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High Throughput Parallel Computing (HTPC)

High Throughput Parallel Computing (HTPC). Dan Fraser, UChicago Greg Thain , Uwisc. The two familiar HPC Models . High Throughput Computing Run ensembles of single core jobs Capability Computing A few jobs parallelized over the whole system Use whatever parallel s/w is on the system.

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High Throughput Parallel Computing (HTPC)

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  1. High Throughput Parallel Computing (HTPC) Dan Fraser, UChicago Greg Thain, Uwisc

  2. The two familiar HPC Models • High Throughput Computing • Run ensembles of single core jobs • Capability Computing • A few jobs parallelized over the whole system • Use whatever parallel s/w is on the system

  3. HTPC – an emerging model Ensembles of small- way parallel jobs (10’s – 1000’s) Use whatever parallel s/w you want  (It ships with the job)

  4. CurrentHTPC Mechanism https://twiki.grid.iu.edu/bin/view/Documentation/HighThroughputParallelComputing • Submit jobs thatconsume an entire processor • Typically 8 cores (today) • Package jobs with a parallel library (schedd) • HTPC jobs as portable as any other job • MPI, OpenMP, your own scripts, … • Parallel libraries can be optimized for on-board memory access • All memory is available for efficient utilization • Some jobs just need more memory • Submit jobs via WMS glidein on the OSG • A separate list of resources for HTPC (by VO)

  5. Where we are heading • Condor 7.6.x now supports: • Node draining • Partial node usage (e.g. 4 out of 8 cores) • Fixes a job priority issue with HTPC jobs • Now being tested at Wisconsin (CHTC) • Plan is to create a “best practice” template to help with Condor configuration • Will add to RPM CE doc • Currently in Pacman OSG CE doc

  6. Configuring Condor for HTPC • Two strategies: • Suspend/drain jobs to open HTPC slots • Hold empty cores until HTPC slot is open • http://condor-wiki.cs.wisc.edu • See the HTPC twiki for the straightforward PBS setup • https://twiki.grid.iu.edu/bin/view/Documentation/HighThroughputParallelComputing

  7. How to submit universe = vanilla requirements = (CAN_RUN_WHOLE_MACHINE =?= TRUE) +RequiresWholeMachine=true executable = some job arguments = arguments should_transfer_files = yes when_to_transfer_output = on_exit transfer_input_files = inputs queue

  8. MPI on Whole machine jobs Whole machine mpi submit file universe = vanilla requirements = (CAN_RUN_WHOLE_MACHINE =?= TRUE) +RequiresWholeMachine=true executable = mpiexec arguments = -np 8 real_exe should_transfer_files = yes when_to_transfer_output = on_exit transfer_input_files = real_exe queue

  9. How to submit to OSG universe = grid GridResource = some_grid_host GlobusRSL = MagicRSL executable = wrapper.sh arguments = arguments should_transfer_files = yes when_to_transfer_output = on_exit transfer_input_files = inputs transfer_output_files = output queue

  10. Chemistry Usage Example of HTPC

  11. What’s the magic RSL? Site Specific Documentation is in the OSG CE ( PBS (host_xcount=1)(xcount=8)(queue=?) LSF (queue=?)(exclusive=1) Condor (condorsubmit=(‘+WholeMachine’ true))

  12. What’s with the wrapper? Chmod executable Create output files #!/bin/sh chmod 0755 real.ex touch output ./mpiexec –np 8 real.ex

  13. Next steps …?

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