[phenixbb] phenix.composite-omit-map and PBScluster

Mark A Saper saper at umich.edu
Tue Feb 18 12:37:19 PST 2014


This is a technical question for cluster experts.

I tried to run phenix.composite-omit-map which can divide the calculations into separate jobs, on a very large cluster controlled by the PBS system. I used this command of which the first 2 lines specify to divide the work up into 16 processes, and each process will use 1 of the CPU's in the cluster. 

phenix.composite_omit_map nproc=16 background=False technology=pbs \
    qsub_command="qsub -V -l procs=1,walltime=00:30:00,mem=2000mb,qos=flux -j oe -M saper at umich.edu -q flux -m abe " \
    omit_type=anneal map_type=2mFo-Dfc output.file_name=composite_omit_map9.mtz \
    reflections3_5percent.mtz  Refine_122.pdb

This is the end of the log file before it aborted:

              ----------Calculating individual omit maps----------             

| target_work(ml) = 4.65539  r_work = 0.1750  r_free = 0.2066                 |

And this is the error log:

Traceback (most recent call last):
  File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 238, in <module>
  File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 166, in run
  File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py", line 395, in __init__
  File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py", line 502, in parallel_map
    display_stderr = not preserve_exception_message,
  File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/queuing_system_utils/processing/__init__.py", line 405, in PBS
    raise RuntimeError, "PBS does not support synchronous submission"
RuntimeError: PBS does not support synchronous submission

I know that PBS doesn't support synchronous submission.  Perhaps each job (or map region) requires more than one processor?


Mark A. Saper, Ph.D.				
Associate Professor of Biological Chemistry, University of Michigan
c/o Biophysics, Chem 3040
930 N University Ave
Ann Arbor MI  48109-1055 U.S.A.
saper at umich.edu     phone (734) 764-3353     fax (734) 764-3323

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