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Supporting MPI Applications on EGEE Grids Zolt án Farkas MTA SZTAKI

Supporting MPI Applications on EGEE Grids Zolt án Farkas MTA SZTAKI. Contents. MPI Standards Implementations EGEE and MPI History Current status Working/research groups in EGEE Future Works P-GRADE Grid Portal Workflow execution, file handling Direct job submission

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Supporting MPI Applications on EGEE Grids Zolt án Farkas MTA SZTAKI

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  1. Supporting MPI Applications onEGEE GridsZoltán FarkasMTA SZTAKI

  2. Contents • MPI • Standards • Implementations • EGEE and MPI • History • Current status • Working/research groups in EGEE • Future Works • P-GRADE Grid Portal • Workflow execution, file handling • Direct job submission • Brokered job submission

  3. MPI Budapest, 5 July 2006 • MPI stands for Message Passing Interface • Standards 1.1 and 2.0 • MPI Standard features: • Collective communication (1.1+) • Point-to-Point communication (1.1+) • Group management (1.1+) • Dynamic Processes (2.0) • Programming Language APIs • …

  4. MPI Implementations Budapest, 5 July 2006 • MPICH • Freely available implementation of MPI • Runs on many architectures (even on Windows) • Implements Standards 1.1 (MPICH) and 2.0 (MPICH2) • Supports Globus (MPICH-G2) • Nodes are allocated upon application execution • LAM/MPI • Open-source implementation of MPI • Implements Standards 1.1 and parts of 2.0 • Many interesting features (checkpoint) • Nodes are allocated before application execution • Open MPI • Implements Standard 2.0 • Uses technologies of other projects

  5. MPICH execution on x86 clusters Budapest, 5 July 2006 • Application can be started … • … using ‘mpirun’ • … specifying: • number of requested nodes (-np <nodenumber>), • a file containing the nodes to be allocated (-machinefile <arg>) [OPTIONAL], • the executable, • executable arguments. • $ mpirun –np 7 ./cummu –N –M –p 32 • Processes are spawned using ‘rsh’ or ‘ssh’, depending on the configuration

  6. MPICH x86 execution – requirements Budapest, 5 July 2006 • Executable (and input files) must be present on worker nodes: • Using Shared Filesystem, or • User distributes the files before invoking ‘mpirun’. • Accessing worker nodes from the host running ‘mpirun’: • Using ‘rsh’ or ‘ssh’ • Without user interaction (host-based authentication)

  7. EGEE and MPI Budapest, 5 July 2006 • MPI became important at the end of 2005/beginning of 2006: • Intructions about CE/jobmanager/WN configuration • The user has to start a wrapper script • the input sandbox isn’t distributed to worker nodes • sample wrapper script, which works for PBS, LFS and assumes ssh • Current status (according to experiments): • No need to use wrapper scripts • MPI jobs fail in case on no shared filesystems • Remote file handling not supported, so user has to take care

  8. EGEE and MPI - II Budapest, 5 July 2006 • Research/Working groups formed: • MPI TCG WG: • User requirements: • „Shared” filesystem: distribute executable and input files • Storage Element handling • Site requirements: • Solution must be compatible with a big number of jobmanagers • Infosystem extensions (max. number of concurent CPUs used by a job, …) • MSc research group (1-month project, 2 students): • Created wrapper scripts for MPICH, LAM/MPI, OpenMPI • Application source is compiled before execution • Executable and input files are distributed to allocated worker nodes, ‘ssh’ is assumed • No remote file support

  9. EGEE and MPI – Future work Budapest, 5 July 2006 • Add support for: • all possible jobmanagers • all possible MPI implementations • Storage Element handling in case of legacy applications • input sandbox distribution in case of no shared filesystems before application execution • output file collection in case of no shared filesystems after the application has been executed

  10. P-GRADE Grid Portal Budapest, 5 July 2006 • Workflow execution: • DAGMan as workflow scheduler • pre and post script to perform tasks around job exeution • Direct job execution using GT-2: • GridFTP, GRAM • pre: create temporary storage directory, copy input files • job: Condor-G is executing a wrapper script • post: download results • Job execution using EGEE broker (both LCG/gLite): • pre: create application context as input sandbox • job: Scheduler universe Condor job executing a script, which does job submission, status polling, output downloading. A wrapper script is submitted to the broker • post: error checking

  11. Portal: File handling Budapest, 5 July 2006 • „Local” files: • User has access to these files through the Portal • Local input files are uploaded from the user machine • Local output files are downloaded to the user machine • „Remote” files: • Files reside on EGEE Storage Elements or are accessible using GridFTP • EGEE SE files: • lfn:/… • guid:… • GridFTP files: gsiftp://…

  12. Portal: Direct job execution Budapest, 5 July 2006 • The resource to be used is known before job execution • The user must have a valid, accepted certificate • Local files are supported • Remote GridFTP files are supported, even in case of grid-unaware applications • Jobs may be sequential or MPI applications

  13. Direct exec: step-by-step I. Budapest, 5 July 2006 • Pre script: • creates a storage directory on the selected site’s front-end node, using the ‘fork’ jobmanager • local input files are copied to this directory from the Portal machine using GridFTP • remote input files are copied using GridFTP (in case of errors, a two-phase copy is tried using Portal machine) • Condor-G job: • a wrapper script (wrapperp) is specified as the real executable • a single job is submitted to the requested jobmanager, for MPI jobs the ‘hostcount’ RSL attribute is used to specify the number of requested nodes

  14. Direct exec: step-by-step II. Budapest, 5 July 2006 • LRSM: • allocate the number of requested nodes (if needed) • start wrapperp on one of the allocated nodes (master worker node) • Wrapperp (running on master worker node): • copies the executable and input files from the front-end node (‘scp’ or ‘rcp’) • in case of PBS jobmanagers, executable and input files are copied to the allocated nodes (PBS_NODEFILE). In case of non-PBS jobmanagers, shared filesystem is required, as the host names of the allocated nodes cannot be determined • wrapperp searches for ‘mpirun’ • the real executable is started using the found ‘mpirun’ • in case of PBS jobmanagers, output files are copied from the allocated worker nodes to the master worker node) • output files are copied to the front-end node

  15. Direct exec: step-by-step III. Budapest, 5 July 2006 • Post script: • local output files are copied from the temporary working directory created by the pre script to the Portal machine using GridFTP • remote output files are copied using GridFTP (in case of errors, a two-phase copy is tried using Portal machine) • DAGMan: schedule next jobs…

  16. Direct execution: animated Portal machine Remote file storage 1 2 5 1 5 Fork GridFTP Temp. Storage PBS Master WN 3 Wrapperp 4 Slave WN1 Slave WNn-1 In/exe mpirun In/exe In/exe Executable 4 Executable Executable Output Output Output Budapest, 5 July 2006

  17. Direct Submission Summary Budapest, 5 July 2006 • Pros: • Users can add remote file support to legacy applications • Works for both sequential and MPI(CH) applications • For PBS jobmanagers, there is no need to have a shared filesystem (support for other jobmanagers can be added, depends on informations provided by jobmanagers) • Works in case of jobmanagers, which do not support MPI • Faster, than submitting with the broker • Cons: • doesn’t integrate into the EGEE middleware • user needs to specify the execution resource • currently doesn’t work on non-PBS jobmanagers without shared filesystems

  18. Portal: Brokered job submission Budapest, 5 July 2006 • The resource to be used is unknown before job execution • The user must have a valid, accepted certificate • Local files are supported • Remote files residing on Storage Elements are supported, even in case of grid-unaware applications • Jobs may be sequential or MPI applications

  19. Broker exec: step-by-step I. Budapest, 5 July 2006 • Pre script: • creates the Scheduler universe Condor submit file • Scheduler Universe Condor job: • the job is a shell script • the script is responsible for: • job submission: a wrapper script (wrapperrb) is specified as the real executable in the JDL file • job status polling • job output downloading

  20. Broker exec: step-by-step II. Budapest, 5 July 2006 • Resource Broker: • handles requests of the Scheduler universe Condor job • sends the job to a CE • watches its exeution • reports errors • … • LRMS on CE: • allocates the requested number of nodes • starts wrapperrb on the master worker node using ‘mpirun’

  21. Broker exec: step-by-step III. Budapest, 5 July 2006 • Wrapperrb: • the script is started by ‘mpirun’, so this script starts on every allocated worker node like an MPICH process • checks if remote input files are already present. If not, they are downloaded from the storage element • if the user specified any remote output files, they are removed from the storage • the real executable is started with the arguments passed to the script. These arguments already contain MPICH-specific ones • after the executable has been finished, remote output files are uploaded to the storage element (only in case of gLite) • Post script: • nothing special…

  22. Broker execution: animated Budapest, 5 July 2006 Portal Machine 2 Storage Element Resource Broker 5 3 Master WN … mpirun Globus Front-end node 5 4 Slave WN1 Slave WNn-1 PBS wrapperrb wrapperrb wrapperrb Real exe Real exe Real exe 5

  23. Broker Submission Summary Budapest, 5 July 2006 • Pros: • adds support for remote file handling in case of legacy applications • extends the functionality of the EGEE broker • one solution supports both sequential and MPI applications • Cons: • slow application execution • status polling generates high load with 500+ jobs

  24. Experimental results • Tested some selected SEEGRID CEs using the broker from command line and the direct job submission from P-GRADE Portal with a job requesting 3 nodes Budapest, 5 July 2006

  25. Budapest, 5 July 2006 Thank you for your attention ?

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