 xpbs Hosts Panel The Hosts panel is composed of a leading horizontal HOSTS bar a listbox and a set of command buttons The HOSTS bar contains a mini
28. e mail 48 Enterprise wide Resource Sharing 4 Environment Variables 159 Error _Path 57 etime 60 euser 60 Exclusive VP 10 exec_host 60 Execution Time 57 Executor 9 Exit Status job arrays 151 External Reference Specifi cation vii 11 F Fairshare job arrays 152 File output 113 output and error 54 rhosts 25 specify name of 46 stage in 13 stage out 13 staging 5 12 114 Files cshre 22 hosts equiv 26 login 22 pbs conf 27 76 profile 22 rhosts 26 xpbsrc 76 files login 23 logout 23 G GASS 129 Global Grid Forum 4 Globus 9 127 128 129 130 131 defined 127 globusrun 127 128 Grid Toolkit 5 job states 129 jobs 128 Graphical user interface 20 Grid 4 5 Group defined 12 ID GID 12 group list 57 GUI 20 H hashname 60 here document 32 Hitchhiker s Guide 155 Hold defined 12 job 51 or release job 100 Hold_ Types 57 Holding a Job Array 148 I identifier 31 Identifier Syntax 136 Information Power Grid 4 interactive 60 Interactive job submission job arrays 138 Interactive batch jobs 55 Interdependency 5 IRIX 156 J ja 126 Job batch 12 checkpoint 57 comment 59 88 depend 57 dependencies 111 identifier 31 management vii name 48 priority 58 selecting using xpbs 94 sending messages to 103 sending signals to 104 states 129 tracking 96 Job Array Attributes 138 Staging Syntax 143 States 139 status 145 Job array range 136 Job Array Dependencies 151 Job array iden
29. hosts space separated to automatically select highlight in the HOSTS listbox List of queues space separated to automatically select high light in the QUEUES listbox List of jobs space separated to automatically select highlight in the JOBS listbox List of owners checked when limiting the jobs appearing on the Jobs listbox in the main xpbs window Specify value as Own ers lt list_of_owners gt See u option in qselect 1B for format of lt list_of_owners gt List of job states to look for do not space separate when limit ing the jobs appearing on the Jobs listbox in the main xpbs window Specify value as Job States lt states_string gt See s option in gselect 1B for format of lt states_string gt List of resource amounts space separated to consult when lim iting the jobs appearing on the Jobs listbox in the main xpbs window Specify value as Resources lt res_string gt See 1 option in qselect 1B for format of lt res_string gt The Execution Time attribute to consult when limiting the list of jobs appearing on the Jobs listbox in the main xpbs window Specify value as Queue Time lt exec_time gt See a option in gselect 1B for format of lt exec_time gt The name of the account that will be checked when limiting the jobs appearing on the Jobs listbox in the main xpbs window Specify value as Account Name lt account_name gt See A 78 Chapter 5 Using the xpbs GUI selectCheckpoi
30. manpage on ja for details PBS Professional 7 127 User s Guide The starting and ending ja commands must be used before and after any other commands the user wishes to monitor Here are examples of command line and a script On the command line qsub N myjobname 1 ncpus 1 ja myrawfile sleep 50 ja c gt myreport ja t myrawfile ctrl D Accounting data for the user s job sleep 50 is written to myreport If the user creates a file foo with these commands PBS N myjobname PBS 1 ncpus 1 ja myrawfile sleep 50 ja c gt myreport ja t myrawfile The user could run this script via qsub qsub foo This does the same thing via the script foo 8 10 Globus Support Globus is a computational software infrastructure that integrates geographically distrib uted computational and information resources Jobs are normally submitted to Globus using the utility globusrun When Globus support is enabled for PBS jobs can be routed between Globus and PBS Contact your PBS system administrator to learn if Glo 128 Chapter 8 Advanced PBS Features bus support has been enabled on your PBS systems Important Globus is currently supported on UNIX not Windows 8 10 1 Running Globus jobs To submit a Globus job users must specify the globus resource name gatekeeper as the following example shows qsub 1l site globus globus resource name pbsjob The pbs_mom_globus daemon service must be running on the same ho
31. neneiia aiai 135 qsub Submitting a Job Array 0 eects 137 Job Array Attributes ec ceeeceesseeeteceteeeeees 138 JODsATIAY Stat Sareananunrinenn 139 PBS Environmental Variables ce cesses 140 File Sta 112535 savhadusnsashsdacSavnen ara a 140 PBS Commands isinai 143 Other PBS Commands Supported for Job Arrays 149 Job Arrays and XpDSvicsisscscastsscassvivisotnatccmattycnss 150 More on Job Arrays ss seesessssessesessssessessrssressesses 150 10 Multiprocessor Jobs e ssoesssessoesssesssoossoossoossssesssese 153 Submitting SMP MPI and Multi threaded Jobs 153 MPI Jobs with PBS sssessesesseseseseesesessssesesresesese 154 PVM Jobs with PBS caries atennaeacucamnes 156 OpenMP Jobs with PBS cee eeeeeseeteeeeees 156 Cpusets with PBS sisscuncss puiowiawentodseasine 156 Checkpointing SGI MPI Jobs 0 0 ee eeeeeeeteeee 157 11 Appendix A PBS Environment Variables 159 12 Appendix B Converting From NQS to PBS 161 D3 VV S CEEE asisstestedscadcccieseessachsecccescdecstatecscsceteess 163 vi PBS Professional 7 vii User Guide Preface Intended Audience PBS Professional is the professional workload management system from Altair that pro vides a unified queuing and job management interface to a set of computing resources This document provides the user with the information required to use the Portable Batch System PBS including creating submitting and manipulating batch jobs querying
32. on the xpbs main display and if you then click it xpbs will display a list of all completed jobs that you were previously tracking Selecting one of those jobs will launch a window con taining the standard output and standard error files associated with the job Important The Track Job feature is not currently available on Windows To enable xpbs job tracking click on the Track Job button at the top center of the main xpbs display Doing so will bring up the Track Job dialog box shown below From this window you can name the users whose jobs you wish to monitor You also need to specify where you expect the output files to be either local or remote e g will the files be retained on the Server host or did you request them to be delivered to another host Next click the start reset tracking button and then the close window button Note that you can disable job tracking at any time by clicking the Track Job button on the main xpbs display and then clicking the stop tracking button PBS Professional 7 97 User s Guide Chapter 7 Working With PBS Jobs This chapter introduces the reader to various commands useful in working with PBS jobs Covered topics include modifying job attributes holding and releasing jobs sending mes sages to jobs changing order of jobs within a queue sending signals to jobs and deleting jobs In each section below the command line method for accomplishing a particular task is presented first f
33. open The File Selection Dialog window is shown below Clicking on the Select File but ton will load the file into xpbs just as does the oad button described above The various fields in the Submit window will get loaded with values found in the script file The script file text box will only be loaded with executable lines non PBS found in the script The job script header box has a Prefix entry box that can be modified to specify the PBS directive to look for when parsing a script file for PBS options If you don t have a existing script file to load into xpbs you can start typing the execut able lines of the job in the file text box Next review the Destination listbox This box lists all the queues found in the host that you selected A special entry called host refers to the default queue at the indicated host Select appropriately the destination queue for the job Next define any required resources in the Resource List subwindow Important The resources specified in the Resource List section will be job wide resources only In order to specify chunks or job PBS Professional 7 75 User s Guide placement use a script Finally review the optional settings to see if any should apply to this job For example o Use the one of the buttons in the Output region to merge out put and error files o Use Stdout File Name to define standard output file and to redirect output o Use the Env
34. represented by the option argument The available options to qselect are a op date_time A account string Restricts selection to a specific time or a range of times The qselect command selects only jobs for which the value of the Execution_Time attribute is related to the date_time argu ment by the optional op operator The date_time argument is in the POSIX date format CC YY MMDDhhmn SS where the MM is the two digits for the month DD is the day of the month hh is the hour mm is the minute and the optional SS is the seconds CC is the century and YY the year If op is not specified jobs will be selected for which the Execution_Time and date_time values are equal Restricts selection to jobs whose Account Name attribute matches the specified account_string c op interval h hold list J l resource list PBS Professional 7 91 User s Guide Restricts selection to jobs whose Checkpoint interval attribute matches the specified relationship The values of the Check point attribute are defined to have the following ordered rela tionship n gt s gt c minutes gt c gt u If the optional op is not specified jobs will be selected whose Checkpoint attribute is equal to the interval argument Restricts the selection of jobs to those with a specific set of hold types Only those jobs will be selected whose Hold Types attribute exactly match the value of the hold list argument The hold l
35. s Guide The ghold command can be used on job arrays but not on subjobs or ranges of subjobs On job arrays the qhold command can be applied only in the Q B or W states This will put the job array in the H held state If any subjobs are running they will run to completion Job arrays cannot be moved in the H state if any subjobs are running Checkpointing is not supported for job arrays Even on systems that support checkpoint ing no subjobs will be checkpointed they will run to completion Similarly the qrls command releases a hold on a job However the user executing the qrls command must have the necessary privilege to release a given hold The same rules apply for releasing a hold as exist for setting a hold The qrls command can only be used with job array objects not with subjobs or ranges The job array will be returned to its pre hold state which can be either Q B or W The usage syntax of the qr1s command is qrls h hold list job identifier For job arrays the job_identifier must be enclosed in double quotes The following examples illustrate how to use both the qhold and qrls commands Notice that the state S column shows how the state of the job changes with the use of these two commands 102 Chapter 7 Working With PBS Jobs qstat a Queue Jobname Sess NDS 54 south workq engine qhold 54 qstat a Queue Jobname Sess NDS 54 south workq engine
36. sta tus of jobs queues and systems and otherwise making effective use of the computer resources under the control of PBS Related Documents The following publications contain information that may also be useful to the user of PBS PBS Professional Quick Start Guide offers a short overview of the installation and use of PBS Professional PBS Professional Administrator s Guide provides the system administrator with information required to install configure and manage PBS as well as a thorough discussion of how the various components of PBS interoperate PBS Professional External Reference Specification discusses in detail the PBS application programming interface API security within PBS and inter daemon service communication viii Ordering Software and Publications To order additional copies of this and other PBS publications or to purchase additional software licenses contact an authorized reseller or the PBS Sales Department Contact information is included on the copyright page of this document Document Conventions PBS documentation uses the following typographic conventions abbreviation Ifa PBS command can be abbreviated such as sub commands to qmgr the shortest acceptable abbreviation is underlined command This fixed width font is used to denote literal commands filena mes error messages and program output input Literal user input is shown in this bold fixed width font manpage x Following U
37. the de facto standard for batch queueing Over time distributed parallel systems began to emerge and NQS was inadequate to han dle the complex scheduling requirements presented by such systems In addition com puter system managers wanted greater control over their compute resources and users wanted a single interface to the systems In the early 1990 s NASA needed a solution to this problem but found nothing on the market that adequately addressed their needs So NASA led an international effort to gather requirements for a next generation resource management system The requirements and functional specification were later adopted as an IEEE POSIX standard 1003 2d Next NASA funded the development of a new resource management system compliant with the standard Thus the Portable Batch Sys tem PBS was born PBS was quickly adopted on distributed parallel systems and replaced NQS on traditional supercomputers and server systems Eventually the entire industry evolved toward distrib uted parallel systems taking the form of both special purpose and commodity clusters Managers of such systems found that the capabilities of PBS mapped well onto cluster systems For information on converting from NQS to PBS see Appendix B The PBS story continued when MRJ Veridian the R amp D contractor that developed PBS for NASA released the Portable Batch System Professional Edition PBS Pro a com mercial enterprise ready workload management
38. the specified destination path does not exist 2 A directory in the specified destination path is not searchable by the user 3 The target directory is not writable by the user 8 6 Input Output File Staging File staging is a way to specify which files should be copied onto the execution host before the job starts and which should be copied off the execution host when it completes For file staging under Globus see PBS File Staging through GASS on page 129 The W stagein file list and W stageout file list options to qsub specify which files are staged copied in before the job starts or staged out after the job completes execution On completion of the job all staged in and staged out files are removed from the execution system The file _list is in the form local file hostname remote filel PBS Professional 7 115 User s Guide regardless of the direction of the copy Note that the character is used for separating the local specification from the remote specification The name ocal_file is the name of the file on the system where the job executes It may be an absolute path or relative to the home directory of the user The name remote_file is the destination name on the host spec ified by hostname The name may be absolute or relative to the user s home directory on the destination host Thus for stage in the direction of travel is local file remote host remote file and for stage out
39. then the job s standard error stream will be merged inter mixed with the job s stan 58 Chapter 4 Submitting a PBS Job Keep Files Mail Points Mail Users no stdio sockets Output _ Path Priority Rerunnable Resource List Shell Path List dard output stream and placed in the file determined by the Output Path attribute The Error Path attribute is main tained but ignored However if the Join Paths attribute is eo then the job s standard output stream will be merged inter mixed with the job s standard error stream and placed in the file determined by the Error Path attribute and the Output_ Path attribute will be ignored If Keep Files contains the values o KEEP OUTPUT and or e KEEP ERROR the corresponding streams of the batch job will be retained on the execution host upon job termination Keep Files overrides the Output Path and Error Path attributes Identifies when the Server will send email about the job The set of users to whom mail may be sent when the job makes certain state changes Flag to indicate whether a multinode job should have the stan dard output and standard error streams of tasks running on other nodes returned to mother superior via sockets These sockets may cause a job to be not checkpointable Default false sock ets are created The final path name for the file containing the job s standard output stream See the qsub and qalter command descrip tio
40. to check status of a job and request status of queues nodes systems or PBS Servers Chapter 7 discusses commonly used commands and features of PBS and explains how to use each one Chapter 8 describes and explains how to use the more advanced features of PBS Chapter 9 describes and explains the job array features in PBS Chapter 10 explains how PBS interacts with multi node and parallel appli cations and illustrates how to run such applications under PBS Appendix A provides a quick reference summary of PBS environment vari ables Appendix B includes information for converting from NQS NQE to PBS 1 2 What is PBS Professional PBS Professional is the professional version of the Portable Batch System PBS a flexi ble workload management system originally developed to manage aerospace computing resources at NASA PBS has since become the leader in supercomputer workload man agement and the de facto standard on Linux clusters Today growing enterprises often support hundreds of users running thousands of jobs across different types of machines in different geographical locations In this distributed heterogeneous environment it can be extremely difficult for administrators to collect detailed accurate usage data or to set system wide resource priorities As a result many computing resources are left under utilized while other are over utilized At the same time users are confronted with an ever expanding array of oper
41. will have a user level access control list set to the user who submitted the reservation and any other users the owner specified The queue will accept jobs in the same manner as normal queues When the reservation start time is reached the queue will be started Once the reservation is complete any jobs remaining in the queue running or not will be deleted and the reservation removed from the Server When a reservation is requested and confirmed it means that a check was made to see if the reservation would conflict with currently running jobs other confirmed reservations and dedicated time A reservation request that fails this check is denied by the Scheduler If the submitter did not indicate that the submission command should wait for confirma tion or rejection I option he will have to periodically query the Server about the status of the reservation via pbs_rstat or wait for a mail message regarding its denial or confirmation Important Hosts nodes that have been configured to accept jobs only from a specific queue node queue restrictions cannot be used for advance reservations See your local PBS Administrator to determine if this affects your site 8 8 1 Submitting a PBS Reservation The pbs_rsub command is used to request a reservation of resources If the request is granted PBS provides for the requested resources to be available for use during the speci fied future time interval A queue is dynamically allocated to s
42. xpbs Preferences The Preferences button is in the Menu Bar at the top of the main xpbs window Click ing it will bring up a dialog box that allows you to customize the behavior of xpbs Define Server hosts to query Select wait timeout in seconds Specify xterm command for interactive jobs UNIX only Specify which rsh ssh command to use te 72 Chapter 5 Using the xpbs GUI 5 5 Relationship Between PBS and xpbs xpbs is built on top of the PBS client commands such that all the features of the com mand line interface are available through the GUI Each task that you perform using xpbs is converted into the necessary PBS command and then run Table 12 xpbs Buttons and PBS Commands Location Command Button PBS Command Hosts Panel detail qstat B f selected server_host s Hosts Panel submit qsub options selected Server s Hosts Panel terminate qterm selected server_host s Queues Panel detail qstat Q f selected queue s Queues Panel stop qstop selected queue s Queues Panel start qstart selected queue s Queues Panel enable qenable selected queue s Queues Panel disable qdisable selected queue s Jobs Panel detail qstat f selected job s Jobs Panel modify qalter selected job s Jobs Panel delete qdel selected job s Jobs Panel hold qhold selected job s Jobs Panel release qrls selected job s Jobs Panel run qrun selected job s Jobs Panel rerun
43. 11Forwarding yes parameter in the sshd_ config file Your local system administrator can provide details on this process if needed An alternative but less secure method is to direct your X Windows session to permit the xpbs client to connect to your local X server Do this by running the xhost command with the name of the host from which you will be running xpbs as shown in the example below xhost server mydomain com Next on the system from which you will be running xpbs set your X Windows DIS PLAY variable to your local workstation For example if using the C shell setenv DISPLAY myWorkstation 0 0 However if you are using the Bourne or Korn shell type the following export DISPLAY myWorkstation 0 0 5 2 Using xpbs Definitions of Terms The various panels boxes and regions collectively called widgets of xpbs and how they are manipulated are described in the following sections A listbox can be multi select able a number of entries can be selected highlighted using a mouse click or single select able one entry can be highlighted at a time For a multi selectable listbox the following operations are allowed e left click to select highlight an entry e shift left click to contiguously select more than one entry e control left click to select multiple non contiguous entries e click the Select All Deselect All button to select all entries or deselect all entries at once PBS Professional
44. 9 qstop 21 72 qsub 21 22 24 37 38 40 41 42 44 56 72 110 111 133 qterm 21 72 qtime 61 Queue defined 10 queue 61 Queuing vii 7 Quick Start Guide vii R rep 22 42 Releasing a Job Array 148 report 126 requeue 13 Requeuing a Job Array 149 rerunnable 58 Reservation deleting 125 showing status of 124 submitting 119 Resource Requests 16 Resource_List 58 resources 30 resources list 44 resources_used 61 rhosts 25 run limits job arrays 150 run_count 61 Running a Job Array 149 S schedselect 61 Scheduler 9 Scheduling 7 job Arrays 152 scp 22 Selection of Job Arrays 150 Sequence number 135 Server 8 server 61 session_id 61 SGI cpusets 156 SGI MPI 157 sh 30 shell 29 shell script 30 Shell Path List 58 SIGKILL 104 SIGNULL 104 SIGTERM 104 single signon 40 size 42 stagein 59 115 stageout 45 59 115 Staging Job Array 141 143 state job 80 States Job Array 139 states 77 93 95 Status Job Array 145 stepping factor 137 Subjob 135 Subjob index 135 Submitting a Job Array 137 Submitting a PBS Job 29 Suppressing job identifier 55 syntax identifier 136 System integration 6 monitoring 5 T Task 13 Task Manager 117 TCL 63 TGT 133 time 42 TK 63 tm 3 117 TMPDIR 28 160 tracejob 21 job arrays 149 tracejob on Job Arrays 149 tracking 96 PBS Pro 5 4 167 User s Guide U umask 59 110 User defined 13 ID UID 13 interfaces 5 name mapping 6 user job accounting 126 User _Lis
45. 9 5 PBS Environmental Variables Suspended by keyboard activity Table 19 PBS Environmental Variables Environment Variable Namie Used For Description PBS ARRAY INDEX subjobs Subjob index in job array e g 7 PBS_ ARRAY ID subjobs Identifier for a job array Sequence num ber of job array e g 1234 PBS_JOBID Jobs sub Identifier for a job or a subjob For sub jobs job sequence number and subjob index in brackets e g 1234 7 9 6 File Staging File staging for job arrays is like that for jobs with an added variable to specify the subjob index This variable is array_index This is the name of the variable that will be used for the actual array index The stdout and stderr files follow the naming convention for jobs but include the identifier of the job array which includes the subscripted index As with jobs the stagein and stageout keywords require the W option to qsub PBS Professional 7 141 User s Guide 9 6 1 Job Array File Staging Syntax on UNIX stagein local_path host remote_path stageout local_path host remote_path Local_path is the path on the execution host Local_path is either relative to the user s home directory or an absolute path Host is the machine where the data normally resides Remote_path is the path on the machine where the data normally resides Examples Remote_path film Data files used as input framel frame2 frame3 Ho
46. Altaire PBS Professional 7 User s Guide UNIX LINUX and Windows Portable Batch System User s Guide Altair PBS Professional 7 Service Pack 1 Updated September 8 2005 Edited by Anne Urban Copyright 2004 2005 Altair Grid Technologies LLC All rights reserved Trademark Acknowledgements PBS Professional PBS Pro Portable Batch Sys tem and the PBS Juggler logo are trademarks of Altair Grid Technologies LLC All other trademarks are the property of their respective owners Altair Grid Technologies is a subsidiary of Altair Engineering Inc For more information and for product sales and technical support contact Altair at URL www altair com www pbspro com Email sales pbspro com pbssupport altair com Location Telephone e mail North America 1 248 614 2425 pbssupport altair com China 86 0 21 5393 0011 support altair com cn France 33 0 1 4133 0990 francesupport altair com Germany 49 0 7031 6208 22 support altair de India 91 80 658 8540 91 80 658 8542 pbs support india altair com Italy 39 832 315573 39 800 905595 support altairtorino it Japan 81 3 5396 1341 support altairjp co jp Korea 82 31 728 8600 support altair co kr Scandinavia 46 0 46 286 2050 support altair se UK 44 0 1327 810 700 support uk altair com This document contains proprietary information belonging to Altair Grid Technologies PBS Professional
47. Concepts and Terms Batch or Batch Processing Complex Destination Destination Identifier Directive File Staging Group ID GID Group Hold Job or Batch Job This refers to the capability of running jobs outside of the interactive login environment A complex is a collection of hosts managed by one batch sys tem It may be made up of nodes that are allocated to only one job at a time or of nodes that have many jobs executing at once on each node or a combination of these two scenarios This is the location within PBS where a job is sent A destination may be a single queue at a single Server or it may map into multiple possible locations tried in turn until one accepts the job This is a string that names the destination It is composed of two parts and has the format queue server where server is the name of a PBS Server and queue is the string identifying a queue on that Server A means by which the user specifies to PBS the value of a variable such as number of cpus the name of a job etc The default start of a directive is PBS PBS directives either specify resource requirements or attribute values See page 38 File staging is the movement of files between a specified location and the execution host See Stage In and Stage Out below This unique number represents a specific group see Group Group refers to collection of system users see Users A user must be a member of a grou
48. Headings Heading Meaning Max Maximum number of jobs permitted Tot Count of jobs currently enqueued in any state Ena Is queue enabled yes or no PBS Professional 7 69 User s Guide Table 10 xpbs Queue Column Headings Heading Meaning Str Is queue started yes or no Que Count of jobs in the Queued state Run Count of jobs in the Running state Hld Count of jobs in the Held state Wat Count of jobs in the Waiting state Tm Count of jobs in the Transiting state Ext Count of jobs in the Exiting state Type Type of queue execution or route Server Name of Server on which queue exists 5 3 4 xpbs Jobs Panel The Jobs panel is composed of a leading horizontal JOBS bar a listbox and a set of com mand buttons The JOBS bar lists the queues that are consulted when listing jobs the bar also contains a minimize maximize button for displaying or iconizing the Jobs region The listbox displays information about jobs that are found in the queue s selected from the Queues listbox each listbox entry can be selected as described above for the Hosts panel The region just above the Jobs listbox shows a collection of command buttons whose labels describe criteria used for filtering the Jobs listbox contents The list of jobs can be selected according to the owner of jobs Owners job state Job_ States name of the job Job Name type of hold placed on the job Hold_Types the
49. INDEX 140 159 PBS DEFAULT 27 82 PBS DEFAULT SERVE R 76 PBS_DPREFIX 27 PBS ENVIRONMENT 22 23 27 159 PBS_HOME 13 pbs_hostid 21 pbs_hostn 21 PBS_JOBCOOKIE 159 PBS_JOBID 140 159 PBS_JOBNAME 159 pbs migrate users 21 pbs mom globus 128 PBS MOMPORT 159 PBS _NODEFILE 159 PBS NODENUM 159 PBS_O HOME 159 PBS_O_HOST 159 PBS_O LANG 159 PBS_O_LOGNAME 159 PBS _O MAIL 159 PBS_O PATH 159 PBS_O QUEUE 159 PBS_O SHELL 160 PBS _O SYSTEM 160 PBS _O TZ 160 PBS_O WORKDIR 27 160 pbs_passwd 21 pbs_password 40 41 pbs_probe 21 PBS QUEUE 160 pbs rcp 21 42 114 pbs_rdel 21 125 pbs_rstat 21 124 pbs_rsub 21 119 PBS_TASKNUM 160 pbs _tclsh 21 pbsdsh 21 117 pbsfs 21 pbsnodes 21 pbs report 21 pdbx 155 Peer Scheduling job arrays 152 Placing Jobs on Nodes 17 POE 155 Portable Batch System 11 POSIX defined 13 Preemption job arrays 152 printjob 21 priority 58 Pro Pack 126 PROFILE PATH 25 Prologues and Epilogues job arrays 151 PVM 156 Q qalter 21 24 72 job array 148 qdel 21 72 102 job array 148 qdisable 21 72 qenable 21 72 qhold 21 72 100 102 job arrays 148 qmer 21 qmove 21 72 106 job array 148 qmsg 21 72 103 149 qorder 21 72 105 106 job arrays 148 qrerun 21 72 job array 149 qrls 21 72 101 102 job array 148 qrun 21 72 job array 149 qselect 21 77 78 89 90 93 94 job arrays 150 qsig 21 72 104 qstart 21 72 qstat 21 72 79 80 81 82 83 84 85 86 87 88 89 94 99 102 106 12
50. M option to gst at displays all jobs at the requested or default Server using the alternative display showing all size information in megawords MW rather than the default of smallest displayable units A word is considered to be 8 bytes 6 1 11 List Nodes Assigned to Jobs The n option to qstat displays the nodes allocated to any running job at the option ally specified PBS Server in addition to the other information presented in the alternative display The node information is printed immediately below the job see job 51 in the example below and includes the node name and number of virtual processors assigned to the job i e south 0 where south is the node name followed by the virtual pro cessor s assigned A text string of is printed for non running jobs Notice the differ ences between the queued and running jobs in the example below Jobname Sess NDS aims14 aimsl airfoil my job 88 Chapter 6 Checking Job System Status 6 1 12 Display Job Comments The s option to qstat displays the job comments in addition to the other informa tion presented in the alternative display The job comment is printed immediately below the job By default the job comment is updated by the Scheduler with the reason why a given job is not running or when the job began executing A text string of is printed for jobs whose comment has not yet bee
51. M program you would use the pvmexec command For example here is a sample PBS script for a PVM job PBS 1 nodes 32 pvmexec a out inputfile data in 10 4 OpenMP Jobs with PBS To provide support for OpenMP jobs the environment variable OMP_NUM THREADS is created for the job with the value of the number of CPUs allocated to the job The variable NCPUS is also set to this value 10 5 Cpusets with PBS PBS Professional software supports SGI cpusets on both Altix and IRIX systems Using cpusets improves performance by exclusively allocating chunks of the system to individ ual jobs This may affect where and when your jobs run PBS does not support cpusets with multinode jobs PBS Professional 7 157 User s Guide 10 6 Checkpointing SGI MPI Jobs Under Irix 6 5 and later MPI parallel jobs as well as serial jobs can be checkpointed and restarted on SGI systems provided certain criteria are met SGI s checkpoint system call cannot checkpoint processes that have open sockets Therefore it is necessary to tell mpirun to not create or to close an open socket to the array services daemon used to start the parallel processes One of two options to mpi run must be used cpr This option directs mpirun to close its connection to the array services daemon when a checkpoint is to occur miser This option directs mpirun to directly create the parallel process rather than use the array services This avoids opening the socket conne
52. NIX tradition manual page references include the corresponding section number in parentheses appended to the man page name terms Words or terms being defined as well as variable names are in italics PBS Professional 7 ix User s Guide Acknowledgements PBS Professional is the enhanced commercial version of the PBS software originally developed for NASA The NASA version had a number of corporate and individual con tributors over the years for which the PBS developers and PBS community is most grate ful Below we provide formal legal acknowledgements to corporate and government entities then special thanks to individuals The NASA version of PBS contained software developed by NASA Ames Research Cen ter Lawrence Livermore National Laboratory and MRJ Technology Solutions In addi tion it included software developed by the NetBSD Foundation Inc and its contributors as well as software developed by the University of California Berkeley and its contribu tors Other contributors to the NASA version of PBS include Bruce Kelly and Clark Streeter of NERSC Kent Crispin and Terry Heidelberg of LLNL John Kochmar and Rob Penning ton of Pittsburgh Supercomputing Center and Dirk Grunwald of University of Colorado Boulder The ports of PBS to the Cray T3e and the IBM SP SMP were funded by DoD USAERDC the port of PBS to the Cray SV1 was funded by DoD MSIC No list of acknowledgements for PBS would possibly be complete without spe
53. Q in the original script nqs2pbs existing NQS script new PBS script Important Converting NQS date specifications to the PBS form may result in a warning message and an incomplete converted date PBS does not support date specifications of today tomorrow or the name of the days of the week such as Monday If any of these are encoun tered in a script the PBS specification will contain only the time portion of the NQS specification i e PBS a hhmnf ss It is suggested that you specify the execution time on the qsub com mand line rather than in the script All times are taken as local time If any unrecognizable NQS directives are encountered an error message is displayed The new PBS script will be deleted if any errors occur Section Setting Up Your UNIX Linux Environment on page 22 discusses PBS environ ment variables A queue complex in NQS was a grouping of queues within a batch Server The purpose of a complex was to provide additional control over resource usage The advanced schedul ing features of PBS eliminate the requirement for queue complexes 162 Appendix B Converting From NQS to PBS Index A Access Control 5 126 Account 11 Account Name 57 Accounting 5 126 job arrays 151 accounting 126 accounting id 59 ACCT_TMPDIR 126 Administrator 11 Administrator Guide vii 9 16 20 Aerospace computing 2 AIX 155 alt_id 59 Altair Engineering 4 Altair Grid Technologies ii 4
54. Us allocated to the job C does not appear if it is one If the job is queued in an execution queue this attribute is set to the group name under which the job is to be run This attribute is available only to the batch administrator If the job is queued in an execution queue this attribute is set to the user name under which the job is to be run This attribute is available only to the batch administrator The name used as a basename for various files such as the job file script file and the standard output and error of the job This attribute is available only to the batch administrator True if the job is an interactive PBS job The login name on the submitting host of the user who submit ted the batch job The state of the job The time that the job was last modified changed state or changed locations qtime queue resources used run_count schedselect server session id PBS Professional 7 61 User s Guide The time that the job entered the current queue The name of the queue in which the job currently resides The amount of resources used by the job This is provided as part of job status information if the job is running The number of times the server has run the job Format inte ger This is set to the union of the select resource of the job and the queue and server defaults for resources in a chunk The name of the server which is currently managing the job If the job is
55. X 2 PBS directives 3 Tasks programs or commands 30 Chapter 4 Submitting a PBS Job To submit a PBS job the user can type qsub lt name of script gt 4 1 1 1 Specifying the shell UNIX Users Windows Users 4 1 1 2 PBS Directives Since the job file under UNIX is a shell script the first line of the job file specifies which shell to use to execute the script The Bourne shell sh is the default but you can change this to your favorite shell This first line can be omitted if it is accept able for the job file to be interpreted using the Bourne shell The remainder of the examples in this manual will assume these conditions are true If this is not true for your site simply add the shell specifier Windows does not use a shell specification This line will not appear for a Windows job PBS directives are at the top of the script file They are used to request resources or set attributes A directive begins with the default string PBS Attributes can also be set using options to the qsub command which will override directives 4 1 1 3 The User s Tasks These can be programs or commands This is where the user specifies an application to be run Important 4 1 2 Job Attributes In Windows if you use notepad to create a job script the last line does not automatically get newline terminated Be sure to put one explicitly otherwise PBS job will get the following error message More wh
56. a priority of zero This option allows the user to specify a priority for their jobs However this option is dependant upon the local scheduling policy By default the sort jobs by job priority fea ture is disabled If your local PBS administrator has enabled it then all queued jobs will be sorted based on the user specified priority If you need an absolute ordering of your own jobs see Specifying Job Dependencies on page 111 qsub p 120 my job PBS p 300 4 10 11 Deferring execution The a date time option declares the time after which the job is eligible for execu tion The date_time argument is in the form CC YY MM DD hhmn SS where CC is the first two digits of the year the century YY is the second two digits of the year MM is the two digits for the month DD is the day of the month hh is the hour mm is the minute and the optional SS is the seconds If the month MM is not specified it will default to the current month if the specified day DD is in the future Otherwise the month will be set to next month Likewise if the day DD is not specified it will default to today if the time hhmm is in the future Otherwise the day will be set to tomorrow For example if you submit a job at 11 15am with a time of 1110 the job will be eligible to run at PBS Professional 7 User s Guide 51 11 10am tomorrow Other examples include qsub a 0700 my job PBS a 10220700 4 10 12
57. aces a command line interface CLI and a graphical user interface GUI The CLI lets you type commands at the system prompt The GUI is a graphical point and click interface The user commands are discussed in this book the administrator commands are discussed in the PBS Professional Administrator s Guide The subsequent chapters of this book will explain how to use both the CLI and GUI versions of the user commands to create submit and manipulate PBS jobs PBS Professional 7 21 User s Guide Table 2 PBS Professional User and Manager Commands User Commands Administrator Commands Command Purpose Command Purpose nqs2pbs Convert from NQS pbs report Report job statistics pbs_rdel Delete Adv Reservation pbs hostid Report host identifier pbs_rstat Status Adv Reservation pbs _hostn Report host name s pbs_password Update per user per pbs_migrate_ Migrate per user per server password cae server passwords pbs_rsub Submit Adv Reservation pbs probe PBS diagnostic tool pbsdsh PBS distributed shell pbs op File transfer tool qalter Alter job pbs_tcilsh TCL with PBS API qdel Delete job pbsfs Show fairshare usage qhold Hold a job pbsnodes Node manipulation qmove Move job printjob Report job details qmsg Send message to job qdisable Disable a queue gorder Reorder jobs genable Enable a queue qris Release hold on job
58. across a server and its execution hosts but not across a submission host and a server A user may have access to more than one server and may have a different username on each server In this environment if a user wishes to submit a job to any of the available servers the username for each server is specified The wildcard username will be used if the job ends up at yet another server not specified but only if that wildcard username is valid For example our user is UserS on the submission host HostS UserA on server ServerA and UserB on server ServerB and is UserC everywhere else Note that this user must be UserA on all ExecutionA and UserB on all ExecutionB machines Then our user can use qsub u UserA ServerA UserB ServerB UserC for the job The job owner will always be UserS 4 10 14 1 qsub u User ID with UNIX The server s flatuid attribute determines whether it assumes that identical usernames mean identical users If true it assumes that if UserS exists on both the submission host and the server host then UserS can run jobs on that server If not true the server calls ruserok which uses etc hosts equiv and rhosts to authorize UserS to run as UserS Table 6 UNIX User ID and flatuid Value of Submission host username server host username flatuid Same UserS UserS Different UserS UserA True Server assumes user has permis Server checks whether UserS can sion to run job run job as UserA Not true Serve
59. added to the corresponding piece of the selection directive as host NAME f If a property is specified that is not a node name it will be added to the corresponding piece of the selection directive as a boolean resource requesting a vaue of True The above rules are demonstrated by the following examples Nodespec Selection directive nodes 2 ncpus 1 select 2 npus 1 nodes 3 ncpus 1 ppn 2 select 3 ncpus 2 nodes 4 ncpus 2 ppn 3 select 4 ncpus 6 PBS Professional 7 35 User s Guide nodes NodeA NodeB select 1 host NodeA ncpus 1 1 host NodeB ncpus 1 nodes 2 blue 1 green select 2 ncpus 1 blue True 1 ncpus 1 green True It is an error to specify both a node directive and a select specification when submitting a job Please note that the use of 1 nodes specification is deprecated and may not be supported in future versions of PBS Professional Use of the new select and place directives should replace existing use of the node specification 4 3 5 What Happens When no Resources are Specified If neither a node specification nor a selection directive is specified then a selection direc tive will be created requesting 1 chunk with resources as requested by the job as job resource limits or taken from the queue or server default resource list Only certain resource items will be included in the selection directive They are ncpus mem arch host and software For example a job submitted with qsub l ncpus 4 mem 123mb arch li
60. al stepping factor X and Y must be whole numbers and Z must be a positive integer Y must be greater than X If Y is not a multiple of the stepping factor above X i e it won t be used as an index value the highest index used will be the next below Y For example 1 100 2 gives 1 3 5 99 Blocking qsub waits until the entire job array is complete then returns the exit status of the job array Interactive submission of job arrays is not allowed 138 Chapter 9 Job Arrays Examples To submit a job array of 10 000 subjobs with indices 1 2 3 10000 qsub J 1 10000 job scr 1234 server domain com To submit a job array of 500 subjobs with indices 500 501 502 1000 qsub J 500 1000 job scr 1235 server domain com To submit a job array with indices 1 3 5 999 qsub J 1 1000 2 job scr 1236 server domain com 9 2 1 Interactive Job Submission Job arrays do not support interactive submission 9 3 Job Array Attributes Job arrays and subjobs have all of the attributes of a job In addition they have the follow ing when appropriate These attributes are read only Table 16 Job Array Attributes Name Type Applies To Value array boolean job array True if item is job array array_id string subjob Subjob s job array identi fier array_index string subjob Subjob s index number array_state_count string job array Similar to state_count attribute for server and que
61. all jobs at that Server If a full destination identifier quaeue server is given the request is for status of all jobs in the named queue at the named server Important Ifa PBS Server is not specified on the qstat command line the default Server will be used See discussion of PBS DEFAULT in Environment Variables on page 26 6 1 3 Checking Server Status The B option to qstat displays the status of the specified PBS Batch Server One line of output is generated for each Server queried The three letter abbreviations correspond to various job limits and counts as follows Maximum Total Queued Running Held Wait ing Transiting and Exiting The last column gives the status of the Server itself active idle or scheduling qstat B Server Tra Ext Status 0 Active PBS Professional 7 83 User s Guide When querying jobs Servers or queues you can add the option to qstat to change the display to the full or long display For example the Server status shown above would be expanded using f as shown below qstat Bf Server fast mydomain com server state Active scheduling True total jobs 14 state_count Transit 0 Queued 13 Held 0 Waitang 0 Running 1 Exiting 0 managers userl fast mydomain com default queue workq log events 511 mail from adm query other jobs True resources available mem 64mb 1 resources available ncpus 2 resources default ncp
62. ame Sess NDS Mem Time S Time 63 south bob workq airfoil 54 south bob workq twinkie To change the order of two jobs using xpbs select the two jobs and then click the order button The gorder command can only be used with job array objects not on subjobs or ranges This will change the queue order of the job array in association with other jobs or job arrays in the queue 7 7 Moving Jobs Between Queues PBS provides the qmove command to move jobs between different queues even queues on different Servers To move a job is to remove the job from the queue in which it resides and instantiate the job in another queue Important A job in the running state cannot be moved The usage syntax of the qmove command is qmove destination job identifier s Job array job identifiers must be enclosed in double quotes PBS Professional 7 107 User s Guide The first operand is the new destination for queue server queue server If the destination operand describes only a queue then qmove will move jobs into the queue of the specified name at the job s current Server If the dest ination operand describes only a Server then qmove will move jobs into the default queue at that Server If the destination operand describes both a queue and a Server then qmove will move the jobs into the specified queue at the specified Server All following operands are job_identifiers which specify the jobs to be moved to the new destination
63. amount of physical memory workingset used by any single process of the job Job wide limit Units size pvymem Maximum amount of virtual memory used by any single process in the job Job wide limit Units size vmem Maximum amount of virtual memory used by all concurrent processes in the job Establishes a job resource limit or within a chunk establishes a per chunk limit Units size software Site specific software specification Allowable values and effect on job placement are site dependent String 44 Chapter 4 Submitting a PBS Job Table 4 Resource Description walltime Maximum amount of wall clock time during which the job can be in the running state Establishes a job resource limit Units time Default 5 years custom Custom resources are site dependent If used for a floating license must resources be specified outside of a selection statement as a job wide resource limit If used for a node locked license must be specified inside a selec tion statement in a chunk See your system administrator 4 10 Job Submission Options There are many options to the qsub command The table below gives a quick summary of the available options the rest of this chapter explains how to use each one Table 5 Options to the qsub Command Option Function and Page Reference A account string Specifying a local account on page 54 a date time Deferring execu
64. and any that need to be copied off after the job completes The job will be scheduled to run only after the required files have been successfully transferred Parallel Job Support works with parallel programming libraries such as MPI PVM and HPF Applications can be scheduled to run within a single multi processor computer or across multiple systems System Monitoring includes a graphical user interface for system monitoring Displays node status job placement and resource utilization information for both stand alone sys tems and clusters Job Interdependency enables the user to define a wide range of inter dependencies between jobs Such dependencies include execution order and execution conditioned on the success or failure of another specific job or set of jobs Computational Grid Support provides an enabling technology for meta computing and computational grids including support for the Globus Grid Toolkit Comprehensive API includes a complete Application Programming Interface API for sites who desire to integrate PBS with other applications or who wish to support unique job scheduling requirements Automatic Load Leveling provides numerous ways to distribute the workload across a cluster of machines based on hardware configuration resource availability keyboard activity and local scheduling policy Distributed Clustering allows customers to utilize physically distributed systems and clus ters even across wide area netw
65. array this is the number of subjobs completed and deleted divided by the total number of subjobs 6 2 Viewing Job System Status with xpbs The main display of xpbs shows a brief listing of all selected Servers all queues on those Servers and any jobs in those queues that match the selection criteria discussed below Servers are listed in the HOST panel near the top of the display To view detailed information about a given Server i e similar to that produced by qstat fB select the Server in question then click the Detail button Likewise for details on a given queue i e similar to that produced by qstat f Q select the queue in question then click its corresponding Detail button The same applies for jobs as well i e qstat You can view detailed information on any displayed job by selecting it and then clicking on the Detail button Note that the list of jobs displayed will be dependent upon the Selection Criteria currently selected This is discussed in the xpbs portion of the next section 6 3 The qselect Command The qselect command provides a method to list the job identifier of those jobs job arrays or subjobs which meet a list of selection criteria Jobs are selected from those owned by a single Server When qselect successfully completes it will have written to standard output a list of zero or more job identifiers which meet the criteria specified by the options Each option ac
66. atch PBS consists of one Job Server pbs server one or more Job System Schedulers pbs_sched and one or more execution servers pbs mom The PBS System can be set up to distribute the work load to one large system multiple systems a cluster of nodes or any combination of these Virtual Processor A node may be declared to consist of one or more virtual proces VP sors VPs The term virtual is used because the number of VPs declared does not have to equal the number of real processors CPUs on the physical node The default number of virtual proces sors on a node is the number of currently functioning physical pro cessors the PBS Manager can change the number of VPs as required by local policy The remainder of this chapter provides additional terms listed in alphabetical order Account An account is arbitrary character string which may have meaning to one or more hosts in the batch system Frequently account is used by sites for accounting or charge back purposes Administrator See Manager API PBS provides an Application Programming Interface API which is used by the commands to communicate with the Server This API is described in the PBS Professional External Reference Specifi cation A site may make use of the API to implement new com mands if so desired Attribute An attribute is a data item whose value affects the operation or behavior of the object and can be set by the owner of the object 12 Chapter 2
67. ating systems and plat forms Each year scientists engineers designers and analysts must waste countless hours learning the nuances of different computing environments rather than being able to focus on their core priorities PBS Professional addresses these problems for computing inten sive industries such as science engineering finance and entertainment PBS Professional 7 3 User s Guide Now you can use the power of PBS Professional to better control your computing resources This allows you to unlock the potential in the valuable assets you already have while at the same time reducing dependency on system administrators and operators freeing them to focus on other actives PBS Professional can also help you effectively manage growth by tracking real usage levels across your systems and enhancing utiliza tion of future purchases 1 3 History of PBS In the past UNIX systems were used in a completely interactive manner Background jobs were just processes with their input disconnected from the terminal However as UNIX moved onto larger and larger machines the need to be able to schedule tasks based on available resources increased in importance The advent of networked compute servers smaller general systems and workstations led to the requirement of a networked batch scheduling capability The first such UNIX based system was the Network Queueing Sys tem NQS funded by NASA Ames Research Center in 1986 NQS quickly became
68. ceholder for the value obtained from the etc pbs conf file UNIX or PBS Destination Folder pbs conf file Windows timeoutSecs Specify the number of seconds before timing out waiting for a connection to a PBS host xtermCmd The xterm command to run driving an interactive PBS session labelFont Font applied to text appearing in labels fixlabelFont Font applied to text that label fixed width widgets such as list box labels This must be a fixed width font textFont Font applied to a text widget Keep this as fixed width font backgroundColor foregroundColor activeColor disabledColor signalColor shadingColor selectorColor selectHosts selectQueues selectJobs selectOwners selectStates selectRes selectExecTime selectAcctName PBS Professional 7 77 User s Guide The color applied to background of frames buttons entries scrollbar handles The color applied to text in any context The color applied to the background of a selection a selected command button or a selected scroll bar handle Color applied to a disabled widget Color applied to buttons that signal something to the user about a change of state For example the color of the Track Job button when returned output files are detected A color shading applied to some of the frames to emphasize focus as well as decoration The color applied to the selector box of a radiobutton or check button List of
69. ch job submitted The path for the xterm command can be set via the preferences as discussed above in section 5 4 Setting xpbs Preferences on page 71 For further details on usage and restrictions see Interactive batch jobs on page 55 5 7 Exiting xpbs Click on the Close button located in the Menu bar to leave xpbs If any settings have been changed xpbs will bring up a dialog box asking for a confirmation in regards to saving state information The settings will be saved in the xpbsrc configuration file and will be used the next time you run xpbs as discussed in the following section 5 8 The xpbs Configuration File Upon exit the xpbs state may be written to the xpbsrc file in the user s home direc tory See also section 3 8 1 Windows User s HOMEDIR on page 24 Information saved includes the selected host s queue s and job s the different jobs listing criteria the view states i e minimized maximized of the Hosts Queues Jobs and INFO regions and all settings in the Preferences section In addition there is a system wide xpbs con figuration file maintained by the PBS Administrator which is used in the absence of a user s personal xpbsrc file 5 9 xpbs Preferences The resources that can be set in the xpbs configuration file xpbsrc are serverHosts List of Server hosts space separated to query by xpbs A spe cial keyword PBS_ DEFAULT SERVER can be used which will be used as a pla
70. cial recog nition of the first two beta test sites Thomas Milliman of the Space Sciences Center of the University of New Hampshire was the first beta tester Wendy Lin of Purdue University was the second beta tester and holds the honor of submitting more problem reports than anyone else outside of NASA PBS Professional 7 1 User s Guide Chapter 1 Introduction This book the User s Guide to the Portable Batch System Professional Edition PBS Professional is intended as your knowledgeable companion to the PBS Professional soft ware The information herein pertains to PBS in general with specific information for PBS Professional 7 1 1 Book organization This book is organized into 10 chapters plus two appendices Depending on your intended use of PBS some chapters will be critical to you and others may be safely skipped Chapter 1 gives an overview of this book PBS and the PBS team Chapter 2 discusses the various components of PBS and how they interact fol lowed by definitions of terms used in PBS and in distributed work load management Chapter 3 introduces PBS describing both user interfaces and suggested set tings to the user s environment Chapter 4 describes the structure and components of a PBS job and explains how to create and submit a PBS job 2 Chapter 1 Introduction Chapter 5 introduces the xpbs graphical user interface and shows how to submit a PBS job using xpbs Chapter 6 describes how
71. closed in double quotes The hold list defines the type of holds to be placed on the job The hold list argument is a string consisting of one or more of the letters u p o or s in any combina tion or the letter n The hold type associated with each letter is Letter Meaning n none no hold type specified u user the user may set and release this hold type p password set if job fails due to a bad password can be unset by the user o operator require operator privilege to unset s system requires manager privilege to unset If no h option is given the user hold will be applied to the jobs described by the job identifier operand list If the job identified by job _ identifier is in the queued held or waiting states then all that occurs is that the hold type is added to the job The job is then placed into held state if it resides in an execution queue If the job is running then the following additional action is taken to interrupt the execu tion of the job If checkpoint restart is supported by the host system requesting a hold on a running job will cause 1 the job to be checkpointed 2 the resources assigned to the job to be released and 3 the job to be placed in the held state in the execution queue If checkpoint restart is not supported qhold will only set the requested hold attribute This will have no effect unless the job is requeued with the grerun command PBS Professional 7 101 User
72. ction at all The miser option appears the better choice as it avoids the socket in the first place If the cpr option is used the checkpoint will work but will be slower because the socket connection must be closed first Note that interactive jobs or MPMD jobs more than one executable program cannot be checkpointed in any case Both use sockets and TCP IP to communicate outside of the job for interactive jobs and between programs in the MPMD case 158 Chapter 10 Multiprocessor Jobs PBS Professional 7 User s Guide 159 Appendix A PBS Environment Variables Table 23 PBS Environment Variables Variable Meaning NCPUS Number of threads or cpus per process ncpus on the node OMP NUM THREADS Same as NCPUS PBS ARRAY ID Identifier for job arrays Consists of sequence number PBS ARRAY INDEX Index number of subjob in job array PBS ENVIRONMENT Indicates job type PBS_BATCH or PBS_INTERACTIVE PBS JOBCOOKIE Unique identifier for inter MOM job based communication PBS _JOBID The job identifier assigned to the job or job array by the batch system PBS _JOBNAME The job name supplied by the user PBS _MOMPORT Port number on which this job s MOMs will communicate PBS NODEFILE The filename containing a list of nodes assigned to the job PBS NODENUM Logical node number of this node allocated to the job
73. d by one or more users The syntax of the user list is user name host user_ name host Host names may be wild carded on the left end e g mydo main com User_name without a host is equivalent to user name i e at any host Jobs will be selected which are owned by the listed users at the corresponding hosts For example say you want to list all jobs owned by user barry that requested more than 16 CPUs You could use the following gselect command syntax 94 Chapter 6 Checking Job System Status qselect u barry l ncpus gt 16 121 south 133 south 154 south Notice that what is returned is the job identifiers of jobs that match the selection criteria This may or may not be enough information for your purposes Many users will use shell syntax to pass the list of job identifiers directly into qstat for viewing purposes as shown in the next example necessarily different between UNIX and Windows UNIX qstat a qselect u barry 1 ncpus gt 16 Y P g Req d Elap Queue Jobname Sess NDS TSK Mem Time S Time workq workq Windows type the following at the cmd prompt all on one line for F usebackq j in qselect u barry l ncpus gt 16 qstat a j 121 south 133 south 154 south Note This technique of using the output of the gselect command as input to qstat can also be used to supply input to other PBS comman
74. ds as well 6 4 Selecting Jobs Using xpbs The xpbs command provides a graphical means of specifying job selection criteria offer ing the flexibility of the gselect command in a point and click interface Above the JOBS panel in the main xpbs display is the Other Criteria button Clicking it will bring PBS Professional 7 95 User s Guide up a menu that lets you choose and select any job selection criteria you wish The example below shows a user clicking on the Other Criteria button then selecting Job States to reveal that all job states are currently selected Clicking on any of these job states would remove that state from the selection criteria ey You may specify as many or as few selection criteria as you wish When you have com pleted your selection click on the Select Jobs button above the HOSTS panel to have xpbs refresh the display with the jobs that match your selection criteria The selected cri teria will remain in effect until you change them again If you exit xpbs you will be prompted if you wish to save your configuration information this includes the job selec tion criteria 96 Chapter 6 Checking Job System Status 6 5 Using xpbs TrackJob Feature The xpbs command includes a feature that allows you to track the progress of your jobs When you enable the Track Job feature xpbs will monitor your jobs looking for the out put files that signal completion of the job The Track Job button will flash red
75. e List PBS O LOGNAME userl PBS O HOST south user userl egroup groupl The brief option B will only show the identifiers of all the reservations pbs _rstat B Name R226 sout Name R302 sout Name R304 sout 8 8 4 Delete PBS Reservations The pbs_rdel command deletes reservations in the order in which their reservation identifiers are presented to the command A reservation may be deleted by its owner or a PBS operator manager Note that when a reservation is deleted all jobs belonging to the reservation are deleted as well regardless of whether or not they are currently running pbs_rdel R304 126 Chapter 8 Advanced PBS Features 8 8 5 Accounting Accounting records for advance resource reservations are available in the Server s job accounting file The format of such records closely follows the format that exists for job records In addition any job that belongs to an advance reservation will have the reserva tion ID recorded in the accounting records for the job 8 8 6 Access Control A site administrator can inform the Server as to those hosts groups and users whose advance resource reservation requests are or are not to be considered The philosophy in this regard is same as that which currently exists for jobs In a similar vein the user who submits the advance resource reservation request can spec ify to the system those other parties user s or group s that a
76. e host or be scattered across hosts or be grouped by a resource or whether it should run anywhere available It also allows specification of whether the job should have exclusive use of its node s For more information see Placing Jobs on Nodes on page36 and the pbs_resources 7B manual page 3 2 3 Node Types All nodes are now treated alike and are treated the same as what were called time shared nodes The types time shared and cluster are deprecated The ts suffix is deprecated It is silently ignored and not preserved during rewrite The node attribute ntype will only be used to distinguish between PBS and Globus nodes It is read only 3 2 4 Boolean Resources Replace Properties What were properties are now boolean resources These are treated like other resources except that they take on boolean values of True or False The term property is dep recated It will be accepted for the time being in a nodespec 3 2 5 Nodes File The server s node definition file has changed due to the use of boolean resources and the change in node types If an existing nodes file with deprecated forms is used when it is written out it will be in the new form Properties will be written as boolean resources and any ts suffixes will be dropped 3 2 6 The qsub qalter and pbs_rsub Commands The qsub qalter and pbs_rsub command usage has changed due to the change 18 Chapter 3 Getting Started With PBS
77. e sequence number component of the job identifier Both standard output and standard error will be retained Both standard output and standard error will be retained Neither file is retained 4 10 19 Suppressing job identifier The z option directs the gsub command to not write the job identifier assigned to the job to the command s standard output _ 4 10 20 Interactive batch jobs 56 Chapter 4 Submitting a PBS Job PBS provides a special kind of batch job called interactive batch An interactive batch job is treated just like a regular batch job in that it is queued up and has to wait for resources to become available before it can run Once it is started however the user s terminal input and output are connected to the job in a matter similar to a login session It appears that the user is logged into one of the available execution machines and the resources requested by the job are reserved for that job Many users find this useful for debugging their applications or for computational steering The I option declares that the job is an interactive batch job Important Interactive batch jobs are not currently supported on Windows If the I option is specified on the command line the job is an interactive job If a script is given it will be processed for directives but any executable commands will be discarded When the job begins execution all input to the job is from the terminal session in w
78. ect 1B for format of lt jobname gt A boolean value true or false indicating whether or not to iconize the HOSTS region A boolean value true or false indicating whether or not to iconize the QUEUES region A boolean value true or false indicating whether or not to iconize the JOBS region A boolean value true or false indicating whether or not to iconize the INFO region A curly braced list of resource names as according to architec ture known to xpbs The format is as follows lt arch typel gt resnamel resname2 resnameN lt arch type2 gt resnamel resname2 resnameN lt arch typeN gt resnamel resname2 resnameN PBS Professional 7 79 User s Guide Chapter 6 Checking Job System Status This chapter introduces several PBS commands useful for checking status of jobs queues and PBS Servers Examples for use are included as are instructions on how to accomplish the same task using the xpbs graphical interface 6 1 The qstat Command The qstat command is used to the request the status of jobs queues and the PBS Server The requested status is written to standard output stream usually the user s termi nal When requesting job status any jobs for which the user does not have view privilege are not displayed 6 1 1 Checking Job Status Executing the qstat command without any options displays job information in the default format An alternative display format is also provided and
79. ed after the job is queued If an error is detected the new job will be deleted by the server Mail will be sent to the job submitter stating the error PBS Professional 7 113 User s Guide Suppose you have three jobs job1 job2 and job3 and you want job3 to start after job1 and job2 have ended The first example below illustrates the options you would use on the qsub command line to specify these job dependencies qsub job1 16394 jupit qsub job2 16395 jupiter qsub W depend afterany 16394 16395 job3 16396 Jjupiter As another example suppose instead you want job2 to start only if jobl ends with no errors i e it exits with a no error status qsub jobl 16397 Jjupiter qsub W depend afterok 16397 job2 16396 jupiter Similarly you can use before dependencies as the following example exhibits Note that unlike after dependencies before dependencies require the use of the on depen dency qsub W depend on 2 jobl 16397 Jjupiter qsub W depend beforeany 16397 job2 16398 jupiter qsub W depend beforeany 16397 job3 16398 jupiter You can use xpbs to specify job dependencies as well On the Submit Job window in the other options section far left center of window click on one of the three dependency but tons after depend before depend or concurrency These will launch a Depen dency window in which you will be able to set up the dependencies you wish 8 5 Deli
80. emote_ e cfd Ju As with rcp the remote file and local file portions for both stage in and stage out may name a directory For stage in if remote file is a directory then local file must also be a directory Likewise for stage out if local file isa directory then remote file must be a directory If local file on a stage out directive is a directory that directory on the execution host including all files and subdi rectories will be copied At the end of the job the directory including all files and subdi rectories will be deleted Users should be aware that this may create a problem if multiple jobs are using the same directory The same requirements and hints discussed above in regard to delivery of output apply to staging files in and out Wildcards should not be used in either the local file or the remote filename PBS does not expand the wild card character on the local system If wildcards are used in the remote file name since rcp is launched by rsh to the remote system the expansion will occur However at job end PBS will attempt to delete the file whose name actually contains the wildcard character and will fail to find it This will leave all the staged in files in place undeleted File staging is supported for job arrays See File Staging on page 140 Using xpbs to set up file staging directives may be easier than using the command line On the Submit Job window in the miscellany options sect
81. en the Windows command interpreter tries to execute that last line PBS Professional 7 31 User s Guide Job attributes can be set either by using directives or by giving options to the qsub com mand These two methods have the same functionality Options to the qsub command will override PBS directives which override defaults Some job attributes have default values preset in PBS Some job attributes default values are set at the user s site 4 2 Submitting a PBS Job There are a few ways to submit a PBS job using the command line The first is to create a job script and submit it using qsub 4 2 1 Submitting a Job Script For example with job script myjob the user can submit it by typing qsub myjob 16387 foo exampledomain PBS returns a job identifier e g 16387 fo0 exampledomain in the example above Its format will be sequence number servernam or for a job array sequence number servername domain You ll need the job identifier for any actions involving the job such as checking job sta tus modifying the job tracking the job or deleting the job If my_job contains the following the user is naming the job testjob and running a program called myprogram bin sh PBS N testjob myprogram 4 2 1 1 Overriding Directives PBS directives in a script can be overridden by using the equivalent options to qsub For example to override the PBS directive naming the job
82. ent the set of all subjobs of the job array with a single index a job array identifier to represent a single subjob with a range a job array range to represent the subjobs designated by the range 9 1 2 Identifier Syntax Job arrays have three identifier syntaxes e The job array object itself 1234 server or 1234 e A single subjob of a job array with index M 1234 M server or 1234 M e A range of subjobs of a job array 1234 X Y Z server or 1234 X Y Z PBS Professional 7 137 User s Guide Examples 1234 server domain com Full job array identifier 1234 Short job array identifier 1234 73 Subjob identifier of the 73rd index of job array 1234 1234 Error if 1234 is a job array 1234 server domain com Error if 1234 server domain com is a job array The sequence number 1234 in 1234 server is unique so that jobs and job arrays cannot share a sequence number Note Since some shells for example csh and tcsh read and as shell metacharac ters job array names and subjob names will need to be enclosed in double quotes for all PBS commands Example qdel 1234 myhost 5 qdel 1234 myhost Single quotes will work except where you are using shell variable substitution 9 2 qsub Submitting a Job Array To submit a job array qsub is used with the option J range where range is of the form X Y Z X is the starting index Y is the ending index and Z is the option
83. eq d Elap Job ID User Jobname Sess NDS Time S Time 54 south barry workg To alter a job attribute via xpbs first select the job s of interest and the click on modify button Doing so will bring up the Modify Job Attributes dialog box From this window you may set the new values for any attribute you are permitted to change Then click on the confirm modify button at the lower left of the window The qalter command can be used on job arrays but not on subjobs or ranges of subjobs When used with job arrays any job array identifiers must be enclosed in double quotes e g qalter l1 walltime 25 00 1234 south For more information see the qalter 1B manual page 100 Chapter 7 Working With PBS Jobs 7 2 Holding and Releasing Jobs PBS provides a pair of commands to hold and release jobs To hold a job is to mark it as ineligible to run until the hold on the job is released The qhold command requests that a Server place one or more holds on a job A job that has a hold is not eligible for execution There are three types of holds user operator and system A user may place a user hold upon any job the user owns An operator who is a user with operator privilege may place either an user or an operator hold on any job The PBS Manager may place any hold on any job The usage syntax of the qhold com mand is qhold h hold list job identifier Note that for a job array the job_identifier must be en
84. er specified lt output_path gt and lt stderr_path gt v lt variable_list gt environment lt variable_list gt job type single When the job gets submitted to Globus PBS qstat will report various state changes according to the following mapping Table 15 PBS Job States vs Globus States PBS State Globus State TRANSIT T PENDING RUNNING R ACTIVE EXITING E FAILED EXITING E DONE 8 10 3 PBS File Staging through GASS The stagein stageout feature of Globus aware PBS works with Global Access to Sec ondary Storage GASS software Given a stagein directive localfile host inputfile PBS will take care of copying inputfile at host over to localfile at the execut ing Globus machine The same process is used for a stageout directive localfile host outputfile PBS will take care of copying the 1ocalfile on the executing Globus host over to the 130 Chapter 8 Advanced PBS Features outputfileat host Globus file transfer mechanisms are used when transferring files between hosts that run Globus otherwise pbs scp pbs rcp or cp is used This means that if the host given in the stage in stage out argument runs Globus then Globus communication will be opened to that system 8 10 4 Limitation PBS does not currently support co allocated Globus jobs where two or more jobs are simultaneously run distributed over two or more Globus resource managers 8 10 5 Examples Be
85. ervice a confirmed reserva tion Users who are listed as being allowed to run jobs using the resources of this reservation will submit their jobs to this queue via the standard qsub command Although a confirmed resources reservation will accept jobs into its queue at any time the scheduler is not allowed to schedule jobs from the queue before the reservation period arrives Once the reservation period arrives these jobs will begin to run but they will not in aggregate use up more resources than the reservation requested The pbs_rsub command returns an ID string to use in referencing the reservation and an indication of its current status The actual specification of resources is done in the same way as it is for submission of a job Following is a list and description of options to the 120 Chapter 8 Advanced PBS Features pbs_rsub command R datetime E datetime D timestring q destination m mail_ points Specifies reservation starting time If the reservation s end time and duration are the only times specified this start time is cal culated The datetime argument adhers to the POSIX time speci fication LII CC YY MM DD hhmn SS If the day DD is not specified it will default to today if the time hhmm is in the future Otherwise the day will be set to tomor row For example if you submit a reservation having a specifi cation R 1110 at 11 15am it will be interpreted as being for 11 10am tomorrow
86. es a maximum username length of 15 characters Ifa job is submitted to run under a username longer than this limit the job will be rejected 3 7 Setting Up Your UNIX Linux Environment A user s job may not run if the user s start up files i e cshre login or profile contain commands which attempt to set terminal characteristics Any such command sequence within these files should be skipped by testing for the environment variable PBS ENVIRONMENT This can be done as shown in the following sample login setenv MANPATH usr man usr local man SMANPATH if PBS_ ENVIRONMENT then do terminal settings here endif PBS Professional 7 23 User s Guide You should also be aware that commands in your startup files should not generate output when run under PBS As in the previous example commands that write to stdout should not be run for a PBS job This can be done as shown in the following sample login setenv MANPATH usr man usr local man SMANPATH if PBS_ENVIRONMENT then do terminal settings here run command with output here endif When a PBS job runs the exit status of the last command executed in the job is reported by the job s shell to PBS as the exit status of the job We will see later that this is impor tant for job dependencies and job chaining However the last command executed might not be the last command in your job This can happen if your job s shell is csh on t
87. ess 0 of 4 on host pluto at time Mon Aug 29 17 39 01 2004 Example 3 Here is a more complicated example Say you want to transfer and run a SGlI specific MPI job requiring 4 CPUs on host sgi galaxey com via Globus Furthermore let s say that host is running a different batch system and you want the job s out put returned to the submitting host The following job script illustrates this PBS 1 site globus sgi galaxy com jobmanager l1sf PBS W stagein u jill mpi_sgi earth progs mpi_sgi PBS W stageout mpi_sgi out earth mpi_ sgi out mpirun np 4 u jill mpi_sgi gt gt mpi _sgi out echo Done it Upon execution the sample output is Done it And the output of the run would have been written to the file mpi sgi out and returned to the user s home directory on host earth as specified Note Just like a job that s completely managed by PBS a job that s submitted to a Globus 132 Chapter 8 Advanced PBS Features Grid through PBS can be deleted signaled held released rerun have text appended to its output error files and be moved from one location to another 8 11 Running PBS in a UNIX DCE Environment PBS Professional includes optional support for UNIX based DCE By optional we mean that the customer may acquire a copy of PBS Professional with the standard security and authentication module replaced with the DCE module There are two W options available with qsub which will e
88. essional has a major new feature This is the enhancement to job resource requests and job placement on nodes Several existing features are replaced by this new feature and are deprecated All nodes are now treated alike with respect to allocating jobs and specifying resources There is no distinction between time shared and cluster nodes all nodes are treated as time shared but are referred to as nodes The following is a list of new features and changes in PBS Professional release 7 More detail is given in the indicated sections Enhancement to job resource requests and placement See Major Changes on page 16 Requesting Resources on page 32 and Placing Jobs on Nodes on page 36 Improved integration with LAM MPI See PBS Jobs with LAM 16 Chapter 3 Getting Started With PBS MPI on page 156 Improved integration with MPI for HP running HP UX and Linux See PBS MPI Jobs on HP UX and Linux on page 156 Ability to convert a regular job into a reservation job that will run ASAP See Converting a Job into a Reservation Job on page 107 Job Arrays See Job Arrays on page 135 Change to mpirun command See MPICH Jobs With PBS on page 154 Integration with AIX MPI See MPI Jobs Using AIX POE on page 155 Support for CSA user job accounting on Altix machines See Using Comprehensive System Accounting on page 126 Important The full list of new features in this
89. f the job array returned an exit status of 0 No PBS error occurred Deleted subjobs are not considered 1 At least 1 subjob returned a non zero exit status No PBS error occurred 2 A PBS error occurred 9 10 8 Scheduling Job Arrays All subjobs within a job array have the same scheduling priority 9 10 8 1 Preemption Individual subjobs may be preempted by higher priority work 9 10 8 2 Peer Scheduling Peer scheduling does not support job arrays 9 10 8 3 Fairshare Subjobs are treated like jobs with respect to fairshare ordering fairshare accounting and fairshare limits If running enough subjobs of a job array causes the priority of the owning entity to change additional subjobs from that job array may not be the next to start 9 10 8 4 Node Grouping All nodes associated with a single subjob should belong to the same node group Different subjobs can be put on different node groups PBS Professional 7 153 User s Guide Chapter 10 Multiprocessor Jobs 10 1 Submitting SMP MPI and Multi threaded Jobs To submit a job which should run on one host and which requires a certain number of cpus and amount of memory submit the job with qsub l select ncpus N mem M 1 place group host When the job is run the PBS_NODEFILE will contain one entry the name of the selected execution host Generally this is ignored for SMP jobs as all processes in the job are run on the host where the job script is run The job will have t
90. h as working directory Any relative pathnames in stagein stageout output error file delivery will resolve to the above path PBS Professional 7 25 User s Guide Note that Windows can return as PROFILE PATH one of the following forms Documents and Settings username Documents and Settings username local hostname Documents and Settings username local hostname 00N where N is a number Documents and Settings username domain name 3 8 2 Windows Usernames and Job Submission A PBS job is run from a user account and the associated username string must conform to the POSIX 1 standard for portability That is the username must contain only alphanu meric characters dot underscore _ and or hyphen The hyphen must not be the first letter of the username If appears in the username then it will assumed to be in the context of a Windows domain account username domainname An exception to the above rule is the space character which is allowed If a space character appears in a username string then it will be displayed quoted and must be specified in a quoted man ner The following example requests the job to run under account Bob Jones qsub u Bob Jones my _ job 3 8 3 Windows rhosts File The Windows rhosts file is located in the user s PROFILE PATH for example Documents and Settings username rhosts with the format hostname username Important Be sure the rhosts file is owned b
91. h the same API as used by the client commands Note that the Scheduler interfaces with the Server with the same privilege as the PBS man ager 10 Chapter 2 Concepts and Terms 2 2 Defining PBS Concepts and Terms The following section defines important terms and concepts of PBS The reader should review these definitions before beginning the planning process prior to installation of PBS The terms are defined in an order that best allows the definitions to build on previous terms Node Cluster Exclusive VP Load Balance Queue A node to PBS is a computer system with a single operating system OS image a unified virtual memory space one or more CPUs and one or more IP addresses Frequently the term execution host is used for node A computer such as the SGI Origin 3000 which contains multiple CPUs running under a single OS is one node Systems like the IBM SP and Linux clusters which contain separate computational units each with their own OS are collections of nodes If a node has more than one virtual processor the VPs may be assigned to different jobs or used to satisfy the requirements of a single job exclusive This ability to temporarily allocate the entire node to the exclusive use of a single job is important for some multi node parallel applications Note that PBS enforces a one to one allocation scheme of cluster node VPs ensuring that the VPs are not over allocated or over subscribed between multiple j
92. he exe cution host and you have a logout there In that case the last command executed is from the logout and not your job To prevent this you need to preserve the job s exit status in your logout file by saving it at the top then doing an explicit exit at the end as shown below set EXITVAL status previous contents of logout here exit SEXITVAL Likewise if the user s login shell is csh the following message may appear in the stan dard output of a job Warning no access to tty thus no job control in this shell This message is produced by many csh versions when the shell determines that its input is not a terminal Short of modifying csh there is no way to eliminate the message For tunately it is just an informative message and has no effect on the job An interactive job comes complete with a pseudotty suitable for running those commands that set terminal characteristics But more importantly it does not caution the user that starting something in the background that would persist after the user has exited from the interactive environment might cause trouble for some moms They could believe that once the interactive session terminates all the user s processes are gone with it For example applications like ssh agent background themselves into a new session and would prevent a 24 Chapter 3 Getting Started With PBS CPU set enabled mom from deleting the CPU set for the job This in turn might cause subseq
93. he index which has many properties of a job as well as additional semantics defined below Sequence number The numeric part of a job or job array identifier e g 1234 Subjob index The unique index which differentiates one subjob from another This must be a non negative integer Job array The identifier returned upon success when submitting a job array identifier The format is sequence_number or sequence_number server domain com 136 Chapter 9 Job Arrays Job array range A set of subjobs within a job array When specifying a range indices used must be valid members of the job array s indices 9 1 1 Description A job array is a compact representation of one or more jobs called subjobs when part of a Job array which have the same job script and have the same values for all attributes and resources with the following exceptions e each subjob has a unique index Job Identifiers of subjobs only differ by their indices e the state of subjobs can differ All subjobs within a job array have the same scheduling priority A job array is submitted through a single command which returns on success a job array identifier with a server unique sequence number Subjob indices are specified at submis sion time These can be e a contiguous range e g 1 through 100 e a range with a stepping factor e g every second entry in 1 through 100 1 3 5 99 A job array identifier can be used e by itself to repres
94. hich qsub is running The I option is ignored in a script directive When an interactive job is submitted the gsub command will not terminate when the job is submitted qsub will remain running until the job terminates is aborted or the user interrupts qsub with a SIGINT the control C key If qsub is interrupted prior to job start it will query if the user wishes to exit If the user responds yes qsub exits and the job is aborted Once the interactive job has started execution input to and output from the job pass through qsub Keyboard generated interrupts are passed to the job Lines entered that begin with the tilde character and contain special sequences are interpreted by qsub itself The recognized special sequences are qsub terminates execution The batch job is also terminated susp If running under the UNIX C shell suspends the qsub pro gram susp is the suspend character usually CNTL Z asusp If running under the UNIX C shell suspends the input half of qsub terminal to job but allows output to continue to be dis played asusp is the auxiliary suspend character usually con trol Y 4 11 Job Attributes A PBS job has the following attributes which may be set by the various options to gsub PBS Professional 7 57 User s Guide for details see section 4 10 Job Submission Options on page 44 Account Name Checkpoint depend Error Path Execution Time grou
95. host user host If unset the list defaults to the submitting user at the qsub host i e the job owner qsub M userl mydomain com my_job Important PBS on Windows can only send email to addresses that specify an actual hostname that accepts port 25 sendmail requests For the above example on Windows you will need to specify qsub M userl host mydomain com where host mydomain com accepts port 25 connections 4 10 7 Specifying a job name The N name option declares a name for the job The name specified may be up to and including 15 characters in length It must consist of printable non whitespace characters PBS Professional 7 User s Guide 49 with the first character alphabetic and contain no special characters If the N option is not specified the job name will be the base name of the job script file specified on the command line If no script file name was specified and the script was read from the stan dard input then the job name will be set to STDIN 4 10 8 Marking a Job as Rerunnable or Not The r y n option declares whether the job is rerunnable To rerun a job is to termi nate the job and requeue it in the execution queue in which the job currently resides The value argument is a single character either y or n If the argument is y the job is rerunnable If the argument is n the job is not rerunnable The default value is y rerunnab
96. indows Mapped Drives and PBS In Windows XP unlike Windows 2000 when you map a drive it is mapped locally to your session The mapped drive cannot be seen by other processes outside of your session A drive mapped on one session cannot be un mapped in another session even if it s the same user This has implications for running jobs under PBS Specifically if you map a drive chdir to it and submit a job from that location the node that executes the job may not be able to deliver the files back to the same location from which you issued qsub The workaround is to use the 0 or e options to qsub and specify a local non mapped directory location for the job output and error files For details see section 4 10 2 Redi recting output and error files on page 46 3 9 Environment Variables PBS Professional 7 27 User s Guide There are a number of environment variables provided to the PBS job Some are taken from the user s environment and carried with the job Others are created by PBS Still oth ers can be explicitly created by the user for exclusive use by PBS jobs All PBS provided environment variable names start with the characters PBS _ Some are then followed by a capital O PBS O_ indicating that the variable is from the job s originating environ ment i e the user s Appendix A gives a full listing of all environment variables provided to PBS jobs and their meaning The following short example
97. ion far left center of window click on the file staging button This will launch the File Staging dialog box shown below in which you will be able to set up the file staging you desire The File Selection Box will be initialized with your current working directory If you wish to select a different directory double click on its name and xpbs will list the contents of the new directory in the File Selection Box When the correct directory is displayed sim ply click on the name of the file you wish to stage in or out Its name will be written in the File Selected area Next click either of the Add file selected buttons to add the named file to the stage in or PBS Professional 7 117 User s Guide stage out list Doing so will write the file name into the corresponding area on the lower half of the File Staging window Now you need to provide location information For stage in type in the path and filename where you want the named file placed For stage out specify the hostname and pathname where you want the named file delivered You may repeat this process for as many files as you need to stage When you are done selecting files click the OK button 8 6 1 File Staging Between UNIX and Windows If the files being staged are being copied from a UNIX host to a Windows host or the other way around ensure that all pathnames in the stage in stage out specification are absolute not relative For example this directive to qsub
98. ion to qsub in section 4 10 9 Specifying which scripting language to use on page 49 The Windows script will be a exe or bat file Lines 2 8 of both files are almost identical The primary differences will be in file and directory path specification such as the use of drive letters and slash vs backslash as the path separator Lines 2 4 are PBS directives PBS reads down the shell script until it finds the first line that is not a valid PBS directive then stops It assumes the rest of the script is the list of commands or tasks that the user wishes to run In this case PBS sees lines 6 8 as being user commands We will see shortly how to use the qsub command to submit PBS jobs Any option that you specify to the qsub command line except I can also be provided as a PBS directive inside the PBS script PBS directives come in two types resource requirements and attribute settings In our example above lines 2 3 specify the 1 resource list option followed by a spe PBS Professional 7 39 User s Guide cific resource request Specifically lines 2 3 request 1 hour of wall clock time as a job wide request and 400 megabytes MB of memory in a chunk Line 4 requests that PBS join the stdout and stderr output streams of the job into a single stream Finally lines 6 8 are the command lines for executing the program s we wish to run You can specify as many programs tasks or job steps as you need 4 7 Cha
99. ired and may be wild carded on the left end e g mydo main com user name without a host is equivalent to user name that is at any host qstat u Req d Elap Jobname Sess NDS Time S Time qstat u userl barry 51 south barry workq airfoil 52 south userl workq my_job 54 south barry workq airfoil 6 1 7 List Running Jobs The r option to qst at displays the status of all running jobs at the optionally speci fied PBS Server Running jobs include those that are running and suspended One line of output is generated for each job reported and the information is presented in the alterna tive display 6 1 8 List Non Running Jobs The i option to qstat displays the status of all non running jobs at the optionally specified PBS Server Non running jobs include those that are queued held and waiting One line of output is generated for each job reported and the information is presented in the alternative display see description above PBS Professional 7 87 User s Guide 6 1 9 Display Size in Gigabytes The G option to gst at displays all jobs at the requested or default Server using the alternative display showing all size information in gigabytes GB rather than the default of smallest displayable units Note that if the size specified is less than 1 GB then the amount if rounded up to 1 GB 6 1 10 Display Size in Megawords The
100. ironment Variables to Export subwindow to have current environment variables exported to the job o _Use the Job Name field in the OPTIONS subwindow to give the job a name o Use the Notify email address and one of the buttons in the OPTIONS subwindow to have PBS send you mail when the job terminates Now that the script is built you have four options of what to do next Reset options to default Save the script to a file Submit the job as a batch job Submit the job as an interactive batch job UNIX only Reset clears all the information from the submit job dialog box allowing you to create a job from a fresh start Use the FILE field in the upper left corner to define a filename for the script Then press the Save button This will cause a PBS script file to be generated and written to the named file Pressing the Confirm Submit button at the bottom of the Submit window will submit the PBS job to the selected destination xpbs will display a small window containing the job identifier returned for this job Clicking OK on this window will cause it and the Submit window to be removed from your screen On UNIX systems not Windows you can alternatively submit the job as an interactive batch job by clicking the nteractive button at the bottom of the Submit Job window 76 Chapter 5 Using the xpbs GUI Doing so will cause an X terminal window xterm to be launched and within that win dow a PBS interactive bat
101. is discussed below The default display includes the following information The job identifier assigned by PBS The job name given by the submitter The job owner The CPU time used 80 Chapter 6 Checking Job System Status The job state The queue in which the job resides The job state is abbreviated to a single character State Description B Job arrays only job array has started E Job is exiting after having run H Job is held A job is put into a held state by the server or by a user or administrator A job stays in a held state until it is released by a user or administrator Q Job is queued eligible to run or be routed R Job is running S Job is suspended by server A job is put into the suspended state when a higher priority job needs the resources T Job is in transition being moved to a new location U Job is suspended due to workstation becoming busy W Job is waiting for its requested execution time to be reached or job spec ified a stage in request which failed for some reason X Subjobs only subjob is finished expired The following example illustrates the default display of qstat PBS Professional 7 81 User s Guide Time Use airfoil 00 21 03 airfoil 21 09 12 my job 0 tns3d O airfoil 0 seq_35 3 donald O O OO0OO0OJJVZZT An alternative display accessed via the a option is also provided that includes extra info
102. ist argument is a string consisting of one or more occur rences the single letter n or one or more of the letters u o p or s in any combination If letters are duplicated they are treated as if they occurred once The letters represent the hold types Letter Meaning n none u user o operator p bad password Windows only S system Shows only job array identifiers Restricts selection of jobs to those with specified resource amounts Only those jobs will be selected whose Resource List attribute matches the specified relation with each resource and value listed in the resource _list argument The relation operator op must be present The resource list is in the following for mat resource nameopvalue resource_nameopval 92 Chapter 6 Checking Job System Status N name p op priority q destination r rerun s States Restricts selection of jobs to those with a specific name Restricts selection of jobs to those with a priority that matches the specified relationship If op is not specified jobs are selected for which the job Priority attribute is equal to the prior ity Restricts selection to those jobs residing at the specified desti nation The destination may be one of the following three forms queue server queue server If the q option is not specified jobs will be selected from the default Server If the destination describes only a queue only job
103. ith n The program is spawned on a single node which is the N th node allocated This option is mutual exclusive with c The program will not wait for the tasks to finish If this option is given the program is run sequentially on each node one after the other Verbose output about error messages and task exit status is pro duced When run without the c or the n option pbsdsh will spawn the program on all nodes allocated to the PBS job The execution take place concurrently all copies of the task exe cute at about the same time The following example shows the pbsdsh command inside of a PBS batch job The options indicate that the user wants pbsdsh to run the myapp program with one argu ment app arg1 on all four nodes allocated to the job i e the default behavior PBS se PBS wa ect mem 10GB ltime 1 00 00 pbsdsh myapp app arg1 8 8 Advance Reservation of Resources PBS Professional 7 119 User s Guide An Advance Reservation is a set of resources with availability limited to a specific user or group of users a specific start time and a specified duration The user submits an advance reservation with the ppbs_rsub command PBS will then confirm that the reser vation can be met or else reject the request Once the scheduler has confirmed the reserva tion the queue that was created to support this reservation will be enabled allowing jobs to be submitted to it The queue
104. le qsub r n my_ job 4 10 9 Specifying which scripting language to use The S path _1list option declares the path and name of the scripting language to be used in interpreting the job script The option argument path list is in the form pathi host path host Only one path may be specified for any host named and only one path may be specified without the corresponding host name The path selected will be the one with the host name that matched the name of the execution host If no matching host is found then the path specified without a host will be selected if present If the S option is not specified the option argument is the null string or no entry from the path_list is selected then PBS will use the user s login shell on the execu 50 Chapter 4 Submitting a PBS Job tion host qsub S usr local bin perl my job PBS S bin bash mars usr bin bash jupiter Important Using this option under Windows is more complicated because if you change from the default shell of cmd then a valid PATH is not automatically set Thus if you use the S option under Windows you must explicitly set a valid PATH as the first line of your job script 4 10 10 Setting a job s priority The p priority option defines the priority of the job The priority argument must be an integer between 1024 lowest priority and 1023 highest priority inclusive The default is no priority which is equivalent to
105. lecting Jobs Using xpbs 00 0 ee ceecceesseeeteeeeeeeeeee 94 Using xpbs TrackJob Feature cceccesseeeteees 96 7 Working With PBS Jobs ccsscccssscsssrsesssseseees 97 Modifying Job Attributes eee cecceeeeeereeeteees 97 Holding and Releasing Jobs ceeceeseeeeeeeeee 100 D leting J ODS Acie va ceriohs ater e a bees 102 Sending Messages to JODS ccceeceeseeeteeeteees 103 Sending Signals to Jobs eeceeccceseceteeeteeeteees 104 Changing Order of Jobs Within Queue 105 Moving Jobs Between Queues eeeesceeeeeeeee 106 Converting a Job into a Reservation Job 107 8 Advanced PBS Features cscsssccssscsssesseossees 109 UNIX Job Exit Statuis cisscssessassccdacstessanestaenneesteats 109 Changing UNIX Job umask 0 ce eeeeeeeeteeee 110 Requesting qsub Wait for Job Completion 110 Specifying Job Dependencies eee 111 PBS Professional 7 v User s Guide Delivery of Output Files ccccaserscaccctadasvecdes 113 Input Output File Staging 00 0 0 ee eeeeeeeeeeeeee 114 The pbsdsh Command s icnccacseecctiancancgiens 117 Advance Reservation of Resources eeeee 118 Using Comprehensive System Accounting 126 Globus Support xccscrlpotsvas scott ccs Beeseoe eaters 127 Running PBS in a UNIX DCE Environment 132 Running PBS in a UNIX Kerberos Environment 132 9 SOD ATTA ionini tssis reas sioi 135 Definitionsiseee nenn
106. lists some of the more useful variables and typical values PBS _O HOME u userl PBS O LOGNAME userl1 PBS O PATH usr new bin usr local bin bin PBS O SHELL sbin csh PBS _ O HOST cray1 PBS O WORKDIR u userl PBS O QUEUE submit PES _JOBID 16386 cray1 PBS QUEUE crayq PBS ENVIRONMENT PBS_ INTERACTIVE There are a number of ways that you can use these environment variables to make more efficient use of PBS In the example above we see PBS_ ENVIRONMENT which we used earlier in this chapter to test if we were running under PBS Another commonly used vari able is PBS_O_WORKDIR which contains the name of the directory from which the user submitted the PBS job There are also two environment variables that you can set to affect the behavior of PBS The environment variable PBS_DEFAULT defines the name of the default PBS Server Typically it corresponds to the system name of the host on which the Server is running If PBS DEFAULT is not set the default is defined by an administrator established file usu ally etc pbs conf on UNIX and PBS Destination Folder pbs conf on Windows The environment variable PBS_DPREFIX determines the prefix string which identifies directives in the job script The default prefix string is PBS however the Windows user may wish to change this as discussed in section 4 7 Changing the Job s PBS Direc tive on page 39 3 10 Temporary Scratch Space TMPDIR 28 Chap
107. lly delete the reservation request from the system If automatic deletion isn t being requested and if the scheduler doesn t make a decision in the specified number of seconds the command will return the ID string for the reservation and show the status as unconfirmed The requester may periodically issue the pbs_rstat com mand with ID string as input to monitor the reservation s status W other attributes value This allows a site to define any extra attributes for the reserva tion The following attribute is supported qmove jobid Converts the normal job with job ID jobid into a reservation job that will run as soon as possible Creates the reservation and reservation queue and places the job in the queue Uses the resources requested by the job to create the reservation In creating the reservation resources requested through the pbs_rsub command override existing job resources There PBS Professional 7 123 User s Guide fore if the existing job resources are greater than those requested for the reservation the job will be rejected by the reservation The R and E options to pbs_rsub are disabled when using the qmove jobid attribute See Converting a Job into a Reservation Job on page 107 The following example shows the submission of a reservation asking for 1 node 30 min utes of wall clock time and a start time of 11 30 Note that since an end time is not speci fied PBS will calculate the end
108. low are some examples of using PBS with Globus They all assume that the user has acquired a valid grid proxy certificate beforehand by running Globus grid proxy init utility Example 1 If you want to run a single processor job on globus gatekeeper mars mydomain com using whatever job manager is cur rently configured at that site then you could create a PBS script like the following example cat job script PBS 1 site globus mars mydomain com echo hostname Hello world Globus style Upon execution this will give the sample output mars Hello world Globus style Example 2 If you want PBS to submit a multi processor job to the Globus gatekeeper pluto mydomain com jobmanager fork with CPU count set to 4 and shipping the architecture compati ble executable mpitest over to the Globus host pluto for execution then compose a script and submit as follows PBS 1 site globus pluto domain com 763 jobmanager fork C US O Communications Package OU Stellar Divi sion CN shirley com org PBS Professional 7 131 User s Guide PBS W stagein mpitest earth domain com progs mpitest mpirun n 4 mpitest wait Upon execution this sample script would produce the following output Process 2 of 4 on host pluto at time Mon Aug 29 17 39 01 2004 Process 3 of 4 on host pluto at time Mon Aug 29 17 39 01 2004 Process 1 of 4 on host pluto at time Mon Aug 29 17 39 01 2004 Proc
109. ly places the job into execution This process pbs_mom is informally called MOM as it is the mother of all executing jobs MOM is a reverse engineered acronym that stands for Machine Oriented Mini server MOM places a job into execution when it receives a copy of the job from a Server MOM creates a new session that is as identical to a user login session as is possible For example under UNIX if the user s login shell is csh then MOM creates a session in which login is run as well as cshrc MOM also has the responsibility for returning the job s output to the user when directed to do so by the Server One MOM runs on each computer which will execute PBS jobs A special version of MOM called the Globus MOM is available if it is enabled during the installation of PBS It handles submission of jobs to the Globus environment Globus is a software infrastructure that integrates geographically distributed computational and infor mation resources Globus is discussed in more detail in the PBS Professional Administrator s Guide To find out if Globus sup port is enabled at your site contact your PBS system administrator The Job Scheduler daemon service pbs_sched implements the site s policy controlling when each job is run and on which resources The Scheduler communicates with the various MOMs to query the state of system resources and with the Server for avail ability of jobs to execute The interface to the Server is throug
110. mand requests that a signal be sent to executing PBS jobs The signal is sent to the session leader of the job Usage syntax of the qs ig command is qsig s signal job_identifier Job array job_identifiers must be enclosed in double quotes If the s option is not specified SIGTERM is sent If the s option is specified it declares which signal is sent to the job The signal argument is either a signal name e g SIGKILL the signal name without the STG prefix e g KILL or an unsigned signal number e g 9 The signal name SIGNULL is allowed the Server will send the signal 0 to the job which will have no effect Not all signal names will be recognized by qsig If it doesn t recognize the signal name try issuing the signal number instead The request to signal a batch job will be rejected if The user is not authorized to signal the job The job is not in the running state The requested signal is not supported by the execution host The job is exiting Two special signal names suspend and resume note all lower case are used to sus pend and resume jobs When suspended a job continues to occupy system resources but is not executing and is not charged for walltime Manager or operator privilege is required to suspend or resume a job The three examples below all send a signal 9 SIGKILL to job 34 qsig s SIGKILL 34 qsig s KILL 34 qsig s 9 34 PBS Professional 7 105 User s Guide Important On m
111. mechanism a The hostname of the machine from which the current user is logged in appears in the server s hosts equiv file or b The current user has an entry in user s HOMEDIR rhosts file Note that pbs password encrypts the password obtained from the user before sending it to the PBS Server The pbs password command does not change the user s pass word on the current host only the password that is cached in PBS 4 8 2 Per Job Password Method If you are running in a password protected Windows environment but the single signon method has not been configured at your site then you will need to supply a password with the submission of each job You can do this via the qsub command with the Wpowd option and supply the password when prompted gqsub Wpwd lt password gt job script The password specified will be shown on screen and will be passed onto the program which will then encrypt it and save it securely for use by the job The password should be enclosed in double quotes If you only type the pair of double quotes you will be prompted for the password The password can also be specified in xpbs using the SUBMIT PASSWORD entry box in the Submit window The password you type in will not be shown on the screen Important Both the Wpwd option to qsub and the xpbs SUBMIT PASS WORD entry box can only be used when submitting jobs to Win dows The UNIX qsub does not support the Wpwd option and if you type a passwo
112. mize maximize button identified by a dot or a rectangular image for displaying or iconizing the Hosts region The listbox dis plays information about favorite Server host s and each entry is meant to be selected via a single left click shift left click for contiguous selection or control left click for non contiguous selection To the right of the Hosts Panel are buttons that represent actions that can be performed on selected host s Use of these buttons will be explained in detail below detail Provides information about selected Server host s This functional ity can also be achieved by double clicking on an entry in the Hosts listbox submit For submitting a job to any of the queues managed by the selected host s terminate For terminating shutting down PBS Servers on selected host s Visible via the admin option only Important Note that some buttons are only visible if xpbs is started with the admin option which requires manager or operator privilege to function The middle portion of the Hosts Panel has abbreviated column names indicating the infor mation being displayed as the following table shows Table 9 xpbs Server Column Headings Heading Meaning Max Maximum number of jobs permitted Tot Count of jobs currently enqueued in any state Que Count of jobs in the Queued state Run Count of jobs in the Running state Hld Count of jobs in the Held state Wat Count of jobs in
113. n for more detail The job scheduling priority assigned by the user The rerunnable flag given by the user The resource list is a set of resources required by the job The value also establishes the limit of usage of that resource If not set the value for a resource may be determined by a queue or Server default established by the administrator A set of absolute paths of the program to process the job s script file stagein stageout umask User List Variable List comment PBS Professional 7 59 User s Guide The list of files to be staged in prior to job execution The list of files to be staged out after job execution The initial umask of the job is set to the value of this attribute when the job is created This may be changed by umask commands in the shell initialization files such as profile or cshrc Default value 077 The list of user hosts which determines the username under which the job is run on a given host This is the list of environment variables passed with the Queue Job batch request An attribute for displaying comments about the job from the system Visible to any client The following attributes are read only they are established by the Server and are visible to the user but cannot be set or changed by a user accounting id alt_id array array _id array_index Accounting ID for tracking accounting data not produced by PBS For a few systems such as Irix 6 x running
114. n set The example below illustrates the different type of messages that may be displayed Req d Queue Jobname Sess NDS TSK Mem Time L workgq aimsl 1 held by userl on Wed Aug 22 13 06 11 2 userl workgq aims14 re d Waiting on user requested start time south barry workg airfoil 930 I o Job run on node south started Thu Aug 23 south userl workgq my job E Ji te Not Running No available resources on nodes N soul susan workq solver Se 2 0 6 1 13 Display Queue Limits The q option to qstat displays any limits set on the requested or default queues Since PBS is shipped with no queue limits set any visible limits will be site specific The limits are listed in the format shown below qstat q server south Memory CPU Time Walltime Node Run Que Im State 6 1 14 Show State of Job Job Array or Subjob The t option to qstat will show the state of a job a job array object and all non X sub jobs In combination with J qstat will show only the state of subjobs PBS Professional 7 89 User s Guide 6 1 15 Show state of Job Arrays The J option to qstat will show only the state of job arrays In combination with t qstat will show only the state of subjobs 6 1 16 Print Job Array Percentage Completed The p option to qstat prints the default display with a column for Percentage Com pleted For a job
115. nable a dcelogin context to be set up for the job when it eventually executes The user may specify either an encrypted password or a forwardable renewable Kerberos V5 TGT Specify the W cred dce option to qsub if a forwardable renewable Kerberos VS TGT ticket granting ticket with the user as the listed principal is what is to be sent with the job If the user has an established credentials cache and a non expired forwardable renewable TGT is in the cache that information is used The other choice W cred dce pass causes the qsub command to interact with the user to generate a DES encryption of the user s password This encrypted password is sent to the PBS Server and MOM processes where it is placed in a job specific file for later use by pbs_mom in acquiring a DCE login context for the job The information is destroyed if the job terminates is deleted or aborts Important The W pwd option to qsub has been superseded by the above two options and therefore should no longer be used Any acquired login contexts and accompanying DCE credential caches established for the job get removed on job termination or deletion qsub Wcred dce lt other qsub options gt job script Important The W cred option to qsub is not available under Win dows 8 12 Running PBS in a UNIX Kerberos Environment PBS Professional includes optional support for Kerberos only i e no DCE environment PBS Professional 7
116. nd SIGKILL are not trapped and thus will immediately terminate the qsub process leaving the associated job either running or queued If the job runs to completion qsub will exit with the exit status of the job See also section 8 1 UNIX Job Exit Status on page 109 for further discussion of the job exit status For job arrays blocking qsub waits until the entire job array is complete then returns the exit status of the job array PBS Professional 7 111 User s Guide 8 4 Specifying Job Dependencies PBS allows you to specify dependencies between two or more jobs Dependencies are use ful for a variety of tasks such as 1 Specifying the order in which jobs in a set should execute 2 Requesting a job run only if an error occurs in another job 3 Holding jobs until a particular job starts or completes execution The W depend dependency list option to qsub defines the dependency between multiple jobs The dependency list has the format type arg list type arg list where except for the on type the arg_1list is one or more PBS job IDs in the form jobid jobid There are several types after arg_list This job may be scheduled for execution at any point after all jobs in arg list have started execution afterok arg_ list This job may be scheduled for execution only after all jobs in arg list have terminated with no errors See Warning about exit status with csh in EXIT STATUS afternotok arg list Thi
117. ndows environment you will need to spec ify to PBS the password needed in order to run your jobs There are two methods of doing this 1 by providing PBS with a password once to be used for all jobs single signon method or 2 by specifying the password for each job when submitted per job method Check with your system administrator to see which method was configured at your site 4 8 1 Single Signon Password Method To provide PBS with a password to be used for all your PBS jobs use the pbs password command This command can be used whether or not you have jobs enqueued in PBS The command usage syntax is pbs password s server r d user When no options are given to pbs_password the password credential on the default PBS server for the current user i e the user who executes the command is updated to the prompted password Any user jobs previously held due to an invalid password are not released The available options to pos_password are r Any user jobs previously neld due to an invalid password are released s server Allows user to specify server where password will be changed d Deletes the password user The password credential of user user is updated to the prompted password Ifuseris not the current user this action is only allowed if PBS Professional 7 41 User s Guide 1 The current user is root or admin 2 User user has given the current user explicit access via the ruserok
118. ng a Job Array The qrerun command will take a job array identifier subjob identifier or job array range If a job array identifier is given as an argument it is returned to its initial state at submis sion time or to its altered state if it has been qaltered All of that job array s subjobs are requeued which includes those that are currently running and completed and deleted If a subjob or range is given those subjobs are requeued as jobs would be 9 7 10 qrun Running a Job Array The qrun command takes a subjob or a range of subjobs not a job array object Ifa single subjob is given as the argument it is run as a job would be Ifa range of subjobs is given as the argument the non running subjobs within that range will be run 9 7 11 tracejob on Job Arrays The tracejob command can be run on job arrays and individual subjobs When tracejob is run on a job array or a subjob the same information is displayed as for a job with addi tional information for a job array Note that subjobs do not exist until they are running so tracejob will not show any information until they are When tracejob is run on a job array the information displayed is only that for the job array object not the subjobs Job arrays themselves do not produce any MOM log information Running tracejob on a job array will give information about why a subjob did not start 9 7 12 qsig Signaling a Job Array If a job array object subjob or job array range is given
119. nging the Job s PBS Directive By default the text string PBS is used by PBS to determine which lines in the job file are PBS directives The leading symbol was chosen because it is a comment delimiter to all shell scripting languages in common use on UNIX systems Because directives look like comments the scripting language ignores them Under Windows however the command interpreter does not recognize the symbol as a comment and will generate a benign non fatal warning when it encounters each PBS string While it does not cause a problem for the batch job it can be annoying or disconcerting to the user Therefore Windows users may wish to specify a different PBS directive via either the PBS DPREFIX environment variable or the C option to qsub For example we can direct PBS to use the string REM PBS instead of PBS and use this directive string in our job script REM PBS 1 walltime 1 00 00 REM PBS 1 select mem 400mb REM PBS j oe date t my_ application date t Given the above job script we can submit it to PBS in one of two ways set PBS DPREFIX REM PBS qsub my_job_ script or qsub C REM PBS my job script 40 Chapter 4 Submitting a PBS Job For additional details on the C option to qsub see section 4 10 Job Submission Options on page 44 4 8 Passwords and Windows Jobs When running PBS in a password protected Wi
120. nt selectHold selectPriority selectRerun selectJobName iconizeHosts View iconizeQueues View iconizeJobs View iconizeInfo View jobResourceList option in gselect 1B for format of lt account_name gt The checkpoint attribute relationship including the logical operator to consult when limiting the list of jobs appearing on the Jobs listbox in the main xpbs window Specify value as Checkpoint lt checkpoint_arg gt See c option in qse lect 1B for format of lt checkpoint_arg gt The hold types string to look for in a job when limiting the jobs appearing on the Jobs listbox in the main xpbs window Spec ify value as Hold Types lt hold_string gt See h option in qselect 1B for format of lt hold_string gt The priority relationship including the logical operator to con sult when limiting the list of jobs appearing on the Jobs listbox in the main xpbs window Specify value as Priority lt prior ity_value gt See p option in qselect 1B for format of lt priority_value gt The rerunnable attribute to consult when limiting the list of jobs appearing on the Jobs listbox in the main xpbs window Spec ify value as Rerunnable lt rerun_val gt See r option in qse lect 1B for format of lt rerun_val gt Name of the job that will be checked when limiting the jobs appearing on the Jobs listbox in the main xpbs window Spec ify value as Job Name lt jobname gt See N option in qse l
121. nux will have the following selection directive created select 1 ncpus 4 mem 123mb arch linux 4 3 6 Limits on Resource Usage Job resource limits are established both by requesting job wide resources and when per chunk consumable resources are summed Chunk requests set limits for per chunk resource usage and job resource limits seta limit for per job resource usage Job resource limits from job wide resource requests override those from sums of chunks If a job s resource limit exceeds queue or server restrictions it will not be put in the queue or accepted by the server If a job exceeds its limit for a consumable or time based resource it will be terminated 36 Chapter 4 Submitting a PBS Job If a resource is not specified by the job in qsub 1 then it will inherit a value limit for a resource from a queue s resource default server s resource_default queue s resource_max server s resource_max not set one If both job resource limits and a selection directive are specified when a job is submitted the sum of the resources in the directive must not exceed the specified limits For example qsub 1 ncpus 4 mem 200mb lselect 2 ncpus 2 mem 100mb is accepted because neither the sum of the number of CPUs nor the sum of the requested memory exceeds the specified limits However qsub l ncpus 2 lselect 1 ncpus 3 will be rejected because the requested number of CPUs 3 is greater than the specified
122. obs See also node and virtual processors This is any collection of nodes controlled by a single instance of PBS i e by one PBS Server An exclusive VP is one that is used by one and only one job at a time A set of VPs is assigned exclusively to a job for the dura tion of that job This is typically done to improve the perfor mance of message passing programs A policy wherein jobs are distributed across multiple time shared hosts to even out the workload on each host Being a policy the distribution of jobs across execution hosts is solely a function of the Job Scheduler A queue is a named container for jobs within a Server There are two types of queues defined by PBS routing and execution A routing queue is a queue used to move jobs to other queues including those that exist on different PBS Servers A job must reside in an execution queue to be eligible to run and remains in an execution queue during the time it is running In spite of the PBS Professional 7 11 User s Guide name jobs in a queue need not be processed in queue order first come first served or FIFO Node Attribute Nodes have attributes associated with them that provide control information The attributes defined for nodes are state the list of jobs to which the node is allocated properties max running max user run max group run and both assigned and available resources resources assigned and resources available Portable B
123. of eo directs that the two streams will be merged intermixed as standard error If the join argu ment is n or the option is not specified the two streams will be two separate files 4 10 18 Retaining output and error files on execution host The k keep option defines which if either of standard output STDOUT or stan dard error STDERR of the job will be retained on the execution host If set this option overrides the path name for the corresponding file If not set neither file is retained on the PBS Professional 7 55 User s Guide execution host The argument is either the single letter e or o yor the letters e and o combined in either order Or the argument is the letter n If k is not re neither file is retained CO oe The standard error file is to be retained on the execution host The file will be placed in the home directory of the user under whose user id the job executed The file name will be the default file name given by job _name esequence where job_name is the name specified for the job and sequence is the sequence number component of the job identifier The standard output file is to be retained on the execution host The file will be placed in the home directory of the user under whose user id the job executed The file name will be the default file name given by job_name osequence where job name is the name specified for the job and sequence is th
124. ollowed by the xpbs method 7 1 Modifying Job Attributes Most attributes can be changed by the owner of the job or a manager or operator while the job is still queued However once a job begins execution the only resources that can be modified are cputime and walltime These can only be reduced When the qalter 1 option is used to alter the resource list of a queued job it is important to understand the interactions between altering the select directive and job limits 7 1 1 Changing the Selection Directive If the selection directive is altered the job limits for any consumable resource in the direc tive are also modified For example if a job is queued with the following resource list 98 Chapter 7 Working With PBS Jobs select 2 ncpus 1 mem S5gb ncpus 2 mem 10gb and the selection directive is altered to request select 3 ncpus 2 mem 6gb then the job limits are reset to ncpus 6 and mem 1 8gb 7 1 2 Changing the Job wide Limit However if the job wide limit is modified the corresponding resources in the selection directive are not modified It would be impossible to determine where to apply the changes in a compound directive Reducing a job wide limit to a new value less than the sum of the resource in the directive is strongly discouraged This may produce a situation where the job is aborted during exe cution for exceeding its limits The actual effect of such a modification is not specified If a job is queued re
125. onsumable resource or a time based resource such as walltime Job wide resources are used for requesting floating licenses or other resources not tied to specific nodes such as cput and walltime 4 3 3 Boolean resources 34 Chapter 4 Submitting a PBS Job A resource request can specify whether a boolean resource should be true or false For example if some nodes have green true and some are red true a selection statement for two nodes each with one CPU all green and no red would be 1 select 2 green true red false ncpus 1 The next example Windows script shows a job wide request for walltime and a chunk request for ncpus and memory litime 1 00 00 lect ncpus 4 mem 400mb 4 3 4 What Happens When Jobs are Submitted Using l nodes If a job is submitted with a nodes specification it will be converted into a new select directive according to the following rules a Each plus sign piece of the nodespec will be converted into a chunk b The number of times the chunk will be repeated is the same as the number of nodes requested for that piece of the nodespec c The product of the number of ncpus in a piece times the number of processes per node ppn will be the number of cpus ncpus in the chunk d Ifeither ncpus X or ppn P is not specified in the nodespec the value of X or P is assumed to be 1 e If a property is specified that is recognized as a node name it will be
126. orks 6 Chapter 1 Introduction Common User Environment offers users a common view of the job submission job query ing system status and job tracking over all systems Cross System Scheduling ensures that jobs do not have to be targeted to a specific com puter system Users may submit their job and have it run on the first available system that meets their resource requirements Job Priority allows users the ability to specify the priority of their jobs defaults can be provided at both the queue and system level Username Mapping provides support for mapping user account names on one system to the appropriate name on remote server systems This allows PBS to fully function in envi ronments where users do not have a consistent username across all hosts Fully Configurable PBS was designed to be easily tailored to meet the needs of different sites Much of this flexibility is due to the unique design of the scheduler module which permits significant customization Broad Platform Availability is achieved through support of Windows 2000 and XP and every major version of UNIX and Linux from workstations and servers to supercomput ers New platforms are being supported with each new release System Integration allows PBS to take advantage of vendor specific enhancements on dif ferent systems such as supporting cpusets on SGI systems Job Arrays are a mechanism for containerizing related work making it possible to submit quer
127. ost UNIX systems the command kill 1 that s minus ell will list all the available signals To send a signal to a job using xpbs first select the job s of interest then click the signal button Doing so will launch the Signal Running Job dialog box From this window you may click on any of the common signals or you may enter the sig nal number or signal name you wish to send to the job Click the Signal button to complete the process 7 6 Changing Order of Jobs Within Queue PBS provides the qorder command to change the order or reorder two jobs To order two jobs is to exchange the jobs positions in the queue or queues in which the jobs resides The two jobs must be located at the same Server and both jobs must be owned by the user No attribute of the job such as priority is changed The impact of changing the order within the queue s is dependent on local job scheduling policy contact your sys tems administrator for details Important A job in the running state cannot be reordered Usage of the qorder command is gorder job identifierl job identifier2 Job array identifiers must be enclosed in double quotes 106 Chapter 7 Working With PBS Jobs Both operands are job _ identifiers which specify the jobs to be exchanged qstat u bob Req d Elap Jobname Sess NDS TSK Mem Time S Time 54 south bob twinkie 63 south bob workg airfoil gorder 54 63 qstat u bob Req d Elap Jobn
128. ould change them to be based on ncpus The neednodes resource is obsolete The ssinodes resource is obsolete e Properties are replaced by boolean resources 3 3 Using PBS 20 Chapter 3 Getting Started With PBS From the user s perspective a workload management system allows you to make more efficient use of your time You specify the tasks you need executed The system takes care of running these tasks and returning the results to you If the available computers are full then the workload management system holds your work and runs it when the resources are available With PBS you create a batch job which you then submit to PBS A batch job is a file a shell script under UNIX or a cmd batch file under Windows containing the set of com mands you want to run on some set of execution machines It also contains directives which specify the characteristics attributes of the job and resource requirements e g memory or CPU time that your job needs Once you create your PBS job you can reuse it if you wish Or you can modify it for subsequent runs For example here is a simple PBS batch job Windows bin sh PBS 1 walltime 1 00 00 walltime 1 00 00 mem 400mb ncpus 4 PBS 1 mem 400mb ncpus 4 my_ application lication Don t worry about the details just yet the next chapter will explain how to create a batch job of your own 3 4 PBS Interfaces PBS provides two user interf
129. p and may be a member of more than one Membership in a group establishes one level of privilege and is also often used to control or limit access to system resources A restriction which prevents a job from being selected for processing There are three types of holds One is applied by the job owner another is applied by a PBS Operator and a third applied by the system itself or the PBS Manager See also Operator and Manager in this glossary The basic execution object managed by the batch subsystem A job is a collection of related processes which is managed as a Manager Operator Owner PBS_HOME POSIX Requeue Rerunnable Stage In Stage Out User Task User ID UID PBS Professional 7 13 User s Guide whole A job can often be thought of as a shell script running a set of tasks A manager is authorized to use all capabilities of PBS The Manager may act upon the Server queues or jobs The Manager is also called the administrator A person authorized to use some but not all of the restricted capabilities of PBS is an operator The user who submitted a specific job to PBS Refers to the path under which PBS was installed on the local system Your local system administrator can provide the specific location This acronym refers to the various standards developed by the Technical Committee on Operating Systems and Application Environments of the IEEE Computer Society under standard P1003
130. p list Hold Types Job Name Join Path Reserved for local site accounting If specified using the A option to qsub this value is carried within the job for its dura tion and is included in the job accounting records If supported by the Server implementation and the host operat ing system the checkpoint attribute determines when check pointing will be performed by PBS on behalf of the job The legal values for checkpoint are described under the galter and qsub commands The type of inter job dependencies specified by the job owner The final path name for the file containing the job s standard error stream See the qsub and qalter command description for more detail The time after which the job may execute The time is main tained in seconds since Epoch If this time has not yet been reached the job will not be scheduled for execution and the job is said to be in wait state A list of group_names hosts which determines the group under which the job is run on a given host When a job is to be placed into execution the Server will select a group name according to the rules specified for use of the qsub command The set of holds currently applied to the job If the set is not null the job will not be scheduled for execution and is said to be in the hold state Note the hold state takes precedence over the wait state The name assigned to the job by the qsub or qalter com mand If the Join Paths attribute is oe
131. pecifying job groupID on page 53 W stagein list Input Output File Staging on page 114 W stageout list Input Output File Staging on page 114 W cred dce Running PBS in a UNIX DCE Environment on page 132 W block opt Requesting qsub Wait for Job Completion on page 110 W pwd password Per Job Password Method on page 41 and Running PBS in a UNIX DCE Environment on page 132 umask nnn Changing UNIX Job umask on page 110 Suppressing job identifier on page 55 4 10 1 Specifying Queue and or Server 46 Chapter 4 Submitting a PBS Job The q destination option to qsub allows you to specify a particular destination to which you want the job submitted The destination names a queue a Server or a queue at a Server The qsub command will submit the script to the Server defined by the desti nation argument If the destination is a routing queue the job may be routed by the Server to a new destination If the q option is not specified the qsub command will submit the script to the default queue at the default Server See also the discussion of PBS DEFAULT in Environment Variables on page 26 The destination specification takes the following form q queue Ghost q queue my_ job PBS q queueName q server my job q queueName serverName my _ job q queueName serverName domain com my_job 4 10 2 Redirecting output and error files
132. ple PBS J 1 2 PBS W stagein homedir work data array_index host1 homedir inputs data array index PBS W stagein homedir work extra array index hostl homedir inputs extra array index PBS W stageout homedir work newdata array index hostl homedir outputs newdata array_ index echo Main script index PBS ARRAY INDEX cd homedir work cat data PBS ARRAY INDEX extra PBS ARRAY INDEX gt gt newdata PBS ARRAY INDEX Local path execution directory homedir work Remote path for inputs original data files dataX and extraXx homedir inputs Remote path for results output of computation newdataX homedir outputs Host data storage host host1 StageScript resides in homedir testdir In that directory we can run it by typing qsub StageScript It will run in homedir our home directory which is why the line cd homedir work is in the script PBS Professional 7 143 User s Guide 9 6 1 2 Output filenames The name of the job array will default to the script name if no name is given via qsub N For example if the sequence number were 1234 PBS N fixgamma would give stdout for index number 7 the name fixgamma o1234 7 and stderr the name fixgamma e1234 7 The name of the job array can also be given through stdin 9 6 2 Job Array Staging Syntax on Windows In Windows the stagein and stageout string must be contained in double quotes when using array_index Example of a s
133. ption defines the group name under which the job is to run on the execution system The g ist argument is of the form groupf host group Ghost 54 Chapter 4 Submitting a PBS Job Only one group name may be given per specified host Only one of the group specifica tions may be supplied without the corresponding host specification That group name will used for execution on any host not named in the argument list If not set the group_list defaults to the primary group of the user under which the job will be run Under Win dows the primary group is the first group found for the user by PBS when querying the accounts database qsub W group list grpA grpB jupiter my job 4 10 16 Specifying a local account The A account string option defines the account string associated with the job The account_string is an opaque string of characters and is not interpreted by the Server which executes the job This value is often used by sites to track usage by locally defined account names Important Under IRIX and Unicos if the Account string is specified it must be a valid account as defined in the system User Data Base UDB 4 10 17 Merging output and error files The j join option declares if the standard error stream of the job will be merged with the standard output stream of the job A join argument value of oe directs that the two streams will be merged intermixed as standard output A join argument value
134. qmgr Manager interface qselect Select jobs by criteria qrerun Requeue running job qsig Send signal to job qrun Manually start a job qstat Status job queue Server qstart Start a queue qsub Submit a job qstop Stop a queue tracejob Report job history qterm Shutdown PBS xpbs Graphical User Interface xpbsmon GUI monitoring tool Notes 1 Available on Windows only 22 Chapter 3 Getting Started With PBS 3 5 User s PBS Environment In order to have your system environment interact seamlessly with PBS there are several items that need to be checked In many cases your system administrator will have already set up your environment to work with PBS In order to use PBS to run your work the following are needed User must have access to the resources hosts that the site has configured for PBS User must have a valid account username and group on the execution hosts User must be able to transfer files between hosts e g via rcp or scp The subsequent sections of this chapter discuss these requirements in detail and provide various setup procedures 3 6 Usernames Under PBS By default PBS will use your login identifier as the username under which to run your job This can be changed via the u option to qsub see section 4 10 14 Specifying Job User ID on page 52 The user submitting the job must be authorized to run the job under the execution user name whether explicitly specified or not Important PBS enforc
135. qrerun selected job s Jobs Panel signal qsig selected job s Jobs Panel msg qmsg selected job s Jobs Panel move qmove selected job s Jobs Panel order qorder selected job s Indicates command button is visible only if xpbs is started with the admin option PBS Professional 7 73 User s Guide 5 6 How to Submit a Job Using xpbs To submit a job using xpbs perform the following steps First select a host from the HOSTS listbox in the main xpbs display to which you wish to submit the job Next click on the Submit button located next to the HOSTS panel The Submit button brings up the Submit Job Dialog box see below which is composed of four distinct regions The Job Script File region is at the upper left The OPTIONS region containing various widgets for setting job attributes is scattered all over the dialog box The OTHER OPTIONS is located just below the Job Script file region and COMMAND BUTTONS region is at the bottom 74 Chapter 5 Using the xpbs GUI The job script region is composed of a header box the text box FILE entry box and two buttons labeled oad and save If you have a script file containing PBS options and execut able lines then type the name of the file on the FILE entry box and then click on the load button Alternatively you may click on the FILE button which will display a File Selec tion browse window from which you may point and click to select the file you wish to
136. quested modifications must still fit within the queue s and server s job resource limits If a requested modification to a resource would exceed the queue s or server s job resource limits the resource request will be rejected Resources are modified by using the 1 option either in chunks inside of selection state ments or in job wide modifications using resource_name value pairs The selec tion statement is of the form 1 select N chunk N chunk where N specifies how many of that chunk and a chunk is of the form resource name value resource name value Job wide resource _name value modifications are of the form l resource name value resource name value Placement of jobs on nodes is changed using the place statement l place modifier modifier PBS Professional 7 99 User s Guide where modifier is any combination of group excl and or one of free pack scatter The usage syntax for galter is galter job resources job list The following examples illustrate how to use the galter command First we list all the jobs of a particular user Then we modify two attributes as shown increasing the wall clock time from 20 to 25 minutes and changing the job name from airfoil to engine qstat u barry Req d Elap Job ID User Queue Jobname Sess NDS Time S Time th barry workq airfoil 1 0 16 R 0 01 th barry workgq airfoil il 0 20 Q qalter 1 walltime 20 00 N engine 54 qstat a 54 R
137. r checks whether UserS can Server checks whether UserS can run job as UserS run job as UserA PBS Professional 7 53 User s Guide Note that if different names are listed via the u option then they are checked regardless of the value of flatuid 4 10 14 2 qsub u User ID with Windows Under Windows if a user has a non admin account the server s hosts equiv file is used to determine whether that user can run a job on a given server For an admin account PROFILE PATH rhosts is used and the server s acl_roots attribute must be set to allow job submissions Usernames containing spaces are allowed as long as the username length is no more than 15 characters and the usernames are quoted when used in the command line Table 7 Requirements for Admin User to Submit Job Locatio Action Submission host username Server host username Same UserS UserS Different UserS UserA PROFILE PATH For UserS on ServerA For UserA on ServerA thosts contains add lt HostS gt UserS add lt HostS gt UserS set ServerA s qmgr gt set server qmgr gt set server acl roots attribute acl_roots UserS acl_roots UserA Table 8 Requirements for Non admin User to Submit Job File Submission host username Server host username Same UserS UserS Different UserS UserA hosts equiv on ServerA lt HostS gt lt HostS gt UserS 4 10 15 Specifying job groupID The W group _list g_1ist o
138. r jobs or job arrays in the queue 9 7 6 qmove Moving a Job Array The qmove command can only be used with job array objects not with subjobs or ranges Job arrays can only be moved from one server to another if they are in the Q H or W states and only if there are no running subjobs The state of the job array object is pre served in the move The job array will run to completion on the new server As with jobs a qstat on the server from which the job array was moved will not show the job array A qstat on the job array object will be redirected to the new server Note The subjob accounting records will be split between the two servers 9 7 7 qhold Holding a Job Array The qhold command can only be used with job array objects not with subjobs or ranges A hold can be applied to a job array only from the Q B or W states This will put the job array in the H held state If any subjobs are running they will run to completion No queued subjobs will be started while in the H state 9 7 8 qris Releasing a Job Array The qrls command can only be used with job array objects not with subjobs or ranges If PBS Professional 7 149 User s Guide the job array was in the Q or B state it will be returned to that state If it was in the W state it will be returned to that state unless its waiting time was reached it will go to the Q state 9 7 9 qrerun Requeui
139. r requeueing selected job s that are running admin only The middle portion of the Jobs Panel has abbreviated column names indicating the infor mation being displayed as the following table shows Heading Table 11 xpbs Job Column Headings Meaning Job id Name Job Identifier Name assigned to job or script name User User name under which job is running PEs CputUse Number of Processing Elements CPUs requested Amount of CPU time used WalltUse Amount of wall clock time used S Queue State of job Queue in which job resides 5 3 5 xpbs Info Panel The Info panel shows the progress of the commands executed by xpbs Any errors are written to this area The INFO panel also contains a minimize maximize button for dis playing or iconizing the Info panel PBS Professional 7 71 User s Guide 5 3 6 xpbs Keyboard Tips There are a number of shortcuts and key sequences that can be used to speed up using xpbs These include Tip 1 All buttons which appear to be depressed in the dialog box sub window can be activated by pressing the return enter key Tip 2 Pressing the tab key will move the blinking cursor from one text field to another Tip 3 To contiguously select more than one entry left click then drag the mouse across multiple entries Tip 4 To non contiguously select more than one entry hold the con trol left click on the desired entries 5 4 Setting
140. rd into the xpbs SUBMIT PASSWORD entry box under UNIX the job will be rejected Keep in mind that in a multi node job the password supplied will be propagated to all the sister nodes This requires that the password be the same on the user s accounts on all the nodes The use of domain accounts for a multi node job will be ideal in this case 42 Chapter 4 Submitting a PBS Job Important Because of enhanced security features found in Windows 2003 Server you may not be able to run non passworded jobs Accessing network share drives resources within a job session also requires that you sub mit the job with a password via qsub W pwd or the SUBMIT PASSWORD entry box in xpbs Furthermore if the job is submitted without a password do not use the native rcp com mand from within the job script as it will generate the error unable to get user name Instead please use pbs_ rcp 4 9 PBS System Resources Jobs can request a variety of resources that can be allocated and used by the job For information on how to request resources see the pbs_resources 7B manual page and Requesting Resources on page 32 The resource values are specified using the following data types time specifies a maximum time period the resource can be used Time is expressed in seconds as an integer or in the form hours minutes seconds milliseconds size specifies the maximum amount in terms of bytes default or words It i
141. re authorized to submit jobs to the reservation queue that s to be created When this queue is instantiated these specifications will supply the values for the queue s user group access control lists Likewise the party who submits the reservation can if desired control the username and group name at the Server that the Server associates with the reservation 8 9 Using Comprehensive System Accounting PBS supports Comprehensive System Accounting CSA on SGI Altix machines that are running SGI s Pro Pack 2 4 3 0 3 2 or 4 0 and have the Linux job container facility avail able CSA provides accounting information about user jobs called user job accounting CSA works the same with and without PBS To run user job accounting either the user must specifiy the file to which raw accounting information will be written or an environ ment variable must be set The environment variable is ACCT _TMPDIR This is the directory where a temporary file of raw accounting data is written To run user job accounting the user issues the CSA command ja lt filename gt or if the environment variable ACCT_TMPDIR is set ja In order to have an accounting report produced the user issues the command ja lt options gt where the options specify that a report will be written and what kind To end user job accounting the user issues the command ja t the t option can be included in the previous set of options See the
142. release of PBS is given in the PBS Professional Administrator s Guide 3 2 Major Changes The way in which jobs request resources and placement on nodes has changed All nodes are now treated alike with respect to allocating jobs and specifying resources Node prop erties are replaced The nodes file is changed Several commands have different usage There may be incompatibilities with prior versions when converting from the deprecated form to the current form The scheduler groups nodes differently The major changes and deprecations are listed below 3 2 1 Resource Requests Jobs now request resources in two new ways They can use the select statement to define chunks and specify the quantity of each chunk A chunk is a set of resources that are to be allocated as a unit Jobs can also use a job wide resource request which uses resource value pairs The 1 nodes form is deprecated and if it is used it will be converted into a request for chunks and job wide resources PBS Professional 7 17 User s Guide The qsub qalter and pbs_rsub commands are used to request resources For more information see Requesting Resources on page 32 and the qsub 1B qalter 1B pbs_rsub 1B and pbs _resources 7B manual pages 3 2 2 Placing Jobs on Nodes All nodes are treated alike with respect to allocating jobs to nodes Jobs are placed on nodes using the place statement This allows specification of whether the job should run on a singl
143. resources that is allocated to a job Jobs can specify how many of these units they need Job wide resources are associated with the entire job and are specified differently from PBS Professional 7 33 User s Guide chunks Jobs request resources either in chunks within a selection statement or in job wide resource requests A job s resource specification is also its resource limit Some resources can only be requested inside of chunks and some establish job wide limits See the pbs_resources 7B manual page Boolean resources now replace properties which are deprecated 4 3 1 Requesting resources in chunks Chunks are described in a selection statement which specifies how many of each kind of chunk A selection statement has this form 1l select N Jchunk N chunk If N is not specified it is taken to be 1 A chunk declares the value of each resource in a set of resources which are to be allocated as a unit to a job It is the smallest set of resources that will be allocated to a job It is one or more resource _name value statements separated by a colon e g ncpus 2 mem 10GB host Hostl ncpus 1 mem 20GB arch linux Example of multiple chunks in a selection statement 1 select 2 ncpus 1 mem 10GB 3 ncpus 2 mem 8GB arch solaris 4 3 2 Requesting job wide resources Job wide resources are requested outside of a selection statement this way l keyword value keyword value where keyword identifies either a c
144. rmation about jobs including the following additional fields Session ID Number of nodes requested Number of parallel tasks or CPUs Requested amount of memory Requested amount of wallclock time Elapsed time in the current job state Jobname Ses NDS TSK Mem aims1l serl aims1l barry airfoil 930 userl kq myjob susan tns3d EE barry airfoil donald worl SEG oo Other options which utilize the alternative display are discussed in subsequent sections of this chapter 82 Chapter 6 Checking Job System Status 6 1 2 Viewing Specific Information When requesting queue or Server status qstat will output information about each desti nation The various options to qstat take as an operand either a job identifier or a desti nation If the operand is a job identifier it must be in the following form sequence number server name server where sequence number server name is the job identifier assigned at submittal time see qsub Ifthe server name is omitted the name of the default Server will be used If server is supplied the request will be for the job identifier currently at that Server If the operand is a destination identifier it takes one of the following three forms queue server queue server If queue is specified the request is for status of all jobs in that queue at the default Server If the server form is given the request is for status of
145. roup grouping is ignored This behavior is unchanged PBS Professional 7 19 User s Guide Table 1 place group Node grouping enabled Node grouping disabled resource Scatter No scatter Scatter No scatter Requested Scatter Scatter Scatter Scatter place group place group place group place group resource resource resource resource Not requested Scatter Scatter Scatter No scatter no node grouping node grouping no place no place no node node grouping grouping 3 2 10 Administrator Can Set Chunk Defaults The administrator can set server and queue defaults for resources used in chunks See Server Configuration Attributes on page 76 Attributes for execution queues only on page 92 and the pbs server_attributes 7B and pbs_queue_attributes 7B manual pages 3 2 11 Deprecations e The 1 nodes nodespec form is replaced by the 1 select and l place statements The nodes resource is no longer used e The l resource rescspec form is replaced by the 1 select statement e The time shared node type is no longer used and e the ts suffix is obsolete e The cluster node type is no longer used e The resource arch is only used inside of a select statement e The resource host is only used inside of a select statement e The nodect resource is obsolete The ncpus resource should be used instead Sites which currently have default values or limits based on nodect sh
146. running this is set to the session id of the first executing task 62 Chapter 4 Submitting a PBS Job PBS Professional 7 63 User s Guide Chapter 5 Using the xpbs GUI The PBS graphical user interface is called xpbs and provides a user friendly point and click interface to the PBS commands xpbs utilizes the tcl tk graphics tool suite while providing the user with most of the same functionality as the PBS CLI commands In this chapter we introduce xpbs and show how to create a PBS job using xpbs 5 1 Starting xpbs If PBS is installed on your local workstation or if you are running under Windows you can launch xpbs by double clicking on the xpbs icon on the desktop You can also start xpbs from the command line with the following command UNIX Windows Doing so will bring up the main xpbs window as shown below 5 1 1 Running xpbs Under Unix Before running xpbs for the first time under UNIX you may need to configure your work station for it Depending on how PBS is installed at your site you may need to allow 64 Chapter 5 Using the xpbs GUI xpbs to be displayed on your workstation However if the PBS client commands are installed locally on your workstation you can skip this step Ask your PBS administrator if you are unsure The most secure method of running xpbs remotely and displaying it on your local XWin dows session is to redirect the XWindows traffic through ssh secure shell via setting the X
147. s For a job it is time used divided by time requested Examples We run an example job and an example job array on a machine with 2 processors demoscript bin sh PBS N JobExample sleep 60 arrayscript bin sh PBS N ArrayExample PBS J 1 5 sleep 60 We run these scripts using qsub qsub arrayscript 1235 host 146 Chapter 9 Job Arrays qsub demoscript 1236 host 1235 host ArrayExample 1236 host JobExample qstat J Name 1235 host ArrayExample qstat p Name 1235 host ArrayExample 1236 host JobExample qstat t 1235 host 1235 1 host 1235 2 host 1235 3 host 1235 4 host 1235 5 host 1236 host Name ArrayExample ArrayExample ArrayExample ArrayExample ArrayExample ArrayExample JobExample qstat Jt Name userl userl userl userl 1235 1 host 1235 2 host 1235 3 host 1235 4 host 1235 5 host ArrayExample ArrayExample ArrayExample ArrayExample ArrayExample Time Use S Time Use S Time Use S 00 00 00 R 00 00 00 R 0Q 0Q 0Q PBS Professional 7 147 User s Guide After the first two subjobs finish qstat Jtp Job id Name User done S Queue 1235 1 host ArrayExample userl 100 X workq 1235 2 host ArrayExample userl 100 X workq 1235 3 host ArrayExample userl R workgq 1235 4 host ArrayExample userl R workgq 1235 5 host ArrayExample userl Q workgq qstat pt Job id Name User
148. s expressed in the form integer suffix The suffix is a multiplier defined in the following table The size of a word is the word size on the execution host b or w bytes or words kb or kw Kilo 1024 bytes or words mb ormw Mega 1 048 576 bytes or words gb or gw Giga 1 073 741 824 bytes or words Different resources are available on different systems often depending on the architecture of the computer itself The table below lists the available resources that can be requested PBS Professional 7 43 User s Guide by PBS jobs on any system Table 4 Resource Description arch Required system architecture For use inside chunks only One archi tecture can be specified Allowable values and effect on job placement are site dependent String cput Maximum amount of CPU time used by the job for all processes on all nodes Establishes a job resource limit Units time file Limit on size of any single file that may be created by the job Units size host Name of execution host For use inside chunks only Site dependent string mem Maximum amount of physical memory i e workingset allocated to the job on any single node Units size ncpus Number of processors requested Integer nice Nice value under which the job is to be run Host dependent integer pcput Maximum amount of CPU time allocated to any single process in the job Job wide limit Units time pmem Maximum
149. s in that queue on the default batch Server will be selected If the destination describes only a Server then jobs in all queues on that Server will be selected If the destination describes both a queue and a Server then only jobs in the named queue on the named Server will be selected Restricts selection of jobs to those with the specified Rerunna ble attribute The option argument must be a single character The following two characters are supported by PBS y and n Restricts job selection to those in the specified states The states argument is a character string which consists of any combina tion of the characters B E H Q R S T U W and X The characters in the states argument have the following interpreta tion Shows job job array and subjob identifiers State PBS Professional 7 93 User s Guide Table 13 Job States Meaning Job array has started execution Job is in the process of Exiting Job has been placed on Hold Job is in the Queued state Job is in the Running state Job has been Suspended Job is Transiting between states Job suspended due to workstation user activity Job is in the Waiting state x S clH a w ola m Subjob has completed execution Jobs will be selected which are in any of the specified states uuser list Restricts selection to jobs owned by the specified user names This provides a means of limiting the selection to jobs owne
150. s job may be scheduled for execution only after all jobs in arg list have terminated with errors See Warning about exit status with csh in EXIT STATUS afterany arg list 112 Chapter 8 Advanced PBS Features This job may be scheduled for execution after all jobs in arg_list have terminated with or without errors before arg list Jobs in arg list may begin execution once this job has begun execution beforeok arg_ list Jobs in arg list may begin execution once this job terminates without errors See Warning about exit status with csh in EXIT STATUS beforenotok arg list If this job terminates execution with errors the jobs in arg_ list may begin See Warning about exit status with csh in EXIT STATUS beforeany arg list Jobs in arg list may begin execution once this job terminates execution with or without errors on count This job may be scheduled for execution after count depen dencies on other jobs have been satisfied This type is used in conjunction with one of the before types listed count is an integer greater than 0 Job IDs in the arg list of before types must have been submitted with a type of on To use the before types the user must have the authority to alter the jobs inarg_list Otherwise the dependency is rejected and the new job aborted Error processing of the existence state or condition of the job on which the newly submit ted job is a deferred service i e the check is perform
151. s_ rsub are disabled when using the w qmove option For more information see Advance Reservation of Resources on page 118 and the pbs_rsub 1B qsub 1B and qmove 1B manual pages Important A job s default walltime is 5 years Therefore an ASAP reser vation s start time can be in 5 years if all the jobs in the system have the default walltime PBS Professional 7 109 User s Guide Chapter 8 Advanced PBS Features This chapter covers the less commonly used commands and more complex topics which will add substantial functionality to your use of PBS The reader is advised to read chap ters 5 7 of this manual first 8 1 UNIX Job Exit Status On UNIX systems the exit status of a job is normally the exit status of the shell executing the job script If a user is using csh and has a Logout file in the home directory the exit status of csh becomes the exit status of the last command in logout This may impact the use of job dependencies which depend on the job s exit status To preserve the job s exit status the user may either remove Logout or edit it as shown in this example set EXITVAL Sstatus logout s original content exit SEXITVAL Doing so will ensure that the exit status of the job persists across the invocation of the logout file The exit status of a job array is determined by the status of each of the completed subjobs 110 Chapter 8 Advanced PBS Features It is only
152. soessoossossssse 29 iii PBS JODS2 isis erie att Pisciotta hie eee 29 Submitting a PBS Job ccsescesccesecsssrsessnceeees 31 Requesting Resources 03 wsstactenaca diate aaties 32 Placing Jobs on Nodes 0 ccccecsseesseesteceteeeeeeeeseees 36 How PBS Parses a Job Script cceeceeseeesseeeteees 37 A Sample PBS J bnircirsesserirenn 38 Changing the Job s PBS Directive eee 39 Passwords and Windows Jobs eeeeseeseereeeeees 40 PBS System Resources iicciesacdsiss daira ssaenveacdnesias 42 Job Submission Options cccccceeeeeeeseeeteeeeees 44 JOVA MODUS nenanem cannes 56 5 Using the xpbs GUI sesssesssesssecssooesoosssoesssesssesssosee 63 Starline XPOS onana hne tien ana 63 Using xpbs Definitions of Terms cesses 64 Introducing the xpbs Main Display ee 65 Setting xpbs Preferences isscxidcsitvisendonsiedcuans 71 Relationship Between PBS and xpbs 0 12 How to Submit a Job Using xpbs e eee 73 Exiting SD OS 25 costoostearcs ain Gusk seseaantca deta suueaecretonenieues 76 The xpbs Configuration File ccecceseeeeteeees 76 KDDS PRELEPENCES 4 c iersaasbajaveataqodecsteadyeetneiecdbavtad 76 6 Checking Job System Status ccsssecsseeseeee 79 The qstat Command secs Jays vesetutsnsasescaascouslnaae vies 79 Viewing Job System Status with xpbs 89 The qseleet Command sagessytasiesgeatseaianigetesvetistoens 89 Se
153. solution Three years later the MRJ Ver 4 Chapter 1 Introduction idian PBS Products business unit was acquired by Altair Engineering Inc Altair set up the PBS Products unit as a subsidiary company named Altair Grid Technologies focused on PBS Professional and related Grid software 1 4 About the PBS Team The PBS Professional product is developed by the same team that originally designed PBS for NASA In addition to the core engineering team Altair Grid Technologies includes individuals who have supported PBS on computers around the world including some of the largest supercomputers in existence The staff includes internationally recognized experts in resource management and job scheduling supercomputer optimization mes sage passing programming parallel computation and distributed high performance com puting In addition the PBS team includes co architects of the NASA Metacenter the first full production geographically distributed meta computing grid co architects of the Department of Defense MetaQueueing prototype Grid Project co architects of the NASA Information Power Grid and co chair of the Global Grid Forum s Scheduling Group 1 5 About Altair Engineering Through engineering consulting and high performance computing technologies Altair Engineering increases innovation for more than 1 500 clients around the globe Founded in 1985 Altair s unparalleled knowledge and expertise in product development and manu fac
154. st store Local_path tmp Executable a out The filename prefix frame is optional Using it will prevent collisions on the execution machine For this example a out produces frame2 out from frame2 PBS W stagein tmp in frame array_index store film frame array_index PBS W stageout tmp out frame array_index out store film PBS J 1 3 a out N frame tmp in tmp out Note that the stageout statement is all one line broken here for readability The result will be that the user s directory named film contains the original files frame frame2 frame3 plus the new files framel out frame2 out and frame3 out 9 6 1 1 Scripts Example 1 In this example we have a script named ArrayScript which calls scriptlet1 and scriptlet2 All three scripts are located in homedir testdir bin sh PBS N ArrayExample 142 Chapter 9 Job Arrays PBS J 1 2 echo Main script index PBS ARRAY INDEX homedir testdir scriptlet PBS ARRAY INDEX In our example scriptletl and scriptlet2 simply echo their names We run ArrayScript using the qsub command qsub ArrayScript Example 2 In this example we have a script called StageScript It takes two input files dataX and extraX and makes an output file newdataX as well as echoing which iteration it is on The dataX and extrax files will be staged from inputs to work then new dataX will be staged from work to outputs bin sh PBS N StagingExam
155. st where the pbs_server is running Be sure the pbs_server has a nodes file entry server host gl in order for Globus job status to be communicated back to the Server by pbs_mom_globus Before a user can use the Globus infrastructure to successfully send work to some execu tion host s in the Globus Grid a valid grid proxy certificate must be obtained by the user The utility grid proxy init is used to obtain a valid grid proxy certificate If a user s job fails to run due to an expired proxy credential or non existent credential then the job will be put on hold and the user will be notified of the error by email 8 10 2 PBS and Globusrun If you re familiar with the gLobusrun utility the following mappings of options from PBS to an RSL string may be of use to you Table 14 qsub Option vs Globus RSL PBS Option Globus RSL Mapping l site globus lt gatekeeper gt specifies the gatekeeper to contact ncpus yy count yy A lt account_name gt project lt account_name gt l cput yy maxcputime yy in minutes l pcput yy maxtime yy in minutes 1 walltime yy maxwalltime yy in minutes mem zz maxmemory zz in megabytes PBS Professional 7 129 User s Guide Table 14 qsub Option vs Globus RSL PBS Option Globus RSL Mapping o lt output_path gt stdout lt local_output_path gt e lt error_path gt stderr lt local_error_path gt PBS will deliver from lt local_path gt to us
156. t 59 username 25 maximum 22 Vv Variable List 59 Veridian 3 Viewing Job Information 84 Virtual Processor VP 11 W Wait for Job Completion 110 Widgets 64 Windows 24 25 password 40 Windows 2000 6 Windows 2003 42 Windows command inter preter 30 Workload management 2 X xpbs 21 41 42 73 76 77 78 buttons 72 configuration 76 job arrays 150 usage 63 89 94 103 168 Index 105 113 xpbsmon 21 xpbsrce 76
157. tagein qsub W stagein foo array_index host 1 C WINNT Temp foo array_index J 1 5 stage_script Example of a stageout qsub W stageout C WINNT Temp foo array_index host 1 Q my_username foo array_index out J 1 5 stage_ script 9 7 PBS Commands 9 7 1 PBS Commands Taking Job Arrays as Arguments Note Some shells such as csh and tcsh use the square bracket as a metacharac ter When using one of these shells and a PBS command taking subjobs job arrays or job array ranges as arguments the subjob job array or job array range must be enclosed in double quotes The following table shows PBS commands that take job arrays subjobs or ranges as argu ments The cells in the table indicate which objects are acted upon In the table Atray the job array object Array Range the set of subjobs of the job array with indices in range given 144 Chapter 9 Job Arrays Array Index Array RUNNING Array QUEUED Array REMAINING Array DONE the individual subjob of the job array with the index given the set of subjobs of the job array which are currently running the set of subjobs of the job array which are currently queued the set of subjobs of the job array which are queued or running the set of subjobs of the job array which have finished running Table 20 PBS Commands Taking Job Arrays as Arguments Argument to Command
158. tand how the pieces fit together and how they affect you Commands Server Server PBS Commands Scheduler Batch Job PBS supplies both command line programs that are POSIX 1003 2d conforming and a graphical interface These are used to submit monitor modify and delete jobs These client com mands can be installed on any system type supported by PBS and do not require the local presence of any of the other com ponents of PBS There are three command classifications user commands which any authorized user can use operator commands and manager or administrator commands Operator and manager commands which require specific access privileges are dis cussed in the PBS Professional Administrator s Guide The Job Server daemon service is the central focus for PBS Within this document it is generally referred to as the Server or by the execution name pbs_server All commands and the other Job Executor MOM Scheduler PBS Professional 7 9 User s Guide daemons services communicate with the Server via an Internet Pro tocol IP network The Server s main function is to provide the basic batch services such as receiving creating a batch job modify ing the job and running the job Normally there is one Server man aging a given set of resources However if the Server Failover feature is enabled there will be two Servers The Job Executor or MOM is the daemon service which actual
159. ter 3 Getting Started With PBS PBS creates an environment variable TMPDIR which contains the full path name to a temporary scratch directory created for each PBS job The directory will be removed when the job terminates Under Windows TMP will also be set to the value of s TMPDIR amp The temporary directory will be created under either winnt temp or windows temp unless an alternative directory was specified by the administrator in the MOM configuration file Users can access the job specific temporary space by changing directory to it inside their job script For example UNIX Windows cd STMPDIR cd sTMPDIR PBS Professional 7 29 User s Guide Chapter 4 Submitting a PBS Job The way in which jobs request resources and specify placement on nodes has changed with this release There are several associated new features and deprecations The current method of requesting resources is deprecated Please see Requesting Resources on page 32 and Placing Jobs on Nodes on page 36 as well as the pbs_resources 7B manual page 4 1 PBS Jobs A PBS job can be submitted at the command line or via xpbs At the command line the user can create a job script and submit it During submission it is possible to override elements in the job script Alternatively PBS will read from input typed at the command line 4 1 1 PBS Job Script A PBS job script consists of 1 An optional shell specification UNI
160. tfile to POE This should not be supplied by the user and if the user specifies it PBS will print a warning that it is replacing the hostfile Notes 1 Debugging using pdbx will work in the expected fashion 2 Your system administrator may have set PBS up so that applications which are directly invoked will be part of a PBS job 3 Since PBS is tracking tasks started by poe these tasks are counted towards a user s run limits 4 Usernames must be identical across nodes For more information on using IBM s Parallel Operating Environment see IBM Parallel Environment for AIX 5L Hitchhiker s Guide 156 Chapter 10 Multiprocessor Jobs 10 2 3 PBS Jobs with LAM MPI You can use the same arguments to the mpirun command as you would outside of PBS If you are running a single program PBS will track resource usage and manage processes If you are running multiple programs specified in an application file PBS does not track resources or manage processes 10 2 4 PBS MPI Jobs on HP UX and Linux PBS is more tightly integrated with the mpirun command on HP UX so that resources can be tracked and processes managed When running a PBS MPI job you can use the same arguments to the mpirun command as you would outside of PBS The h host and 1 user options will be ignored and the np number option will be modified to fit the available resources 10 3 PVM Jobs with PBS On a typical system to execute a Parallel Virtual Machine PV
161. the Waiting state 68 Chapter 5 Using the xpbs GUI Table 9 xpbs Server Column Headings Heading Meaning Tm Count of jobs in the Transiting state Ext Count of jobs in the Exiting state Status Status of the corresponding Server PEsInUse Count of Processing Elements CPUs PEs Nodes in Use 5 3 3 xpbs Queues Panel The Queues panel is composed of a leading horizontal QUEUES bar a listbox and a set of command buttons The QUEUES bar lists the hosts that are consulted when listing queues the bar also contains a minimize maximize button for displaying or iconizing the Queues panel The listbox displays information about queues managed by the Server host s selected from the Hosts panel each listbox entry can be selected as described above for the Hosts panel To the right of the Queues Panel area are buttons for actions that can be performed on selected queue s detail provides information about selected queue s This functional ity can also be achieved by double clicking on a Queue listbox entry stop for stopping the selected queue s admin only start for starting the selected queue s admin only disable for disabling the selected queue s admin only enable for enabling the selected queue s admin only The middle portion of the Queues Panel has abbreviated column names indicating the information being displayed as the following table shows Table 10 xpbs Queue Column
162. tifier 135 Job Array Run Limits 150 Job Arrays 135 Job Arrays and xpbs 150 Job Attributes 30 job container 126 Job Script 29 job state 80 Job States 93 Job_Name 57 Job_Owner 60 141 job_state 60 Join Path 57 K Keep Files 58 Kerberos 132 KRB5 133 krb5 133 L Linux job container 126 Listbox 64 Load Balance 10 Load Leveling 5 M Mail Points 58 Mail Users 58 man pages SGI 24 management vii Manager 13 MANPATH 24 Message Passing Interface 154 meta computing 4 Modifying Job Attributes 97 MOM 9 Monitoring 7 Moving 148 jobs between queues 106 Moving a Job Array 148 MPI 154 MPICH 154 mpirun 154 MRJ Technology Solutions PBS Pro 5 4 165 User s Guide ix MRJ Veridian 3 mtime 60 N name 48 NASA Ames Research Center 3 and PBS ix 2 Information Grid 4 Metacenter 4 NCPUS 159 Network Queueing System NQS 3 nqs2pbs 161 network share 42 no stdio_ sockets 58 Node attribute 11 defined 10 Node Grouping job arrays 152 Node Types 17 nqs2pbs 21 Power O OMP NUM _ THREADS 156 159 OpenMP 156 Operator 13 Ordering Job Arrays in the Queue 148 Ordering Software and Publications viii Output _Path 58 override 31 Owner 13 166 Index P Parallel job support 5 Virtual Machine PVM 156 password 42 single signon 40 Windows 40 xpbs 41 PBS availability 6 PBS Commands Taking Job Arrays as Arguments 143 PBS Environmental Vari ables 140 PBS_ARRAY ID 140 159 PBS ARRAY
163. time based on the reservation start time and duration pbs_rsub R 1130 D 30 00 00 R226 south UNCONFIRMED A reservation queue named R226 was created on the local PBS Server Note that the reservation is currently unconfirmed Email will be sent to the reservation owner either confirming the reservation or rejecting it Upon confirmation the owner of the reserva tion can submit jobs against the reservation using the qsub command naming the reser vation queue on the command line with the q option e g qsub q R226 aims14 299 south Important The ability to submit query or delete advance reservations using the xpbs GUI is not available 8 8 2 Waiting for Confirmation When the user requests an advance reservation of resources via the pos _rsub command an option I n is available to wait for confirmation response The value n that is specified is taken as the number of seconds that the command is willing to wait This value can be either positive or negative A non negative value means that the Server scheduler response is needed in n or less seconds After that time the submitter will need to use pbs_rstat or some other means to discern success or failure of the request For a nega tive value the command will wait up to n seconds for the request to be either confirmed 124 Chapter 8 Advanced PBS Features or denied If the response does not come back in n or fewer seconds the Server
164. tion on page 50 C DPREFIX Changing the Job s PBS Directive on page 39 c interval Specifying job checkpoint interval on page 51 e path Redirecting output and error files on page 46 h Holding a job delaying execution on page 51 I Interactive batch jobs on page 55 J _X Y Z Job Array on page 135 J Join Merging output and error files on page 54 k keep Retaining output and error files on execution host on page 54 1 resources list Requesting Resources on page 32 PBS Professional 7 45 User s Guide Table 5 Options to the qsub Command Option Function and Page Reference user list Setting e mail recipient list on page 48 m MailOptions Specifying e mail notification on page 48 N name Specifying a job name on page 48 0o path Redirecting output and error files on page 46 p priority Setting a job s priority on page 50 q destination Specifying Queue and or Server on page 45 r value Marking a Job as Rerunnable or Not on page 49 S path list Specifying which scripting language to use on page 49 u user Vist Specifying Job User ID on page 52 V Exporting environment variables on page 47 variable list Expanding environment variables on page 47 depend list Specifying Job Dependencies on page 111 group list list S
165. to qsig all currently running sub jobs within the specified set will be sent the signal 9 7 13 qmsg Sending Messages The qmsg command is not supported by job arrays 9 8 Other PBS Commands Supported for Job Arrays 150 Chapter 9 Job Arrays 9 8 1 qselect Selection of Job Arrays The default behavior of qselect is to return the job array identifier without returning sub job identifiers Note qselect will not return any job arrays when the state selection s option restricts the set to R S T or U because a job array will never be in any of these states How ever qselect can be used to return a list of subjobs by using the t option Options to qselect can be combined For example to restrict the selection to subjobs use both the J and the T options To select only running subjobs use J T sR Table 22 Options to qselect for Job Arrays Option Selects Result none jobs Shows job and job array identifiers job arrays J job arrays Shows only job array identifiers T jobs Shows job and subjob identifiers subjobs 9 9 Job Arrays and xpbs xpbs does not support job arrays 9 10 More on Job Arrays 9 10 1 Job Array Run Limits Jobs and subjobs are treated the same way by job run limits For example if max_user_run is set to 5 a user can have a maximum of 5 subjobs and or jobs running 9 10 2 Starving A job array s starving status is based on the q
166. ts as a filter restricting the number of jobs which might be listed With no options the gselect command will list all jobs at the Server which the user is authorized to list query status of The u option may be used to limit the selection to jobs owned by this user or other specified users 90 Chapter 6 Checking Job System Status When an option is specified with a optional op component to the option argument then op specifies a relation between the value of a certain job attribute and the value compo nent of the option argument If an op is allowable on an option then the description of the option letter will indicate that op is allowable The only acceptable strings for the op component and the relation the string indicates are shown in the following list eq ene ge Sgt The value represented by the attribute of the job is equal to the value represented by the option argument The value represented by the attribute of the job is not equal to the value represented by the option argument The value represented by the attribute of the job is greater than or equal to the value represented by the option argument The value represented by the attribute of the job is greater than the value represented by the option argument The value represented by the attribute of the job is less than or equal to the value represented by the option argument The value represented by the attribute of the job is less than the value
167. turing extend throughout North America Europe and Asia Altair specializes in the development of high end open CAE software solutions for modeling visualization opti mization and process automation 1 6 Why Use PBS PBS Professional provides many features and benefits to both the computer system user and to companies as a whole A few of the more important features are listed below to give the reader both an indication of the power of PBS and an overview of the material that will be covered in later chapters in this book Enterprise wide Resource Sharing provides transparent job scheduling on any PBS sys tem by any authorized user Jobs can be submitted from any client system both local and remote crossing domains where needed PBS Professional 7 5 User s Guide Multiple User Interfaces provides a graphical user interface for submitting batch and interactive jobs querying job queue and system status and monitoring job progress PBS also provides a traditional command line interface Security and Access Control Lists permit the administrator to allow or deny access to PBS systems on the basis of username group host and or network domain Job Accounting offers detailed logs of system activities for charge back or usage analysis per user per group per project and per compute host Automatic File Staging provides users with the ability to specify any files that need to be copied onto the execution host before the job runs
168. ue objects Lists num ber of subjobs in each state Name PBS Professional 7 139 User s Guide Table 16 Job Array Attributes Type Applies To Value array_indices_ remaining array indices submitted string string job array job array List of indices of subjobs still queued Range or list of ranges e g 500 552 596 1000 Complete list of indices of subjobs given at submis sion time Given as range e g 1 100 9 4 Job Array States Job array states map closely to job states except for the B state The B state applies to job arrays and indicates that at least one subjob has left the queued state and is running or has run but not all subjobs have run Job arrays will never be in the R S or U states State Table 17 Job Array States Indication The job array has started The job array has a wait time in the future The job array is held The job array is in transit between servers The job array is queued or has been qrerun m o 4a m lt oe All subjobs are finished and the server is cleaning up the job array 140 Chapter 9 Job Arrays 9 4 1 Subjob States Subjobs can be in one of six states listed here Table 18 Subjob States State Indication Queued Running Ending Expired subjob has completed execution Suspended C A Kx m a O
169. uent failed attempts to run new jobs resulting in them being placed in a held state 3 7 1 Setting MANPATH on SGI Systems The PBS man pages UNIX manual entries are installed on SGI systems under usr bsd or for the Altix in usr pbs man In order to find the PBS man pages users will need to ensure that usr bsd is set within their MANPATH The following example illus trates this for the C shell setenv MANPATH usr man usr local man usr bsd SMANPATH 3 8 Setting Up Your Windows Environment This section discusses the setup steps needed for running PBS Professional in a Microsoft Windows environment including host and file access passwords and restrictions on home directories 3 8 1 Windows User s HOMEDIR Each Windows user is assumed to have a home directory HOMEDIR where his her PBS job would initially be started The home directory is also the starting location of files when users specify relative path arguments to gsub qalter W stagein stage out options If a user has not been explicitly assigned a home directory then PBS will use this Win dows assigned default as the base location for the user s default home directory More specifically the actual home path will be PROFILE PATH My Documents PBS Pro For instance if a userA has not been assigned a home directory it will default to a local home directory of Documents and Settings userA My Documents PBS Pro UserA s job will use the above pat
170. ueued portion of the array This means that if PBS Professional 7 151 User s Guide there is a queued subjob which is starving the job array is starving A running subjob retains its sarving status when it was started 9 10 3 Job Array Dependencies Job dependencies are supported e between job arrays and job arrays e between job arrays and jobs between jobs and job arrays Note Job dependencies are not supported for subjobs or ranges of subjobs 9 10 4 Accounting Job accounting records for job arrays and subjobs are the same as for jobs When a job array has been moved from one server to another the subjob accounting records are split between the two servers except that there will be no Q records for subjobs 9 10 5 Checkpointing Checkpointing is not supported for job arrays On systems that support checkpointing subjobs are not checkpointed instead they run to completion 9 10 6 Prologues and Epilogues If defined prologues and epilogues will run at the beginning and end of each subjob but not for job arrays 9 10 7 Job Array Exit Status The exit status of a job array is determined by the status of each of the completed subjobs It is only available when all valid subjobs have completed The individual exit status of a completed subjob is passed to the epilogue and is available in the E accounting log record of that subjob 152 Chapter 9 Job Arrays Exit Status Meaning 0 All subjobs o
171. us resources assigned sncpus 1 resources assigned nodect 1 scheduler iteration 600 pbs_ version PBSPro 7 1 41640 6 1 4 Checking Queue Status The Q option to qstat displays the status of all or any specified queues at the optionally specified PBS Server One line of output is generated for each queue queried The three letter abbreviations correspond to limits queue states and job counts as follows Maximum Total Enabled Status Started Status Queued Running Held Waiting Tran siting and Exiting The last column gives the type of the queue routing or execution Q Max Tot Ena Str Que Run Hld Wat Trn Ext Type O 10 yes yes 7 1 1 1 0 0 Execution 84 Chapter 6 Checking Job System Status The full display for a queue provides additional information qstat Qf Queue workg queue type Execution total _ jobs 10 state_count Transit 0 Queued 7 Held 1 Waiting 1 Running 1 Exiting 0 resources _ assigned ncpus 1 hasnodes False nabled Tru started True 6 1 5 Viewing Job Information We saw above that the f option could be used to display full or long information for queues and Servers The same applies to jobs By specifying the option and a job identifier PBS will print all information known about the job e g resources requested resource limits owner source destination queue etc as shown in the following exam ple See Job Attrib
172. utes on page 56 for a description of attribute PBS Professional 7 85 User s Guide qstat f 89 Job Id 89 south Job Name tns3d Job Owner susan south mydomain com resources used cput 00 00 00 resources _ used mem 2700kb resources _ used ncpus 1 resources used vyvmem 5500kb resources used walltime 00 00 00 job _ state R queue workq server south Checkpoint u ctime Thu Aug 23 10 11 09 2004 Error Path south u susan tns3d e89 exec host south 0 Hold Types n Join Path oe Keep Files n Mail Points a mtime Thu Aug 23 10 41 07 2004 Output_Path south u susan tns3d 089 Priority 0 qtime Thu Aug 23 10 11 09 2004 Rerunnable True Resource List mem 300mb Resource List nepus 1 Resource List walltime 00 20 00 session id 2083 Variable List PBS _ O HOME u susan PBS O LANG en_US PBS O LOGNAME susan PBS O PATH bin usr bin PBS O SHELL bin csh PBS O HOST south PBS O WORKDIR u susan PBS O SYSTEM Linux PBS _ O QUEUE workq euser susan egroup myegroup queue type E comment Job run on node south started at 10 41 etime Thu Aug 23 10 11 09 2004 86 Chapter 6 Checking Job System Status 6 1 6 List User Specific Jobs The u option to qstat displays jobs owned by any of a list of user names specified The syntax of the list of users is user name host user name Ghost Host names are not requ
173. variables The v option declares that all environment variables in the qsub command s environ ment are to be exported to the batch job 4 10 4 Expanding environment variables The v variable list option to qsub allows you to specify additional environ ment variables to be exported to the job variable_list names environment variables from the qsub command environment which are made available to the job when it executes The variable_list is a comma separated list of strings of the form variable or vari able value These variables and their values are passed to the job qsub v DISPLAY myvariable 32 my job 48 Chapter 4 Submitting a PBS Job 4 10 5 Specifying e mail notification The m MailOptions defines the set of conditions under which the execution server will send a mail message about the job The Mai Options argument is a string which con sists of either the single character n or one or more of the characters a b and e If no email notification is specified the default behavior will be the same as for m a send mail when job is aborted by batch system send mail when job begins execution send mail when job ends execution do not send mail 4 10 6 Setting e mail recipient list 5 0 O fm The M user list option declares the list of users to whom mail is sent by the exe cution server when it sends mail about the job The user_ ist argument is of the form user G
174. very of Output Files To transfer output files or to transfer staged in or staged out files to from a remote destina 114 Chapter 8 Advanced PBS Features tion PBS uses either rcp or scp depending on the configuration options The version of rcp used by PBS always exits with a non zero exit status for any error Thus MOM knows if the file was delivered or not The secure copy program scp is also based on this version of rcp and exits with the proper status code If using rcp the copy of output or staged files can fail for at least two reasons 1 The user lacks authorization to access the specified system See discussion in User s PBS Environment on page 22 2 Under UNIX if the user s cshrc outputs any characters to standard output e g contains an echo command pbs_ rcp will fail If using Secure Copy scp then PBS will first try to deliver output or stage in out files using scp If scp fails PBS will try again using rcp assuming that scp might not exist on the remote host If rcp also fails the above cycle will be repeated after a delay in case the problem is caused by a temporary network problem All failures are logged in MOM s log and an email containing the errors is sent to the job owner For delivery of output files on the local host PBS uses the cp command UNIX or the xcopy command Windows Local and remote delivery of output may fail for the fol lowing additional reasons 1 A directory in
175. will automatically delete the request from the system 8 8 3 Showing Reservation Status The pbs_rstat command is used to show the status of all the reservations on the PBS Server There are three different output formats brief short default and long The fol lowing examples illustrate these three options The short option S will show all the reservations in a short concise form This is the default display if no options are given The information provided is the identifier of the reservation name of the queue that got created for the reservation user who owns the res ervation the state the start time duration in seconds and the end time pbs _rstat S Name Queu State Start Duration End R226 R226 L Lis 1800 Today 1 R302 R302 15 1800 Today 1 R304 R304 L 15s 1800 Today 1 The full option f will print out the name of the reservation followed by all the attributes of the reservation PBS Professional 7 125 User s Guide pbs _rstat f R226 Name R226 south Reserve Owner userl south reserve_type 2 reserve state RESV_CONFIRMED reserve _substate 2 reserve_start Fri Aug 24 11 30 00 2004 reserve_end Fri Aug 24 12 00 00 2004 reserve duration 1800 queue R226 Resource List ncpus Resource List mem 500kb Resource List nodes Resource List walltime 00 30 00 uthorized Users userl south south Fri Aug 24 06 30 53 2004 time Fri Aug 24 06 30 53 2004 ariabl
176. wo environment variables NCPUS and OMP_NUM_THREADS set to N the number of CPUs allocated If you have a cluster of small systems with for example 2 CPUs each and you wish to sub mit an MPI job that will run on four separate hosts then submit qsub l select 4 ncpus 1 l place scatter The PBS_NODEFILE file will contain one entry for each of the hosts allocated to the job In the example above it would contain 4 lines The variables NCPUS and OMP_NUM_THREADS will be set to one 154 Chapter 10 Multiprocessor Jobs If you do not care where the four MPI processes are run you may submit qsub l select 4 ncpus 1 place free and the job will run on 2 3 or 4 hosts depending on what is available For this example PBS NODEFILE will contain 4 entries either four separate hosts or 3 hosts one of which is repeated once or 2 hosts each repeated twice NCPUS and OMP_NUM_THREADS will be set 1 or 2 depending on the number of cpus allocated from the first listed host Most multi threaded jobs will request all CPUs on the same host This defaults to case 1 above Should you have a job that is both MPI and multi threaded you will need to be careful in determining the number of CPUs and nodes allocated The total number of entries in the PBS_NODEFILE will be the same as the total number of CPUs allocated NCPUS and OMP_NUM_THREADS will be set to the number of CPUs allocated from the first host In order to run only one MPI process on each host
177. y modify and display a set of jobs as a single unit PBS Professional 7 7 User s Guide Chapter 2 Concepts and Terms PBS is a distributed workload management system As such PBS handles the manage ment and monitoring of the computational workload on a set of one or more computers Modern workload management solutions like PBS Professional include the features of tra ditional batch queueing but offer greater flexibility and control than first generation batch systems such as NQS Workload management systems have three primary roles Queuing The collecting together of work or tasks to be run on a computer Users submit tasks or jobs to the resource management system where they are queued up until the system is ready to run them Scheduling The process of selecting which jobs to run when and where according to a predetermined policy Sites balance competing needs and goals on the system s to maximize efficient use of resources both computer time and people time Monitoring The act of tracking and reserving system resources and enforcing usage policy This includes both software enforcement of usage limits and user or administrator monitoring of scheduling policies to see how well they are meeting stated goals 8 Chapter 2 Concepts and Terms 2 1 PBS Components PBS consist of two major component types user level commands and system daemons services A brief description of each is given here to help you unders
178. y user or an administrator type group and has write access granted only to the owning user or an administrator or group This file can also determine if a remote user is allowed to submit jobs to the local PBS Server if the mapped user is an Administrator account For example the following entry in user susan s rhosts file on the server would permit user susan to run jobs sub mitted from her workstation wks031 wks031 susan 26 Chapter 3 Getting Started With PBS Furthermore in order for Susan s output files from her job to be returned to her automati cally by PBS she would need to add an entry to her rhosts file on her workstation naming the execution host Host1 If instead Susan has access to several execution hosts she would need to add all of them to her crhosts file tl susan t2 susan t3 susan Note that Domain Name Service DNS on Windows may return different permutations for a full hostname thus it is important to list all the names that a host may be known For instance if Host4 is known as Host4 Host4 lt subdomain gt or Host4 lt subdo main gt lt domain gt you should list all three in the rhosts file t4 susan t4 subdomain susan t4 subdomain domain susan As discussed in the previous section usernames with embedded white space must also be quoted if specified in any hosts equiv or rhosts files as shown below Host5 subdomain domain Bob Jones 3 8 4 W

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