[phenixbb] mr_rosetta pause & resume
juergen.koepke at biophys.mpg.de
Thu Jul 30 02:57:32 PDT 2015
thank you very much for your help. I launched the command in command line mode in a new parallel directory and it works :-D It even writes its further results again directly into the original directory (MR_ROSETTA_3) :-))
But now I wonder if it might be possible to restart a crashed run directly from a certain *.pkl-file inside of the phenix-GUI. If not yet possible, wouldn’t that be a wonderful must-have option for a future release? When will MR-Rosetta be out of the beta stage?
My job with 906 residues to place is currently still running on a machine with 8 processors after the restart. Therefore we are discussing possibilities how to speed things further up for future runs. We have seen some hints in the documentation about distributing Rosetta onto more nodes with BOINC. Would that be helpful in MR-Rosetta? Have you experience with this option?
Dr. Juergen Koepke
Project Leader ESFRI-Instruct Core Centre
Max-Planck-Inst. of Biophysics
Dept. Molecular Membrane Biol.
Max-von-Laue Str. 3
T:  69 6303 1055
F:  69 6303 1002
C:  151 2263 6736
Email: juergen.koepke at biophys.mpg.de
> On 28 Jul 2015, at 15:17, Terwilliger, Thomas Charles <terwilliger at lanl.gov> wrote:
> Hi Juergen,
> I think the answer to your question is that you want to be in the same directory where you originally started your run when you issue the command to re-run mr_rosetta (not in the MR_ROSETTA_3 directory). Let me know if that does not help!
> All the best,
> Tom T
> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Juergen Koepke [juergen.koepke at biophys.mpg.de]
> Sent: Tuesday, July 28, 2015 5:00 AM
> To: phenixbb at phenix-online.org
> Cc: Thorsten Luft
> Subject: Re: [phenixbb] mr_rosetta pause & resume
> Dear Tom,
> I found in the phenixbb exactly my case discribed as you wrote on July 22nd, 2013 on reply of Morten Grøftehauge:
> Hi Morten,
> Yes, you'll need to specify the start_point (otherwise it will start from the beginning considering the solutions you have in the .pkl file along with ones that it finds along the way).
> I don't know if rosetta3.5 makes a difference in mr_rosetta; I'd be happy to hear from anyone on this.
> All the best,
> Tom T
> but unfortunately after launching the command "phenix.mr_rosetta mr_rosetta_params.eff start_point=rosetta_rescore mr_rosetta_solutions=./rebuild_results.pkl" I get the following error message:
> Sorry: Unable to create temporary directory MR_ROSETTA_3
> Error message is: The directory MR_ROSETTA_3 could not be created (it may already exist)
> but this looks not logical to me since I am in directory MR_ROSETTA_3 because I want to restart were the program stopped after the crash. Do I have to restart the program from within another directory or what ist the trick? I must admit I first started without the start_point=rosetta_rescore until I realized the program had started my job from the very beginning. Thus i killed the processes again and tried the above with the start_point included. Has my previous attempt already confused something?
> Dr. Juergen Koepke
> Project Leader ESFRI-Instruct Core Centre
> Max-Planck-Inst. of Biophysics
> Dept. Molecular Membrane Biol.
> Max-von-Laue Str. 3
> D-60438 Frankfurt/Main
> T:  69 6303 1055
> F:  69 6303 1002
> C:  151 2263 6736
> Email: juergen.koepke at biophys.mpg.de <mailto:juergen.koepke at biophys.mpg.de>
> URL: https://registration.cc.biophys.mpg.de <https://registration.cc.biophys.mpg.de/>
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