[phenixbb] Autobuild on parallel

[Kaushik Hatti]

Hi,

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 (
https://www.phenix-online.org/documentation/reference/autobuild.html#parallel-jobs-nproc-nbatch-number-of-parallel-models-and-how-autobuild-works-in-parallel).
When I tried the same through PBS script, I got the following error,

XXXXXXXXXXXXXX
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:
~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1.log
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
    self.AutoBuild_rebuild_cycle_run()
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
4647, in AutoBuild_rebuild_cycle_run
    always_reuse_model=always_reuse_model)
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
7452, in AutoBuild_build_refine
    mtz_file=mtz_file,mtz_ref_file=mtz_ref_file)
  File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line
7696, in run_standard_build_in_parallel
    r.run(out=sys.stdout)
  File
"~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line
294, in run
    self.start_run(run_file,last=is_last)
  File
"~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line
604, in start_run
    cmd+"
"+self.add_double_quote(run_file,escape_space=False)).raise_if_errors()
  File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in
raise_if_errors
    raise Error(msg)
RuntimeError: child process stderr output:
  command: 'qsub background=False nproc=20
"~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"'
  /bin/sh: qsub: command not found

XXXXXXXXXXXXXX

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

Please advice,
Kaushik


-- 
People living deeply have no fear of death - Anais Nin
Caution: I am still the dumbest person I have ever known :-)
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