High Performance Beowulf Cluster Environment User Manual
Contents
1. M clustervision ITS Information Technology Service High Performance Beowulf Cluster Environment Hamilton Cluster User Manual Version 1 01 15 December 2005 Table of Contents TiINtrdUGHO Mesan a n a a a vests pete aaa den neti 4 2 The physical hardware layout of HAMiltON cccseeeeeeeeeeeeeeeeeeeeeeeaeeeeeeeeeeeesaeeeeeeeas 4 3 Getting an account on HAMIMOM x cfenes fee Soecadecesdenssdenpctaacuce ccndanchecplanadnte Madersateptorageces 5 A ACCESSING the CIUSIOM wesc ceeceveenciserensauasirstooamezedeustselssp doen oeet EAEE Ra DEAA AARE ANEKERE Suk 5 S THe Hamilton Cluster a roana a Ra aaa a A cee a EE E elas 6 6 The Modules Environment nssssrrrrrrrsssrrnrrnnnnsssrnnnnntneeesseernrrrrrnnerrrrnnnnnnnnnnnnnnneneeeea 7 7 Running your application on the cluster eeeeeeeeeeeeeeeeeeeeeeeerenrrirrrrrnnnnnsssssnsssrrreeenn 8 8 Selecting the correct module environment ssssssessssserersseerrnrertnrrtserrtnnrrsrtrrnsrrrnnne 8 9 Compiling your C d rss mrar a e A E earns 10 10 MPI compile and link COMMANAS 4ci25 Mawes ae ena lo eho 11 11 Executing the PIO OMA eet ccsclac Aah cyten Ros ee ek Ae Oe eae octashe aiesds steed 11 Tti USING AA PIC Pics gate occas tenors ented aeaesn sha e araa AE a a E 12 11 2 USING MPIC HAG ioe oeoa ature saare tes aeae ces eae aa a aE Ea ati aai 12 12 Running your program from the Grid Engine queuing SyStem ccceeeeeeeeeeees 13 12 Grid EA2. ssh Y dxyOabc hamilton From a computer running Windows we would recommend using PuTTY which can be obtained from http www chiark greenend org uk sgtatham putty download html 5 The Hamilton cluster Once you login you will be in your ITS home space users username Files here are stored on the main ITS file servers hudson and stevens and are backed up overnight but there is limited space available This is where you should store your source code and other important files Each user is given space on the master node in a directory called data hamilton Your space will be in the directory with your username e g data hamilton username Please use this directory to run jobs from as it is close to the slave nodes and will place less load on the main file servers Files will not be deleted from here but are not backed up The filestore is a RAID device however You can also access the ITS scratch space scratch share This is accesible from all ITS Unix or Linux computers and can be used to transfer files or data across Data here is not backed up and is deleted regularly Each of the slave nodes on the hamilton cluster has local scratch space available as scratch local You can use this for temporary storage whilst your job runs on the slave node Locally installed software is in usr local packagename e g usr local dlpoly which is mounted from the file servers or on the master itself under usr local Cluster Apps pac
3. Makefile for a Beowulf cluster Frequently it is sufficient to choose a Makefile specifically for a Linux MPI environment and to adapt the cc and F77 parameters in the Makefile These parameters should point to mpicc and mpif77 or mpif90 in the case of Fortran 90 code respectively 11 Executing the program There are two methods for executing a parallel or serial batch program using the queuing system or directly from the command line In general you should use the queuing system as this is a production environment with multiple users and example scripts which you can copy are discussed below However if a quick test of the application is necessary you can use the command line and run outside the queuing system on the master node but only with 1 or 2 processes To run a serial program such as the executable monte above you only need to type the name of the executable to run it monte All installed parallel MPI environments need to know on what slave nodes to run the program The methods for telling the program which nodes to use differ however 11 1 Using MPICH The command line for MPICH would look like this mpirun machinefile configuration_file np 4 program_name program options Where the configuration file is chosen by the Grid Engine software and looks something like this node02 2 node03 2 The 2 extension tells MPICH that it is intending to run two processes on each node Please refer to the specific man pages and t
4. CE may be used optionally to receive a message of any tag and from any sending process MPI_Recv buffer maxcount datatype source tag MPI_COMM_WORLD amp status Information about the received message is returned in a status variable The received message tag is status MPI_TAG and the rank of the sending process is status MPI_SOURCE Another function not used in the sample code returns the number of data type elements received It is used when the number of elements received might be smaller than maxcount MPI_Get_count amp status datatype amp nelements With these few functions you are ready to program almost any application There are many other more exotic functions in MPI but all can be built upon those presented here so far
5. QING sees a a e a a aa a a E Eaa EA RE REA EE ERRE REAT 14 12 2 Sample batch submission SCIP lL siisrciceesiencccessisstoteny wae eaadeededeatemaade 14 12 3 Sample script for MPU CH oiiiicc cceazagereeccnvedecadoevsdues ela nueseupdees bdeticbeeacevteseeieeeetoir ts 15 12 4 Grid Engine GOMMANGS rrara orn a aape a a s 16 13 SOMWA O a a e E et aa ee eee 18 13 1 BLAS LAPACK FFT and SCALAPACK libraries 0 cccceceseeeeteeeeeeeteee 18 13 2 Numerical Algorithms Group NAG Fortran Library ecceeeeeeeeeeeeeeeeeeeee 19 Ted os MAUNA Diiia a a ans agile oes devas A ENUS a tes 19 13 4 MGIB Oss size ce te asetettnad edabetia he Mone lures aAa NAANA ENa ATENE tee Mele Ae ecto pia Siaa 20 14 Creating your own modules Advanced USEIS ccccceeeeeeeeeeeeeeeeneeeeeeeeeeeeseeeeeeees 20 15 An example MPI PrOGrarn is ovscsescesesresseese ch vgeasibecetrpdernngamuuceoed coeueedaa ated taddeevenensaeds 21 15 1 Ent r and Exit MP nr a Anse Nena seis aac esds 23 15 2 Who Am Who Are They ccicisctes cnsecetayianinsseesieahinaecinlaedenelauaeecedeee 23 15 3 Sending MESSAGES so lt ine nasecbs se cche scnenedessatiesnaweacaeeenasaderestvssdedendaesatsteneas 23 15 4 Receiving MESSAQSS se sccrei ccc euelits Mantes tate tone tall ata de tam etadls 23 1 Introduction This guide introduces the ClusterVision Beowulf Cluster Environment running on the Hamilton Cluster at the University of Durham hamilton It explains how to use the MPI a
6. change the name of the module file such that it reflects the version number of the application For instance this is the name of the location of the mute module usr local Cluster Config Modulefiles mute 1 9 5 Now by issuing the command module load mute you will automatically load the new module The advantage is that if you have different version of the same application this command will always loads the most recent version of that application 15 An example MPI program The sample code below contains the complete communications skeleton for a dynamically load balanced master slave application Following the code is a description of the few functions necessary to write typical parallel applications include lt mpi h gt define WORKTAG ib define DIETAG 2 main argc argv Mnet rge Ohar arga int myrank MPI_Init amp argce amp argv initialize MPI MPI_Comm_rank MPI_COMM_WORLD always use this amp myrank process rank O thru N 1 if myrank 0 master else slave MPI_Finalize cleanup MPI master int ntasks rank work double result MPI_Status status MPI_Comm_size MPI_COMM_WORLD always use this amp ntasks processes in application Seed the slaves REM Processes are represented by a unique rank integer and ranks are numbered 0 1 2 N 1 MPI_COMM_WORLD means all the processes in the MPI application It is called a c
7. d pathscale module add mpich 1 2 6 pathcc12 The naming scheme for this combination can be explained as follows The first part of the name is the type of MPI library mpich for MPI over gigabit ethernet it would be mpich gm for MPI over Myrinet This is followed by the version number of the MPI library 1 2 6 The last part of the name is the compiler used when the mpicc command is run pathcc the PathScale compilers 9 Compiling your code There are three compilers groups available on the master node GNU Portland Group http AWwww pgroup com and PathScale http www pathscale com compilers The Portland compilers have 5 floating licences and are recommended for general use We have one PathScale licence which is on trial The following table summarises the compiler commands available on hamilton Language GNUcompiler Portland PathScale compiler compiler C gec pgec pathcc C C pgCC pathCC Fortran77 77 pgf77 pathf90 Fortran90 pgf90 pathf90 The most common code optimisation flag for the GNU compiler is 03 For the Portland compiler the fast option expands out to basic compiler optimsation flags type pgf90 fast help for more details For the PathScale compilers use 0 For maximum application speed it is recommended to use the Portland or PathScale compilers Please refer to the respective man pages for more information about optimisation for GNU Portland and PathScale HTML and PDF documentation may be found in
8. de polling blocking or hybrid Tram reeveverb specifies verbose for recv mode selection ms specifies totalview debugger Options gm use shmem is highly recommended to use as it improves performance Another recommended option is gm ki1l11 It is possible for a program to get stuck on a machine and MPI is unable to pick up the error The problem is that the program will keep the port locked and no other program will be able to use that Myrinet port The only way to fix this is to manually kill the MPI program on the slave node If the option gm kill 1 is used MPI make a better effort to properly kill programs after a failure 12 Running your program from the Grid Engine queuing system A workload management system also known as a batch or queuing system allows users to make more efficient use of their time by allowing you to specify tasks to run on the cluster It allows administrators to make more efficient use of cluster resources spreading load across processors and scheduling tasks according to resource needs and priority The Grid Engine queuing system allows parallel and batch programs to be executed on the cluster The user asks the queuing system for resources and the queuing system will reserve machines for execution of the program The user submits jobs and instructions to the queuing system through a shell script The script will be executed by the queuing system on one machine only the comma
9. e 6 0ul module info mpich_gm 1 2 5 12 gnu333 use own modules mpich_gm 1 2 5 12 pathcce version This indicates that there are several different modules available on the system including application software e g castep compilers e g pathscape pgi and MPI parallel environments e g mpich and mpich_gm To get more information on available modules try typing module help Ormodule whatis There is a default module available called default ethernet which loads several other modules namely the Portland compilers Grid Engine sge the queue manager and mpich for the ethernet To see what modules you have currently loaded type module list Currently Loaded Modulefiles i rg teal i 4 modules 7 default ethernet 2 Veg 5 mpich 1 2 6 pgi522 3 sge 6 0ul 6 pgi 5 2 2 If you want to remove any of these you can run module rm name To Clear all modules type module purge and you can then load other modules For example if you wanted to use the Myrinet interface you would load the default myrinet module 7 Running your application on the cluster In order to use and run your application on the cluster four steps are necessary e selecting the correct module environment e compiling your application e creating an batch script for the queuing system and e submitting your application to the queuing system 8 Selecting the correct module environment As mentioned above the module system is used to select from a number of poss
10. he command mpirun nh for more information 11 2 Using MPICH GM A typical command line for MPICH GM Myrinet based communication in the directory where the program can be found is the following mpirun ch_gm gm kill 1 gm f configuration_file np 4 program_name program_options The configuration_file consists typically of the following lines node02 node02 node03 node03 The configuration_file chosen by Grid Engine shows that the application using this configuration file will be started with two processes on each node as in the case of dual CPU slave nodes The np switch on the mpirun ch_gm command line indicates the number of processes to run in this case 4 The list of options is aoran ea om gm Lone lt n esom h stiles samehi prog oerione Option Explanation ASN verbose includes comments pee nn specifies the number of processes to run OMS RPS same as np use one or the other le a a specifies a configuration file gm use shmem enable the shared memory support gm shmem file lt file gt pecifies a shared memory file name gn she explicitly removes the shared memory file et ag generates this message TERE start machines in reverse order HAGMSW SNZ wait n secs between starting each machine gm kill lt n gt n secs after first process exits kill all other processes gn ay ean Don t actually execute the commands just print them gm recv lt mode gt specifies the recv mo
11. ible running environments If you are running single processor serial jobs or parallel jobs on the Gigabit ethernet then the default environment default ethernet should be sufficient and you can skip this part If you want run parallel code on the Myrinet interface or change compilers you will have to change from the default module There are two different MPI libraries on the cluster MPICH for Ethernet based communication and MPICH GM for Myrinet For each network system there is a choice of compilers the open source GNU gcc or the higher performance compilers from Portland or PathScale In order to select between the different compilers and MPI libraries you should use the module environment During a single login session use the command line tool module This makes it easy to switch between versions of software and will set variables such as the PATH to the executables However such changes will only be in effect for this login session and subsequent sessions will not use these settings To select a non default combination of compiler and MPI library on a permanent basis you must edit your login file You first need to get rid of the deafult setup and then add in your new set up For example to use the default setup for the Myrinet you would add module purge module add default myrinet to the end of the file To use the PathScale compilers together with the gigabit ethernet you would add module purge module ad
12. information about their configuration 1l attr val show only certain hosts j job_list shows detailed information on pending running job q shows detailed information on queues at each host The command qsub is used to submit jobs qsub scriptname submits a script for execution a time run the job at a certain time 1 request a certain resource q queues jobs is run in one of these queues There are many other options to qsub consult the man page for more information The command qde1 is used to delete jobs qdel jobid s deletes one or more jobs u username deletes all jobs for that user f force deletion of running jobs So to submit your job you would type qsub serial csh and to check its status you can type qstat If there are lots of jobs in the system you might use the u option together with your username to show only your jobs qstat u dxy0Oabc To get more detail about an individual job you can specify a job number qstat j 304 You can use the qmon graphical user interface GUI to get information about your jobs and account status qmon amp To see the state of your account or project click on Policy Configuration fourth from left bottom row and then select Share Tree Policy at the bottom You should then see a list of departments which you can click on to see groups and users At the bottom is a list of the attributes of the highlighted group or user The Shares entry is the numbe
13. kagename e g usr local Cluster Apps castep 6 The Modules Environment On a complex computer system with a choice of software packages and software versions it can be quite hard to set up the correct computing environment For instance managing different MPI software packages on the same system or even different versions of the same MPI software package is almost impossible on a standard Suse or Red Hat system as a lot of software packages use the same names for the executables and libraries As a user you end up with the problem that you can never be quite sure which libraries are used for the compilation of a program as multiple libraries with the same name might be available Also very often you would like to test new versions of a software package before permanently installing it Within Red Hat or Suse this would be a quite complex task to achieve The module environment makes this process easy The command to use is module module no arguments print usage instructions avail list available software modules load modulename add a module to your environment add modulename add a module to your environment unload modulename remove a module clear remove all modules This is an example output from module avail Caste pA O eee ENE maa molpro 2002 6 MpAehmcm A on 2E pgo default ethernet mpich 1 2 6 32b pgi522 nu default myrinet mpich 1 2 6 gee333 pathscale 1 2 dot mpich 1 2 6 pathcc12 BISAR gm 2 0 13 mpich 1 2 6 pgi522 sg
14. le to create new modules and add them to the module environment After installing an application in for instance my_application and creating a new module directory in my_modules you can modify the MODULEPATH to include the new search path If you use the tcsh shell the default the command would be setenv MODULEPATH SMODULEPATH my_modules If you use the bash shell this command would be export MODULEPATH SMODULEPATH my_modules To make the change permanent please add this command to your cshre or bashrc file The contents of a module look like this HHSMOdULEL OFFFHHHH HH HH HHH HHH HHH HH HH HH HH HH HH HH HH HE HH mpich gnu modulefile E proc ModulesHelp puts stderr tAdds myrinet mute to your environment module whatis Adds myrinet mute to your environment set root usr local Cluster Apps mute 1 9 5 setenv GM_HOME Sroot setenv gm_home roor append path PATH Sroot bin append path MANPATH Sroot man append path LD_LIBRARY_PATH Sroot lib Typically you only have to fill in the root path usr local Cluster Apps mute 1 9 5 and the description to make a new and fully functional module For more information please load the modules module module load modules and read the module and modulefile man pages The best policy is to make an additional directory underneath the modules directory for each application and to place your new module in there Then you can
15. ml 2 5 0 Doc e g usr local atlas acml 2 5 0 Doc html index html or usr local atlas acml 2 5 0 Doc acml pdf and also at http www pgroup com support libacml htm To compile a program foo f with the Portland compiler and link it with the acml library the following command may be used pgf90 foo f o foo Mcache_align tp k8 64 l usr local atlas acml 2 5 0 pgi64 include usr local atlas acml 2 5 0 pgi64 lib libacml a 13 2 Numerical Algorithms Group NAG Fortran Library This is installed in usr local nag current Documentation is available in usr local nag current doc An overview is provided by pointing mozilla at the User Note mozilla usr local nag current doc un html The nagexample script demonstrates use of the library e g nagexample x02ajf and you can compile a fortran program thus pgf77 x02ajfe f usr local nag current lib libnag a usr local nag current acml libacml a 13 3 Matlab Matlab commands in a matlab file Untitled m can be run using the following command in a serial batch file such as usr local Cluster Examples sge serial csh module add matlab matlab nodisplay lt Untitled m 13 4 Molpro Single processor molpro jobs e g in a file called h2o_eom test can be run by adding the following commands to a serial batch file such as usr local Cluster Examples sge serial csh module add molpro molpros 2002 _6 v lt h20_eom test 14 Creating your own modules Advanced users It is possib
16. n be embedded in the script using lines starting with see below The name of the job is set by default to the name of the script and the output will go into a file with this name with the suffix o appended with the jobid e g out put from the script with job number 304 will go into file serial csh o304 The nm flag is used to request the user be emailed at start s and end e of the job The job output is directed into the directory you are currently working from by cwd If you prefer to have standard error and standard output combined leave the flag j y You can adda P flag to specify which project the job should be charged from e g P ITSall When a job is submitted the queuing system takes into account the requested resources and allocates the job to a queue which can satisfy these resources If more than one queue is available load criteria determine which node is used so there is load balancing There are several requestable resources including system memory and max CPU time for a job for details type qstat F 12 3 Sample script for MPICH This example script which can be found in usr local Cluster Examples sge mpich ethernet csh submits an MPICH job to run on the ethernet system bin csh simple test script for submission of a parallel mpi job using the gigabit ethernet on hamilton please edit the mailname below use current working directory cwd combine error and output files S J y send email a
17. n order to solve a particular computational problem and need to exchange large amounts of information The Myrinet network can send information at a maximum rate of 4000 Mbits per second The AMD Opteron CPUs are 64 bit and are referred to as x86_64 architecture This architecture allows addressing of large memory sizes However one of the additional advantages of Opterons is that they can also run executables built for Intel x86 32 bit processors Known as x86_32 such as ITS linux computers like vega 3 Getting an account on Hamilton If you already have an account on hal you will be able to use hamilton under the ITS project allocation If you do not already have an account please apply by submitting the application form available from http Awww dur ac uk resources its helpdesk registration forms HighPerfRegistration pdf to the ITS helpdesk You account will be ready for use the next day with the same password as your standard ITS account 4 Accessing the cluster The master node is called hamilton From outside the cluster it is known by this name only If you wish to access the master node use ssh secure shell The command structure for ssh is ssh user hostname So if you are user dxyOabc then the command ssh dxyOabc hamilton will log you into the cluster From outside Durham it would be hamilton dur ac uk If you wish to use X11 graphics the Y option requests X11 forwarding and for programs such as qmon or nedit
18. nd batch environments how to submit jobs to the queuing system and how to check your job progress If you are short of time and would like a quick guide please see quick sxw 2 The physical hardware layout of Hamilton Hamilton is an example of a Beowulf Cluster and consists of a login compile and job submission node called the master node and 135 compute nodes normally referred to as slave nodes A second fail over master is available in case the main master node fails Each of the slave nodes consists of two 2 GHz AMD Opteron processors and 4 Gbytes of memory An additional second fast network called a Myrinet is available for fast communication between 32 of the 135 slave nodes see figure Local network Master Failover node z node Myrinet 000000 D on slaves Slave 2 Slave 3 Slave a Slav The master node is used to compile software to submit a parallel or batch program to a job queuing system and to analyse produced data Therefore it should rarely be necessary for a user to login to one of the slave nodes The master node and slave nodes communicate with each other through a Gigabit Ethernet network This can send information at a maximum rate of 1000 Mbits per second The additional Myrinet network is added to the cluster for faster communication between 32 of the slave nodes This faster network is mainly used for MPI programs that can use multiple machines in parallel i
19. nds in the script will have to make sure that it starts the actual application on the machines the queuing system has assigned for the job The system takes care of holding jobs until computing resources are available scheduling and executing jobs and returning the results to you 12 1 Grid Engine Grid Engine is a software package for distributed resource management on compute clusters and grids Utilities are available for job submission queuing monitoring and checkpointing The Grid Engine software is made available by Sun Microsystems and the project homepage is at http gridengine sunsource net where extensive documentation can be found 12 2 Sample batch submission script This is an example script used to submit non parallel scripts to Grid Engine This script can be found in usr local Cluster Examples sge serial csh bin csh simple test script for submission of a serial job on hamilton please change the mail name below use current working directory cwd combine error and output files S Y send email at start s and end e m se email address M my_mail_name durham ac uk execute commands myprogl In order to submit a script to the queuing system the user issues the command qsub scriptname Usage of qsub and other queueing system commands will be discussed in the next section Note that qsub accepts only shell scripts not executable files All options accepted by the command line qsub ca
20. ommunicator and it provides all information necessary to do message passing Portable libraries do more with communicators to provide synchronisation protection that most other systems cannot handle 15 1 Enter and Exit MPI As with other systems two functions are provided to initialise and clean up an MPI process MPI_Init amp argc amp argv MPI_Finalize 15 2 Who Am I Who Are They Typically a process in a parallel application needs to know who it is its rank and how many other processes exist A process finds out its own rank by calling MPI_Comm_rank Int myrank MPI_Comm_rank MPI_COMM_WORLD amp myrank The total number of processes is returned by MPI_Comm_size AYHIE LayS Kates MPI_Comm_size MPI_COMM_WORLD amp nprocs j 15 3 Sending messages A message is an array of elements of a given data type MPI supports all the basic data types and allows a more elaborate application to construct new data types at runtime A message is sent to a specific process and is marked by a tag integer value specified by the user Tags are used to distinguish between different message types a process might send receive In the sample code above the tag is used to distinguish between work and termination messages MPI_Send buffer count datatype destination tag MPI_COMM_WORLD 15 4 Receiving messages A receiving process specifies the tag and the rank of the sending process MPI_ANY_TAG and MPI_ANY_SOUR
21. r of shares allocated The level percentage is the percentage that the allocated number of shares represents out of that level So for example if you click on Chemistry you can see they have 15400 shares which is 23 5 of the resource at the departmental level Level Percentage and which represents 23 5 of the total resource Total Percentage Now you can also see Chemistry has three groups namely chemmodel coldmols and liquidcrystal Clicking on them indicates the relative distribution of the 15400 shares within Chemistry If you click on say chemmodel you can see it has 4000 shares which is 26 of Chemistry s allocation and 6 1 of the total resource The Actual Resource Share indicates the percentage the level has used so far The quick queue for short jobs There is a quick queue called all q set up for jobs requiring less than 12 hours CPU time To run your job in this queue you should add q all q I quick I h_cpu 12 0 0 to your job submission script 13 Software 13 1 BLAS LAPACK FFT and SCALAPACK libraries The AMD Core Maths Libraries ACML incorporating BLAS Basic Linear Algebra Subprograms _http www netlib org blas LAPACK Linear Algebra Package http www netlib org lapack FFT and SCALAPACK http www netlib org scalapack routines are installed in usr local atlas acml 2 5 0 These routines have been tuned for the AMD Opteron processor Documentation for the libraries is available in usr local atlas ac
22. t start s and end e m se email address M my_mail_name durham ac uk request between 2 and 4 slots pe mpich 2 4 setenv MPICH_PROCESS_GROUP no set up the mpich version to use load the module module purge module load default ethernet Gridengine allocates the max number of free slots and sets the variable SNSLOTS echo Got SNSLOTS slots execute command mpirun np NSLOTS machinefile STMPDIR machines mympiexecutable It requests from 2 to 4 parallel slots and runs the job A similar file mpich myrinet csh can be used to submit jobs to run on the Myrinet network 12 4 Grid Engine commands The Grid Engine queuing system is used to submit and control batch jobs The queuing system takes care of allocating resources accounting and load balancing jobs across the cluster Job output and error messages are returned to the user The most convenient method to update or see what happens with the queuing system is using the X11 based command qmon The command qstat is used to show the status of queues and submitted jobs qstat show job queue status no arguments show currently running pending jobs f show full listing of all queues their status and jobs j job_list shows detailed information on pending running job u user shows current jobs by user The command ghost is used to show information about nodes qhost show job host status no arguments show a table of all execution hosts and
23. the usr local Cluster Docs directory By default the compiler will try to compile and link in one step So for example if you have a Fortrang0 file called monte 90 you would type pgf90 o monte monte f90 to compile and link it in one step to produce the executable monte If you wish to compile and link in different steps you would use the c option to the compiler to prevent the link stage pgf90 c monte f90 which would produce an object file monte o You could then link it in a separate step pgf90 o monte monte o 10 MPI compile and link commands The commands referred to in the table above are specific for serial single processor applications For parallel applications it is preferable to use MPI based compilers The correct compilers are automatically available after choosing the parallel environment The following MPI compiler commands are available Code Compiler C mpicc C mpiCC Fortran77 mpif77 Fortran90 mpif90 These MPI compilers are wrappers around the GNU Portland and PathScale compilers and ensure that the correct MPI include and library files are linked into the application Dynamic MPI libraries are not available on the cluster Since they are wrappers the same optimisation flags can be used as with the standard GNU or Portland compilers Typically applications use a Makefile that has to be adapted for compilation Please refer to the application s documentation in order to adapt the
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