[phenixbb] Autobuild on parallel

Kaushik Hatti hskaushik at gmail.com
Sun Apr 26 23:05:49 PDT 2015


What is the best way to run Autobuild if I need to run it on hundreds of
datasets (through command-line)?  I have a single machine with 24 cores and
access to a cluster with 128 cores (on parallel; accessible only through
PBS script).

Each Autobuild job with nproc=4 on a single core machine takes ~12 hours to
run (nproc > 4 wouldn't make any difference in the speed of
computation?!).  However, I read that I could set nproc=10 (or
more) and run on parallel (
When I tried the same through PBS script, I got the following error,

Running up to  1  jobs in parallel... with total of  3  jobs

Splitting work into 3 jobs and running with 1 processors using qsub
background=False nproc=20
background=False in ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0
Final job will be run with sh  with background=True
Starting job 1...Log will be:
Traceback (most recent call last):
  File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line
989, in DoNextMethod
    self.CarryOutBest()     # to be obtained after it is finished
  File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line
2147, in CarryOutBest
    getattr(self,str(self.application_method))()  # call this fn
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
2364, in AutoBuild_build_cycle
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
4647, in AutoBuild_rebuild_cycle_run
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
7452, in AutoBuild_build_refine
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
7696, in run_standard_build_in_parallel
"~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line
294, in run
"~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line
604, in start_run
  File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in
    raise Error(msg)
RuntimeError: child process stderr output:
  command: 'qsub background=False nproc=20
  /bin/sh: qsub: command not found


Please let me know if I can share eff and log files of the run.

Please advice,

People living deeply have no fear of death - Anais Nin
Caution: I am still the dumbest person I have ever known :-)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150427/284a2101/attachment.htm>

More information about the phenixbb mailing list