Dear Jacob,
Is it just that your system has run out of memory? If the jobs are swapping heavily, that would lead to the behaviour you describe.
Randy
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> On 10 Jul 2015, at 18:30, Keller, Jacob <[log in to unmask]> wrote:
>
> Dear Crystallographers,
>
> I have been running three MR jobs concurrently, one MrBump and two Phasers, but things have not only slowed to a snail's pace but also the GUI has locked up, meaning I cannot click on anything to see what's happening. I've looked at the log files manually, however, and the jobs are still adding to the log files, albeit quite slowly.
>
> -The MrBump job was going very slowly, and I was able to kill it last night. It currently appears as killed on the gui, but the CCP4_session_log file still thinks it's running, although in the task manager there is no indication of this. Also its own log file shows it's terminated. I put the tail of this below.
>
> -It seems Phaser has gone into compulsively-deep mode, and is therefore very slow.
>
> -I am not sure why having heavy jobs should kill the gui--that seems pretty weird.
>
> So the question--is there any way to wake up the GUI, or do I have to resort to killing it, and possibly have to re-run these long jobs? If I do kill it, will the information be lost, or could I resume at roughly the same place? I would just let it run over the weekend, but there's other stuff I would like to get going as well.
>
> All the best,
>
> Jacob Keller
>
>
> *******************************************
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: [log in to unmask]
> *******************************************
>
>
>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: C:/CCP4/6.5/bin/ccp4-python.bat -u C:/CCP4/6.5/bin/mrbump HKLIN D:/CRYSTAL/CamPepA33Redo/ThreeSets_p3_scaled1.mtz SEQIN D:/CRYSTAL/CamPepA33Redo/Nlobe.seq HKLOUT D:/CRYSTAL/CamPepA33Redo/REDOscratch/ThreeSets_p3_scaled1_mrbump_soln1.mtz XYZOUT D:/CRYSTAL/CamPepA33Redo/REDOscratch/ThreeSets_p3_scaled1_mrbump_soln1.pdb KEYIN C:/ccp4temp/REDO_18_1_com.tmp
> has failed with error message
> Traceback (most recent call last):
> File "C:/CCP4/6.5/bin/mrbump", line 109, in <module>
> master.runMR(init, target_info, mstat, queue)
> File "C:\CCP4\6.5\share\mrbump\include\initialisation\MRBUMP_master.py", line 695, in runMR
> MR.MR_start(target_info, init, mstat, init.keywords.QSIZE, None)
> File "C:\CCP4\6.5\share\mrbump\include\mr\MRBUMP_MR.py", line 608, in MR_start
> best.write_results_log(init, mstat)
> File "C:\CCP4\6.5\share\mrbump\include\output\MRBUMP_writebest.py", line 138, in write_results_log
> self.report += " SHELXE CC: %.3f\n" % mstat.model_list[MODEL_SOURCE].shelxe_molrep_CCscore
> TypeError: float argument required, not NoneType
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 "Traceback (most recent call last): File "C:/CCP4/6.5/bin/mrbump", line 109, in <module> master.runMR(init, target_info, mstat, queue) File "C:\CCP4\6.5\share\mrbump\include\initialisation\MRBUMP_master.py", line 695, in runMR MR.MR_start(target_info, init, mstat, init.keywords.QSIZE, None) File "C:\CCP4\6.5\share\mrbump\include\mr\MRBUMP_MR.py", line 608, in MR_start best.write_results_log(init, mstat) File "C:\CCP4\6.5\share\mrbump\include\output\MRBUMP_writebest.py", line 138, in write_results_log self.report += " SHELXE CC: %.3f\n" % mstat.model_list[MODEL_SOURCE].shelxe_molrep_CCscore TypeError: float argument required, not NoneType"
> #CCP4I TERMINATION TIME 07 Jul 2015 20:45:38
> #CCP4I TERMINATION OUTPUT_FILES D:/CRYSTAL/CamPepA33Redo/REDOscratch/search_18
> #CCP4I MESSAGE Task failed
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