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ANL/MCS-TM-ANL-01/x Rev x Installation and User's Guide to

1. A We have been informed that there is a error in the 77 script in some versions of Linux which causes this problem Try either getting a patch for the 77 script or reconfiguring with nof77 2 Q The build fails for the ch_p4 device when using the Compaq C compiler A There is an incompatibility with the system include files not the MPICH include files If you can modify usr include rpc xdr h add the following near the top of that file if defined __DECC defined __DECCXX typedef long int int64_t endif 53 6 7 6 Compaq ULTRIX and Tru64 1 Q When trying to build the make aborts early during the cleaning phase amon MPICH mpich gt make clean bin rm f o nupshot Error code 1 A This is a bug in the shell support on some Compaq ULTRIX systems You may be able to work around this with setenv PROG_ENV SYSTEM_FIVE Configuring with make s5make may also work 6 8 Problems in testing The MPICH test suite in examples test performs a fairly complete test of an MPI imple mentation If there is an error it usually indicates a problem with the implementation of MPI if you encounter such a problem please report it tompi bugs mcs anl gov However there are a few exceptions that are described here 6 8 1 General 1 Q The test pt2pt structf fails with O Error in MPI_ADDRESS Invalid argument Address of location given to MPI_ADDRESS does not fit in Fortran integer
2. Q When trying to start a large number of processes on a workstation network I get the message p4_error latest msg from perror Too many open files A There is a limitation on the number of open file descriptors On some systems you can increase this limit yourself on others you must have help from your system administrator You could experiment with the secure server but it is not a complete solution Q When I try to run a program on more than one processor I get an error message mpirun np 2 cpi home me cpi error in loading shared libraries libcxa so 1 cannot open shared object file No such file or directory There is no trouble running on one processor A This means that some shared library used by the system cannot be found on remote processors There are two possibilities a The shared libraries are not installed on the remote processor To fix this have your system administrators install the libraries b The shared libraries are not in the default path This can happen if the path is in an environment variable that is set in your current shell but that is not part of your default or remote shell environment The fix in this case is harder because you must communicate the location of the shared library to the executable a major deficiency in most Unix shared library designs is that executables do not by default remember where a shared library was found when linking The simplest fix may be to have your sy
3. A fourth possiblity is to get an AFS version of rsh that fixes this bug As we are not running AFS ourselves we do not know whether such a fix is available 2 Q Not all processes start A This can happen when using the ch_p4 device and a system that has extremely small limits on the number of remote shells you can have Some systems using Ker beros a network security package allow only three or four remote shells on these systems the size of MPI_COMM_WORLD will be limited to the same number plus one if you are using the local host The only way around this is to try the secure server this is documented in the MPICH installation guide Note that you will have to start the servers by hand since the chp4_servs script uses remote shell to start the servers 6 13 Programs fail after starting 6 13 1 General 1 Q I use MPI_Allreduce and I get different answers depending on the number of processes I m using A The MPI collective routines may make use of associativity to achieve better par allelism For example an MPI_Allreduce gin amp out MPI_DOUBLE 1 might compute a b e d e f g h or it might compute a 6 c d e f g h where a b are the values of in on each of eight processes These expressions are equivalent for integers reals and other familar objects from mathematics but are not equivalent for datatypes such as floating point used in computers The assoc
4. automountfix program This is sometimes necessary for systems with automounter prob lems see Section 4 11 2 with comm name Select a communication option for the device Only for the ch_p4 device the values shared for SMP nodes and bproc for Scyld are supported rsh commandname Set the name of the program used to start remote processes Only the ch_p4 device uses this and if no name is provided configure will attempt to determine the appropropriate program This usage is deprecated instead use the environment variable RSHCOMMAND In addition configure makes use of environment variables such as MAKE CC FC CFLAGS and FFLAGS Normally you should use configure with as few arguments as you can If you leave all arguments off configure will usually guess the correct architecture arch unless you are in a cross compiling environment and will usually choose an appropriate device device as well Where TCP IP is an appropriate mechanism for communication the TCP device ch_p4 will be chosen by default 4 1 1 MPI and PMPI routines The MPI standard requires that each routine be available with both the MPI and PMPI prefix for example MPI_Send and PMPI_Send MPICH attempts to use weak symbols to provide this feature this reduces the size of the MPICH library You can force MPICH to make separate libraries for the MPI and PMPI versions by adding the configure option disable weak symbols configure disable weak symbol
5. id_dsa and id_dsa pub for dsa key types 3 Copy the file id_dsa pub to authorized_keys2 rather than to authorized_keys Py P y y 4 6 Special Configure Options There are several configure options that modify the behavior of the ch_p4 device These include 27 enable lazy gethostbyname Use a more scalable approach in initializing connections This may cause the first message to a process to take longer than otherwise enable threaded listener Use a separate thread rather than a separate process for the listener that is used to initiate connections 4 7 Alternate C Compilers More and more systems particularly clusters come with multiple compilers In many cases you can build MPICH using just one of these compilers and then allow users to use their favorite compiler when building their code In many cases no extra steps are needed Users can simply use the command line argument cc or the environment variable MPICH_CC to specify a different compiler Unfortunately this won t always work For example in some cases different libraries may be needed by different compilers when linking programs Some compilers may need different options to support ANSI ISO C In particular support for the longer datatypes such as long long and long double may rely on runtime library support routines that are specific to each compiler For C and C you can create a file with the name mpicc lt compilename gt
6. segmentation violation during program execution This is usually due to an error in the user s program such as an array overwrite or use of an uninitialized variable in referencing storage 6 4 Troubleshooting Shared Libraries Shared libraries provide a useful and powerful tool for speeding linking and execution of programs However the implementation of shared libraries in most operating systems leaves much to be desired This section covers some of the problems and workarounds for them Some most systems do not remember where the shared library was found when the executable was linked Instead they depend on finding the shared library in either a default location such as 1ib or in a directory specified by an environment variable such as LD_LIBRARY_PATH or by a command line argument such as R or rpath more on this below The MPICH configure tests for this and will report whether an executable built with shared libraries remembers the location of the libraries It also attemps to use a compiler command line argument to force the executable to remember the location of the shared library If you need to set an environment variable to indicate where the MPICH shared libraries are you need to ensure that both the process that you run mpirun from and any processes 3There is a reason for this unfortunate choice that has to do with distributing executables linked with shared libraries However the capability to save the l
7. It is necessary that the wish program be accessible to users the other parts of Tcl and Tk do not need to be installed but make sure that everything that wish itself needs is installed To build Tcl and Tk we recommend the following approach 1 Fetch the compressed tar files and the patch file into an empty directory preferably in a local not NFS file system such as tmp but make sure that you have enough space in that file system xxx should be adequate 2 Unpack the tar files gunzip c tcl7 3 tar Z tar xf gunzip c tk3 6 tar Z tar xf 3 Apply the patch to Tk cd tk3 6 patch p 1 lt tk3 6p1patch cd Note that the instructions say to use patch p newer versions of patch require an argument and the correct value in this case is one other versions of patch will want p1 no space between p and the one 4 Configure Tcl Pick an installation directory that clearly indicates the Tcl and Tk versions For example to build Tcl to install into usr local tc173tk36 use cd tcl7 6 configure prefix usr local tcl73tk36 5 Build and install Tcl Before you execute the make install step make sure that the directory specified in the prefix argument to configure exists mkdir usr local tc173tk36 make make install 6 Configure build and install Tk Use the same installation directory for Tk that you used for Tcl 97 cd tcl7 6 configure prefix usr local tcl73tk36 make
8. JM_PARTIONCREATIONFAILURE ERROR 0031 635 Non zero status 1 returned from pm_mgr_init A This means that either mpirun is trying to start jobs on your SP in a way different than your installation supports or that there has been a failure in the IBM software that manages the parallel jobs all of these error messages are from the IBM poe command that mpirun uses to start the MPI job Contact your system administrator for help in fixing this situation You system administrator can use dsh av ps aux egrep i poel pmd jmd from the control workstation to search for stray IBM POE jobs that can cause this behavior The files tmp jmd_err on the individual nodes may also contain useful diagnostic information Q When trying to run on an IBM SP I get the message from mpirun ERROR 0031 214 pmd chdir lt a user gamma home mpich examples basic gt ERROR 0031 214 pmd chdir lt a user gamma home mpich examples basic gt A These are messages from tbe IBM system not from mpirun They may be caused by an incompatibility between POE the automounter especially the AMD auto mounter and the shell especially if you are using a shell other than ksh There is no good solution IBM often recommends changing your shell to ksh Q When trying to run on an IBM SP I get this message ERROR 0031 124 Less than 2 nodes available from pool 0 A This means that the IBM POE MPL system could not allocate the requested nodes when you trie
9. ssh identity pub ssh authorized_keys 26 If the machine you are connecting to does not share a common file system then ssh identity pub should be copied over to the ssh authorized_keys file of the machine you will be connecting to ssh will insist that authorized _keys have its permissions set so that it is not group writable so do chmod go rwx ssh authorized_keys This step avoids the need to enter your password each time you want to run a secure shell command 4 In order to avoid typing in your pass phrase each time ssh is invoked an ssh agent needs to be created and your pass phrase added ssh agent SHELL ssh add 5 Configure with rsh ssh so that the ch_p4 device will use ssh instead of rsh configure rsh ssh In case of trouble e Make sure that the hosts listed in your util machines machine xxxx are also listed in the etc ssh_known_hosts file on your network or your ssh known_hosts file in your home directory e It is important that tmp has permissions set to 03777 with root as owner and group 0 e openssh has a v flag which is very useful for tracking down handshaking problems 4 5 2 SSH Version 2 Follow the instructions for Original SSH with the following changes 1 Give the option t dsaor t rsatossh keygen Otherwise an rsal key is generated that cannot be used by ssh2 2 Instead of the files identity ssh keygen creates files with names
10. vides for far faster and more scalable startup Grids The globus2 device uses Globus www globus org to provide a grid enabled im plementation of MPI This device is appropriate for collections of systems on which Globus is installed Symmetric Multiprocessors The ch_shmem device is appropriate for a single shared memory system such as a SGI Origin or Sun E10000 This device uses shared memory to pass messages between processes and makes use of facilities provided by the oper ating system such as System V shared memory or anonymous mmap regions for data and System V semaphores or OS specific mutex routines for synchronization The ch_1fshmem device is a version of ch_shmem that uses a lock free approach and that we developed for the NEC SX 4 9 The ch_shmem is appropriate for most systems the ch_1fshmem requires special assembly language coding but can be ported to most systems However the ch_1fshmem supports only the NEC SX 4 Massively Parallel Processors MPPs MPICH was originally developed to provide an implementation of MPI for many of the massively parallel processors each of which had its own propritary message passing system We still include the devices ch_ meiko ch_nx and ch_mpl with MPICH releases though most of these systems have now disappeared Others MPICH was designed to enable other groups to use it when developing their own MPI implementations Both vendors and research groups have used MPICH as the bas
11. In fact it prides itself on gathering the stdouts for you You can do one of the following a Use Unix built in commands for redirecting stdout from inside your program dup2 etc The MPE routine MPE_10_Stdout_to_file in mpe src mpe_ io c shows one way to do this Note that in Fortran the approach of using dup2 will work only if the Fortran PRINT writes to stdout This is common but by no means universal b Write explicitly to files instead of to stdout use fprintf instead of printf etc You can create the file name from the process s rank This is the most portable way 6 143 HP UX 1 Q When trying to run upshot under HP UX I get error messages like set Variable name must begin with a letter or upshot syntax error at line 35 unexpected 71 A Your version of HP UX limits the shell names to very short strings Upshot is a program that is executed by the wish shell and for some reason HP UX is both refusing to execute in this shell and then trying to execute the upshot program using your current shell e g sh or csh instead of issuing a sensible error message about the command name being too long There are two possible fixes a Add a link with a much shorter name for example ln s usr local tk3 6 bin wish usr local bin wish Then edit the upshot script to use this shorter name instead This may require root access depending on where you put the link b Create a regula
12. The MPICH implementation is not thread safe and does not support either fork or the creation of new processes Note that the MPI specification is thread safe but implementations are not required to be thread safe At this writing few implemen tations are thread safe primarily because this reduces the performance of the MPI implementation you at least need to check to see if you need a thread lock actually getting and releasing the lock is even more expensive The MPICH implementation supports the MPI_Init_thread call with this call new in MPI 2 you can find out what level of thread support the MPI implementation sup ports As of version 1 2 0 of MPICH only MPI_THREAD_SINGLE is supported We believe that version 1 2 0 and later support MPI_THREAD_FUNNELED and some users have used MPICH in this mode particularly with OpenMP but we have not rigourously tested MPICH for this mode Future versions of MPICH will support MPI_THREAD_MULTIPLE Q C programs execute global destructors or constructors more times than ex pected For example class Z public ZO cerr lt lt Z lt lt endl ZO 4 cerr lt lt Z lt lt endl ES Z Zs int main int argc char argv MPI_Init amp argc amp argv MPI_Finalize when running with the ch_p4 device on two processes executes the destructor twice for each process 69 A The number of processes running before MPI_Init or after MPI_Finalize is not define
13. ch_nc native nCUBE calls requires arch ncube ch_cmmd native TMC CM 5 CMMD calls These are no longer distributed with the MPICH distribution Known architectures include case is important alpha Compaq alpha CRAY CRAY XMP YMP C90 J90 T90 cray_t3d CRAY T3D EWS_UX_V NEC EWS4800 360AD Series workstation Untested freebsd PC clones running FreeBSD hpux HP UX intelnx Intel i860 or Intel Delta IRIX synonym for sgi IRIX32 IRIX with 32bit objects 32 IRIXN32 IRIX with n32 IRIX64 IRIX with 64bit objects ksr Kendall Square KSR1 and KSR2 LINUX PC clones running LINUX LINUX_ALPHA Linux on Alpha processors meiko Meiko CS2 netbsd PC clones running NetBSD paragon Intel Paragon rs6000 AIX for IBM RS6000 sgi Silicon Graphics IRIX 4 x 5 x or 6 x sgi5 Silicon Graphics IRIX 5 x on R4400 s for the MESHINE solaris Solaris solaris86 Solaris on Intel platforms sppux SPP UX sun4 SUN OS 4 x SX_4_floatO NEC SX 4 Floating point format float0 92 Conforms IEEE 754 standard C3 sizeof int 4 sizeof float 4 FORTRAN sizeof INTEGER 4 sizeof REAL 4 SX_4_floati NEC SX 4 Floating point format float1 IBM floating point format Ca sizeof int 4 sizeof float 4 FORTRAN sizeof INTEGER 4 sizeof REAL 4 SX_4_float2 NEC SX 4 Floating point format float2 CRAY floating point format C sizeof int 4 sizeof float 8 FORTRAN sizeof INTEG
14. operating system etc first followed by questions that are specific to a particular environment Problems with workstation clusters are collected together as well To make it easier to find solutions the most common problems are described first 6 3 The Most Common Problems This section describes some of the most common problems encountered when building and using MPICH See also Section A which covers frequently asked questions including some additional problems Permission Denied Q When I use mpirun I get the message Permission denied A If you see something like this 45 mpirun np 2 cpi Permission denied or mpirun np 2 cpi socket protocol failure in circuit setup when using the ch_p4 device it probably means that you do not have permission to use rsh to start processes The script tstmachines can be used to test this Try tstmachines t If this fails then you may need a rhosts or etc hosts equiv file you may need to see your system administrator or you may need to use the p4 server see Section B 3 4 Another possible problem is the choice of the remote shell program some systems have several Check with your systems administrator about which version of rsh or remsh you should be using If you must use ssh see the section on using ssh in the nstallation Manual If your system policy allows a rhosts file do the following 1 Create a file rhosts in your home directory
15. p udp i ethO j ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i eth1 j ACCEPT A input s 0 0 d 0 0 i lo j ACCEPT New rules for ssh traffic incoming or outgoing A input p tcp s 0 0 d 0 0 22 b j ACCEPT End of new rules A input p tcp s 0 0 d 0 0 0 1023 y j REJECT A input p tcp s 0 0 d 0 0 2049 y j REJECT A input p udp s 0 0 d 0 0 0 1023 j REJECT A input p udp s 0 0 d 0 0 2049 j REJECT A input p tcp s 0 0 d 0 0 6000 6009 y j REJECT A input p tcp s 0 0 d 0 0 7100 y j REJECT At this point users on remote systems should be able to ssh into the machine but they will still need a password Users should set up a private public authentication key pair in order for ssh to operate without passwords This process is documented in the installation guide but a summary of the steps for RH7 2 will be included here First run the ssh keygen t rsa application to create the private public key pair By default this will create the files ssh id_rsa and ssh id_rsa pub Use a password Next place the public key ssh id_rsa pub in the file ssh authorized_keys If more than one machine is going to be used then this key must be put in the ssh authorized_keys file on each machine The permissions on the ssh directory should be set to 700 otherwise the sshd may choose to not accept the keys This will allow you to connect using rsa k
16. 0 d 0 0 514 b j ACCEPT End of new rules A input p tcp s 0 0 d 0 0 0 1023 y j REJECT A input p tcp s 0 0 d 0 0 2049 y j REJECT A input p udp s 0 0 d 0 0 0 1023 j REJECT A input p udp s 0 0 d 0 0 2049 j REJECT A input p tcp s 0 0 d 0 0 6000 6009 y j REJECT A input p tcp s 0 0 d 0 0 7100 y j REJECT At this point users on remote systems with accounts on this system should be able to rsh rlogin to this machine without using a password Enabling ssh Enabling ssh is somewhat easier First the ssh server sshd must be installed This is part of the openssh server RPM This RPM is located on the first disc of the RedHat 7 2 distribution Once the server is installed it must be started etc rc d init d sshd start The service will be automatically started on reboot 78 At this point ssh on the localhost should work although a password will still be required However our firewall rules will be preventing connections from other machines We again modify etc sysconfig ipchains this time to allow ssh traffic in and out See the above section for a discussion of what we are doing here Firewall configuration written by lokkit Manual customization of this file is not recommended Note ifup post will punch the current nameservers through the H firewall such entries will not be listed here input ACCEPT forward ACCEPT output ACCEPT A input s 0 0 67 68 d 0 0 67 68
17. 2 Change the protection on it to user read write only chmod og rwx rhosts 3 Add one line to the rhosts file for each processor that you want to use The format is host username For example if your username is doe and you want to user machines a our org and b our org your rhosts file should contain a our org doe b our org doe Note the use of fully qualified host names some systems require this On networks where the use of rhosts files is not allowed you should use the secure server to run on machines that are not trusted by the machine that you are initiating the job from Finally you may need to use a non standard rsh command within MPICH MPICH must be reconfigured with rsh command_name and perhaps also with rshnol if the remote shell command does not support the 1 argument Systems using Kerberos and or AFS may need this See the section in the Installation Guide on using the secure shell ssh An alternate source of the Permission denied message is that you have used the su command to change your effective user id On some systems the ch_p4 device will not work in this situation Log in normally and try again Connection Refused This problem may be caused by Internet security settings on your system that restrict the number and frequency of interprocess connection operations Check with your systems administrator Linux users depending on the Linux distri bution should try running the fol
18. For example a user created datatype that was not later freed would be reported The option tracing enables tracing of internal calls This should be used only for debugging the MPICH implementation itself The option dlast enables tracing of the most recent operations performed by the device These can be output when a signal like SIGINT error or call to a special routine occurs There is a performance penalty for this option but it can be very useful for implementors attempting to debug problems Sample Configure Usage To make for running on Sun s running Solaris with ch_p4 as the device 91 and with the installation directory equal to the current directory configure with device ch_p4 with arch solaris make Known devices are ch_nx native Intel NX calls ch_mpl native IBM EUI or MPL calls ch_p4 p4 ch_p4mpd p4 with the MPD startup system globus2 Globus globus_io vMPI ch_meiko for Meiko CS2 using NX compatibility library ch_shmem for shared memory systems such as SMPs ch_lfshmem for shared memory systems such as SMPs uses lock free message buffers ch_cenju3 native NEC Cenju 3 calls The following devices were supported with ADI 1 but are currently unsupported Please contact us if you are interested in helping us support these devices meiko for Meiko CS2 using elan tport library and nx for Intel Paragon t3d for the Cray T3D using Cray shmem library
19. MPIR_F_FALSE ld 0711 317 ERROR Undefined symbol MPIR_InitFortran ld 0711 317 ERROR Undefined symbol MPIR_1_DCOMPLEX ld 0711 317 ERROR Undefined symbol MPIR_Free_Fortran_dtes ld 0711 317 ERROR Undefined symbol MPIR_Free_Fortran_keyvals this usually indicates an error in the make process For some reason the Fortran part which is where these symbols come from is particularly fragile To fix this try the following steps cd src fortran src make clean make ar lib libmpich a o ranlib lib libmpich a If weak symbols are not supported then in addition do these additional steps 83 make clean make profile ar lib libpmpich a o ranlib lib libpmpich a The problem is that some versions of make have logic errors that cause them to create files but not to act on them this causes make to build the object file but then fail to include it in the archive The above steps should work around this problem A 15 Warning messages while building MPICH Some compilers may generate a large number of warnings of the form commreq_free c line 70 warning 187 use of where may have been intended There is nothing wrong with these statements The compiler is warning about a legal but often misused feature of the C language The statements have been crafted so that most compilers recognize that the was used intentionally unfortunately some compilers insists on warning a
20. The option disable short longs may be used to suppress support for the C types long long a common extension and long double ANSI ISO C when they are the same size as long and double respectively Some systems allow these long C types but generate a warning message when they are used this option may be used to suppress these messages and support for these types disable long long disables just long long gt disable long double disables just long double The option ar_nolocal prevents the library archive command from attempting to use the local directory for temporary space This option should be used when a there isn t much space less than 20 MB available in the partition where MPICH resides and b there is enough space in tmp or wherever ar places temporary files by default 90 The option noranlib causes the ranlib step needed on some systems to build an object library to be skipped This is particularly useful on systems where ranlib is optional allowed but not needed because it is allowed configure chooses to use it just in case but can fail some ranlib s are implemented as scripts using ar if they don t use the local directory they can fail destroying the library in the process if the temporary directory usually tmp does not have enough space This has occured on some OSF systems The option rsh allows
21. You can set the directory into which the man pages will be placed with manpath lt path gt The option help shows the full set of options for mpiinstall You can test the installation by using the configure in mpich examples test For example if you have installed MPICH into usr local mpich 1 2 7p1 for architecture solaris and device ch_p4 execute cd examples test configure mpichpath usr local mpich 1 2 7 solaris ch_p4 bin make testing The test codes in the mpich examples test directory may be used with any implemen tation of MPI not just the MPICH implementation 4 13 1 User commands The commands mpirun mpicc mpif77 mpicxx and mpif90 should be in the user s search path Note that if several architectures and or MPICH devices are supported it is important that the correct directory be added to the user s path These are installed into the bin directory If multiple architectures or devices are being used be sure that the installation path distinguishes these For example if both the ch_p4 and ch_shmem devices are built on a Solaris system set the installation prefix to include these names prefix usr local mpich 1 2 7p1 solaris ch_p4 and prefix usr local mpich 1 2 7p1 solaris ch_shmem respectively Alternately set the prefix to usr local mpich 1 2 7p1 and set the ex ecprefix to 36 usr local mpich 1 2 7p1 solaris ch_p4 and usr local mpich 1 2 7p1 solaris c
22. ch_p4mpd device e Improvements to the SMP support in the ch_p4 device thanks to Pete Wykcoff e Support for IA64 systems running Linux and for Mac OS X e Support for version 2 of Globus in the globus2 device e Many bug fixes and code improvements See www mcs anl gov mpi mpich r1_2_ 3changes html for a complete list of changes New and improved in 1 2 2 e A greatly improved ch_p4mpd device e Improved support for assorted Fortran 77 and Fortran 90 compilers including compile time evaluation of Fortran constants used in the MPICH implementation e An improved globus2 device providing better performance e A new bproc mode for the ch_p4 device supports Scyld Beowulfs e Many TCP performance improvements for the ch_p4 and ch_p4mpd devices as well as e Many bug fixes and code improvements See www mcs anl gov mpi mpich r1_2_ 2changes htm1 for a complete list of changes 1 2 Choosing the correct device and release MPICH is designed to be ported and optimized for a variety of systems though implemen tations of an abstract device interface ADI Many different implementations of the ADI exist each is called a device Workstation Networks Beowulf Clusters and Individual Workstations The im portant devices are ch_p4 and ch_p4mpd The ch_p4 device is the most general and supports SMP nodes MPMD programs and heterogeneous collections of systems The ch_p4mpd device supports only homogenous clusters of uniprocessors but pro
23. chp4_servs port 1234 The secure server propagates all environment variables to the remote process and ensures that the environment in which that process containing your MPI program contains all environment variables that start with LD_ just in case the system uses LD_SEARCH_PATH or some other name for finding shared libraries 3 3 10 Setting the Working Directory for the p4 Device By default the working directory for processes running remotely with ch_p4 device is the same as that of the executable To specify a different working directory use p4wdir as follows mpirun np 4 myprog p4wdir myrundir 3 4 MPMD Programs It is possible to run a parallel program with different executables with several of the devices including the ch_p4 ch_mpl1 and globus2 devices It is not possible to do this with the ch_shmem or ch_p4mpd devices This style of parallel programming is often called MPMD for multiple program multiple data In many cases it is easy to convert a MPMD program into a single program that uses the rank of the process to invoke a different routine doing so makes it easier to start parallel programs and often to debug them If converting a MPMD program to a SPMD single program multiple data not to be confused with single instruction multiple data or SIMD is not feasible then you can run MPMD programs using MPICH However you will not be able to use mpirun to start the programs instead you will need to follow the in
24. conf e g mpicc gcc conf or mpicc pgcc conf that contains any specifications that are needed by the mpicc command mpicxx uses mpicxx lt name gt conf These files must be created by hand starting from the file mpichlib conf that is created in the mpich util directory by the MPICH configure The simplest way to create each file is to use configure setenv CC cc configure prefix usr local mpich 1 2 7 make make install cp util mpichlib conf usr local mpich 1 2 7 etc mpicc cc conf setenv CC gcc configure prefix usr local mpich 1 2 7 make cp util mpichlib conf usr local mpich 1 2 7 etc mpicc gcc conf In this example the default value of sysconfdir prefix etc is used For example if MPICH was built with cc as the compiler but a user wanted to use gcc instead either the commands setenv MPICH_CC gcc mpicc or mpicc config gcc would case mpicc to load mpich gcc conf and use the appropriate definitions 28 4 8 Fortran Compilers MPICH provides support for both Fortran 77 and Fortran 90 Because MPICH is implemented in C using MPICH from Fortran can sometimes require special options This section discusses some of the issues Note that configure tries to determine the options needed to support Fortran You need the information in this section only if you have problems Section 4 8 6 discusses how to support multiple Fortran compilers e g g77 and pgf77 with a sing
25. directory available to all machines This attempts to 1s a file that tstmachines creates by running 1s using the remote shell command Note that ch_p4 does not require that all processors have access to the same file system see Section 3 3 7 but the mpirun command does require this 11 3 Can user programs be run on remote systems This checks that shared libraries and other components have been properly installed on all machines 3 3 2 Changing the Remote Shell Program You can change the remote shell command that the ch_p4 device uses to start the remote processes with the environment variable P4_RSHCOMMAND For example if the default remote shell program is rsh but you wish to use the secure shell ssh you can do setenv P4_RSHCOMMAND ssh mpirun np 4 a out This only works for different remote shell commands that accept the same command line arguments If you are having trouble using the remote shell commands consider using either the secure server Section 3 3 4 or the ch_p4mpd device 3 3 3 Using the Secure Shell Section 4 5 explains how to set up your environment so that the ch_p4 device on networks will use the secure shell ssh instead of rsh This is useful on networks where for security reasons the use of rsh is discouraged or disallowed 3 3 4 Using the Secure Server Because each workstation in a cluster usually requires that a new user log into it and because this process can be very time consuming MPICH provid
26. discussed in the Users Guide 4 14 3 Stopping the P4 servers To stop the servers their processes must be killed This is easily done with the Scalable Unix Tools 6 with the command 39 pt ps all tn serv_p4 and o LOGNAME ki11 INT Alternately you can log into each system and execute something like ps auxww egrep LOGNAME serv_p4 if using a BSD style ps or ps flu LOGNAME egrep serv_p4 if using a System V style ps The System V style will work only if the command name is short the System V ps only gives you the first 80 characters of the command name and if it was started with a long but valid directory path the name of the command may have been lost An alternative approach is discussed in Section 4 14 4 Managing the servers An experimental per15 program is provided to help you manage the p4 secure servers This program is chkserv and is installed in the sbin directory You can use this program to check that your servers are running start up new servers or stop servers that are running Before using this script you may need to edit it check that it has appropriate values for serv_p4 portnum and machinelist you may also need to set the first line to your version of perl5 To check on the status of your servers use chkserv port 2345 To restart any servers that have stopped use chkserv port 2345 restart This does not restart servers that are already running you can use this as a cron j
27. ee 44 E 45 6 3 The Most Common Problems 0 000002 e eee 45 ag Me eek ae ee eee vs a Se As 47 6 5 Other Problemsl a 48 6 6 Problems configuring 2 2 ea 49 6 6 1 Gemerall ai a E i ee ca 49 ek aui gok pos WE ag a A BO i Eee eS 49 6 7 Problems building MPICH o oaaae 50 6 7 1 General 000000000 00000 ee ee 50 6 7 2 Workstation Networks 0 0 0 0 0 0 0084 51 careta adas A 52 6 74 25G4 oca a A e Re 52 ad aie oe Ek Re he Pe A eee 53 6 7 6 Compaq ULTRIX and Tru64 0 0 54 6 8 Problems in testidgl ee 54 6 81 General cosida A ae Eh A a we de 54 pena pudes 55 6 9 1 Remera 55 a E E E E ee es 56 6 10 1 General 2 ee ee 56 ee Ue A ee eee ek te Ate ee eens 56 Bf GE Mock Sask e ic Rees tee ad Ie eg Sk te Ree 57 E E ho a E Pe 57 oL EL Generali a Go y y aie Gales Gs bug eee abet Gy eerie ae eee 57 6 11 2 Workstation Networks 0 0 0 0 0008 4 60 6 11 3 IBM RS6O00 ssri erra ee 65 6 11 4 IBM SP 020 000 000 000 000000000 65 6 12 Programs fail at startup ee 67 6 12 1 General 67 6 12 2 Workstation Networks 0 0 0 0 00084 67 6 13 Programs fail after starting ooa a ee 68 6 13 General ec 2 6 ie hme CARS ASAE RA SS He De RES 68 Son Pee a ee ee ee ee Se ee E 70 iy tinsel Hae Tn ot Wht tek Oy Bae etme we a tee See ee Se ae 70 6 13 4 Workstation Network
28. examples Directory containing further directories of example MPI programs Of particular note are basic with a few small examples to try first test with a test suite for exercising MPICH and perftest containing benchmarking code include The include files both user and system bin Contains the programs and executable scripts such as mpicc and mpirun used to build and run MPI programs man Man pages for MPI MPE and internal routines mpe The source code for the MPE extensions for logging and X graphics The contrib directory contains examples Best are the mandel and mastermind subdirectories The profiling subdirectory contains the profiling subsystem including a system for automatically generating the wrappers for the MPI profiling interface MPE also includes the performance visualization programs such as jumpshot see Section 3 6 1 mpid The source code for the various devices that customize MPICH for a particular ma chine operating system and environment romio The ROMIO parallel I O system which includes an implementation of most of the MPI 2 parallel I O standard src The source code for the portable part of MPICH There are subdirectories for the various parts of the MPI specification util Utility programs and files www HTML versions of the man pages D Configure Usage The command configure help will print out Configuring with args help Configuring MPICH Version 1 2 3 pre alpha of 20
29. local mpich bin machines if using the execer h This help machine lt machine name gt use startup procedure for lt machine name gt paragon p4 sp1 ibmspx anlspx sgi_mp ipsc860 inteldelta cray_t3d execer smp symm_ptx machinefile lt machine file name gt Take the list of possible machines to run on from the file lt machine file name gt This is a list of all available machines use np lt np gt to request a specific number of machines np lt np gt specify the number of processors to run on nodes lt nodes gt specify the number of nodes to run on for SMP systems only ch_mpl device supports this nolocal don t run on the local machine only works for ch_p4 jobs all cpus allcpus Use all available CPUs on all the nodes all local Run all processes on the master node exclude lt list gt Exclude nodes in a colon delimited list map lt list gt Use the colon delimited list to specify which rank runs on which nodes stdin filename Use filename as the standard input for the program This is needed for programs that must be run as batch jobs such as some IBM SP systems and Intel Paragons using NQS see paragontype below use stdin dev null if there is no input and you intend to run the program in the background An alternate is to redirect standard input from dev null as in mpirun np 4 a out lt dev null t Testing do not actually run just print what would be executed 94 v V
30. main alaska 3 afs u graphics It is not possible to provide different command line argument to different MPI processes 3 3 8 Using special or multiple interconnects In some installations certain hosts can be connected in multiple ways For example the normal Ethernet may be supplemented by a high speed FDDI ring Usually alternate host names are used to identify the high speed connection All you need to do is put these alternate names in your machines xxxx file In this case it is important not to use the form local O but to use the name of the local host For example if hosts host1 and host2 have ATM connected to hosti atm and host2 atm respectively the correct ch_p4 procgroup file to connect them running the program home me a out is hosti atm 0 home me a out host2 atm 1 home me a out 15 3 3 9 Using Shared Libraries with the ch p4 device As described at the end of Section 4 10 it is sometime necessary to ensure that environment variables have been communicated to the remote machines before the program that makes use of shared libraries starts The various remote shell commands e g rsh and ssh do not do this Fortunately the secure server Section does communicate the environment variables This server is built and installed as part of the ch_p4 device and can be installed on all machines in the machines file for the current architecture assuming that there is a working remote shell command with
31. make install This will provide you with a Tcl and Tk installation that can be used with the Tcl and Tk tools provided with MPICH If you have installed these into a non standard location such as the one used above you can set the environment variable TCL73TK36_DIR to the location used as the prefix in the configure commands setenv TCL73TK36_DIR usr local tc173tk36 This will allow MPICH to find these versions of Tcl and Tk We no longer use or recommend Tcl Tk because of the lack of compatibility between versions of Tcl Tk F 2 Obsolete Systems To configure for the Intel Paragon use configure with device ch_nx with arch paragon Two troubleshootings tip for the Paragon are 1 Q I got the following messages when I tried to build on the Paragon PGC W 0115 Duplicate standard type init c 576 PGC Paragon Paragon Rel R5 0 compilation completed with warnings PGC W 0115 Duplicate standard type init c 576 PGC Paragon Paragon Rel R5 0 compilation completed with warnings A This is because the compiler doesn t handle long long but doesn t reject it either It causes no harm 2 Q I get errors compiling or running Fortran programs A Fortran programs will need to use a absolute path for the mpif h include file due to a bug in the if77 compiler it searches include directories in the wrong order A troubleshooting tip for the older Intel i860 system is 1 Q The link test fails on an Intel i860 with icc
32. of the MPI module is that it is very difficult to provide a completely correct module that includes all of the functions with choice arguments As it is on many systems the size of the Fortran 90 module to handle the routines with choice arguments will be larger than the entire C version of the MPI library If you are uninterested in the Fortran 90 MPI module or you wish to keep the installed version of MPICH small you can turn off the creation of the Fortran 90 MPI module with the configure option disable f90modules 4 8 5 Configuring with the Absoft Fortran Compiler The Absoft compiler can be told to generate external symbols that are uppercase lowercase and lowercase with a trailing underscore the most common case for other Unix Fortran compilers or use mixed case an extension of Fortran which is only monocase Each of these choices requires a separate MPICH configure and build step MPICH has been tested in the mode where monocase names are generated this case is supported because only this case supports common and necessary for MPICH extensions such as getarg and iargc By default MPICH forces the Absoft compiler to use lowercase this matches most Unix Fortran compilers MPICH will find the appropriate versions of getarg and iargc for this case Because the examples and the test suite assume that the Fortran compiler is case insensitive the Fortran library produced by MPICH will only work with source code that uses monocase ei
33. of those problems Shared libraries are not supported from C In order to build shared libraries for MPICH you must have configured and built MPICH with the enable sharedlib option Because each Unix system and in fact each com piler uses a different and often incompatible set of options for creating shared objects and libraries MPICH may not be able to determine the correct options MPICH understands So laris GNU gcc on most platforms including Linux and Solaris and IRIX Information on building shared libraries on other platforms should be sent to mpi bugs mcs anl gov Once the shared libraries are built you must tell the MPICH compilation and linking commands to use shared libraries the reason that shared libraries are not the default will become clear below You can do this either with the command line option shlib or by setting the environment variable MPICH_USE_SHLIB to yes For example mpicc o cpi shlib cpi c or setenv MPICH_USE_SHLIB yes mpicc o cpi cpi c Using the environment variable MPICH_USE_SHLIB allows you to control whether shared libraries are used without changing the compilation commands this can be very useful for projects that use makefiles Running a program built with shared libraries can be tricky If you have trouble particular if programs will either not start or start and issue error messages about missing libraries see Section 6 4 4 11 File System Issues Most users do not need to wor
34. old style and prototype parameters does not agree cc 142 cc WARNING File p4_error c Line 162 The number of old style and prototype parameters does not agree cc 142 cc WARNING File p4_error c Line 169 The number of old style and prototype parameters does not agree cc 142 cc WARNING File p4_error c Line 174 The number of old style and prototype parameters does not agree A These have to do with declarations for a signal handler and can be ignored Specifically P4 is using the SIG_IGN ignore signal and SIG_DFL default behavior which are defined in usr include signal h and these definitions are not correct 6 7 3 Cray T3D 1 Q When linking I get mppldr 133 cf77 CAUTION Unsatisfied external references have been encountered Unsatisfied external references Entry name Modules referencing entry GETARG equivalenced to USX1 MPIR_GETARG A You may have specified the Fortran compiler with the F77 environment variable or the fc argument to configure The MPICH Fortran implemenation of MPI uses a com mon Fortran extension GETARG to get the command line arguments Most Fortran runtime systems support this but Cray uses call pxfgetarg i s len s ierr in stead You can change the file src env farg f manually to call the correct routine but note that configure builds a new farg f from farg f in each time that it is run MPICH now attempts to determine the correct names of the rou
35. use the same signal causing the program to fail For example by default the ch_p4 device uses SIGUSR1 some thread packages also use SIGUSR1 In a few cases you can change the signal before calling MPI_Init In those cases your signal handler will be called after the MPICH implementation acts on the signal For example if you want to change the behavior of SIGSEGV to print a message you can establish such a signal handler before calling MPI_Init With devices such as the ch_p4 device that handle SIGSEGV this will cause your signal handler to be called after MPICH processes it this is what it means to chain signals each part of the application is given the opportunity to respond to the signal 4 2 Workstation Networks with the ch p4 device Many users of MPICH will be using a Beowulf cluster typically running Linux Windows NT users should consult the installations instructions for the NT version of MPICH The ch_p4 device is one of two devices that are appropriate for Beowulf and other clusters the other is the ch_p4mpd device described in the installation and user s guide for that device Linux The ch p4 device will be chosen by default Using shared memory when the config ure option comm shared is given is supported as of MPICH version 1 2 0 through Unix System V IPC s Use of mmap is not supported as Linux does not support the use of MAP_SHARED with MAP_ANONYMOUS Because the System V IPC s cannot by design reliably be f
36. what is printed at what levels see the p4 Users Guide 2 Acknowledgments The work described in this report has benefited from conversations with and use by a large number of people We also thank those that have helped in the implementation of MPICH particularly Patrick Bridges and Edward Karrels Particular thanks goes to Nathan Doss and Anthony Skjellum for valuable help in the implementation and development of MPICH Debbie Swider who worked with the MPICH group for several years helped support and enrich the MPICH implementation More recent extensive contributions have been made by Omer Zaki for Jumpshot Anthony Chan has helped with SLOG and Jumpshot 3 David Ashton who has developed the Windows NT version of MPICH and was supported by a grant from the Microsoft corporation has also contributed to MPICH The C bindings have been contributed by Andrew Lumsdaine and Jeff Squyres of Notre Dame Rajeev Thakur of Argonne is responsible for the ROMIO implementation of the MPI 2 I O functions The Globus2 device is due to Nick Karonis of Northern Illinois University and Brian Toonen of Argonne National Laboratory Appendices A Frequently Asked Questions The web page www mcs anl gov mpi mpich faq html contains answers for many fre quently asked questions This section contains the same information as that web site e Introduction e Installing MPICH e Using MPICH e Permission Denied e Notes on getting MPICH running Under
37. you to select an alternative remote shell command by default configure will use rsh or remsh from your PATH If your remote shell command does not support the 1 option some AFS versions of rsh have this bug also give the option rshnol These options are useful only when building a network version of MPICH e g with device ch_p4 Special Tuning Options There are a number of options for tuning the behavoir of the ADI Abstract Device Interface which is the low level message passing interface These should NOT be used unless you are sure you know what you are doing The option pkt_size LENGTH allows you to choose the message length at which the ADI Abstract Device Interface switches from its short to long message format LENGTH must be positive The option adi_collective allows the ADI to provide some collective operations in addition to the basic point to point operations Currently most systems do not support this option it is ignored and on the others it has not been extensively tested Options for Experts The option memdebug enables extensive internal memory debugging code This should be used only if you are trying to find a memory problem it can be used to help find memory problems in user code as well Running programs with the option mpidb memdump will produce a summary when gt MPI_Finalize is called of all unfreed memory allocated my MPI
38. 0 Aborting program A This is not an error it is a gap in the MPI 1 definition that is fixed in MPI 2 with the routine MPI_Get_address This indicates that Fortran integers are not large enough to hold an address This does indicate that MPI programs written in Fortran should not use the MPI_Address function on this system 2 Q The test env timers fails with Timer around sleep 1 did not give 1 second gave 0 399949 A The low level software that MPICH uses probably makes use of the SIGALRM signal thus denying it to the user s program This is not an error the standard permits systems to make use of any signals though it is unfortunate 54 6 9 Problems compiling or linking Fortran programs 6 9 1 General 1 Q When linking the test program the following message is generated 77 g o secondf secondf o L usr local mpich lib lmpich invalid option L usr local mpich lib ld lmpich No such file or directory A This 77 program does not accept the L command to set the library search path Some systems provide a shell script for 77 that is very limited in its abilities To work around this use the full library path instead of the L option 77 g o secondf secondf o usr local mpich lib libmpich a As of the MPICH 1 2 0 release the MPICH configure attempts to find the correct option for indicating library paths to the Fortran compiler If you find that the MPICH configure has made an error please submit
39. 01 08 20 18 08 23 Usage configure with arch ARCH_TYPE with comm COMM_TYPE with device DEVICE 86 with mpe without mpe disable f77 disable f90 with f90nag with f95nag disable f90modules disable gencat disable doc enable cxx disable cxx enable mpedbg disable mpedbg enable devdebug disable devdebug enable debug disable debug enable traceback disable traceback enable long long disable long long enable long double disable long double prefix INSTALL_DIR c C _COMPILER noc opt OPTFLAGS cc C_COMPILER fc FORTRAN_COMPILER clinker C_LINKER flinker FORTRAN_LINKER c linker CC_LINKER cflags CFLAGS fflags FFLAGS c flags CCFLAGS optcc C_OPTFLAGS optf 77 F77_OPTFLAGS 90 F90_COMPILER f 90flags F90_FLAGS f90inc INCLUDE_DIRECTORY_SPEC_FORMAT_FOR_F90 901inker F90_LINKER 901ibpath LIBRARY_PATH_SPEC_FORMAT_FOR_F90 1ib LIBRARY mpilibname MPINAME mpe_opts MPE_OPTS make MAKEPGM memdebug ptrdebug tracing dlast listener_sig SIGNAL_NAME cross adi_collective automountfix AUTOMOUNTFIX noranlib ar_nolocal rsh RSHCOMMAND rshnol noromio file_system FILE_SYSTEM p4_opts P4_0PTS where ARCH_TYPE COMM_TYPE DEVICE INSTALL_DIR MPE_OPTS P4_OPTS C _COMPILER OPTFLAGS CFLAGS FFLAGS MAKEPGM LENGTH AUTOMOUNTFIX
40. 33 Unresolved data symbol MPI_COMM_WORLD ist referenced by overtake o ld ERROR 33 Unresolved text symbol MPI_Send ist referenced by overtake o A Check that the ar and ranlib programs are compatible One site installed the Gnu ranlib in such a way that it would be used with the vendors ar program with which it was incompatible Use the noranlib option to configure if this is the case 6 7 2 Workstation Networks 1 Q When building MPICH the make fails with errors like this making p4 in directory lib make libp4 a cc Aa g 1 include 1 include c p4_globals c cc usr include netinet in h line 69 error 1000 Unexpected symbol u_long cc usr include netinet in h line 127 error 1000 Unexpected symbol u_short etc A The problem here is that the system not MPICH include files are incompatible with your choice of compiler Check to see if cc is aliased in C shell do alias cc If it is either unalias it or set the environment variable CC to the full path for the compiler To get the full path do unalias cc setenv CC which cc and then reconfigure 5l 2 Q When building the ch_p4 device I get errors of the form making p4 in directory lib make libp4 a cc 1 include 1 include c p4_globals c cc 1 include 1 include c p4_MD c cc I include 1 include c p4_error c cc 142 cc WARNING File p4_error c Line 152 The number of
41. 4 1 1 MPI and PMPI routines 20 0000022 ae 23 ies Want x oP Peas 23 111 AS ENAS eve san ia a Go E we rae ws AA Gey 24 4 2 Workstation Networks with the ch_p4 device 24 pei 25 4 4 Setting UpIShl o a a 25 4 5 Configuring with SSh e 26 4 5 1 Original SSH version Ij ace eed ds oe be deb be ebeess 26 Laia A a ee Shaheed PER Es 27 ee i a am A a S 27 a e a Gee ate a ee a 28 aea a God Gt Ho a a Gee 4 29 4 8 1 What if there is no Fortran compiler 29 822 FOr anoU sec ae ek pe Sd BR BaP he Se Se TE oS Oe a 29 4 8 3 Fortran 77 and Fortran 90 2 4 29 4 8 4 Fortran 90 Modules o e o 30 eee ee 30 a eee de ees 31 AQ CA cece eee PE ee ek a Se De ew ee ee ee es 31 bee op St ee a es ee 32 pee Bs ee ete ee Ge Eee ay ee es ee 32 Lia AER a Qe BED Eee ee Ee 33 Owe Rode HOR E hae Sy Gu HA Ges 34 4 12 Building MPICH 02 0 02 2 eee ee 34 Ad Sous a ak Gow a Bee eee 35 4 13 1 User commands 2 0 0 00 a 36 Lato he hab a a ROS be Oe wes 37 oR OE OD we ee Se eS ee hea ee G 37 ee a e ee ee a eee 37 boa eet a Gta ee ee etn 37 eT o toe ee oe eee bow ta Tk ae es 37 eis ae sage TR eae 38 pe ade Big Sage ee oe ee hoe ge A S 39 MEG 2 OG oi oe ae Se 40 4 15 Thorough Testing 2 aaa ee Al op GRR ed ne Sh en os ROG A BAS ce ce eS 41 DA a at a a Ee eS 42 43 44 6 1 Things to try first
42. 7 2 distribution The rlogin server in rlogind is also included in this package The xinetd server controls the availability of the rsh and rlogin services This server is installed by default but by default rsh and rlogin services are disabled To enable these services you must edit the files etc xinetd d rsh and etc xinetd d rlogin Here is the rsh file as it looks by default default on description The rshd server is the server for the rcmd 3 routine and consequently for the rsh 1 program The server provides remote execution facilities with authentication based on privileged port numbers from trusted hosts service shell socket_type stream wait no user root log_on_success USERID log_on_failure USERID server usr sbin in rshd disable yes You must enable the service by changing disable yes to disable no The same must be done to the rlogin config file to enable that service At this point the xinetd daemon must be restarted to register these changes etc rc d init d xinetd restart 76 At this point you should receive a Permission denied if you attempt a command such as rsh localhost hostname as a non root user or as root for that matter To allow users to rsh without passwords you need to edit etc hosts equiv the system wide host file for rsh and rlogin This file should hold hostnames of machines that you would like users to be
43. ANL MCS TM ANL 01 x Rev x Installation and User s Guide to MPICH a Portable Implementation of MPI Version 1 2 7p1 The ch_p4 device for Workstation Networks by William Gropp and Ewing Lusk MONAL w a oe SO quo MATHEMATICS AND COMPUTER SCIENCE DIVISION yw z ARGON y Q Q try oF e Contents 1 1 1 1 Features of recent releases o 2 paa pl dl ergo ae e 4 1 3 Citations and References 2 a a a a 5 2 Quick Start 5 2 1 Downloading MPICH e 5 2 2 Configuring Making and Installing a 6 ea a A a a a oe a e o g 7 O ee 8 8 a eee 8 ee 10 oat A pee Gaede nie Geos Se Se eee 10 ee ee 10 3 3 1 Checking your machines list o a 11 as ap toa tas 12 3 3 3 Using the Secure Sh ell o 12 A E Soa Ueto ae BO e Ay 12 3 3 0 SMP Clusters 0 0 e soe a a Eie a a a E e ara a E a a a G 13 aos 13 AA E eee eee E 14 A 15 ana aora 16 AA 16 e dis Ak e A 16 3 0 DebUpeineys e so a r arat ad ee eee a A ew 16 3 5 1 The printf Approach 2 2220 4 17 3 5 2 Error handlers ooa aa a 17 Dik ESP ae eRe ee aS 17 o 17 oia 18 AA RA EEE RS 18 eee 19 o e as ee et 20 3 0 1 Jumpshot se ee aa eS a ae a h a a A a 20 3 7 Execution tracing 2 a 21 3 8 Performance measurements 2 ao a a 21 4 Details 22 bok hash ote chine Te operas a eg ke Beet a en as Pee 22
44. CH but not in MPICH2 is heterogenity that is support for a single MPI application running on systems that use different data representations e g a mixture of 1A32 and IA64 systems New and improved in 1 2 7 e Numerous ROMIO changes primarily to support MPICH 2 but including a number of bug fixes and more support for PVFS e Numerous MPE changes primarily to improve support for MPICH 2 but including new features and a more robust build process e Improvements to the code that releases SYS V IPC resources on exit these are used in the ch_shmem device and in the ch_p4 device when shared memory support is requested Numerous MPICH G2 changes including support for MPI_Comm_connect and MPI_ Comm_accept from Fortran and support for the mpicxx script for compiling C programs Fixed support for gnuplotps and gnuploteps in the mpptest performance test pro gram Improved support for MPI_STATUS_IGNORE However users looking for MPI 2 features such as this should switch to MPICH2 e Added support to the ch_p4 device for usernames containing more than nine charac ters New and improved in 1 2 6 e Improved build for Mac OSX including use of the IBM compilers Many small fixes Additional improvements to the collective algorithms New and improved in 1 2 5 Updated Globus2 device for Globus 2 2 or later Improved SLOG and Jumpshot New collective algorithms Better handling of startup in the ch_p4 device New and impro
45. Change directory to src fortran 2 Execute setenv F77 pgf77 configure with mpichconfig with flibname mpich pgf77 make clean make make install alt To use a particular Fortran compiler either select it on the mpif77 command line with the config name option e g config pgf77 or by selecting a particular mpif77 command e g mpif77 pgf77 49 C The C support in MPICH has been provided by Indiana University this group was formerly at the University of Notre Dame and uses its own configure process it also supports other MPI implementations This version supports only the MPI 1 functions and does not include support for the MPT 2 functions such as I O or the functions for manipulating MPI_Info Questions comments suggestions and requests for additional information should be sent to mpi2cpp devel osl iu edu Bug reports should also be 31 sent to mpi bugs mcs anl gov More information is available at the web site www osl iu edu research mpi2c Use the environment variable CXX to specify an alternate C compiler 4 10 Using Shared Libraries Shared libraries can help reduce the size of an executable This is particularly valuable on clusters of workstations where the executable must normally be copied over a network to each machine that is to execute the parallel program However there are some practical problems in using shared libraries this section discusses some of them and how to solve most
46. D with a REAL buffer as the first argument and then called it with an INTEGER buffer as the first argument a Fortran compiler can consider this an error Few Fortran 77 compilers would complain about this more Fortran 90 and Fortran 95 compilers check for this There are two solutions One is to use the MPI module in the choice version use the choicemod option for mpif90 the other is to use an option to tell the Fortran 90 compiler to allow argument mismatches For example the argument mismatch will cause the NAG Fortran compilers to allow mismatched arguments Using the MPI module is the preferred approach Fortran 77 users may sometimes see a similar message particularly with later versions of g77 The option Wno globals will suppress these warning messages 6 10 Problems Linking C Programs 6 10 1 General 1 Q When linking programs I get messages about __builtin_saveregs being unde fined A You may have a system on which C and Fortran compilers are incompatible for example using gcc and the vendor s Fortran compiler If you do not plan to use Fortran the easiest fix is to rebuild with the nof77 option to configure You should also look into making your C compiler compatible with your Fortran compiler Because this is very dependent on the specific system and compilers that you are using you may need to find a local expert who can help you The easiest but ugliest possibility is use 2c to convert Fortran to C t
47. E Computer Society Press William Gropp David Gunter and Valerie Taylor FPMPI A fine tuning performance profiling library for MPI November 2001 Poster presented at SC2001 William Gropp Steven Huss Lederman Andrew Lumsdaine Ewing Lusk Bill Nitzberg William Saphir and Marc Snir MPI The Complete Reference Volume 2 The MPI 2 Extensions MIT Press Cambridge MA 1998 William Gropp and Ewing Lusk A high performance MPI implementation on a shared memory vector supercomputer Parallel Computing 22 11 1513 1526 January 1997 William Gropp and Ewing Lusk Sowing MPICH A case study in the dissemination of a portable environment for parallel scientific computing IJSA 11 2 103 114 Summer 1997 William Gropp and Ewing Lusk Installation and user s guide for mpich a portable implementation of MPI Technical Report ANL 01 x Argonne National Laboratory 2001 The updated version is at ftp ftp mcs anl gov pub mpi mpichman ps William Gropp Ewing Lusk Nathan Doss and Anthony Skjellum A high performance portable implementation of the MPI Message Passing Interface standard Parallel Computing 22 6 789 828 1996 William Gropp Ewing Lusk and Anthony Skjellum Using MPI Portable Parallel Programming with the Message Passing Interface 2nd edition MIT Press Cambridge MA 1999 100 14 William Gropp Ewing Lusk and Rajeev Thakur Using MPI 2 Advanced Features of the Message Passing Interface MIT Press Cambr
48. ER 8 sizeof REAL 8 111 WARNING This version will not run together with FORTRAN routines sizeof INTEGER sizeof int SX_4_float2_int64 NEC SX 4 Floating point format float2 and 64 bit int s C sizeof int 8 sizeof float FORTRAN sizeof INTEGER 8 sizeof REAL tflops Intel TFLOPS UXPM UXP M Untested uxpv uxp v Untested ll 00 8 Others may be recognized Special notes For SGI with arch IRIX multiprocessors running the ch_p4 device use comm ch_p4 to disable the use of the shared memory p4 communication device and comm shared to enable the shared memory p4 communication device The default is to enable the shared memory communication device E Mpirun Usage The options for mpirun as shown by mpirun help are note that not all options are supported by all devices Depending on the specific device the output of mpirun help may differ the following is for the globus2 device mpirun mpirun_options lt progname gt options mpirun_options arch lt architecture gt specify the architecture must have matching machines lt arch gt file in usr local mpich bin machines if using the execer h This help machine lt machine name gt use startup procedure for lt machine name gt 93 mpirun mpirun_options lt progname gt options mpirun_options arch lt architecture gt specify the architecture must have matching machines lt arch gt file in usr
49. Intel CPUs do this this can also lead to inconsistent rounding You may be able to force the compiler to round to 64 bits 6 6 2 Linux 1 Q The configure step issues the message checking that the compiler f77 runs no Fortran compiler returned non zero return code Output from test was f2ctmp_conftest f MAIN main A This is probably caused by a problem in the Fortran compiler in older versions of Linux The 77 command in Linux was often a shell script that uses the 2c program to convert the Fortran program to C and then compile it with the C compiler In many versions of Linux this script has an error that causes a non zero return code even when the compilation is successful To fix this problem you need a corrected 77 script If you can edit the script yourself change the last 3 lines from case cOPT in 2 CC G o OUTF OFILES 1f2c lm esac rc exit rc to case cOPT in 2 CC G o 0UTF OFILES 1f2c lm esac rc trap 0 exit rc 2 Q The link test fails on Linux with messages like overtake o text 0x59 undefined reference to MPI_COMM_WORLD overtake o text 0x81 undefined reference to MPI_COMM_WORLD 49 A This is probably caused by a problem in the Fortran compiler in Linux In some early versions of Linux the 77 command in Linux is often a shell script that uses the f2c program to convert the Fortran program to C and then compile it with the C compiler In many versi
50. Linux e poll protocol failure during circuit creation e Using SSH e Mac OS X and hostname e SIGSEGV e semop lock failed e Compiler Switches 73 e C Builds Fail Fortran programs give errors about mismatched types Missing Symbols When Linking Warning messages while building MPICH e MPMD Multiple Program Multiple Data Programs Reporting problems and support Algorithms used in MPICH Jumpshot and X11 A 1 Introduction MPICH is a freely available portable implementation of MPI the Standard for message passing libraries A 2 Installing MPICH Building and installing MPICH often requires only configure prefix home me mpich make make install where the value of the prefix argument to configure is the directory in which MPICH should be installed See the Installation Guide for more detailed instructions A 3 Using MPICH Information on using MPICH can be found in the Installation and Users Guide There are versions of this guide for each MPICH device make sure that you read the one the applies to your device You can find out which device is installed by running a simple MPI program with the option mpiversion mpirun np 1 a out mpiversion All of the guides are available at http www mcs anl gov mpi mpich docs html 74 A 4 Permission Denied Question When I use mpirun I get the message Permission denied connection reset by peer or poll protocol failure in circuit setup when try
51. RSHCOMMAND MPILIBNAME the type of machine that MPI is to be configured for communications layer or option to be used communications device to be used directory where MPI will be installed optional options to pass to the mpe configure options to pass to the P4 configure device ch_p4 default is to use x1C g or CC optional optimization flags to give the compilers e g g flags to give C compiler flags to give Fortran compiler version of make to use Length of message at which ADI switches from short to long message protocol Command to fix automounters Command to use for remote shell Name to use instead of mpich in the name of the MPI library If set lLibMPILIBNAME will be used instead 87 or libmpich This can be used on systems with several different MPI implementations FILE_SYSTEM name of the file system ROMIO is to use Currently supported values are nfs ufs pfs Intel piofs IBM hfs HP sfs NEC and xfs SGI SIGNAL_NAME name of the signal for the P4 device ch_p4 device to use to indicate that a new connection is needed By default it is SIGUSR1 All arguments are optional but if arch comm or prefix arguments are provided there must be only one arch must be specified before gt comm if they both appear Packages that may be included with MPICH with device name Use the named device for communication Known names include ch_p4 ch_mpl ch_shmem an
52. TotalView will be familiar to users of command line based debuggers such as gdb or dbx Starting an MPICH program under TotalView control To start a parallel program under TotalView control simply add dbg totalview to your mpirun arguments mpirun dbg totalview np 4 cpi TotalView will come up and you can start the program by typing G A window will come up asking whether you want to stop processes as they execute MPI_Init You may find it more convenient to say no and instead to set your own breakpoint after MPI_Init see Section 3 5 7 This way when the process stops it will be on a line in your program instead of somewhere inside MPI_Init Attaching to a running program TotalView can attach to a running MPI program which is particularly useful if you suspect that your code has deadlocked To do this start TotalView with no arguments and then press N in the root window This will bring up a list of the processes that you can attach to When you dive through the initial MPICH process in this window TotalView will also acquire all of the other MPICH processes even if they are not local See the TotalView manual for more details of this process Debugging with TotalView You can set breakpoints by clicking in the left margin on a line number Most of the TotalView GUI is self explanatory You select things with the left mouse button bring up an action menu with the middle button and dive into 19 funct
53. a bug report to mpi bugs mcs anl gov 2 Q When linking Fortran programs I get undefined symbols such as 77 c secondf f secondf f MAIN main 77 o secondf secondf o L home mpich lib solaris ch_shmem lmpich Undefined first referenced symbol in file getdomainname home mpich lib solaris ch_shmem libmpi a shmempriv o ld fatal Symbol referencing errors No output written to secondf There is no problem with C programs A This means that your C compiler is providing libraries for you that your Fortran compiler is not providing Find the option for the C compiler and for the Fortran compilers that indicate which library files are being used alternately you may find an option such as dryrun that shows what commands are being used by the compiler Build a simple C and Fortran program and compare the libraries used usually on the 1d command line Try the ones that are present for the C compiler and missing for the Fortran compiler MPICH attempts to determine these libraries for you If you have trouble send a bug report and include the contents of the file mpich src fortran config 1log 3 Q When trying to compile Fortran code with a Fortran 90 or Fortran 95 compiler I get error messages like Error foo f line 30 Inconsistent datatype for argument 1 in MPI_SEND 55 A The Fortran language requires that in two calls to the same subroutine the types of arguments must be the same That is if you called MPI_SEN
54. a ch_p4 procgroup file is a set of lines of the form lt hostname gt lt procs gt lt progname gt lt login gt An example of such a file where the command is being issued from host sun1 might be 14 sunt 0 users jones myprog sun2 1 users jones myprog sun3 1 users jones myprog hp1 1 home mbj myprog mbj The above file specifies four processes one on each of three suns and one on another work station where the user s account name is different Note the 0 in the first line It is there to indicate that no other processes are to be started on host sun1 than the one started by the user by his command You might want to run all the processes on your own machine as a test You can do this by repeating its name in the file suni 0 users jones myprog sunt 1 users jones myprog sunt 1 users jones myprog This will run three processes on sun1 communicating via sockets To run on a shared memory multiprocessor with 10 processes you would use a file like sgimp 9 u me prog Note that this is for 10 processes one of them started by the user directly and the other nine specified in this file This requires that MPICH was configured with the option comm shared see the installation manual for more information If you are logged into host gyrfalcon and want to start a job with one process on gyrfalcon and three processes on alaska where the alaska processes communicate through shared memory you would use local O home jbg
55. able to start MPICH processes from For example simply adding localhost localdomain Should allow users to perform the command rsh localhost hostname successfully Like wise adding other hostnames will allow users on those hosts to rsh to this host However there is another catch By default with medium security packet filtering is enabled as well and this will prevent users from remote hosts from connecting to this machine using the rsh or rlogin services This packet filter or firewall is administered using the ipchains package which is installed by default The firewall configuration is written out by a program called lokkit at installation time I think The configuration is stored in etc sysconfig ipchains and by default looks like this Firewall configuration written by lokkit Manual customization of this file is not recommended Note ifup post will punch the current nameservers through the firewall such entries will not be listed here input ACCEPT forward ACCEPT output ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i ethO j ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i eth1 j ACCEPT A input s 0 0 d 0 0 i lo j ACCEPT A input p tcp s 0 0 d 0 0 0 1023 y j REJECT A input p tcp s 0 0 d 0 0 2049 y j REJECT A input p udp s 0 0 d 0 0 0 1023 j REJECT A input p udp s 0 0 d 0 0 2049 j REJECT A input p tcp s 0 0 d 0 0 6000 6009 y j REJECT A input p t
56. achines file to list the machines or nodes that are available for running MPICH programs 4 14 1 The Machines File The easiest way to create a machines file is to edit the file mpich util machines machines xxxx to contain names of machines of architecture xxxx The xxxx matches the arch given when MPICH was configured Then whenever mpirun is executed the required number of hosts will be selcted from this file for the run There is no fancy scheduling the hosts are selected starting from the top To run all your MPI processes on a single workstation just make all the lines in the file the same A sample machines solaris file might look like 37 mercury venus earth mars earth mars The names should be provided in the same format as is output by the hostname command For example if the result of hostname on earth is earth my edu and similarly for the other names then the machines file should be mercury my edu venus my edu earth my edu mars my edu earth my edu mars my edu For nodes that contain multiple processors indicate the number of processors by fol lowing the name with a colon and the number of processors For example if mars in the previous example had two processors then the machines file should be mercury venus earth mars 2 earth mars 2 4 14 2 Faster job startup for the ch _p4 device When using the ch_p4 device it is possible to speedup the process of starting jobs by using the secure
57. ail in Section 3 1 1 Compiling and Linking without the Scripts In some cases it is not possible to use the scripts supplied by MPICH for compiling and linking programs For example another tool may have its own compilation scripts In this case you can use compile_info and link_info to have the MPICH compilation scripts indicate the compiler flags and linking libraries that are required for correct operation of the MPICH routines For example when using the ch_shmem device on Solaris systems the library thread 1thread must be linked with the application If the thread library is not provided the application will still link but essential routines will be replaced with dummy versions contained within the Solaris C library causing the application to fail For example to determine the flags used to compile and link C programs you can use these commands whose output for the ch_p4 device on a Linux workstation is shown mpicc compile_info cc DUSE_STDARG DHAVE_STDLIB_H 1 DHAVE_STRING_H 1 DHAVE_UNISTD_H 1 DHAVE_STDARG_H 1 DUSE_STDARG 1 DMALLOC_RET_VOID 1 I usr local mpich include c mpicc link_info cc DUSE_STDARG DHAVE_STDLIB_H 1 DHAVE_STRING_H 1 DHAVE_UNISTD_H 1 DHAVE_STDARG_H 1 DUSE_STDARG 1 DMALLOC_RET_VOID 1 L usr local mpich lib 1mpich 3 2 Running programs with mpirun To run an MPI program use the mpirun command which is located in usr local mpich 1 2 7p1 bin For almost all systems you can u
58. ailable for the MPI 1 functions e Both Fortran 77 and Fortran 90 bindings including both mpif h and an MPI module e A Windows NT version is available as open source The installation and use for this version is different this manual covers only the Unix version of MPICH e Supports a wide variety of environments including clusters of SMPs and massively parallel computers e Follows many but not all of GNU recommended build and install targets including VPATH Parts of MPI 2 are also supported Most of MPI IO is supported through the ROMIO implementation See romio README for details Support for MPI_INIT_THREAD but only for MPI_THREAD_SINGLE and MPI_ THREAD_FUNNELLED Miscellaneous new MPI_Info and MPI_Datatype routines e MPICH also includes components of a parallel programming environment including Tracing and logfile tools based on the MPI profiling interface including a scalable logfile format SLOG Parallel performance visualization tools upshot and jumpshot Extensive correctness and performance tests Both large and small application examples 1 1 Features of recent releases Version 1 2 7 of MPICH is primarily a bug fix and increased portability release particularly for Linux based clusters This is primarily a bug fix release New users should use MPICH2 instead of MPICH As of version 1 2 7 of MPICH and version 1 0 of MPICH2 the only major feature supported in MPI
59. ble implementation of the full MPI 1 specification for a wide variety of parallel and distributed computing environments MPICH contains along with the MPI library itself a programming environment for working with MPI programs The programming environment includes a portable startup mechanism several profiling libraries for studying the performance of MPI programs and an X interface to all of the tools This document describes how to install and use the MPICH implementation of MPI This document describes how to obtain install and use MPICH 12 the portable imple mentation of the MPI Message Passing Standard This document describes version 1 2 7p1 1 Introduction MPICH is a freely available implementation of the MPI standard that runs on a wide variety of systems The details of the MPICH implementation are described in 12 related papers include 9 and 10 MPICH is no longer being developed the current release may be the last release of MPICH A new version of MPI MPICH2 is available from www mcs anl gov mpi mpich2 This all new implementation of MPI includes all of both MPI 1 and MPI 2 If you believe you have found a bug in MPICH we recommend that you try MPICH2 we ll probably recommend that when you send in a bug report Major Features of MPICH Full MPI 1 2 compliance including cancel of sends e MPMD programs see Section 3 4 and heterogeneous clusters are supported e The MPI 2 standard C bindings are av
60. both gethostname and hostname If you are using a single machine in a standalone configuration the easiest option is to change the name of the machine in etc hostconfig to localhost use sudo If you wish to use another name you need to make the name in etc hostconfig match the name in the NetInfo database Thanks to Victor Fijkhout for this information A 9 SIGSEGV If your program fails with p4_error interrupt SIGSEGV the problem is probably not with MPI Instead check for program bugs including 1 Array overwrites or accesses beyond array bounds Be particularly careful of a size in C where a is declared as int a size 2 Invalid pointers including null pointers 3 Missing or mismatched parameters to subroutines or functions Fortran users should check that all MPI calls include the integer error return parameter and that any status variable is dimensioned as an array of size MPI_STATUS_SIZE A 10 semop lock failed When running the ch_p4 device with SMP support comm shared you may occasionally see the message p1_13043 p4_error OOPS semop lock failed To fix this try running the script cleanipcs that is included with MPICH You can also use the command ipcs to list the shared memory and semaphore resources that are in use on a node This can help you track down resources that are held by a different user that are preventing your MPI program from running A 11 Compiler Switches Normally you should let config
61. bout this valid use of C and provide no way to indicate to the compiler that the warning is unnecessary A 16 MPMD Multiple Program Multiple Data Programs MPICH depending on the device supports MPMD programs However the mpirun script currently does not support MPMD programs For the ch_p4 device the user must create a procgroup file and invoke the program that will have rank zero in MPI_COMM_WORLD with the command line option p4pg filename See the Installation and User s Guide for more information A 17 Reporting problems and support 1 First check the list of known bugs and patches for the problem you are seeing 2 Also check the troubleshooting guides in the Installation and Users guides 3 If that doesn t help send mail to mpi bugs mcs anl gov A 18 Algorithms used in MPICH 1 Does MPICH use IP Multicast for MPI_Bcast No In principle MPICH could use multicast but in practice this would be very difficult To start with IP multicast is unreliable additional code to make it reliable needs to be added In fact there is an effort to provide a reliable multicast built ontop of the unreliable multicast The second problem is that not all systems allow user programs or any program to perform an IP multicast In fact that is the 84 case for the systems that we have been developing on Thus we will always need the point to point version There is a fairly easy way to replace any collective routine in MPI but no
62. ch system on which you want to start the secure server and start the server manually The command to start an individual server using port 2345 is serv_p4 o p 2345 amp For example if you had chosen a port number of 2345 and were using Solaris then you would give the command sbin chp4_servs port 2345 with arch solaris The server will keep a log of its activities in a file named Secure_Server Log xxxx in the current directory where xxxx is the process id of the process that started the server note that the server may be running as a child of that initial process To make use of the secure servers using the ch_p4 device you must inform mpirun of the port number You can do this in two ways The first is to give the p4ssport n option to mpirun For example if the port is 2345 and you want to run cpi on four processors use mpirun np 4 p4ssport 2345 cpi The other way to inform mpirun of the secure server is to use the environment variables MPI_USEP4SSPORT and MPI_P4SSPORT In the C shell you can set these with setenv MPI_USEP4SSPORT yes setenv MPI_P4SSPORT 2345 The value of MPI_P4SSPORT must be the port with which you started the secure servers When these environment variables are set no extra options are needed with mpirun Note that when MPICH is installed the secure server and the startup commands are copied into the bin directory so that users may start their own copies of the server This is
63. cluded Our use of configure does not follow these rules because configure is too useful but we need the flexibility that allows the user to produce variations of MPICH More notes on command line parameters You can select a different C and Fortran compiler by using the cc and fc switches The environment variables CC and FC can also provide values for these but their settings may be overridden by the configure script Using cc CC fc FC will force configure to use those compilers The option opt allows you to specify optimization options for the compilers both C and Fortran For example opt 0 chooses optimized code generation on many systems optcc and optf77 allow you to specify options for just the C or Fortran compilers Use cflags and fflags for options not related to optimization Note that the opt options are not passed to the mpicc mpif77 gt mpiCC and mpif90 scripts The opt options are used only in building MPICH The option lib allows you to specify the location of a library that may be needed by a particular device Most devices do NOT need this option check the installation instructions for those that might The option make may be used to select an alternate make program For example to make use of VPATH builds building in one directory with the source in a different directory make gnumake may be required
64. command df tmp will show you how much space is available Try to insure that at least twice the size of the library is available 50 2 Q When running make on MPICH I get errors when executing ranlib A Many systems implement ranlib with the ar command and they use the tmp directory by default because it seems obvious that using tmp would be faster tmp is often a local disk Unfortunately some systems have ridiculously small tmp partitions making any use of tmp very risky In some cases the ar commands used by MPICH will succeed because they use the 1 option this forces ar to use the local directory instead of tmp The ranlib command on the other hand may use tmp and cannot be fixed In some cases you will find that the ranlib command is unnecessary In these cases you can reconfigure with noranlib If you must use ranlib either reduce the space used in tmp or increase the size of the tmp partition your system administrator will need to do this There should be at least 20 30 MBytes free in tmp 3 Q When doing the link test the link fails and does not seem to find any of the MPI routines homes me mpich IRIX32 ch_p4 bin mpicc o overtake overtake o test o ld WARNING 126 The archive homes me mpich IRIX32 ch_p4 lib libmpi a defines no global symbols Ignoring ld WARNING 84 usr lib libsun a is not used for resolving any symbol ld ERROR
65. cp s 0 0 d 0 0 7100 y j REJECT While an in depth discussion of ipchains rules is outside the context of this document it s worth talking about how this works a bit First the rules are applied in order from top of the list to the bottom of the list The argument to j says what to do if a packet matches it s usually either ACCEPT let the packet in or REJECT toss it out If a packet makes it through the entire list then the default policy is applied In this case the default policy is ACCEPT The following line tells the packet filter to allow all localhost i lo traffic to pass unmolested A input s 0 0 d 0 0 i lo j ACCEPT TT This line blocks all new TCP connections going to ports 0 1023 which is the range of most services including rsh rlogin A input p tcp s 0 0 d 0 0 0 1023 y j REJECT We re going to modify this file to allow rsh and rlogin traffic Firewall configuration written by lokkit Manual customization of this file is not recommended Note ifup post will punch the current nameservers through the firewall such entries will not be listed here input ACCEPT forward ACCEPT output ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i ethO j ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i eth1 j ACCEPT A input s 0 0 d 0 0 i lo j ACCEPT New rules for rlogin rsh traffic incoming or outgoing A input p tcp s 0 0 d 0 0 513 b j ACCEPT A input p tcp s 0
66. d by the MPI standard you can not rely on any specific behavior In the ch_p4 case a new process is forked to handle connection requests it terminates with the end of the program You can use the threaded listener with the ch_p4 device or use the ch_p4mpd device instead Note however that this code is not portable because it relies on behavior that the MPI standard does not specify 6 13 2 HPUX 1 Q My Fortran programs seem to fail with SIGSEGV when running on HP workstations A Try compiling and linking the Fortran programs with the option T This may be necessary to make the Fortran environment correctly handle interrupts used by MPICH to create connections to other processes 6 133 LINUX 1 Q Processes fail with messages like p0_1835 p4_error Found a dead connection while looking for messages 1 A What is happening is that the TCP implementation on this platform is deciding that the connection has failed when it really hasn t The current MPICH implemen tation assumes that the TCP implementation will not close connections and has no code to reanimate failed connections Future versions of MPICH will work around this problem In addition some users have found that the single processor Linux kernel is more stable than the SMP kernel 6 13 4 Workstation Networks 1 Q My job runs to completion but exits with the message Timeout in waiting for processes to exit This may be due to a defective rsh program Som
67. d globus2 If not specified a default is chosen Special options for the device are specified after the device name separated by a colon E g with device globus2 flavor mpi nothreads Use ROMIO to provide MPI 1 0 from MPI 2 default The options include file_system FSTYPE where fstype can be any combination of nfs ufs pfs intel piofs IBM hfs HP sfs NEC and with romio OPTIONS xfs SGI combined with If romio is not included the Fortran 90 modules cannot be built with mpe Build the MPE environment default with f90nag Choose the NAG 90 compiler for Fortran preliminary version intended for use instead of a Fortran 77 compiler with f95nag Choose the NAG 95 compiler for Fortran with cross file Use the file for cross compilation The file should contain assignments of the form CROSS_SIZEOF_INT 4 for each cross compilation variable The command egrep CROSS_ A Z_ configure sed s g will list each variable You can use without lt featurename gt to turn off a feature except for device Options for device ch_l1fshmenm with device ch_lfshmem usesysv The option usesysv applies to the ch_shmem device and causes the device to attempt and use System V shared memory and semaphore routines rather than what would be chosen by default often mmap or a system specific method Options for device ch_meiko with device ch_meiko Options for d
68. d look something like mpirun np 2 cpi p4norem waiting for process on host shakey mcs anl gov home me cpi sys2 foo edu 38357 p4amslave The unnecessary changes in the command syntax for programs such as dbx contributes to the poor state of software 18 on the first machine and gdb cpi GNU gdb 5 0 Copyright 2000 Free Software Foundation Inc GDB is free software covered by the GNU General Public License and you are welcome to change it and or distribute copies of it under certain conditions Type show copying to see the conditions There is absolutely no warranty for GDB Type show warranty for details This GDB was configured as i586 mandrake linux gdb run sys2 foo edu 38357 p4amslave Starting program home me cpi sys2 foo edu 38357 p4amslave 3 5 7 Debugging MPI programs with TotalView TotalView is a powerful commercial grade portable debugger for parallel and mul tithreaded programs available from Etnus http www etnus com TotalView under stands multiple MPI implementations including MPICH By understand is meant that if you have TotalView installed on your system it is easy to start your MPICH program un der the control of TotalView even if you are running on multiple machines manage your processes both collectively and individually through TotalView s convenient GUI and even examine internal MPICH data structures to look at message queues 4 The general opera tion model of
69. d to run your program most likely someone else was using the system You can try to use the environment variables MP_RETRY and MP_RETRYCOUNT to cause the job to wait until the nodes become available Use man poe to get more information Q When running on an IBM SP my job generates the message Message number 0031 254 not found in Message Catalog and then dies A If your user name is eight characters long you may be experiencing a bug in the IBM POE environment The only fix at the time this was written was to use an account whose user name was seven characters or less Ask your IBM representative about PMR 4017X poe with userids of length eight fails and the associated APAR 1X56566 66 6 12 Programs fail at startup 6 12 2 6 12 1 General Q With some systems you might see lib dld s1 Bind on reference call failed lib dld sl Invalid argument This example is from HP UX or ld so libc so 2 not found This example is from SunOS 4 1 similar things happen on other systems A The problem here is that your program is using shared libraries and the libraries are not available on some of the machines that you are running on To fix this relink your program without the shared libraries To do this add the appropriate command line options to the link step For example for the HP system that produced the errors above the fix is to use W1 Bimmediate to the link step For Solaris the appropriate option
70. dbg to make MPE_Errors_call_dbx_in_xterm the default error handler instead of MPI_ERRORS_ARE_FATAL 3 5 3 Starting jobs with a debugger The dbg lt name of debugger gt option to mpirun causes processes to be run under the control of the chosen debugger For example enter mpirun dbg gdb or mpirun dbg gdb a out invokes the mpirun_dbg gdb script located in the mpich bin directory This script cap tures the correct arguments invokes the gdb debugger and starts the first process under gdb where possible There are five debugger scripts ddd gdb xxgdb ddd and totalview These may need to be edited depending on your system There is another debugger script for dbx but this one will always need to be edited as the debugger commands for dbx varies between versions You can also use this option to call another debugger for ex ample dbg mydebug All you need to do is write a script file mpirun_dbg mydebug which follows the format of the included debugger scripts and place it in the mpich bin directory More information on using the Totalview debugger with MPICH can be found in Section 3 5 7 3 5 4 Starting the debugger when an error occurs It is often convenient to have a debugger start when a program detects an error If MPICH was configured with the option enable mpedbg then adding the command line option mpedbg to the program will cause MPICH to attempt to start a debugger usually dbx or gdb when an err
71. discussions are available at e Books Using MPI Portable Parallel Programming with the Message Passing Interface Second Edition by Gropp Lusk and Skjellum 13 43 Using MPI 2 Advanced Features of the Message Passing Interface by Gropp Lusk and Thakur 14 MPI The Complete Reference Volume 1 The MPI Core by Snir et al 19 MPI The Complete Reference Volume 2 The MPI 2 Extensions by Gropp et al B Parallel Programming with MPI by Peter S Pacheco 18 e Newsgroup comp parallel mpi Mailing lists mpi comments mpi forum org The MPI Forum discussion list mpi implOmcs anl gov The implementors discussion list mpi bugs mcs anl govjis the address to which you should report problems with mpich e Implementations available from the web MPICH is available from http www mcs anl gov mpi mpich or by anonymous ftp from ftp mcs anl govin the directory pub mpi mpich file mpich tar gz Links to other implementations are available at www mcs anl gov mpi implementations html e Test code repository ftp ftp mcs anl gov pub mpi mpi test 6 In Case of Trouble This section describes some of the problems that you may run into and some solutions along with information on submitting bug reports 6 1 Things to try first If something goes wrong the first thing to do is to check the output of configure or make for some obviou
72. e to your users how to compile and run MPI programs using the installation you have just built in usr local mpich 1 2 7p1 or wherever you have installed it See Section B for commands they can use They can also copy the Makefile in usr local mpich 1 2 7p1 examples and adapt it for their own use 2 4 Sample MPI programs The MPICH distribution contains a variety of sample programs which are located in the MPICH source tree Most of these will work with any MPI implementation not just MPICH examples basic contains a few short programs in Fortran C and C for testing the simplest features of MPI examples test contains multiple test directories for the various parts of MPI Enter make testing in this directory to run our suite of function tests examples perftest Performance benchmarking programs See the script runmpptest for information on how to run the benchmarks These are relatively sophisticated mpe contrib mandel A Mandelbrot program that uses the MPE graphics package that comes with mpich It should work with any other MPI implementation as well but we have not tested it This is a good demo program if you have a fast X server and not too many processes mpe contrib mastermind A program for solving the Mastermind puzzle in parallel It can use graphics gmm or not mm Additional examples from the book Using MPI 13 are available at Tutorial material on MPI can also be found at 3 Program
73. e versions of Kerberos rsh have been observed to have this problem This is not a problem with P4 or mpich but a problem with the operating environment For many applications this problem will only slow down process termination What does this mean A If anything causes the rundown in MPI_Finalize to take more than about 5 minutes it becomes suspicious of the rsh implementation The rsh used with some Kerberos installations assumed that sizeof FD_SET sizeof int This meant that the rsh program assumed that the largest FD value was 31 When a program 70 uses fork to create processes that launch rsh while maintaining the stdin stdout and stderr to the forked process this assumption is no longer true since the FD that rsh creates for the socket may be greater than 31 if there are enough processes running When using such a broken implementation of rsh the symptom is that jobs never terminate because the rsh jobs are waiting with select for the socket to close The ch_p4mpd device eliminates this problem 6 14 Trouble with Input and Output 6 14 1 General 1 Q I want output from printf to appear immediately A This is really a feature of your C and or Fortran runtime system For C consider setbuf stdout char 0 or setvbuf stdout NULL _IONBF O 6 14 2 Workstation Networks 1 Q I want standard output stdout from each process to go to a different file A MPICH has no built in way to do this
74. easons to have separate Fortran 90 and Fortran 77 builds then execute the following commands where MPICH is to be installed into the directory usr local setenv FC 77 configure disable f90 prefix usr local mpich 1 2 7 f77 nof90 make make install 29 setenv FC f90 setenv F90 f90 configure prefix usr local mpich 1 2 7 90 make make install This sequence of commands will build and install two versions of MPICH An alternative approach that installs only a single version of MPICH is decribed in Section 4 8 6 4 8 4 Fortran 90 Modules If configure finds a Fortran 90 compiler by default MPICH will try to create a Fortran 90 module for MPI In fact it will create two versions of an mpi module one that includes only the MPI routines that do not take choice arguments and one that does include choice argument A choice argument is an argument that can take any datatype typically these are the buffers in MPI communication routines such as MPI_Send and MPI_Recv The two different modules can be accessed with the nochoice and choice option to mpif90 The choice version of the module supports a limited set of datatypes numeric scalars and numeric one and two dimensional arrays This is an experimental feature please send mail to mpi bugsOmcs anl gov if you have any trouble Neither of these modules offer full extended Fortran support as defined in the MPI 2 standard The reason for having two versions
75. ect parameters for the MPICH that was installed 99 References 1 James Boyle Ralph Butler Terrence Disz Barnett Glickfeld Ewing Lusk Ross Over 10 11 12 13 beek James Patterson and Rick Stevens Portable Programs for Parallel Processors Holt Rinehart and Winston New York NY 1987 Ralph Butler and Ewing Lusk User s guide to the p4 parallel programming system Technical Report ANL 92 17 Argonne National Laboratory Argonne IL 1992 Anthony Chan William Gropp and Ewing Lusk User s guide for mpe extensions for mpi programs Technical Report ANL 98 xx Argonne National Laboratory 1998 The updated version is at ftp ftp mcs anl gov pub mpi mpeman ps James Cownie and William Gropp A standard interface for debugger access to message queue information in MPI In Jack Dongarra Emilio Luque and Tomas Margalef editors Recent Advances in Parallel Virtual Machine and Message Passing Interface volume 1697 of Lecture Notes in Computer Science pages 51 58 Springer Verlag 1999 Message Passing Interface Forum MPI A message passing interface standard Com puter Science Dept Technical Report CS 94 230 University of Tennessee Knoxville TN 1994 W Gropp and E Lusk Scalable Unix tools on parallel processors In Proceedings of the Scalable High Performance Computing Conference May 23 25 1994 Knoxville Tennessee pages 56 62 1109 Spring Street Suite 300 Silver Spring MD 20910 USA 1994 IEE
76. ent p4ssport to mpirun may be used instead of these environment variables mpirun help will give you more information 3 3 5 SMP Clusters When using a cluster of symmetric multiprocessors SMPs with the ch_p4 device con figured with comm shared you can control the number of processes that communicate with shared memory on each SMP node First you need to modify the machines file see Section to indicate the number of processes that should be started on each host Nor mally this number should be no greater than the number of processors on SMPs with large numbers of processors the number should be one less than the number of processors in order to leave one processor for the operating system The format is simple each line of the machines file specifies a hostname optionally followed by a colon and the number of processes to allow For example the file containing the lines mercury venus earth mars 2 jupiter 15 specifies three single processor machines mercury venus and earth a 2 processor ma chine mars and a 15 processor machine jupiter By default mpirun will use at most the number of processors specified in the machines list for each node upto 16 processes on each machine By setting the environment variable MPI_MAX_CLUSTER_SIZE to a positive integer value mpirun will use upto that many pro cesses sharing memory for communication on a host For example if MPI_MAX_CLUSTER_ SIZE had the value 4 then mpiru
77. erbose throw in some comments dbg The option dbg may be used to select a debugger For example dbg gdb invokes the mpirun_dbg gdb script located in the mpich bin directory This script captures the correct arguments invokes the gdb debugger and starts the first process under gdb where possible There are 4 debugger scripts gdb xxgdb ddd totalview These may need to be edited depending on your system There is another debugger script for dbx but this one will always need to be edited as the debugger commands for dbx varies between versions You can also use this option to call another debugger for example dbg mydebug All you need to do is write a script file mpirun_dbg mydebug which follows the format of the included debugger scripts and place it in the mpich bin directory ksq Keep the send queue This is useful if you expect later to attach totalview to the running or deadlocked job and want to see the send queues Normally they are not maintained in a way which is visible to the debugger Options for the globus2 device With the exception of h these are the only mpirun options supported by the globus device machinefile lt machine file name gt Take the list of possible machines to run on from the file lt machine file name gt np lt np gt specify the number of processors to run on dumprsl display the RSL string that would have been used to submit the job using this option does not run t
78. es This uses weak symbols if available for the profiling interface default enable debug Enable support for debuggers to access message queues enable traceback Enable printing of a call stack when MPI and the user s program is built with certain compilers currently only some versions of gcc are supported enable mpedbg Enable the mpedbg command line argument e g errors can start an xterm running a debugger Only works with some workstation systems enable sharedlib Attempt to build shared libraries Static enable sharedlib dir libraries are always built If a directory is specified the shared libraries will be placed in that directory This can be used to place the shared libraries in a uniform location in local disks on a cluster enable f90modules Build Fortran 90 module support default if a Fortran 90 or 95 compiler is found If ROMIO is not built no Fortran 90 modules will be built 89 The following are intended for MPI implementors and debugging of configure enable strict Try and build MPICH using strict options in Gnu gcc enable echo Cause configure to echo what it does enable devdebug Enable debugging code in the ADI You can use disable lt featurename gt to turn off a feature Notes on configure usage The suggestions for GNU configure usage suggest that configure not be used to build different tools only controlling some basics of the features enabled or the packages in
79. es a program that may be used to speed this process This is the secure server and is located in serv_p4 in the directory usr local mpich bin The script chp4_servs in the same directory may be used to start serv_p4 on those workstations that you can rsh programs on You can also start the server by hand and allow it to run in the background this is appropriate on machines that do not accept rsh connections but on which you have accounts Before you start this server check to see if the secure server has been installed for general use if so the same server can be used by everyone In this mode root access is required to install the server If the server has not been installed then you can install it for your own use without needing any special privileges with chp4_servs port 1234 This starts the secure server on all of the machines listed in the file usr local mpich share machines lt arch gt The port number provided with the option port must be different from any other port in use on the workstations To make use of the secure server for the ch_p4 device add the following definitions to your environment 12 setenv MPI_USEP4SSPORT yes setenv MPI_P4SSPORT 1234 The value of MPI_P4SSPORT must be the port with which you started the secure server When these environment variables are set mpirun attempts to use the secure server to start programs that use the ch_p4 device The command line argum
80. et buffer size in 1K 1024 bytes E g bufsize 32 requests 32K byte socket buffers The default is 16 winsize Winshift size Available only on systems that define TCP_WINSHFT and is ignored otherwise netsendw Use select to wait for write to proceed Values are y default or n netreadw Use select to wait for read to proceed Values are y default or n writev Use writev to send the header MPI envelope and data in a single message Values are y default or n readb Switch a socket to blocking mode while wait to read instead of busy waiting or using select Values are y or n default stat Print out statistics on write and read operations Useful only for experts For example to use 64K socket buffers and turn off the use of writev you could use mpirun np 2 mpptest p4sctrl bufsize 64 writev n SMP Tuning By default the ch_p4 device uses the sched_yield system call if it is available to avoid spin waiting when in a blocking receive You can override this with the disable yield to configure See http www mcs anl gov mpi mpich micronotes for some graphs showing the effect of using or not using sched_yield 4 17 Internationalization MPICH has support for providing error messages in different languages This makes use of the X Open message catalog services which are a standard way of providing multi language support This multi language support is often called NLS for National Language Support MPICH comes with e
81. evice ch_mpl with device ch_mpl Options for device ch_p4 88 configure mpid ch_p4 setup_ch_p4 Permission denied Options for device ch_p4mpd with device ch_p4mpd listener_sig SIGNALNAME dlast socksize BYTES The option listener_sig applies to the ch_p4mpd device and changes the Signal that is used to signal that a new connection should be made By default SIGUSRi is used The option dlast causes the p4 device to remember the last few debugging messages printing them out only when the job terminates abnormally The option socksize changes the size of the socket buffers used Options for device ch_shmem with device ch_shmem usesysv The option usesysv applies to the ch_shmem device and causes the device to attempt and use System V shared memory and semaphore routines rather than what would be chosen by default often mmap or a system specific method Options for device globus with device globus globusdir GLOBUSDIR globusdir GLOBUS allows one to specify the location of an installed version of Globus You can acquire Globus from http www globus org Options for device globus2 GLOBUS_INSTALL_PATH must be set Features that may be included with MPICH enable c Build C interfaces to the MPI 1 routines default enable f77 Build Fortran 77 interfaces to the MPI routines default enable weak symbols Use weak symbols for MPI PMPI routin
82. eys rather than simple UNIX passwords The next step is to enable an SSH agent so that you do not need to repeatedly type your password 79 The agent is started with ssh agent lt cmd gt Typically lt cmd gt is SHELL so that your default shell is started The agent will then handle authentication on your behalf any time you attempt to use ssh from this shell To give the ssh agent your password type ssh add This will query you for the passphrase that accompanies your rsa key Once you have completed this you will be able to ssh to other systems on which your key is authorized without typing a password Interprocess communication MPICH processes use the standard UNIX mechanisms for allocating ports for intercommunication Using this mechanism processes are given ports in the range of 1024 65535 Unfortunately for us the default firewall configuration blocks some port ranges that our MPICH processes might be given to use for communication This leads to a situation where MPICH applications will occasionally fail to communicate when they happen to get the wrong port value We re going to modify the ipchains configuration file to remove lines disabling ranges of ports that our processes might use for intercommunication The two default rules of interest are the following A input p tcp s 0 0 d 0 0 6000 6009 y j REJECT A input p tcp s 0 0 d 0 0 7100 y j REJECT The first blocks incoming TCP connections to po
83. gov type blocking 34 T T T T T 33 F 7 32 5 F J time us 32 4 31 5 J 31 b J 0 200 400 600 800 1000 1200 Size bytes 30 5 Figure 1 Sample output from mpptest 4 Details This section covers details that you should not normally need Read this section if you need more detailed control over configuring building installing or operating MPICH 4 1 Configure options The configure script documents itself in the following way If you type configure usage you will get a complete list of arguments and their meanings these are also shown in Appendix D The most important options are prefix dir The installation prefix configure understands all of the usual GNU instal lation directory arguments including libdir and mandir We recommend that all users specify an installation directory with prefix with device devname Set the MPICH device to use devname must be the name of one of the directories in the mpid directory such as ch_p4 ch_shmem globus2 or ch_ p4mpd enable g Add the g option to the compile scripts This is a prerequisite for using most debuggers including dbx and gdb 22 enable debug Turn on support for the Totalview Debugger This allows Totalview to display information on message queues enable sharedlib Build both static and shared libraries for MPICH This supports only a few systems including those using gcc e g most Linux Beowulf systems
84. h_shmem respectively That is use a configure command of the form configure prefix usr local mpich 1 2 7 execprefix usr local mpich 1 2 7 solaris ch_p4 4 13 2 Installing documentation The MPICH implementation comes with several kinds of documentation Installers are en couraged to provide site specific information such as the location of the installation par ticularly if it is not in usr local mpich 1 2 7p1 4 133 Man pages A complete set of Unix man pages for the MPICH implementation are in mpich man man man1 contains the commands for compiling linking and running MPI programs man man3 contains the MPI routines man man4 contains the MPE routines and man man5 contains the MPID routines these are for the low level part of the MPICH implementation are not of interest to users 4 13 4 Examples Users often prefer working from example Makefile s and programs The directory that is installed in the examples directory contains a C and Fortran version of the pi program along with a Makefile in Other examples there include a simple parallel I O program and an MPI program written using the C bindings for the MPI functions Users may be interested in some of the examples that are in the source tree also in the examples directory 4 14 Setting up mpirun for the ch_p4 device When used with the ch_p4 device the mpirun program uses a file called a m
85. he internal shared memory queue 13 Q My programs seem to hang in MPI_Init A There are a number of ways that this can happen a One of the workstations you selected to run on is dead try tstmachines if you are using the ch_p4 device b You linked with the FSU pthreads package this has been reported to cause problems particularly with the system select call that is part of Unix and is used by MPICH Another is if you use the library ldxml extended math library on Com paq Alpha systems This has been observed to cause MPI_Init to hang No workaround is known at this time contact Compaq for a fix if you need to use MPI and 1dxm1 together The root of this problem is that the ch_p4 device uses SIG_USR1 and so any library that also uses this signal can interfere with the operation of MPICH if it is using ch_p4 You can rebuild MPICH to use a different signal by using the configure argument with device ch_p4 listener_sig SIGNAL_NAME and remaking MPICH 14 Q My program using device ch_p4 fails with p0_2005 p4_error fork_p4 fork failed 1 p4_error latest msg from perror Error 0 A The executable size of your program may be too large When a ch_p4 or ch_tcp device program starts it may create a copy of itself to handle certain communication tasks Because of the way in which the code is organized this at least temporarily is a full copy of your original program and occupies the same amount of
86. he job globusrsl lt globus rsl file name gt lt globus rsl file name gt must contain a Globus RSL string When using this option all other mpirun options are ignored Special Options for Batch Environments mvhome Move the executable to the home directory This is needed when all file systems are not cross mounted Only used by anlspx mvback files Move the indicated files back to the current directory Needed only when using mvhome has no effect otherwise maxtime min Maximum job run time in minutes Used only by anlspx Default value is max_time minutes nopoll Do not use a polling mode communication 95 Available only on IBM SPs Special Options for IBM SP2 cac name CAC for ANL scheduler Used only by anlspx If not provided will choose some valid CAC On exit mpirun returns a status of zero unless mpirun detected a problem in which case it returns a non zero status When using the ch_p4 device multiple architectures may be handled by giving multiple arch and np arguments For example to run a program on 2 sun4s and 3 rs6000s with the local machine being a sun4 use mpirun arch sun4 np 2 arch rs6000 np 3 program This assumes that program will run on both architectures If different executables are needed the string a will be replaced with the arch name For example if the programs are program sun4 and program rs6000 then the command is mpirun arch sun4 np 2 arch rs6000 np 3 program a If i
87. hen use the C compiler to compile everything If you take this route remember that every Fortran routine has to be compiled using f2c and the C compiler Alternatively you can use various options check the man pages for your compilers to see what libraries that add when they link Add those libraries to the link line for the other compiler If you find a workable set of libraries edit the appropriate scripts e g mpicc to include the necessary libraries MPICH attempts to find all the libaries that you need but is not always successful 6 10 2 HPUX 1 Q When linking on HPUX I get an error like this cc 0 pgm pgm o L usr local mpich lib hpux ch_p4 lmpich lm bin ld Unsatisfied symbols sigrelse code sigset code sighold code Error code 1 56 A You need to add the link option 1V3 The ch_p4 device uses the System V signals on the HP these are provided in the V3 library 6 10 3 LINUX 1 Q When linking a Fortran program I get Linking foo o data 0x0 undefined reference to pmpi_wtime_ A This is a bug in the pg 77 compiler which is itself a workaround for a bug in the LINUX 1d command You can fix it by either adding lpmpich to the link line or modifying the mpif h to remove the external pmpi_wtime pmpi_wtick statement The MPICH configure attempts to determine if pmpi_wtime and pmpi_wtick can be declared in mpif h and removes them if there is a problem If this happens and y
88. her this needs only be done when linking the program For example to create a log file of a program such as cpi the following steps are needed mpicc c cpi c mpicc o cpi mpilog cpi o The log file will be written to a file with the name cpi clog or cpi slog depending on the value of the environment variable MPE_LOG_FORMAT clog is the default The logfile can be graphically displayed using the Jumpshot program described in Section 3 6 1 Another tool of interest is FPMPI 7 this tool reports a summary of all MPI calls providing information about message lenghts communication patterns 3 6 1 Jumpshot Jumpshot is a program for displaying logfiles produced using the MPE logging libraries Jumpshot is described in more detail in the MPE Installation and User s manual 3 Jump shot is a Java program and requires a functioning Java environment You can view a logfile such as cpi clog in the example above by using logviewer cpi clog There are several available log formats and logviewer selects the version of jumpshot appropriate for a particular logfile See the MPE manual distributed along with this manual for more details 20 3 7 Execution tracing Execution tracing is easily accomplished using the mpitrace command line argument while linking mpicc c cpi c mpicc o cpi mpitrace cpi o 3 8 Performance measurements The mpich examples perftest directory contains a sophisticated tool for measur
89. iation that MPI uses will depend on the number of processes thus you may not get exactly the same result when you use different numbers of processes Note that you are not getting a wrong result just a different one most programs assume the arithmetic operations are associative All processes do get the same result from a single call to MPI_Allreduce 68 2 Q My Fortran program fails with a BUS error A The C compiler that MPICH was built with and the Fortran compiler that you are using have different alignment rules for variables of type like DOUBLE PRECISION For example the GNU C compiler gcc may assume that all doubles are aligned on eight byte boundaries but the Fortran language requires only that DOUBLE PRECISION align with INTEGERs which may be four byte aligned There is no good fix Consider rebuilding MPICH with a C compiler that supports weaker data alignment rules Some Fortran compilers will allow you to force eight byte alignment for DOUBLE PRECISION for example dalign or f on some Sun Fortran compilers note though that this may break some correct Fortran programs that exploit Fortran s storage association rules Some versions of gcc may support munaligned doubles MPICH should be rebuilt with this option if you are using gcc version 2 7 or later MPICH attemps to detect and use this option where available 3 Q I m using fork to create a new process or I m creating a new thread and my code fails A
90. idge MA 1999 15 William D Gropp and Ewing Lusk Reproducible measurements of MPI performance characteristics In Jack Dongarra Emilio Luque and Tomas Margalef editors Recent Advances in Parallel Virtual Machine and Message Passing Interface volume 1697 of Lecture Notes in Computer Science pages 11 18 Springer Verlag 1999 16 William D Gropp and Barry Smith Chameleon parallel programming tools users manual Technical Report ANL 93 23 Argonne National Laboratory Argonne IL March 1993 17 Message Passing Interface Forum MPI A Message Passing Interface standard Inter national Journal of Supercomputer Applications 8 3 4 165 414 1994 18 Peter S Pacheco Parallel Programming with MPI Morgan Kaufman 1997 19 Marc Snir Steve W Otto Steven Huss Lederman David W Walker and Jack Don garra MPI The Complete Reference Volume 1 The MPI Core 2nd edition MIT Press Cambridge MA 1998 Ww 2 Total View Multiprocess Debugger Analyzer 2000 http www etnus com Products TotalView 101
91. imit of as few as 40 processes per minute When running the MPICH test suite or starting short parallel jobs from a script it is possible to exceed this limit To fix this you can do one of the following 1 Wait a few seconds between running parallel jobs You may need to wait up to a minute 2 Modify etc inetd conf to allow more processes per minute for rsh For example change shell stream tcp nowait root etc tcpd2 in rshd to shell stream tcp nowait 200 root etc tcpd2 in rshd 3 Use the ch_p4mpd device or the secure server option of the ch_p4 device instead Neither of these relies on inetd A 7 Using SSH The secure shell ssh may be used with the ch_p4 device but requires careful setup See configuring with ssh in the Installation and User s manual Make sure that ssh is set up to not require a password The command ssh n hostname date should return the date without any prompts for passwords See the installation manual if you have problems 81 A 8 Mac OS X and hostname Under Mac OS X the hostname handling is unusual The hostname that the hostname command or the gethostname function return is determined by the name set in the Shar ing preference pane If this name contains a space you may get only the leading part of the name upto but not including the first space This name is stored in the file etc hostconfig MPICH for the ch_p4 and ch_p4mpd device needs a sensible name returned by
92. ing Because MPICH was designed to enable ports to other systems many parallel computer vendors and research groups have used MPICH as the basis for their implementation Many users are now familar only with the version of MPICH that uses the ch_p4 device for work station and Beowulf clusters However MPICH continues to support other systems and continues to serve as a platform for research into MPI implementations C File Manifest This section briefly describes the files and directories at the top level of the MPICH source tree COPYRIGHT Copyright statement This code is free but not public domain It is copyrighted by the University of Chicago and Mississippi State University Makefile in Template for the Makefile which will be produced when you run configure MPI 2 C The C system from Notre Dame It includes the C bindings for the MPI 1 functions 85 README Basic information and instructions for configuring aclocal m4 Used for building configure from configure in not needed for most in stallations The file aclocal_tcl m4 is included by aclocal m4 ccbugs Directory for programs that test the C compiler during configuration to make sure that it will be able to compile the system configure The script that you run to create Makefiles throughout the system configure in Input to autoconf that produces configure doc Assorted tools for producing documentation together with this manual
93. ing Run the program using mpirun and the t argument mpirun t np 1 foo This should show what mpirun would do t is for testing Or you can use the echo argument to see exactly what mpirun is doing mpirun echo np 1 foo Depending on the choice made by the installer of MPICH you should select the device specific version of mpirun over a generic version We recommend that the installa tion prefix include the device name for example usr local mpich solaris ch_ p4 If the file is created you may be having trouble with the file system When used with mpirun the ch_p4 device requires that the procgroup file be readable from the initial process the one that will have rank zero in MPI_COMM_WORLD Q When trying to run a program I get this message icy mpirun np 2 cpi mpiversion icy icy No such file or directory A The problem is that usr lib rsh is not the remote shell program Try the following which rsh ls usr rsh You probably have usr 1ib in your path ahead of usr ucb or usr bin This picks the restricted shell instead of the remote shell The easiest fix is to just remove usr 1lib from your path few people need it alternately you can move it to after the directory that contains the remote shell rsh Another choice would be to add a link in a directory earlier in the search path to the remote shell For example I have home gropp bin s
94. ing la tency and bandwidth for MPICH on your system Simply change to the mpich examples perftest directory and do make mpirun np 2 mpptest gnuplot gt out gpl The file out gpl will then contain the necessary gnuplot commands The file mppout gp1 will contain the data To view the data with gnuplot use gnuplot out gpl or use load out gpl from within gnuplot Depending on your environment and version of gnuplot you may need to start gnuplot first and issue the command set terminal x11 before executing load out gpl You can use gnuplot set term postscript eps set output foo eps load out gpl to create an Encapsulated Postscript graph such as the one in Figure I The programs mpptest and goptest have a wide variety of capabilities the option help will list them For example mpptest can automatically pick message lengths to discover any sudden changes in behavior and can investigate the ability to overlap communication with computation These programs are written using MPI and may be used with any MPI implementation not just MPICH See the configure file in the examples perftest directory More information is available at http www mcs anl gov mpi mpptest Benchmarking can be very tricky Some common benchmarking errors are discussed at http www mcs anl gov mpi mpptest hownot html The paper discusses these issues at more length 21 Comm Perf for MPI shakey mcs anl
95. ing to run MPICH Answer If you see something like this mpirun np 2 cpi Permission denied or connection reset by peer or poll protocol failure in circuit setup when using the ch_p4 device it probably means that you do not have permission to use rsh to start processes The script tstmachines can be used to test this For example if the architecture type the arch argument to configure is sun4 then try tstmachines sun4 If this fails then you may need a rhosts or etc hosts equiv file you may need to see your system administrator or you may need to use the p4 server Another possible problem is the choice of the remote shell program some systems have several Check with your systems administrator about which version of rsh or remsh you should be using If your system allows a rhosts file do the following e Create a file rhosts in your home directory e Change the protection on it to user read write only chmod og rwx rhosts e Add one line to the rhosts file for each processor that you want to use The format is host username For example if your username is doe and you want to user machines a our org and b our org your rhosts file should contain a our org doe b our org doe Note the use of fully qualified host names some systems require this On networks where the use of rhosts files is not allowed such as the one in MCS at Argonne you should use the p4 server to run on machines
96. ions variables structures processes etc with the right button Pressing cntl in any TotalView window brings up help relevant to that window In the initial TotalView window it brings up general help The full documentation The TotalView User s Guide is available from the Etnus web site You switch from viewing one process to the next with the arrow buttons at the top right corner of the main window or by explicitly selecting left button a process in the root window to re focus an existing window onto that process or by diving right button through a process in the root window to open a new window for the selected process All the keyboard shortcuts for commands are listed in the menu that is attached to the middle button The commands are mostly the familiar ones The special one for MPI is the m command which displays message queues associated with the process Note also that if you use the MPI 2 function MPI_Comm_set_name on a communicator TotalView will display this name whenever showing information about the communicator making it easier to understand which communicator is which 3 6 Log and tracefile tools The MPE libraries that are distributed with MPICH contain several libraries for either logging information about the execution of each MPI call to a file for later analysis or for tracing each call as it occurs These libraries may be accessed by simply providing a command line argument to the compilation scripts furt
97. is append this directory to the search path such as you get with L Instead many compilers provide only replace the search path with this path Bl Thus if both MPICH and the user provide library search paths with R one of the search paths will be lost mpicc and friends could check for R options and create a unified version but they do not do this You can however provide a complete search path yourself if your compiler supports an option such as R The preceeding may sound like a lot of effort to go to and in some ways it is For large clusters however the effort will be worth it programs will start faster and more reliably because there is less network and file system traffic 6 5 Other Problems The following items describe miscellaneous problems that we have encountered These may help solve less common problems You can make cshrc check for the kind of system that you are running on and pick the paths appropriately This isn t as flexible as the approach of setting the environment variable from the running shell Even though the linker may provide the append to search path form 48 6 6 Problems configuring 6 6 1 General 1 Q Configure reports that floating point is not commutative How do I fix it A Check your compiler s documentation On RS 6000 s the qnomaf no multiply add floating point option On some other systems intermediate results may be stored in 80 bit registers
98. is Bstatic 2 Workstation Networks Q I can run programs using a small number of processes but once I ask for more than 4 8 processes I do not get output from all of my processes and the programs never finish A We have seen this problem with installations using AFS The remote shell program rsh supplied with some AFS systems limits the number of jobs that can use standard output This seems to prevent some of the processes from exiting as well causing the job to hang There are four possible fixes a Use a different rsh command You can probably do this by putting the direc tory containing the non AF S version first in your PATH This option may not be available to you depending on your system At one site the non AF S version was in bin rsh b Use the secure server serv_p4 See the discussion in the Users Guide c Redirect all standard output to a file The MPE routine MPE_10_Stdout_to_ file may be used to do this d Get a fixed rsh command The likely source of the problem is an incorrect usage of the select system call in the rsh command If the code is doing something like int mask mask 1 lt lt fd select fd 1 kmask instead of 67 fd_set mask FD_SET fd amp mask select fd 1 kmask then the code is incorrect the select call changed to allow more than 32 file de scriptors many years ago and the rsh program or programmer hasn t changed with the times
99. is for their implementation One important one in the cluster environment is MPICH GM for Myrinet switch connected clusters it is available directly from Myricom To make it easier to build and use MPICH customized versions of this manual are con structured for each major device 1 3 Citations and References The name MPICH is derived from MPI and Chameleon Chameleon both because MPICH can run adapt its color on a wide range of environments and because the initial implementation of MPICH used the Chameleon message passing portability system MPICH is pronounced Em Pee Eye See Aych not Emm Pitch The proper references for MPICH are the paper in the journal Parallel Computing and this manual 11 BibTeX versions of these citations are available at www mcs anl gov mpi mpich mpich prefer ref html 2 Quick Start Here is a set of steps for setting up and minimally testing MPICH Details and instructions for a more thorough tour of MPICH s features including installing validating benchmarking and using the performance evaluation tools are given in the following sections 2 1 Downloading MPICH The first step is to download MPICH and install any necessary patches 1 The easiest way to get MPICH is to use the web page www mcs anl gov mpi mpich you can also use anonymous ftp from ftp mcs an1 gov in directory pub mpi Get the file mpich tar gz If that file is too big try getting the pieces from pub mpi mp
100. isplit and catting them together 2 Unpack the mpich tar gz file into a build directory We recommend using a locally mounted partition rather than an NFS network file system partition For example on many systems tmp or sandbox are locally mounted Make sure that there is 3 enough space available 100MB should be more than enough To unpack assuming that mpich tar gz has been downloaded into tmp use cd tmp tar zxovf mpich tar gz If your tar does not accept the z option use cd tmp gunzip c mpich tar gz tar zxovf Apply any patches Check the web page www mcs anl gov mpi mpich buglist tb1 html for any patches that need to be applied Normally versions of MPICH that al ready have these important patches applied are available they are indicated by a fourth number in the release name e g 1 2 2 3 But in some cases a patch is made available early The patch page has instructions on applying the patches Now you are ready to build MPICH 2 2 1 Configuring Making and Installing Before you can use MPICH you must configure and make it The configuration process analyzes your system and determines the correct options and settings it also creates the Makefile s that are used to make MPICH Decide where you want to install MPICH This step is not strictly necessary except in the case of the ch_p4mpd device however installing MPICH which can be done with
101. ke log Specific non default targets can also be made See the Makefile to see what they are After running this make the size of the distribution will be about 45 Megabytes de pending on the particular machine it is being compiled for and the selected options before building any of the examples or the extensive test library The Makefile s are built for the various example subdirectories but the example programs themselves have to be made by hand 4 13 Installing MPICH for Others to Use This step is optional However if you are installing MPICH you should make sure that you specified the directory into which MPICH is to be installed when you configure MPICH by using the prefix option For example if you plan to install MPICH into usr local mpich 1 2 7p1 then you should configure with the option prefix usr local mpich 1 2 7p1 If there is any possibility at all that you will build MPICH for several systems and or devices you should include that information in the prefix For example by using prefix usr local mpich 1 2 7p1 solaris ch p4 you can later add prefix usr local mpich 1 2 7p1 solaris ch_p4smp for a version that is built with the configure option comm shared suitable for clusters of symmetric multiprocessors hence the smp in the directory name Once you have tested all parts of the MPI distribution you may install MPICH into a publically available directory and di
102. know By default MPICH uses the value of NLSPATH to find the message catalogs If this fails it tries MPICHNLSPATH and if that fails it uses English language versions that are coded into the library The catalogs are not however installed into these directories Instead you will find them in the library directory for a particular architecture for example mpich rs6000 lib 5 Documentation This distribution of MPICH comes with complete man pages for the MPI routines commands for compiling and linking MPI programs and the MPE extensions The mpich www di rectory contains HTML versions of the man pages for MPI and MPE The mpich doc directory contains this Installation and User s Guide All documentation is also available on the web at www mcs anl gov mpi mpich docs html Information about MPI is available from a variety of sources Some of these particularly WWW pages include pointers to other resources e The Standard itself Asa Technical report 5 As Postscript and HTML at www mpi forum org for both MPI 1 and MPI 2 As a journal article in the Fall 1994 issue of the Journal of Supercomputing Applications for MPI 1 and as a journal article in the International Journal of High Performance Computing Applications in 1998 e MPI Forum discussions The MPI Forum email discussions and both current and earlier versions of the Standard are available from www netlib org MPI 2
103. le MPICH installation 4 8 1 What if there is no Fortran compiler The configure program should discover that there is no Fortran compiler You can force configure to not build the Fortran parts of the code with the option disable f77 In this case only the C programs will be built and tested 4 8 2 Fortran 90 During configuration a number of Fortran 90 specific arguments can be specified See the output of configure help In particular when using the NAG Fortran 90 compiler you should specify f90nag 4 8 3 Fortran 77 and Fortran 90 Selecting Fortran 90 with Fortran 77 should be done only when the two compilers are compatible supporting the same datatypes and calling conventions In particular if the Fortran 90 compiler supports an 8 byte integer type the Fortran 77 compiler must support integer 8 this is needed by the MPI IO routines for the value of MPI_OFFSET_KIND In addition both compilers must support the same functions for accessing the command line and the code for those commands must reside in the same library If the two Fortran compilers are not compatible you should either select the Fortran 90 compiler as both the Fortran 77 and Fortran 90 compiler relying on the upward compatibility of Fortran or build two separate configurations of MPICH For example setenv FC 90 setenv F90 90 configure will use 90 for both Fortran 77 and Fortran 90 programs In many systems this will work well If there are r
104. lowing commands 46 iptables list ipchains list Look for any limits restrictions on source or destination ports or limits on syn a type of TCP packet used in establishing connections If you find such limits study your security documentation and decide how you want to modify the security settings We normally recommend that a cluster be placed behind a firewall rather than having each cluster node limit the use of TCP Also check the file etc inetd conf to ensure that it allow more processes per minute for rsh See the FAQ entry Appendix A on poll protocol failure during circuit creation Missing symbols when linking The most common source of missing symbols is a failure of the MPICH configure step to determine how to pass command line arguments to Fortran Check the output of the configure step for any error messages or warnings about building the Fortran libraries If you do not require Fortran reconfigure MPICH using the configure option disable f77 and remake MPICH If you need Fortran and cannot figure out how to make MPICH work with Fortran send a bug report to mpi bugs mcs anl gov Another common problem with programs that mix Fortran and C is missing libraries The MPICH configure attempts to determine the libraries that are necessary when linking C with Fortran but may miss some There are additional suggestions for this problem in Section SIGSEGV Any message that mentions SIGSEGV is refering to a
105. lue of PROGRAM is sed e s tmp_mnt g This uses the sed command to strip the string tmp_mnt from the file name Simple sed scripts like this may be used as long as they do not involve quotes single or double or use these will interfere with the shell commands in configure that do the replacements If you need more complex processing use a separate shell script or program As another example some systems will generate paths like a thishost root home username which are valid only on the machine thishost but also have paths of the form u home username that are valid everywhere For this case the configure option automountfix sed e s a home u home g will make sure that mpirun gets the proper filename 4 12 Building MPICH Once configure has determined the features of your system all you have to do now is make 2Yes this is nonsensical 34 This will clean all the directories of previous object files if any compile both profiling and non profiling versions of the source code including Romio and the C interface build all necessary libraries and link both a sample Fortran program and a sample C program as a test that everything is working If anything goes wrong check Section 6 to see if there is anything said there about your problem If not follow the directions in Section 6 2 for submitting a bug report To simplify checking for problems it is a good idea to use make amp tee ma
106. ming Tools The MPICH implementation comes with a variety of tools for building running debugging and analyzing MPI programs This section details these tools 3 1 Compiling linking and running programs The MPICH implementation provides four commands for compiling and linking C mpicc C mpicxx Fortran 77 mpif77 and Fortran 90 mpif90 programs Use these commands just like the usual C Fortran 77 C or Fortran compilers For example mpicc c foo c mpif77 c foo f mpicxx c foo cxx mpif90 c foo f90 and mpicc o foo foo o mpif77 o foo foo o mpicxx o foo foo o mpif90 o foo foo o Commands for the linker may include additional libraries For example to use routines from the C math library library use mpicc o foo foo o lm Combining compilation and linking in a single command as shown here mpicc o foo foo c mpif77 o foo foo f mpicxx o foo foo cxx mpif90 o foo foo f may also be used on most systems Note that while the suffixes c for C programs and f for Fortran 77 programs are standard there is no consensus for the suffixes for C and Fortran 90 programs The ones shown here are accepted by many but not all systems MPICH tries to determine the accepted suffixes but may not always be able to Earlier versions of MPICH used mpiCC to compile C programs However on some operating systems such as Mac OS X filenames that differ only in case such as mpicc and mpiCc refer to
107. n np 9 with the above machine file create one process on each of mercury venus and earth 2 on mars 2 because the machines file specifies that mars may have 2 processes sharing memory and 4 on jupiter because jupiter may have 15 processes and only 4 more are needed If 10 processes were needed mpirun would start over from the beginning of the machines file creating an additional process on mercury the value of MPI_MAX_CLUSTER_SIZE prevents mpirun from starting a fifth process sharing memory on jupiter 3 3 6 Heterogeneous networks and the ch_p4 device A heterogeneous network of workstations is one in which the machines connected by the network have different architectures and or operating systems For example a network 13 may contain 3 Sun SPARC sun4 workstations and 3 SGI IRIX workstations all of which communicate via the TCP IP protocol The mpirun command may be told to use all of these by using multiple arch and np arguments For example to run a program on 3 sun4s and 2 SGI IRIX workstations use mpirun arch sun4 np 3 arch IRIX np 2 program a The special program name program a allows you to specify the different executables for the program since a Sun executable won t run on an SGI workstation and vice versa The a is replaced with the architecture name in this example program sun4 runs on the Suns and program IRIX runs on the SGI IRIX workstations You can also put the programs into different directories fo
108. nd on your file server it may take anywhere from a few minutes to an hour or more Optional On workstation networks or to run on a single workstation edit the file mpich util machines machines xxx where xxx is MPICH s name for your ma chine s architecture you will recognize it to reflect your local host names for your workstations If you want to you can skip this step because by default five copies of the machine you have built MPICH on will be there to begin with On parallel ma chines this step is not needed See the README file in the mpich util machines directory for a description of the format Running examples Optional Build and run a simple test program cd examples basic make cpi bin mpirun np 4 cpi At this point you have run an MPI program on your system If you have trouble see Section 6 Optional Put the distribution through its complete acceptance test See Section 4 15 for how to do this Optional If you wish to install MPICH in a public place so that others may use it use make install to install MPICH into the directory specified by the prefix option to configure Installation will consist of an include lib bin sbin www and man directories and a small examples directory Should you wish to remove the installation you can run the script sbin mpiuninstall Optional At this point you can announc
109. nstead the executables are in different directories for example tmp me sun4 and tmp me rs6000 then the command is mpirun arch sun4 np 2 arch rs6000 np 3 tmp me a program It is important to specify the architecture with arch before specifying the number of processors Also the first arch command must refer to the processor on which the job will be started Specifically if nolocal is not specified then the first arch must refer to the processor from which mpirun is running F Deprecated Features During the development of MPICH various features were developed for the installation and use of MPICH Some of these have been superceeded by newer features that are described above This section archives the documentation on the deprecated features F 1 Getting Tcl Tk and wish These software packages are available by anonymous ftp from ftp scriptics com pub tcl tcl_old They are needed only for the upshot and nupshot programs you do not 96 need them in order to install MPICH If you cannot find them at ftp scriptics com copies of Tcl and Tk are available at ftp ftp mcs anl gov mpi tcltk You should get tc17 3 tar Z and tk3 6 tar Z and patch tk3 6p1 patch Later versions of both Tcl and Tk are incompatible with these and do not work with nupshot The upshot program has been modified to work with either Tk 3 6 or Tk 4 0 Upshot may work with later versions but we are no longer tracking the changes to Tcl Tk
110. o overtake overtake o test o L mpich lib intelnx lmpi lnode usr ipsc XDEV i860 bin 1d860 Error undefined symbol _MPI_Keyval_create usr ipsc XDEV i860 bin 1d860 Fatal no output file created 98 A You are probably building MPICH on an old 386 running System V release 2 This version of Unix has very severe limitations on the length of filenames more severe than we are willing to cater to The specific problem here is that the name of the file mpich src context keyval_create c is too long for this system and was not properly archived You best bet is to build MPICH on a different more modern system for example a Sun running SunOS or Solaris F 3 More detailed control over compiling and linking Much of MPICH s portability is handled throught the careful construction of system dependant Makefiles by the configure program This is fine for installing MPICH but what can you do when you are building a new application For simple applications the mpicc and mpif77 commands may be the simplest way to build a new application For more complex codes we recommend taking a sample Makefile in file for example in mpich examples test pt2pt Modify those parts that are are relavent such as the EXECS and specific program targets To create a Makefile just execute mpireconfig Makefile mpireconfig is in the same directory as mpirun This generates a new Makefile from Makefile in with the corr
111. ob every morning to make sure that your servers are running Note that this uses the same remote shell command that configure found if you can t use that remote shell command to start the process on the remote systems you ll need to restart the servers by hand In that case you can use the output from chkserv port 1234 to see which servers need to be restarted chkserv port 2345 kill This contacts all running servers and tells them to exit It does not use rsh and can be used on any system This software is experimental If you have comments or suggestions please send them mpi bugs mcs anl gov 40 4 15 Thorough Testing The examples test directory contains subdirectories of small programs that systemati cally test a large subset of the MPI functions The command make testing in the MPICH directory will cause these programs to be compiled linked executed and their output to be compared with the expected output Linking all these test programs takes up considerable space so you might want to do make clean in the test directory afterwards The individual parts of MPI point to point collective topology etc can be tested separately by make testing in the separate subdirectories for examples test If you have a problem first check the troubleshooting guides and the lists of known problems If you still need help send detailed information to 4 16 Tuning P4 Performance There are several enviromen
112. ocation should be provided at least as an option by the linker 47 that mpirun starts gets the enviroment variable The easiest way to do this is to set the environment variable within your cshrc for csh or tesh users or profile for sh and ksh users file However setting the environment variable within your startup scripts can cause prob lems if you use several different systems For example you may have a single cshrc file that you use with both an SGI IRIX and Solaris system You do not want to set the LD_LIBRARY_PATH to point the SGI at the Solaris version of the MPICH shared libraried4 Instead you would like to set the environment variable before running mpirun setenv LD_LIBRARY_PATH LD_LIBRARY_PATH usr local mpich lib shared mpirun np 4 cpi Unfortunately this won t always work Depending on the method that mpirun and MPICH use to start the processes the environment variable may not be sent to the new process This will cause the program to fail with a message like ld so 1 home me cpi fatal libpmpich so 1 0 open failed No such file or directory Killed Some devices support starting new processes with the current environment check the documentation for mpirun Section 3 2 An alternative to using LD_LIBRARY_PATH and the secure server is to add an option to the link command that provides the path to use in searching for shared libraries Unfortunately the option that you would like
113. olaris early in my search path I could use 62 10 11 12 cd home gropp bin solaris ln s usr bin rsh rsh there assuming that usr bin rsh is the remote shell Q When trying to run a program I get this message trying normal rsh A You are using a version of the remote shell program that does not support the 1 argument Reconfigure MPICH with rshnol and rebuild MPICH You may suffer some loss of functionality if you try to run on systems where you have different user names You might also try using ssh Q When I run my program I get messages like ld so warning usr lib libc so 1 8 has older revision than expected 9 A You are trying to run on another machine with an out dated version of the basic C library Unfortunately some manufacturers do not make the shared libraries com patible between minor or even maintenance releases of their software You need to have you system administrator bring the machines to the same software level One temporary fix that you can use is to add the link time option to force static linking instead of dynamic linking for system libraries For some Sun workstations the option is Bstatic Q Programs never get started Even tstmachines hangs A Check first that rsh works at all For example if you have workstations w1 and w2 and you are running on wi try rsh w2 true This should complete quickly If it does not try rsh wi true that is use rsh to run t
114. ond process will not be seen To enable this use the option p4_opts threaded_ listener on the configure command line for MPICH 17 Q MPI_Abort sometimes doesn t work in the ch_p4 device Why A Currently Version 1 2 7p1 a process detects that another process has aborted only when it tries to send or receive a message and the aborting process is one that it has communicated with in the past Thus it is possible for a process busy with computation not to notice that one of its peers has issued an MPI_Abort although for many common communication patterns this does not present a problem This will be fixed in a future release 6 11 3 IBM RS6000 1 Q When trying to run on an IBM RS6000 with the ch_p4 device I got mpirun np 2 cpi Could not load program home me mpich examples basic cpi Could not load library libC al shr o Error was No such file or directory A This means that MPICH was built with the x1C compiler but that some of the machines in your util machines machines rs6000 file do not have x1C installed Either install x1C or rebuild MPICH to use another compiler either xlc or gcc gcc has the advantage of never having any licensing restrictions 6 11 4 IBM SP 1 Q When starting my program on an IBM SP I get this 65 mpirun np 2 hello ERROR 0031 124 Couldn t allocate nodes for parallel execution Exiting ERROR 0031 603 Resource Manager allocation for task 0 node mei myuniv edu rc
115. one has offered us a multicast based MPI_Bcast yet A 19 Jumpshot and X11 Jumpshot relies on the AWT Swing toolkit to perform its graphics operations We have noticed some problems with AWT Swing and X11 window system support on some PC s running Windows In particular the combination of SecureCRT and Exceed or SecureCRT and Xfree86 often have problems sometimes serious including hangs and crashes For now the only workaround is to use OpenSSH and Xfree86 with Cygwin if possible when using a Windows PC B History of MPICH MPICH was developed during the MPI standards process to provide feedback to the MPI Forum on implementation and usability issues With the release of the MPI standard MPICH was designed to provide an implementation of the MPI standard that could replace the proprietary message passing systems on the massively parallel computers of the day such as the Intel Paragon IBM SP and TMC CM5 MPICH used an early version of the abstract device interface ADI based on the Chameleon portability system to provide a light weight implementation layer To enable development on desktop systems a device layered on top of the P4 system was used Over time other devices were developed as systems have vanished e g the TMC CM5 and the Ncube these devices have been dropped from our distribution Because MPICH used P4 for workstation networks MPICH has supported both MIMD programming and heterogeneous clusters from the very beginn
116. ons of Linux this script has an error that causes a non zero return code even when the compilation is successful To fix this problem you need a corrected 77 script If you can edit the script yourself change the last 3 lines from case cOPT in 2 CC G o 0UTF OFILES 1f2c lm esac rc exit rc to case cOPT in 2 CC G o 0UTF OFILES 1f2c lm esac rc trap 0 exit rc 3 Q During the configure step messages like homes me mpich configure 134956160 Permission denied sometimes appear What is wrong A This is a bug in the Linux actually GNU sh shell The shell is attempting to create a file with the name tmp t lt processid gt sh e g tmp t11203 sh but was unable to This may happen if tmp is full however it can also happen when the shell created the same file for another user days before You can see this happen by running configure under strace f The only fix is to have your systems administrator clean old files out of tmp 6 7 Problems building MPICH 6 7 1 General 1 Q When running make on MPICH I get this error ar write error No such file or directory Error code 1 I ve looked and all the files are accessible and have the proper permissions A Check the amount of space in tmp This error is sometimes generated when there is insufficient space in tmp to copy the archive this is a step that ar takes when updating a library The
117. or that generates a signal such as SIGSEGV occurs For example 17 mpirun np 4 a out mpedbg If you are not sure if your MPICH provides this service you can use mpiversion to see if MPICH was built with the enable mpedbg option This feature may not be available with all devices 3 5 5 Attaching a debugger to a running program On workstation clusters you can often attach a debugger to a running process For example the debugger dbx often accepts a process id pid which you can get by using the ps command The form may be either dbx a out 1234 or dbx pid 1234 a out where 1234 is the process idi To do this with gdb start gdb and at its prompt do file a out attach 1234 One can also attach the TotalView debugger to a running program See Section below 3 5 6 Starting processes under a debugger If one specifies p4norem on the command line mpirun will not actually start the processes The master process prints a message suggesting how the user can do it The point of this option is to enable the user to start the remote processes under his favorite debugger for instance The option only makes sense when processes are being started remotely such as on a workstation network Note that this is an argument to the program not to mpirun For example to run myprog this way use mpirun np 4 myprog p4norem For example to run cpi with 2 processes where the second process is run under the debugger the session woul
118. ou use pmpi_wtime or pmpi_wtick in your program you will need to declare them as functions returning double precision values 6 11 Problems starting programs 6 11 1 General 1 Q When trying to start a program with mpirun np 2 cpi either I get an error message or the program hangs A On some systems such as IBM SPs there are many mutually exclusive ways to run parallel programs each site can pick the approach es that it allows The script mpirun tries one of the more common methods but may make the wrong choice Use the v or t option to mpirun to see how it is trying to run the program and then compare this with the site specific instructions for using your system You may need to adapt the code in mpirun to meet your needs See also the next question 2 Q When trying to run a program with e g mpirun np 4 cpi I get usage mpirun options lt executable gt lt dstnodes gt lt args gt or mpirun options lt schema gt A You have a command named mpirun for a different implementation of MPI in your path ahead of the MPICH version Execute the command which mpirun 57 to see which command named mpirun was actually found The fix is to either change the order of directories in your path to put the MPICH version of mpirun first or to define an alias for mpirun that uses an absolute path For example in the csh shell you might do alias mpirun usr local mpich bin mpirun to set mpirun to the MPICH version
119. out any privilages in a user directory both makes it easier to manage updates to MPICH and allows you to reduce the amount disk space that MPICH takes up since the installed version contains only the libraries header files documentation and supporting programs We recommend an install path that contains the version number of MPICH For example if you are installing MPICH for others to use and you have the required access rights you could choose usr local mpich 1 2 7p1i If you are installing it just for your own use you could use something like home me software mpich 1 2 7 Invoke configure with the appropriate prefix configure prefix usr local mpich 1 2 7 amp tee c log This assumes that you are using a C shell such as csh or tcsh if you are using a Bourne shell use configure prefix usr local mpich 1 2 7 2 gt amp 1 tee c log 2 3 instead This will configure MPICH for the default device this is usually the appropriate choice Section 4 1 discusses the options that can be given to configure to customize MPICH The output of configure is piped to tee this program both writes the output to the file specified by its argument here c log and to standard output If you have trouble with the configure or make step the file c 1log will help identify any problems Make MPICH make amp tee make log This may take a while depending on the load on your system a
120. plication On workstation networks long startup times can be due to the time used to start remote processes see the discussion on the secure server in Section 3 3 4 for the ch_ p4 device or consider using the ch_p4mpd device 59 6 11 2 Workstation Networks 1 Q When I use mpirun I get the message Permission denied A See Section 2 Q When I use mpirun I get the message Try again A If you see something like this mpirun np 2 cpi Try again it means that you were unable to start a remote job with the remote shell command on some machine even though you would normally be able to This may mean that the destination machine is very busy out of memory or out of processes The man page for rshd may give you more information The only fix for this is to have your system administrator look into the machine that is generating this message 3 Q When running the ch_p4 device I get error messages of the form stty TCGETS Operation not supported on socket or stty tcgetattr Permission denied or stty Can t assign requested address A This means that one of your login startup scripts i e login and cshrc or profile contains an unguarded use of the stty or tset program For C shell users one typical fix is to check for the variables TERM or PROMPT to be initialized For example if TERM then eval tset s e k U Q I TERM endif Another solution is to see if it is approp
121. pt performs an rsh and a short directory listing this tests that you both have access to the node and that a program in the current directory is visible on the remote node If there are any problems they will be listed These problems must be fixed before proceeding The only argument to tstmachines is the name of the architecture this is the same name as the extension on the machines file For example usr local mpich sbin tstmachines sun4 tests that a program in the current directory can be executed by all of the machines in the sun4 machines list This program is silent if all is well if you want to see what it is doing use the v for verbose argument usr local mpich sbin tstmachines v sun4 The output from this command might look like Trying true on hosti uoffoo edu Trying true on host2 uoffoo edu Trying ls on host1 uoffoo edu Trying ls on host2 uoffoo edu Trying user program on host1 uoffoo edu Trying user program on host2 uoffoo edu If tstmachines finds a problem it will suggest possible reasons and solutions In brief there are three tests 1 Can processes be started on remote machines tstmachines attempts to run the shell command true on each machine in the machines files by using the remote shell command Note that the ch_p4 devices does not require a remote shell command and can use alternative methods for starting processes see Section 3 3 4 and 3 3 3 2 Is current working
122. r Linux distribution and verison there may be a limit of as few as 40 processes per minute When running the MPICH test suite or starting short parallel jobs from a script it is possible to exceed this limit To fix this you can do one of the following a Wait a few seconds between running parallel jobs You may need to wait up to a minute b Modify etc inetd conf to allow more processes per minute for rsh For example change shell stream tcp nowait root etc tcpd2 in rshd to shell stream tcp nowait 200 root etc tcpd2 in rshd c Use the ch_p4mpd device or the secure server option of the ch_p4 device instead Neither of these relies on inetd 6 Q When using mpirun I get strange output like arch No such file or directory A This is usually a problem in your cshrc file Try the shell command 61 which hostname If you see the same strange output then your problem is in your cshrc file You may have some code in your cshrc file that assumes that your shell is connected to a terminal Q When I try to run my program I get p0_4652 p4_error open error on procgroup file procgroup 0 A This indicates that the mpirun program either did not create the expected input file needed to run the program or that the file was not found The most likely reason is that the mpirun command is trying to run a program built with device ch_p4 as a shared memory ch_shmem or other device Try the follow
123. r example mpirun arch sun4 np 3 arch IRIX np 2 tmp a program It is important to specify the architecture with arch before specifying the number of processors Also the first arch command must refer to the processor on which the job will be started Specifically if nolocal is not specified then the first arch must refer to the processor from which mpirun is running 3 3 7 The P4 Procgroup File For even more control over how jobs get started we need to look at how mpirun starts a parallel program on a workstation cluster Each time mpirun runs it constructs and uses a new file of machine names for just that run using the machines file as input The new file is called Plyyyy where yyyy is the process identifier If you specify keep_pg on your mpirun invocation you can use this information to see where mpirun ran your last few jobs You can construct this file yourself and specify it as an argument to mpirun To do this for ch_p4 use mpirun p4pg pgfile myprog where pfile is the name of the file The file format is defined below This is necessary when you want closer control over the hosts you run on or when mpirun cannot construct it automatically Such is the case when e You want to run different executables on different hosts your program is not SPMD e You want to run on a network of shared memory multiprocessors and need to specify the number of processes that will share memory on each machine The format of
124. r shell program containing the lines bin sh usr local tk3 6 bin wish f usr local mpi bin upshot with the appropriate names for both the wish and upshot executables Also file a bug report with HP At the very least the error message here is wrong also there is no reason to restrict general shell choices as opposed to login shells 6 15 Special debugging arguments These are undocumented and some require configure options to have been specified like mpipktsize and chmemdebug The option mpiversion is useful for finding out how your installation of MPICH was configured and exactly what version it is The options include mpedbg If an error occurs start xterms attached to the process that generated the error Requires the MPICH be configured with mpedbg and works on only some workstations systems mpiversion Print out the version and configuration arguements for the MPICH implemen tation being used These arguments are provided to the program not to mpirun For example mpirun np 2 a out mpiversion 6 15 1 p4 Debugging If your configuration of MPICH used device ch_p4 then some of the p4 debugging capa bilities are available to you The most useful of these are the command line arguments to the application program Thus mpirun np 10 myprog p4dbg 20 p4rdbg 20 72 results in program tracing information at a level of 20 being written to stdout during execution For more information about
125. reed by an application when it is done with them you may want to use the cleanipcs command provided with MPICH FreeBSD For a network of PC s running the FreeBSD version of Unix configure with device ch_p4 with arch freebsd SGI multiprocessor such as an Onyx or Origin 2000 using the shared memory for fast message passing configure with device ch_p4 comm shared 24 Use with arch IRIX to force 32 bit pointers and with arch IRIX64 to force 64 bit pointers Sun SunOS configure with device ch_p4 with arch sun4 MPICH now requires a compiler that supports ANSI C prototypes The old SunOS bundled C compiler does not support prototypes If you need a compiler that supports prototypes we recommend the GNU C compiler gcc Sun Solaris configure with device ch_p4 with arch solaris DEC Compaq HP Alpha configure with device ch_p4 with arch alpha Fujitsu For a network of Fujitsu M780s running UXP M the following options have been tested setenv FC frt configure with arch UXPM with device ch_p4 fflags Oe Uep Eml Aabe with mpe mpedbg prefix usr local mpi tcldir usr local tkdir usr local wish usr local bin wish HP HPUX For a network of HP s including the mpe library but leaving out of it the MPE X graphics routines configure with device ch_p4 arch hpux with mpe no_mpegraphics 4 3 Special issues for heterogeneous networks and the ch_p4 device When building MPICH for a hete
126. riate to add if 7USER O prompt 0 exit near the top of your cshrc file but after any code that sets up the runtime envi ronment such as library paths e g LD_LIBRARY_PATH 60 4 Q When running the ch_p4 device and running either the tstmachines script to check the machines file or the MPICH tests I get messages about unexpected output or differences from the expected output I also get extra output when I run programs MPI programs do seem to work however A This means that one of your login startup scripts i e login and cshrc or profile or bashrc contains an unguarded use of some program that generates output such as fortune or even echo For C shell users one typical fix is to check for the variables TERM or PROMPT to be initialized For example if TERM then fortune endif Another solution is to see if it is appropriate to add if 7USER O prompt 0 exit near the top of your cshrc file but after any code that sets up the runtime envi ronment such as library paths e g LD_LIBRARY_PATH 5 Q Occasionally programs fail with the message poll protocol failure during circuit creation A You may see this message if you attempt to run too many MPI programs in a short period of time For example in Linux and when using the ch_p4 device without the secure server or ssh MPICH may use rsh to start the MPI processes Depending on the particula
127. rogeneous collection of workstations you may want to configure with the option no_short_longs This indicates to MPICH that it should not provide support for the C type long double This can improve performance between systems that have the same datatype lengths for all other types some Intel x86 machines have 12 byte 80 bits long doubles many other systems use either 8 or 16 byte long doubles 4 4 Setting up rsh If you are using rsh with the ch_p4 device you may need to set up your machine to allow the use of rsh You should do this only if you are a system administrator and understand what you are doing or you are using an isolated network For example if you are using Linux on a collection of computers at your home or at work and these machines are not connected to a larger network you should follow these directrions If any of the machines are connected to another network talk to the administrator of the network about the policy for using rsh Alternately consider using ssh Section 4 5 or the secure server Section 4 14 2 The following explains how to setup a single machine so that it can use rsh to itself to start processes To setup rsh you need to ensure that you have a file etc hosts equiv that contains at least 25 localhost your_machine_name where your_machine_name is the name that you ve given your machine in etc hosts You may also need to ensure that the files etc hosts allow and etc ho
128. rror messages in US English additional languages will be provided as we get the translations if you wish to provide one please send mail to mpi bugsCncs anl jgov More precisely MPICH uses an English version that uses the ISO Latin 1 character set ISO8859 1 We expect to provide other versions that also use the Latin 1 character set subject to getting translations of the messages To create a new message catalog copy the file mpich En_US msg to mpich mylanguage and translate the entries The value of mylanguage should match the ones used for your system for example mpich De_DE msg for German Many systems put their NLS files in usr 1lib nls msg you can also check the value of the environment variable NLSPATH on your system Note that some systems provide the routines and programs to support NLS but do not make use of it and do not provide a initial NLSPATH value 42 msg For emacs users check the Emacs info under European Display The commands M x standard display european M x iso accents mode can be used to input most European languages You can also load iso transl and use C x 8 to compose characters this sets the high bit in the character MPICH does not support languages that require multi byte character sets such as Japanese However the only changes needed are in the file src env errmsg c if you are interested in developing a multi byte character set version please let us
129. rts 6000 6009 often used by X while the second blocks incoming TCP connections to port 7100 often used by the X font server We simply remove these rules Firewall configuration written by lokkit Manual customization of this file is not recommended Note ifup post will punch the current nameservers through the firewall such entries will not be listed here input ACCEPT forward ACCEPT output ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i ethO j ACCEPT A input s 0 0 67 68 d 0 0 67 68 p udp i eth1 j ACCEPT A input s 0 0 d 0 0 i lo j ACCEPT A input p tcp s 0 0 d 0 0 0 1023 y j REJECT A input p tcp s 0 0 d 0 0 2049 y j REJECT A input p udp s 0 0 d 0 0 0 1023 j REJECT A input p udp s 0 0 d 0 0 2049 j REJECT Removed these rules to eliminate chance of MPICH comm failure A input p tcp s 0 0 d 0 0 6000 6009 y j REJECT 80 A input p tcp s 0 0 d 0 0 7100 y j REJECT End of removed rules This modification in conjunction with one to allow process startup should prepare your system for MPICH jobs A 6 poll protocol failure during circuit creation You may see this message if you attempt to run too many MPI programs in a short period of time For example in Linux and when using the ch_p4 device without the secure server or ssh MPICH uses rsh to start the MPI processes Depending on the particular Linux distribution and verison there may be a l
130. rue on the system that you are running on If you get Permission denied see the help on that If you get krcmd No ticket file tf_util rsh warning using standard rsh can t provide Kerberos auth data then your system has a faulty installation of rsh Some FreeBSD systems have been observed with this problem Have your system administrator correct the problem often one of an inconsistent set of rsh rshd programs Q When running ch_p4 device I get error messages of the form more slaves than message queues 63 A This means that you are trying to run MPICH in one mode when it was configured for another In particular you are specifying in your p4 procgroup file that several processes are to shared memory on a particular machine by either putting a number greater than 0 on the first line where it signifies number of local processes besides the original one or a number greater than 1 on any of the succeeding lines where it indicates the total number of processes sharing memory on that machine You should either change your procgroup file to specify only one process on line or reconfigure MPICH with configure with device ch_p4 comm shared which will reconfigure the p4 device so that multiple processes can share memory on each host The reason this is not the default is that with this configuration you will see busy waiting on each workstation as the device goes back and forth between selecting on a socket and checking t
131. ry about file systems However there are two issues using NFS the Network File System with MPI IO and using NFS with some automounters These issues are covered in the next two sections 32 4 11 1 NFS and MPI IO To use MPI IO multihost on NFS file systems NFS should be version 3 and the shared NFS directory must be mounted with the no attribute caching noac option set the directory cannot be automounted If NFS is not mounted in this manner the following error could occur MPI_Barrier Internal MPI error No such file or directory File locking messages In order to reconfigure NFS to handle MPI IO properly the following sequence of steps are needed root permission required 1 confirm you are running NFS version 3 rpcinfo p hostname grep nfs for example there should be a 3 in the second column fire gt rpcinfo p fire grep nfs 100003 3 udp 2049 nfs 2 edit etc fstab for each NFS directory read written by MPI IO on each machine used for multihost MPI IO The following is an example of a correct fstab entry for epml root gt grep epml etc fstab gershwin epmi rmt gershwin epm1 nfs bg intr noac 0 0 If the noac option is not present add it and then remount this directory on each of the machines that will be used to share MPI IO files root gt umount rmt gershwin epm1 root gt mount rmt gershwin epm1 3 confirm that the directory is mounted noac root gt grep gershwin e
132. s 0 0 0 0 00 0004 70 6 14 Trouble with Input and Output o e 71 6 14 1 Generali ute eck bk a ee e a a 71 6 142 Workstation Networksl 71 2A AA Se A Bie A A e A 71 O 72 6 15 1 p4 Debugging 2 2 ee be ee Re Ewe 72 73 73 ie he ees ws sg ee es ib dde 74 ta esto och wh sons eesti 74 a a eee bs 74 Ope eas ue E Ses Bees ee re we 75 ec atea niobate 76 setae Sica 81 ARNO 81 a ae ee E Seis ez do 82 E ea ae oh Ue E E eos des BOE od E 82 A Bots aie x Geet we ME Souk Bee Pe aes gee eon Bey a Mee sea A 82 AAA hie each ged seule dia 82 A 12 C Builds Fall a L A 13 Fortran programs give errors about mismatched types A 14 Missing Symbols When Linking o e e A 15 Warning messages while building MPICH A 16 MPMD Multiple Program Multiple Data Programs A 17 Reporting problems and support e e A 18 Algorithms used in MPICH o e e A 19 Jumpshot and Xll o 0222 ee ee ee F Deprecated Features F 1 Getting Tcl Tk and wish o a a aa 00 2 0 0000000004 F 2 Obsolete Systems F 3 More detailed control over compiling and linking References vi 85 85 86 93 96 96 98 99 100 Abstract MPI Message Passing Interface is a standard specification for message passing li braries MPICH is a porta
133. s Some MPI routines are implemented in terms of other MPI routines For example in MPICH MPI_Bcast is implemented using MPI_Send When weak symbols are used even the PMPI versions of the routines are implemented using the MPI not PMPI versions If you want the PMPI routines to only use the PMPI routines use disable weak symbols when configuring MPICH Note that this behavior may change in later releases 4 1 2 Configuring MPICH for use with threads The MPICH implementation of MPI is not threadsafe It may however be possible to use MPICH in a threaded application as long as all MPICH calls are made by a single thread An example of this is OpenMP used for loop parallelism combined with MPI However you may run into some problems with signals Many thread packages make use of signals 23 such as SIGUSR1 and or SIGUSR2 By default the ch_p4 device uses SIGUSR1 If you are using MPICH with a thread package that uses SIGUSR1 you will need to reconfigure adding the argument listenersig SIGNAL NAME to the with device ch_p4 line and rebuild MPICH For example configure with device ch_p4 listenersig SIGUSR2 make 4 1 3 Signals In general users should avoid using signals with MPI programs The manual page for MPI_Init describes the signals that are used by the MPI implementation these should not be changed by the user Because Unix does not chain signals there is the possibility that several packages will attempt to
134. s problem such as an improperly specified compiler or inadequate disk space Next check the web page www mcs anl gov mpi mpich buglist tb1 html for any recent patches that may fix your problem After that check Section 6 3 for common problems If you still can t find a solution to your problem submit a bug report and we will try to help you 44 6 2 Submitting bug reports Send any problem that you can not solve by checking this section to mpi bugs mcs anl gov Please include e The version of MPICH e g 1 2 7p1 e The output of running your program with the mpiversion argument e g mpirun np 1 a out mpiversion e The output of uname a for your system If you are on an SGI system also hinv e The files config log and src fortran config 1log e If the problem is with a script such as configure or mpirun run the script with the echo argument e g mpirun echo np 4 a out e If you are using the ch_p4 device also send the output of sbin tstmachines see Section 8 3 1 If you have more than one problem please send them in separate messages this simplifies our handling of problem reports The rest of this section contains some information on trouble shooting MPICH Some of these describe problems that are peculiar to some environments and give suggested work arounds Each section is organized in question and answer format with questions that relate to more than one environment workstation
135. se the command mpirun np 4 a out to run the program a out on four processors The command mpirun help gives you a complete list of options which may also be found in Appendix El On exit mpirun returns the status of one of the processes usually the process with rank zero in MPI_COMM_WORLD 3 3 Workstation clusters and the ch_p4 device Most massively parallel processors MPPs provide a way to start a program on a requested number of processors mpirun makes use of the appropriate command whenever possible In contrast workstation clusters require that each process in a parallel job be started 10 individually though programs to help start these processes exist see Section 3 3 4 below Because workstation clusters are not already organized as an MPP additional information is required to make use of them MPICH should be installed with a list of participating workstations in the file machines lt arch gt in the directory usr local mpich share This file is used by mpirun to choose processors to run on using heterogeneous clusters is discussed in Section 3 3 7 The rest of this section discusses some of the details of this process and how you can check for problems Also see Section 6 particularly the discussion of common problems 3 3 1 Checking your machines list Use the script tstmachines in usr local mpich sbin to ensure that you can use all of the machines that you have listed This scri
136. server The secure server is a program that runs on the machines listed in the machines xxxx file where xxxx is the name of the machine architecture and that allows programs to start faster There are two ways to install this program so that only one user may use it and so all users may use it No special privileges are required to install the secure server for a single user s use However the secure server does use the Unix ruserok routine which usually requires a rhosts or hosts equiv file See the documentation on your system for ruserok to make sure that your environment will support the ruserok routine To use the secure server follow these steps 1 Choose a port This is a number that you will use to identify the secure server different port numbers may be used to allow multiple secure servers to operate A good choice is a number over 1000 If you pick a number that is already being used the server will exit and you ll have to pick another number On many systems you can use the rpcinfo command to find out which ports are in use or reserved For example to find the ports in use on host mysun try 38 rpcinfo p mysun Start the secure server The script sbin chp4_servs sbin chp4_servs port n arch ARCH can be used to start the secure servers This makes use of the remote shell command rsh remsh or ssh to start the servers if you cannot use the remote shell command you will need to log into ea
137. space Thus if your program is over half as large as the maximum space available you wil get this error On SGI systems you can use the command size to get the size of the executable and swap 1 to get the available space Note that size gives you the size in bytes and swap 1 gives you the size in 512 byte blocks Other systems may offer similar commands 64 A similar problem can happen on IBM SPs using the ch_mp1 device the cause is the same but it originates within the IBM MPL library 15 Q Sometimes I get the error Exec format error Wrong Architecture A You are probably using NFS Network File System NFS can fail to keep files updated in a timely way this problem can be caused by creating an executable on one machine and then attempting to use it from another Usually NFS catches up with the existence of the new file within a few minutes You can also try using the sync command mpirun in fact tries to run the sync command but on many systems sync is only advisory and will not guarentee that the file system has been made consistent 16 Q There seem to be two copies of my program running on each node This doubles the memory requirement of my application Is this normal A Yes this is normal In the ch_p4 implementation the second process is used to dynamically establish connections to other processes With Version 1 1 1 of MPICH this functionality can be placed in a separate thread on many architectures and this sec
138. sseminate information for other users so that everyone can use the shared installation To install the libraries and include files in a publicly available place change to the top level MPICH directory and do make install The man pages will have been copied with the installation so you might want to add usr local mpich 1 2 7p1 man to the default system MANPATH It is possible to specify the directory into which MPICH should be installed after building MPICH by setting the value of PREFIX when executing the installation step 35 make install PREFIX usr local mpich 1 2 7 However some features particularly the ability of Totalview to show MPICH message queues will work only if MPICH is configured with the prefix set to the installation directory A good way to handle multiple releases of MPICH is to install them into directories whose names include the version number and then set a link from mpi to that directory For example if the current version is 1 2 7 the installation commands to install into usr local are make install PREFIX usr local mpi 1 2 7 rm usr local mpi ln s usr local mpi 1 2 7 usr local mpi The script bin mpiinstall provides more control over the installation of MPICH in fact make install just runs this script For example you can change the protection of the files when they are installed with the options mode nnnn for regular files and xmode nnnn for executables and directories
139. stem administrators place the necessary shared libraries into one of the directories that is searched by default If this is not possible then you will need to help the compiler and linker out Many linkers provide a way to specify the search path for shared libraries The trick is to a pass this command to the linker program and b specify all of the libraries that are needed For example on Linux systems the linker command to specify the shared library search path is rpath path e g rpath usr lib usr local lib To pass this command to the linker through the Intel C compiler icc the command Qoption link rpath path is used By default the Linux linker looks in usr lib and the directories specified by the environment variable LD_LIBRARY_ PATH Thus to force the linker to include the path to the shared library you can use 58 mpicc o cpi cpi Qoption link rpath LD_LIBRARY_PATH usr lib If this works then consider editing the value of LDFLAGS in the compiler scripts e g mpicc to include this option Unfortunately each compiler has a different way of passing these arguments to the linker and each linker has a different set of arguments for specifying the shared library search path You will need to check the documentation for your system to find this options 5 Q When attempting to run cpilog I get the following message ld so 1 cpilog fatal 1ibX11 so 4 can t open file errno 2 A The X11 version tha
140. structions for each device 3 5 Debugging Debugging parallel programs is notoriously difficult Parallel programs are subject not only to the usual kinds of bugs but also to new kinds having to do with timing and synchro nization errors Often the program hangs for example when a process is waiting for a message to arrive that is never sent or is sent with the wrong tag Parallel bugs often disappear precisely when you adds code to try to identify the bug which is particularly frustrating In this section we discuss several approaches to parallel debugging 16 3 5 1 The printf Approach Just as in sequential debugging you often wish to trace interesting events in the program by printing trace messages Usually you wish to identify a message by the rank of the process emitting it This can be done explicitly by putting the rank in the trace message 3 5 2 Error handlers The MPI Standard specifies a mechanism for installing one s own error handler and specifies the behavior of two predefined ones MPI_ERRORS_RETURN and MPI_ERRORS_ARE_FATAL As part of the MPE library we include two other error handlers to facilitate the use of command line debuggers such as dbx in debugging MPI programs MPE_Errors_call_dbx_in_xterm MPE_Signals_call_debugger These error handlers are located in the MPE directory A configure option mpedbg includes these error handlers into the regular MPI libraries and allows the command line argument mpe
141. sts deny are empty When using a machine that is not networked for example a laptop while travelling you may need to change your network settings Under some versions of Linux use the netcfg and set Hostname to localhost and Domain to localdomain 4 5 Configuring with ssh The normal process startup mechanism for the ch_p4 device on networks is rsh Use of rsh requires that certain permission be set up on the participating machines On some networks it is undesirable to set permissions that way The simplest alternative to the use of rsh is ssh the secure shell It can be used for secure distributed computing It requires some setup described here but then usage is quite simple The exact set of instructions depend unfortunately on exactly which version of ssh you have installed 4 5 1 Original SSH version 1 Here is a set of steps that need to be done before version one of ssh will work properly with MPICH The changes for version two of ssh follow 1 Make sure ssh is installed on your network which ssh If it isn t you can get ssh from http www ssh fi sshprotocols2 index html 2 Create your authentication key ssh keygen This will generate a private public key pair The private key will be saved in ssh identity and the public key will be saved in ssh identity pub 3 Authorize Access Place your public key in your ssh authorized_keys file All keys listed in that file are allowed access cp
142. t configure found isn t properly installed This is a common problem with Sun Solaris systems One possibility is that your Solaris machines are running slightly different versions You can try forcing static linking Bstatic on Solaris Alternately consider adding these lines to your login assuming C shell setenv OPENWINHOME usr openwin setenv LD_LIBRARY_PATH opt SUNWspro 1lib usr openwin lib you may want to check with your system administrator first to make sure that the paths are correct for your system Make sure that you add them before any line like if 7USER O prompt 0 exit 6 Q My program fails when it tries to write to a file A If you opened the file before calling MPI_INIT the behavior of MPI not just the MPICH implementation of MPI is undefined In the ch_p4 device only process zero in MPI_COMM_WORLD will have the file open the other processes will not have opened the file Move the operations that open files and interact with the outside world to after MPI_INIT and before MPI_FINALIZE 7 Q Programs seem to take forever to start A This can be caused by any of several problems On systems with dynamically linked executables this can be caused by problems with the file system suddenly getting requests from many processors for the dynamically linked parts of the exe cutable this has been measured as a problem with some DFS implementations You can try statically linking your ap
143. t variables and command line options that can be used to tune the performance of the ch_p4 device Note that these environment variables must be defined for all processes that are created not just the process that you are launching MPI programs from i e setting these variables should be part of your login or cshrc startup files The environment variables are P4_SOCKBUFSIZE Specifies the socket buffer size in bytes Increasing this value can improve performance on some system P4 WINSHIFT This is another socket parameter that is supported on only a few platforms We recommend leaving it alone P4_GLOBMEMSIZE This is the amount of memory in bytes reserved for communication with shared memory when MPICH is configured with comm shared Increase this if you get error messages about p4_shmalloc returning NULL P4 RSHCOMMAND This specifies the name of the remote shell command that is used to start new processes as part of MPI_Init If no value is given the remote shell command determined by configure will be used If a program name is given it must accept the same command line arguments as the program selected by configure 41 TCP Tuning The command line option p4sctrl takes a parameter that specifies var ious socket options These are in the form of name value separated by colons With the exception of bufsize users should normally not change the defaults for these The names and their meanings are bufsize Sock
144. tc mnttab gershwin epm1 rmt gershwin epm1 nfs noac acregmin 0 acregmax 0 acdirmin 0 acdirmax 0 O O 899911504 Turning off of attribute caching may reduce performance of MPI IO applications as well as other applications using this directory The load on the machine where the NFS directory is hosted will increase 33 4 11 2 Dealing with automounters Automounters are programs that dynamically make file systems available when needed While this is very convenient many automounters are unable to recognize the file system names that the automounter itself generates For example if a user accesses a file home me the automounter may discover that it needs to mount this file system and does so in tmp_mnt home me Unfortunately if the automounter on a different system is presented with tmp_mnt home me instead of home me it may not be able to find the file system This would not be such a problem if commands like pwd returned home me instead of tmp_mnt home me unfortunately it is all too easy to get a path that the automounter should but does not recognize To deal with this problem configure allows you to specify a filter program when you configure with the option automountfix PROGRAM where PROGRAM is a filter that reads a file path from standard input makes any changes necessary and writes the output to standard output mpirun uses this program to help it find necessary files By default the va
145. that are not trusted by the machine that you are initiating the job from Finally you may need to use a non standard rsh command within MPICH MPICH must be reconfigured with rsh command_name and perhaps also with rshnol if the remote shell command does not support the 1 argument Systems using Kerberos and or AFS may need this 79 A 5 Notes on getting MPICH running Under Linux Introduction The purpose of this document is to describe the steps necessary to allow MPICH processes to be started and to communicate with one another The installation that we are focusing on is a RedHat 7 2 installation with medium security the default While other distributions will certainly vary this is a good example of the sorts of problems that one might run across There are three methods for starting MPICH processes that are typically used on clusters today These are rsh ssh and mpd We will first describe getting the rsh service working We will include rlogin in this process because it is helpful for testing Next we will describe getting ssh working and enabling the ssh agent to allow for logins without password typing Finally we will discuss issues related to process communication in MPICH and firewalls Enabling rsh By default the rsh server is not installed and it is necessary for use of the rsh service in starting MPICH processes The rsh server in rshd is part of the rsh server RPM This RPM is located on the first disc of the RedHat
146. the same file To avoid problems caused when scripts and Makefiles that use the MPICH compilation scripts are ported to such systems we have chnaged to using only mpicxx for compiling and linking C programs We also encourage users to use cxx or cc as the file extension for C programs rather than C because it is the same as c on OS X or cpp because some applications use that suffix for files created with the C preprocessor You can override the choice of compiler by specifying the environment variable MPICH_ CC MPICH_F77 MPICH_CCC or MPICH_F90 However be warned that this will work only if the alternate compiler is compatible with the default one by compatible we mean that is uses the same sizes for all datatypes and layouts and generates object code that can be used with the MPICH libraries If you wish to override the linker use the environment variables MPICH_CLINKER MPICH_F77LINKER MPICH_CCLINKER or MPICH_F9OLINKER If you want to see the commands that would be used without actually running them add the command line argument show In addition the following special options are supported for accessing some of the features of the MPE environment for monitoring MPI calls from within an application mpilog Build version that generates MPE log files mpitrace Build version that generates traces mpianim Build version that generates real time animation These are described in more det
147. ther upper or lower for all MPI calls In addition you may need to use N90 if you use character data because the MPICH Fortran interface expects the calling convention used by virtually all Unix Fortran systems 30 Cray UNICOS is handled separately If you are building shared libraries you will also need to set the environment variable FC_SHARED_OPT to none Early versions of the Absoft compiler could not handle multiple I options If you have trouble with this you should get an update from Absoft 4 8 6 Configuring for Multiple Fortran Compilers In some environments there are several different Fortran compilers all of which define Fortran datatypes of the same size and which can be used with the same C libraries These compilers may make different choices for Fortran name mappings e g the external format of the names given to the linker and use different approaches to access the command line This section describes how to configure MPICH to support multiple Fortran compilers However if any of these steps fails the best approach is to build a separate MPICH installation for each Fortran compiler The first step is to configure MPICH with the with flibname option For example if one of the compilers is g77 use setenv F77 g77 configure with flibname mpich g77 other options After you build test and install this version of MPICH you can configure support for additional Fortran compilers as follows 1
148. tines to access the command line If you find that MPICH fails to determine the names correctly please send a bug report to mpi bugs mcs anl gov 6 7 4 SGI 1 Q The build on an SGI Power Challenge fails with 52 Signal SIGSEGV in Back End Driver phase Error Signal SIGSEGV in phase Back End Driver processing aborted 77 ERROR usr 1ib64 cmplrs be died due to signal 4 77 ERROR core dumped k x Error code 2 bu21 k x Error code 1 bu21 Error code 1 bu21 VVVVNVNV oy A Our information is that setting the environment variable SGI_CC to ansi will fix this problem 2 Q The build on an SGI with architecture IRIXN32 fails with cc Warning c should not be used with ucode 03 032 on a single file use j instead to get inter module optimization A Amazingly the standard c option is not valid for the SGI compilers when both 03 and n32 are specified This is a feature of the SGI compiler and there is no way to work around this for MPICH other than a massive and non portable rewrite of all the Makefile s Your only option is to not use the 03 option 6 7 5 Linux 1 Q The link test failed on Linux with cc o overtake overtake o test o L usr local mpich LINUX ch_p4 1ib 1mpi overtake o text 0x71 undefined reference to MPI_COMM_WORLD overtake o text 0x82 undefined reference to MPIR_1_DOUBLE overtake o text 0xe1 undefined reference to MPI_COMM_WORLD
149. ure determine compiler switches However you can use the configure options cflags and fflags to specify special flags See also compiler switches 82 A 12 C Builds Fail If the C build fails with messages about ambiquities in the definitions try reconfiguring and rebuilding with the without profiling options to the C configure In later versions of MPICH a different C interface will be provided that should fix this problem A 13 Fortran programs give errors about mismatched types Some Fortran compilers will complain if a subroutine is passed arguments of different types in the same parameter position For example if MPI_Bcast is used with an integer in one place and a double precision value in another you may see Argument 1 of mpi_bcast is one type at 2 but is some other type at 1 This is a strict interpretation of the Fortran standard To fix this you will need to tell the compiler to allow this usage For the GNU g77 compiler add the command line option Wno globals as in mpif77 Wno globals mycode f An alternative is to use a Fortran 90 or Fortran 95 compiler with the MPI module instead of the mpif h header file A 14 Missing Symbols When Linking If you get errors about missing symbols such as mpicc o overtake overtake o test o ld 0711 317 ERROR Undefined symbol MPIR_F_TRUE ld 0711 317 ERROR Undefined symbol MPIR_InitFortranDatatypes ld 0711 317 ERROR Undefined symbol
150. ved in 1 2 4 Added support for the POSIX sched_yield call This significantly increases the per formance of the ch_shmem device and ch_p4 device when comm shared is chosen when there are more total processes including operating system and other user pro cesses than processors on a node This is now the default where available However when there are fewer processes than processors lower latencies can be achieved by configuring with disable yield The option with common prefix dir can be used to set the directory path for installing tools such as upshot and jumpshot that are independent of the MPICH device For example configure with device ch_p4 prefix usr local mpich 1 2 4 ch_p4 with common prefix usr local mpich 1 2 4 make make install configure with device ch_p4mpd prefix usr local mpich 1 2 4 ch p4mpd with common prefix usr local mpich 1 2 4 Added CYGWIN_NT to known architectures Added more support for the MPI 2 feature MPI_STATUS_NULL Fixed several bugs in the flow control code that could cause programs to hang Many improvements to the MPICH NT version A bug in the autoconf macro AC_CHECK_HEADER has been fixed this caused configure to conclude that header files were not available even though they were Fixes for NETBSD usc code in ch_p4 New and improved in 1 2 3 Reorganized manuals arranged by device and including a frequently asked questions section e Further improvements to the

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