mr_rosetta pause & resume
Hello everybody, Is there a way to pause an mr_rosetta run and resume it with a different number of processors? Thanks, Karolina
Hi Karolina, You can stop after any step in mr_rosetta is completely finished and restart from there. At the time of restarting you could specify a different number of processors. To stop mr_rosetta you would abort it in the GUI or use this procedure 1. Stopping mr_rosetta If you create a file "STOPWIZARD" in the top level directory (i.e., MR_ROSETTA_1/), then each job in the entire process will stop as soon as any Phenix part of the process takes over (i.e., as soon as Rosetta jobs finish). To continue on you would use this approach: 1. Viewing solutions and restarting with saved solutions At each stage, existing solutions are saved as a python "pkl" file and can be read back in to mr_rosetta with "mr_rosetta_solutions=xxx.pkl". These solutions can be displayed with "display_solutions=True". Existing solutions are stored as "mr_rosetta_solution" objects which keep track of the model and its history, the map_coefficients and labels, etc. These can be read in to mr_rosetta with the keyword "mr_rosetta_solutions=results.pkl" and used as inputs for subsequent runs, starting at any step that can use those solutions. NOTE: You can re-start mr_rosetta only at the beginning of major stages (like "place_model", "rosetta_rebuild" etc)...but not in between. Normally at the end of a major stage a .pkl file is written out with text like "type this to see all the results". You can almost always give your original command, the command "start_point=xxx" and "mr_rosetta_solutions=my_pickle_file.pkl" and it should then continue on from there. Let me know if that doesn't do it! All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Karolina Michalska [[email protected]] Sent: Tuesday, June 18, 2013 2:03 PM To: [email protected] Subject: [phenixbb] mr_rosetta pause & resume Hello everybody, Is there a way to pause an mr_rosetta run and resume it with a different number of processors? Thanks, Karolina
Okay, so power got turned off randomly again (or it just failed - who
knows).
So for my interrupted run I go:
phenix.mr_rosetta mr_rosetta_params.eff
mr_rosetta_solutions=./path/to/the/most/recent/results.pkl
?
Or do I need to specify the start point?
Related: Does the new 3.5 version of Rosetta impact the performance
(positively preferably) of phenix.mr_rosetta ?
Cheers,
Morten
On 19 June 2013 16:41, Terwilliger, Thomas C
Hi Karolina,
You can stop after any step in mr_rosetta is completely finished and restart from there. At the time of restarting you could specify a different number of processors.
To stop mr_rosetta you would abort it in the GUI or use this procedure
1. *Stopping mr_rosetta*
If you create a file "STOPWIZARD" in the top level directory (i.e., MR_ROSETTA_1/), then each job in the entire process will stop as soon as any Phenix part of the process takes over (i.e., as soon as Rosetta jobs finish).
To continue on you would use this approach:
1. *Viewing solutions and restarting with saved solutions*
At each stage, existing solutions are saved as a python "pkl" file and can be read back in to mr_rosetta with "mr_rosetta_solutions=xxx.pkl". These solutions can be displayed with "display_solutions=True". Existing solutions are stored as "mr_rosetta_solution" objects which keep track of the model and its history, the map_coefficients and labels, etc. These can be read in to mr_rosetta with the keyword "mr_rosetta_solutions=results.pkl" and used as inputs for subsequent runs, starting at any step that can use those solutions. NOTE: You can re-start mr_rosetta only at the beginning of major stages (like "place_model", "rosetta_rebuild" etc)...but not in between. Normally at the end of a major stage a .pkl file is written out with text like "type this to see all the results". You can almost always give your original command, the command "start_point=xxx" and "mr_rosetta_solutions=my_pickle_file.pkl" and it should then continue on from there.
Let me know if that doesn't do it!
All the best, Tom T
------------------------------ *From:* [email protected] [ [email protected]] on behalf of Karolina Michalska [ [email protected]] *Sent:* Tuesday, June 18, 2013 2:03 PM *To:* [email protected] *Subject:* [phenixbb] mr_rosetta pause & resume
Hello everybody,
Is there a way to pause an mr_rosetta run and resume it with a different number of processors?
Thanks,
Karolina
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Morten K Grøftehauge, PhD Pohl Group Durham University
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
________________________________
From: [email protected] [[email protected]] on behalf of Morten Grøftehauge [[email protected]]
Sent: Monday, July 22, 2013 4:31 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] mr_rosetta pause & resume
Okay, so power got turned off randomly again (or it just failed - who knows).
So for my interrupted run I go:
phenix.mr_rosetta mr_rosetta_params.eff mr_rosetta_solutions=./path/to/the/most/recent/results.pkl
?
Or do I need to specify the start point?
Related: Does the new 3.5 version of Rosetta impact the performance (positively preferably) of phenix.mr_rosetta ?
Cheers,
Morten
On 19 June 2013 16:41, Terwilliger, Thomas C
participants (3)
-
Karolina Michalska -
Morten Grøftehauge -
Terwilliger, Thomas C