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MPI support in gLite

MPI support in gLite. Enol Fernández CSIC. MPI on the Grid. CREAM/WMS. Submission/Allocation Definition of job characteristics Search and select adequate resources Allocate (or coallocate ) resources for the job Execution File distribution Batch system interaction

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MPI support in gLite

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  1. MPI support in gLite Enol Fernández CSIC

  2. MPI on the Grid CREAM/WMS • Submission/Allocation • Definition of job characteristics • Search and select adequate resources • Allocate (or coallocate) resources for the job • Execution • File distribution • Batch system interaction • MPI implementation details MPI-Start

  3. Allocation / Submission • Process count specified with the CPUNumber attribute Type = "Job"; CPUNumber = 23; Executable = "my_app"; Arguments = "-n 356 -p 4"; StdOutput = "std.out"; StdError = "std.err"; InputSandBox = {"my_app"}; OutputSandBox = {"std.out", "std.err"}; Requirements = Member("OPENMPI”, other.GlueHostApplicationSoftwareRunTimeEnvironment);

  4. MPI-Start • Specify a unique interface to the upper layer to run a MPI job • Allow the support of new MPI implementations without modifications in the Grid middleware • Support of “simple” file distribution • Provide some support for the user to help manage his data GridMiddleware MPI-START MPI Resources

  5. MPI-Start Design Goals • Portable • The program must be able to run under any supported operating system • Modular and extensible architecture • Plugin/Component architecture • Relocatable • Must be independent of absolute path, to adapt to different site configurations • Remote “injection” of mpi-start along with the job • “Remote” debugging features

  6. MPI-Start Architecture CORE Scheduler Execution Hooks Local User Compiler File Dist. Open MPI MPICH2 LAM PACX PBS/Torque SGE LSF

  7. Using MPI-Start (I) JobType = "Normal"; CpuNumber = 4; Executable = "starter.sh"; InputSandbox = {"starter.sh”} StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err"}; Requirements = Member("MPI-START”, other.GlueHostApplicationSoftwareRunTimeEnvironment) && Member("OPENMPI”, other.GlueHostApplicationSoftwareRunTimeEnvironment); $ catstarter.sh #!/bin/sh # Thisis a script tocallmpi-start # Setenvironmentvariablesneeded export I2G_MPI_APPLICATION=/bin/hostname export I2G_MPI_APPLICATION_ARGS= exportI2G_MPI_TYPE=openmpi export I2G_MPI_PRECOMMAND=time # Execute mpi-start $I2G_MPI_START stdout: Scientific Linux CERN SLC release 4.5 (Beryllium) Scientific Linux CERN SLC release 4.5 (Beryllium) lflip30.lip.pt lflip31.lip.pt stderr: real 0m0.731s user 0m0.021s sys 0m0.013s

  8. … CpuNumber = 4; Executable = ”mpi-start-wrapper.sh"; Arguments = “userapp OPENMPIsomeappargs…” InputSandbox = {”mpi-start-wrapper.sh”}; Environment = {“I2G_MPI_START_VERBOSE=1”, …} ... Using MPI-Start (II) #!/bin/bash MY_EXECUTABLE=$1 shift MPI_FLAVOR=$1 shift export I2G_MPI_APPLICATION_ARGS=$* # Convertflavortolowercaseforpassingtompi-start. MPI_FLAVOR_LOWER=`echo $MPI_FLAVOR | tr '[:upper:]' '[:lower:]'` # Pull out thecorrectpathsfortherequestedflavor. evalMPI_PATH=`printenv MPI_${MPI_FLAVOR}_PATH` # Ensuretheprefixiscorrectly set. Don'trelyonthedefaults. eval I2G_${MPI_FLAVOR}_PREFIX=$MPI_PATH export I2G_${MPI_FLAVOR}_PREFIX # Setupformpi-start. export I2G_MPI_APPLICATION=$MY_EXECUTABLE exportI2G_MPI_TYPE=$MPI_FLAVOR_LOWER # Invokempi-start. $I2G_MPI_START

  9. MPI-Start Hooks (I) • File Distribution Methods • Copy files needed for execution using the most appropriate method (shared filesystem, scp, mpiexec, …) • Compiler flag checking • checks correctness of compiler flags for 32/64 bits, changes them accordingly • User hooks: • build applications • data staging

  10. MPI-Start Hooks (II) #!/bin/sh pre_run_hook () { # Compile theprogram. echo "Compiling ${I2G_MPI_APPLICATION}" # Actually compile theprogram. cmd="mpicc ${MPI_MPICC_OPTS} -o ${I2G_MPI_APPLICATION} ${I2G_MPI_APPLICATION}.c" $cmd if [ ! $? -eq 0 ]; then echo "Error compilingprogram. Exiting..." exit 1 fi # Everything's OK. echo "Successfullycompiled ${I2G_MPI_APPLICATION}" return 0 } … InputSandbox = {…, “myhooks.sh”…}; Environment = {…, “I2G_MPI_PRE_HOOK=myhooks.sh”}; …

  11. MPI-Start: more features • Remote injection • Mpi-start can be sent along with the job • Just unpack, set environment and go! • Interactivity • A pre-command can be used to “control” the mpirun call • $I2G_MPI_PRECOMMAND mpirun …. • This command can: • Redirect I/O • Redirect network traffic • Perform accounting • Debugging • 3 different debugging levels: • VERBOSE: basic information • DEBUG: internal flow information • TRACE: set –x at the beginning. Full trace of the execution

  12. Future work (I) • New JDL description for parallel jobs (proposed by the EGEE MPI TF): • WholeNodes (True/False): • whether or not full nodes should be reserved • NodeNumber (default = 1): • number of nodes requested • SMPGranularity (default = 1): • minimum number of cores per node • CPUNumber (default = 1): • number of job slots (processes/cores) to use • CREAM team working on how to support them

  13. Future work (II) • Management of non MPI jobs • new execution environments (OpenMP) • generic parallel job support • Support for new schedulers • Condor and SLURM support • Explore support for new architectures: • FPGAs, GPUs,…

  14. More Info… • gLite MPI PT: • https://twiki.cern.ch/twiki/bin/view/EMI/GLiteMPI • MPI-Start trac • http://devel.ifca.es/mpi-start • contains user, admin and developer docs • MPI Wiki @ TCD • http://www.grid.ie/mpi/wiki

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