Just wondering if being able to pause a phenix run would be something useful. Currently, it appears one can only abort. Currently doing refinement of a large structure, and doing several simultaneous runs with different options is slowing down the computer too much. Individual runs take about 72 hrs, so o/n is not an option (o/weekend will be...) (or is it possible and I have missed it?) if the FPLC can do it, why not phenix? Seriously, I don't know how easy or difficult it would be to implement, or if paused runs would still take up too many resources, but it seems like something that might be useful - i.e. set several long runs running, and temporarily interrupt them for other jobs on the same computer (like watching youtube movies, as some people seem to think I do all day...) Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
Hi Mark, On linux or mac you can always hit ctrl-Z in the terminal window where you started phenix. On Windows you'd have to open resource monitor from the task manager and click on the name of the python process to get the option to suspend it. If you were looking for hibernating a phenix job that's a different problem. Robert On Apr 12 2013, Mark J van Raaij wrote:
Just wondering if being able to pause a phenix run would be something useful. Currently, it appears one can only abort. Currently doing refinement of a large structure, and doing several simultaneous runs with different options is slowing down the computer too much. Individual runs take about 72 hrs, so o/n is not an option (o/weekend will be...)
(or is it possible and I have missed it?)
if the FPLC can do it, why not phenix? Seriously, I don't know how easy or difficult it would be to implement, or if paused runs would still take up too many resources, but it seems like something that might be useful - i.e. set several long runs running, and temporarily interrupt them for other jobs on the same computer (like watching youtube movies, as some people seem to think I do all day...)
Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
Hi Robert,
actually I run phenix on a MacPro, directly as an application, so
there is no open terminal window - but yes, I guess I could find the
process from a new window, suspend the whole phenix gui and restart
later. However, I think it would be more useful to be able to
temporarily suspend individual long runs, just to do some other quick
jobs (in phenix or outside).
Mark
Quoting "R.D. Oeffner"
Hi Mark,
On linux or mac you can always hit ctrl-Z in the terminal window where you started phenix. On Windows you'd have to open resource monitor from the task manager and click on the name of the python process to get the option to suspend it.
If you were looking for hibernating a phenix job that's a different problem.
Robert
On Apr 12 2013, Mark J van Raaij wrote:
Just wondering if being able to pause a phenix run would be something useful. Currently, it appears one can only abort. Currently doing refinement of a large structure, and doing several simultaneous runs with different options is slowing down the computer too much. Individual runs take about 72 hrs, so o/n is not an option (o/weekend will be...)
(or is it possible and I have missed it?)
if the FPLC can do it, why not phenix? Seriously, I don't know how easy or difficult it would be to implement, or if paused runs would still take up too many resources, but it seems like something that might be useful - i.e. set several long runs running, and temporarily interrupt them for other jobs on the same computer (like watching youtube movies, as some people seem to think I do all day...)
Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
An approach, which I have used with other software, is to signal the process to stop with the kill command.
You can find the PID at the top of the phenix log, then
kill -STOP PID
will pause the process
kill - CONT PID
will restart the process.
Note, I've not tried this on a Mac or with phenix, but it works under Linux.
Hope this helps,
Andrew
________________________________________
From: [email protected] [[email protected]] On Behalf Of VAN RAAIJ , MARK JOHAN [[email protected]]
Sent: 12 April 2013 13:11
To: PHENIX user mailing list; R.D. Oeffner
Subject: Re: [phenixbb] Pause phenix runs
Hi Robert,
actually I run phenix on a MacPro, directly as an application, so
there is no open terminal window - but yes, I guess I could find the
process from a new window, suspend the whole phenix gui and restart
later. However, I think it would be more useful to be able to
temporarily suspend individual long runs, just to do some other quick
jobs (in phenix or outside).
Mark
Quoting "R.D. Oeffner"
Hi Mark,
On linux or mac you can always hit ctrl-Z in the terminal window where you started phenix. On Windows you'd have to open resource monitor from the task manager and click on the name of the python process to get the option to suspend it.
If you were looking for hibernating a phenix job that's a different problem.
Robert
On Apr 12 2013, Mark J van Raaij wrote:
Just wondering if being able to pause a phenix run would be something useful. Currently, it appears one can only abort. Currently doing refinement of a large structure, and doing several simultaneous runs with different options is slowing down the computer too much. Individual runs take about 72 hrs, so o/n is not an option (o/weekend will be...)
(or is it possible and I have missed it?)
if the FPLC can do it, why not phenix? Seriously, I don't know how easy or difficult it would be to implement, or if paused runs would still take up too many resources, but it seems like something that might be useful - i.e. set several long runs running, and temporarily interrupt them for other jobs on the same computer (like watching youtube movies, as some people seem to think I do all day...)
Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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On Fri, Apr 12, 2013 at 5:17 AM, Andrew Purkiss-Trew
An approach, which I have used with other software, is to signal the process to stop with the kill command. You can find the PID at the top of the phenix log, then kill -STOP PID will pause the process kill - CONT PID will restart the process. Note, I've not tried this on a Mac or with phenix, but it works under Linux.
Somewhat to my surprise, the equivalent calls in the Python API appear to work perfectly (on my Mac) for pausing and resuming jobs from the GUI when run in the default mode (as opposed to "detached" mode, but I'm pretty sure I can get that to work too). It's going to take at least a few more days to thoroughly debug, especially since a) I am rewriting the installers, and b) I desperately need to catch up on other projects, but I'm pretty confident that the next release (and in the nearer future, nightly builds) will have the requested "Pause" button. (Except on Windows, which - as usual - is broken by design.) In theory, I think the process memory will be swapped to/from disk as needed, but I haven't directly tested this. The CPU load definitely decreases when it is paused though. As a side effect, I may have also figured out how to abort jobs almost immediately instead of having to wait for print statements to interrupt the programs. Stay tuned. -Nat
participants (5)
-
Andrew Purkiss-Trew -
Mark J van Raaij -
Nathaniel Echols -
R.D. Oeffner -
VAN RAAIJ , MARK JOHAN