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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt"><span style="font-size: 13.3333330154419px;">Hi Kaushik,</span>
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<div style="font-size: 13.3333330154419px;">I'm sorry for the problem with parallel autobuilding!</div>
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<div style="font-size: 13.3333330154419px;">I think that parallel_autobuild is unfortunately not going to do what you want. It is for running many parallel jobs with the same starting model and combining all the results. It doesn't work with multiple starting
models as I think you want it to.</div>
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<div style="font-size: 13.3333330154419px;">On the error you got, I'm not quite sure what happened but it seems that perhaps the command "qsub" was not found:</div>
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<div style="font-family: Times; font-size: medium;">RuntimeError: child process stderr output:</div>
<div style="font-family: Times; font-size: medium;"> command: 'qsub background=False nproc=20 "~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"'</div>
<div style="font-family: Times; font-size: medium;"> /bin/sh: qsub: command not found</div>
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<div style="font-family: Times; font-size: medium;">It is a little surprising that this would happen in parallel_autobuild and not in autobuild. However perhaps in autobuild you specified that the multiple jobs are to be run with "sh" (run_command=sh) and
in parallel_autobuild it was with qsub (run_command=qsub). <br>
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Let me know if that does not help,</div>
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<div style="font-family: Times; font-size: medium;">All the best,</div>
<div style="font-family: Times; font-size: medium;">Tom T</div>
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<div id="divRpF662470" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Kaushik Hatti [hskaushik@gmail.com]<br>
<b>Sent:</b> Monday, April 27, 2015 12:05 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] Autobuild on parallel<br>
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<div dir="ltr">Hi,
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<div>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). <br>
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<div>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 (<a href="https://www.phenix-online.org/documentation/reference/autobuild.html#parallel-jobs-nproc-nbatch-number-of-parallel-models-and-how-autobuild-works-in-parallel" target="_blank">https://www.phenix-online.org/documentation/reference/autobuild.html#parallel-jobs-nproc-nbatch-number-of-parallel-models-and-how-autobuild-works-in-parallel</a>).
When I tried the same through PBS script, I got the following error,</div>
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<div>XXXXXXXXXXXXXX</div>
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<div>Running up to 1 jobs in parallel... with total of 3 jobs</div>
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<div>Splitting work into 3 jobs and running with 1 processors using qsub background=False nproc=20</div>
<div>background=False in ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0</div>
<div>Final job will be run with sh with background=True</div>
<div>Starting job 1...Log will be: ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1.log</div>
<div>Traceback (most recent call last):</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod</div>
<div> self.CarryOutBest() # to be obtained after it is finished</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest</div>
<div> getattr(self,str(self.application_method))() # call this fn</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 2364, in AutoBuild_build_cycle</div>
<div> self.AutoBuild_rebuild_cycle_run()</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 4647, in AutoBuild_rebuild_cycle_run</div>
<div> always_reuse_model=always_reuse_model)</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7452, in AutoBuild_build_refine</div>
<div> mtz_file=mtz_file,mtz_ref_file=mtz_ref_file)</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7696, in run_standard_build_in_parallel</div>
<div> r.run(out=sys.stdout)</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run</div>
<div> self.start_run(run_file,last=is_last)</div>
<div> File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run</div>
<div> cmd+" "+self.add_double_quote(run_file,escape_space=False)).raise_if_errors()</div>
<div> File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in raise_if_errors</div>
<div> raise Error(msg)</div>
<div>RuntimeError: child process stderr output:</div>
<div> command: 'qsub background=False nproc=20 "~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"'</div>
<div> /bin/sh: qsub: command not found</div>
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<div>XXXXXXXXXXXXXX</div>
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<div>Please let me know if I can share eff and log files of the run.</div>
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<div>Please advice,<br>
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<div>Kaushik</div>
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-- <br>
<div class="gmail_signature">People living deeply have no fear of death - Anais Nin<br>
Caution: I am still the dumbest person I have ever known :-)<br>
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