MPICH User's Guide Version 3.1.3 Mathematics and Computer
Contents
1. Fortran 90 programmers should use the MPI module instead this provides all of the definitions as well as interface definitions for many of the MPI functions However this MPI module does not provide full Fortran 90 support in particular interfaces for the routines such as MPI_Send that take choice arguments are not provided 5 Running Programs with mpiexec The MPI Standard describes mpiexec as a suggested way to run MPI pro grams MPICH implements the mpiexec standard and also provides some extensions 5 1 Standard mpiexec Here we describe the standard mpiexec arguments from the MPI Stan dard I To run a program with n processes on your local machine you can use mpiexec n lt number gt a out To test that you can run an n process job on multiple nodes mpiexec f machinefile n lt number gt a out The machinefile is of the form host1 host2 2 host3 4 Random comments host4 1 host1 host2 host3 and host4 are the hostnames of the machines you want to run the job on The 2 4 1 segments depict the number of processes you want to run on each node If nothing is specified 1 is assumed 5 RUNNING PROGRAMS WITH MPIEXEC 5 5 2 Extensions for All Process Management Environments Some mpiexec arguments are specific to particular communication sub systems devices or process management environments process man agers Our intentio2. MPICH This is a preliminary version and some sections are not com plete yet However there should be enough here to get you started with MPICH 2 Getting Started with MPICH MPICH is a high performance and widely portable implementation of the MPI Standard designed to implement all of MPI 1 MPI 2 and MPI 3 in cluding dynamic process management one sided operations parallel I O and other extensions The MPICH Installer s Guide provides some infor mation on MPICH with respect to configuring and installing it Details on compiling linking and running MPI programs are described below 2 1 Default Runtime Environment MPICH provides a separation of process management and communication The default runtime environment in MPICH is called Hydra Other process managers are also available 2 2 Starting Parallel Jobs MPICH implements mpiexec and all of its standard arguments together with some extensions See Section EI for standard arguments to mpiexec and various subsections of Section Bl for extensions particular to various process management systems 2 3 Command Line Arguments in Fortran MPICH1 more precisely MPICH1 s mpirun required access to command line arguments in all application programs including Fortran ones and 3 QUICK START 2 MPICH1 s configure devoted some effort to finding the libraries that con tained the right versions of iargc and getarg and including those libraries with which the mpifort script lin
3. MPICH User s Guide Version 3 1 3 Mathematics and Computer Science Division Argonne National Laboratory Pavan Balaji Wesley Bland William Gropp Rob Latham Huiwei Lu Antonio J Pena Ken Raffenetti Sangmin Seo Rajeev Thakur Junchao Zhang October 8 2014 This work was supported by the Mathematical Information and Computational Sci ences Division subprogram of the Office of Advanced Scientific Computing Research Sci DAC Program Office of Science U S Department of Energy under Contract DE AC02 06CH11357 Contents L Introduction O a B H 2 tarting Parallel Jobs 2 ommand Line Arguments n Fortra 9 Quick Start 4 p o d g UN pecial Issues tor C H NI pecial Issues tor Fortra eon sae 9 Running Programs with mpiexec tandard mpiexec xtensions for All Process Management Environment nvironment J xtensions for the gtorker Process Management 9 4 mpiexec arguments for giorker O Restrictions of the remshell Process Management B it URM DICK nvironmen co 00 n a a a Ol A A OQ 00 iA p gi 8 o o p A q Question ii 10 10 11 11 13 1 INTRODUCTION 1 1 Introduction This manual assumes that MPICH has already been installed For instruc tions on how to install MPICH see the MPICH Installer s Guide or the README in the top level MPICH directory This manual explains how to compile link and run MPI applications and use certain tools that come with
4. PICH jobs can be launched in two ways i use Hydra s mpiexec with the appropriate options corresponding to PBS or ii using the OSC mpiexec 5 6 1 OSC mpiexec Pete Wyckoff from the Ohio Supercomputer Center provides a alternate util ity called OSC mpiexec to launch MPICH jobs on PBS systems More infor mation about this can be found here http www osc edu pw mpiexec 6 Specification of Implementation Details The MPI Standard defines a number of areas where a library is free to define its own specific behavior as long as such behavior is documented appropriately This section provides that documentation for MPICH where necessary 6 1 MPI Error Handlers for Communicators In Section 8 3 1 Error Handlers for Communicators of the MPI 3 0 Stan dard 2 MPI defines an error handler callback function as 7 DEBUGGING 9 typedef void MPI_Comm_errhandler_function MPI_Comm x int Where the first argument is the communicator in use the second argu ment is the error code to be returned by the MPI routine that raised the error and the remaining arguments to be implementation specific varargs MPICH does not provide any arguments as part of this list So a callback function being provided to MPICH is sufficient if the header is typedef void MPI_Comm_errhandler_function MPI_Comm int 7 Debugging Debugging parallel programs is notoriously difficult Here we describe a number of approaches some of which depend on th
5. WITH MPICH 12 command make testing This test suite should work with any MPI imple mentation not just MPICH A FREQUENTLY ASKED QUESTIONS 13 A Frequently Asked Questions The frequently asked questions are maintained online here http wiki References 1 Message Passing Interface Forum MPI2 A Message Passing Interface standard International Journal of High Performance Computing Appli cations 12 1 2 1 299 1998 2 Message Passing Interface Forum MPI A Message Passing Interface Standard version 3 0 Technical report 2012
6. e exact version of MPICH you are using 7 1 TotalView MPICH supports use of the TotalView debugger from Etnus If MPICH has been configured to enable debugging with TotalView then one can debug an MPI program using totalview a mpiexec a n 3 cpi You will get a popup window from TotalView asking whether you want to start the job in a stopped state If so when the TotalView window appears you may see assembly code in the source window Click on main in the stack window upper left to see the source of the main function TotalView will show that the program all processes are stopped in the call to MPI_Init If you have TotalView 8 1 0 or later you can use a TotalView feature called indirect launch with MPICH Invoke TotalView as totalview lt program gt a lt program args gt da 8 CHECKPOINTING 10 Then select the Process Startup Parameters command Choose the Par allel tab in the resulting dialog box and choose MPICH as the parallel sys tem Then set the number of tasks using the Tasks field and enter other needed mpiexec arguments into the Additional Starter Arguments field 8 Checkpointing MPICH supports checkpoint rollback fault tolerance when used with the Hydra process manager Currently only the BLCR checkpointing library is supported BLCR needs to be installed separately Below we describe how to enable the feature in MPICH and how to use it This information can also be found on the MPICH Wiki index php Ch
7. eckpointing 8 1 Configuring for checkpointing First you need to have BLCR version 0 8 2 installed on your machine If it s installed in the default system location add the following two options to your configure command enable checkpointing with hydra ckpointlib blcr If BLCR is not installed in the default system location you ll need to tell MPICH s configure where to find it You might also need to set the LD LIBRARY PATH environment variable so that BLCR s shared libraries can be found In this case add the following options to your configure command enable checkpointing with hydra ckpointlib blcr with blcr BLCR INSTALL DIR LD LIBRARY PATH BLCR INSTALL DIR 1ib where BLCR INSTALL DIR is the directory where BLCR has been installed whatever was specified in prefix when BLCR was configured Note checkpointing is only supported with the Hydra process manager Hyrda will used by default unless you choose something else with the with pm configure option After it s configured compile as usual e g make make install 9 OTHER TOOLS PROVIDED WITH MPICH 11 8 2 Taking checkpoints To use checkpointing include the ckpointlib option for mpiexec to spec ify the checkpointing library to use and ckpoint prefix to specify the directory where the checkpoint images should be written shell mpiexec ckpointlib blcr ckpoint prefix home buntinas ckpts app ckpoint N f hosts n 4 app While the applicati
8. ked MPI programs Since MPICH does not require access to command line arguments to applications these functions are optional and configure does nothing special with them If you need them in your applications you will have to ensure that they are available in the Fortran environment you are using 3 Quick Start To use MPICH you will have to know the directory where MPICH has been installed Either you installed it there yourself or your systems adminis trator has installed it One place to look in this case might be usr local If MPICH has not yet been installed see the MPICH Installer s Guide We suggest that you put the bin subdirectory of that directory into your path This will give you access to assorted MPICH commands to compile link and run your programs conveniently Other commands in this directory manage parts of the run time environment and execute tools One of the first commands you might run is mpichversion to find out the exact version and configuration of MPICH you are working with Some of the material in this manual depends on just what version of MPICH you are using and how it was configured at installation time You should now be able to run an MPI program Let us assume that the directory where MPICH has been installed is home you mpich installed and that you have added that directory to your path using setenv PATH home you mpich installed bin PATH for tcsh and csh or export PATH home you mpich insta
9. lled bin PATH for bash or sh Then to run an MPI program albeit only on one machine you can do cd home you mpich installed examples mpiexec n 3 cpi 4 COMPILING AND LINKING 3 Details for these commands are provided below but if you can success fully execute them here then you have a correctly installed MPICH and have run an MPI program 4 Compiling and Linking A convenient way to compile and link your program is by using scripts that use the same compiler that MPICH was built with These are mpicc mpicxx and mpifort for C C and Fortran programs respectively If any of these commands are missing it means that MPICH was configured without support for that particular language 4 1 Special Issues for C Some users may get error messages such as SEEK_SET is defined but must not be for the C binding of MPI The problem is that both stdio h and the MPI C interface use SEEK SET SEEK_CUR and SEEK_END This is really a bug in the MPI standard You can try adding undef SEEK_SET undef SEEK_END undef SEEK_CUR before mpi h is included or add the definition DMPICH IGNORE CXX SEEK to the command line this will cause the MPI versions of SEEK SET etc to be skipped 4 2 Special Issues for Fortran MPICH provides two kinds of support for Fortran programs For Fortran 77 programmers the file mpif h provides the definitions of the MPI constants 5 RUNNING PROGRAMS WITH MPIEXEC 4 such as MPI_COMM_WORLD
10. lt all environment variables are provided to each MPI process rationale principle of least surprise for the user envlist lt list gt Pass the listed environment variables names separated by commas with their current values to the processes being run by mpiexec genv lt name gt lt value gt The genv options have the same meaning as their corresponding env version except they apply to all executables not just the current executable in the case that the colon syntax is used to specify multiple execuables genvnone Like envnone but for all executables genvlist lt list gt Like envlist but for all executables usize lt n gt Specify the value returned for the value of the attribute MPI UNIVERSE SIZE 1 Label standard out and standard error stdout and stderr with the rank of the process maxtime lt n gt Set a timelimit of lt n gt seconds exitinfo Provide more information on the reason each process exited if there is an abnormal exit In addition to the commandline argments the gforker mpiexec provides a number of environment variables that can be used to control the behavior of mpiexec MPIEXEC TIMEOUT Maximum running time in seconds mpiexec will ter minate MPI programs that take longer than the value specified by MPIEXEC TIMEOUT MPIEXEC UNIVERSE SIZE Set the universe size MPIEXEC PORT RANGE Set the range of ports that mpiexec will use in com municating with the processes that it starts The for
11. mat of this is lt low gt lt high gt For example to specify any port between 10000 and 10100 use 10000 10100 5 RUNNING PROGRAMS WITH MPIEXEC 7 MPICH PORT RANGE Has the same meaning as MPIEXEC PORT RANGE and is used if MPIEXEC PORT RANGE is not set MPIEXEC PREFIX DEFAULT Ifthis environment variable is set output to stan dard output is prefixed by the rank in MPI COMM WORLD of the process and output to standard error is prefixed by the rank and the text err both are followed by an angle bracket gt If this variable is not set there is no prefix MPIEXEC_PREFIX_STDOUT Set the prefix used for lines sent to standard out put A d is replaced with the rank in MPI COMM WORLD a w is re placed with an indication of which MPI_COMM_WORLD in MPI jobs that involve multiple MPI_COMM_WORLDs e g ones that use MPI_Comm_spawn or MPI_Comm_connect MPIEXEC_PREFIX_STDERR Like MPIEXEC_PREFIX_STDOUT but for standard er ror MPIEXEC_STDOUTBUF Sets the buffering mode for standard output Valid values are NONE no buffering LINE buffering by lines and BLOCK buffering by blocks of characters the size of the block is implemen tation defined The default is NONE MPIEXEC_STDERRBUF Like MPIEXEC_STDOUTBUF but for standard error 5 5 Restrictions of the remshell Process Management Envi ronment The remshell process manager provides a very simple version of mpiexec that makes use of the secure shell command ssh to sta
12. n is to make all arguments as uniform as possible across devices and process managers For the time being we will document these separately 5 3 mpiexec Extensions for the Hydra Process Manager MPICH provides a number of process management systems Hydra is the default process manager in MPICH More details on Hydra and its exten 5 4 Extensions for the gforker Process Management Envi ronment gforker is a process management system for starting processes on a sin gle machine so called because the MPI processes are simply forked from the mpiexec process This process manager supports programs that use MPI Comm spawn and the other dynamic process routines but does not sup port the use of the dynamic process routines from programs that are not started with mpiexec The gforker process manager is primarily intended as a debugging aid as it simplifies development and testing of MPI programs on a single node or processor 5 4 1 mpiexec arguments for gforker In addition to the standard mpiexec command line arguments the gforker mpiexec supports the following options np lt num gt synonym for the standard n argument env lt name gt lt value gt Set the environment variable lt name gt to lt value gt for the processes being run by mpiexec 5 RUNNING PROGRAMS WITH MPIEXEC 6 envnone Pass no environment variables other than ones specified with other env or genv arguments to the processes being run by mpiexec By defau
13. on is running the user can request for a checkpoint at any time by sending a SIGUSR1 signal to mpiexec You can also automati cally checkpoint the application at regular intervals using the mpiexec option ckpoint interval to specify the number of seconds between checkpoints shell mpiexec ckpointlib blcr ckpoint prefix home buntinas ckpts app ckpoint N ckpoint interval 3600 f hosts n 4 app The checkpoint restart parameters can also be controlled with the envi ronment variables HYDRA CKPOINTLIB HYDRA CKPOINT PREFIX and HYDRA CKPOINT_INTERVAL Each checkpoint generates one file per node Note that checkpoints for all processes on a node will be stored in the same file Each time a new checkpoint is taken an additional set of files are created The files are num bered by the checkpoint number This allows the application to be restarted from checkpoints other than the most recent The checkpoint number can be specified with the ckpoint num parameter To restart a process shell mpiexec ckpointlib blcr ckpoint prefix home buntinas ckpts app ckpoint N ckpoint num 5 f hosts n 4 Note that by default the process will be restarted from the first check point so in most cases the checkpoint number should be specified 9 Other Tools Provided with MPICH MPICH also includes a test suite for MPI functionality this suite may be found in the mpich test mpi source directory and can be run with the 9 OTHER TOOLS PROVIDED
14. rt processes on a collection of machines As this is intended primarily as an illustration of how to build a version of mpiexec that works with other process managers it does not implement all of the features of the other mpiexec programs described in this document In particular it ignores the command line options that control the environment variables given to the MPI programs It does support the same output labeling features provided by the gforker version of mpiexec However this version of mpiexec can be used much like the mpirun for the ch_p4 device in MPICH 1 to run programs on a collection of machines that allow remote shells A file by the name of machines should contain the names of machines on which processes can be run one machine name per line There must be enough machines listed to satisfy the requested 6 SPECIFICATION OF IMPLEMENTATION DETAILS 8 number of processes you can list the same machine name multiple times if necessary 5 6 Using MPICH with SLURM and PBS There are multiple ways of using MPICH with SLURM or PBS Hydra provides native support for both SLURM and PBS and is likely the easiest way to use MPICH on these systems see the Hydra documentation above for more details Alternatively SLURM also provides compatibility with MPICH s in ternal process management interface To use this you need to configure MPICH with SLURM support and then use the srun job launching utility provided by SLURM For PBS M
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