[phenixbb] Pause phenix runs

Andrew Purkiss-Trew Andrew.Purkiss-Trew at cancer.org.uk
Fri Apr 12 05:17:17 PDT 2013

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,

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of VAN RAAIJ , MARK JOHAN [mjvanraaij at cnb.csic.es]
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).


Quoting "R.D. Oeffner" <rdo20 at cam.ac.uk>:

> 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
>> phenixbb at phenix-online.org
>> 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
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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