[phenixbb] Autobuild on parallel
Kaushik Hatti
hskaushik at gmail.com
Sun Apr 26 23:05:49 PDT 2015
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 :-)
-------------- 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