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

[Gabor Bunkoczi]

Hi Mark,

I cannot answer your question, but this error message is raised for 
exactly the reason it says, and for some reason, synchronous submission 
mode is the default. It is probably better to switch this over to 
asynchronous, which is more generally supported, and I have just made 
this change.

You can either wait for the next build, or edit 
/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py, line 417, and change:

asynchronous=False
to
asynchronous=True

and hopefully, it will get further.

BW, Gabor

On 2014-02-18 20:37, Mark A Saper wrote:
> Hi,
> 
> 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>
>  run(sys.argv[1:])
>  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
>  out=out)
>  File
> "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py",
> line 395, in __init__
>  preserve_exception_message=True)
>  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?
> 
> Thanks,
> Mark
> 
> _________________________________
> 
> 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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