Problems running pmut in parallel with openmpi

This topic has 2 replies, 2 voices, and was last updated 12 years, 3 months ago by Anonymous.

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- September 21, 2012 at 1:25 pm #1415
  Anonymous
  Hi there,
  
  I am running into problems with pmut using openmpi. We successfully compiled Rosetta3.4 with mpi support, but now that we run pmut with the openmpi command ‘mpirun -np 8’, the job does not distribute ‘the work of creating and scoring all mutants evenly across all available CPUs’ (as it says in the manual), but instead calculates every mutant 8 times: the log file lists every entry 8 times (see below). Am I doing something obvious wrong? Or did the compilation with openmpi fail?
  
  Thanks a lot for your help in this matter.
  
  Rene
  
  ###########
  
  Here’s the command script I use:
  
  mpirun -np 8 pmut_scan_parallel.linuxgccrelease
  -database /opt/rosetta3.4/rosetta_database
  -s XXX.pdb
  -ex1
  -ex2
  -extrachi_cutoff 1
  -use_input_sc
  -ignore_unrecognized_res
  -no_his_his_pairE
  -multi_cool_annealer 10
  -mute basic core
  
  The output log file looks like this:
  
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: go(): master node
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number single mutants possible: 9044
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants possible: 0
  protocols.pmut_scan.PointMutScanDriver: fill_mutations_list(): number double mutants excluded for distance: 0
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average ddG average total energy
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15I A-L15I -2.935 -521.94
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15T A-L15T -1.388 -520.39
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-L15V A-L15V -2.474 -521.47
  protocols.pmut_scan.PointMutScanDriver: A-T16V A-T16V -1.207 -519.48
  protocols.pmut_scan.PointMutScanDriver: A-T16V A-T16V -1.207 -519.48
  protocols.pmut_scan.PointMutScanDriver: A-T16V A-T16V -1.207 -519.48
  protocols.pmut_scan.PointMutScanDriver: A-T16V A-T16V -1.207 -519.48
  protocols.pmut_scan.PointMutScanDriver: A-T16V A-T16V -1.207 -519.48
  protocols.pmut_scan.PointMutScanDriver: A-T16V A-T16V -1.207 -519.48
- September 21, 2012 at 1:38 pm #7834
  Anonymous
  Run pmut_scan_parallel.linuxgccrelease without mpirun and with no options. If it fails with an mpi-related error (mine is
  
  “PMGR_COLLECTIVE ERROR: unitialized MPI task: Missing required environment variable: MPIRUN_RANK”
  
  but yours may be different), then you are using the MPI executable correctly and the problem is elsewhere. If it instead fails with
  
  “basic.options.util: Use either -s or -l to designate one or more start_files
  ERROR:: Exit from: src/basic/options/util.cc line: 109″
  
  then you are not using the MPI executable.
  
  I notice that MPI is not in your executable name: pmut_scan_parallel.linuxgccrelease. There should be a pmut_scan_parallel.mpi.linuxgccrelease in bin/ if you compiled in MPI. There should be a pmut_scan_parallel.default.linuxgccrelease if you compiled not-in-mpi, and both should be present if you compiled both. The pmut_scan_parallel with no insertion (no mpi or default) points to whatever was compiled most recently, so if you compiled mpi then non-mpi, but tried to use the unspecified symlink in bin, you’ll get this behavior.
- September 21, 2012 at 3:43 pm #7836
  Anonymous
  THanks for your help. It works now. Was using the wrong executable
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