Changes between Version 9 and Version 10 of MWLNotes


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Timestamp:
Aug 28, 2010 6:23:36 PM (9 years ago)
Author:
emre
Comment:

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  • MWLNotes

    v9 v10  
    6565From $HOME/mwl/EXP2/: $ perl makegc.pl skip-scan-count - this will create the analysis
    6666files in a subdirectory $HOME/mwl/EXP2/expt-number/[[BR]]
    67 There will be a file created $HOME/wml/EXP2/exps/j'expt-number'.tgz, this needs to be copied to the target analysis cluster[[BR]]
     67There will be a file created $HOME/wml/EXP2/exps/p'expt-number'.tbz, this needs to be copied to the target analysis cluster[[BR]]
    6868
    69 Extract j'expt-number'.tgz on the target cluster and run with target cluster specific instructions. MORE INFO NEEDED. [[BR]]
     69Extract p'expt-number'.tbz on the target cluster and run with target cluster specific instructions. [[BR]]
     70When the jobs have completed on the target cluster, recover the results. MORE INFO NEEDED. [[BR]]
    7071
    71 When the jobs have completed on the target cluster, recover the results. MORE INFO NEEDED. [[BR]]
     72Example on juropa
     73{{{
     74$ cd $HOME/mwl/EXP2/exps/
     75# ----- copy the job over:
     76$ scp p'expt-number'.tbz vip.rzg.mpg.de:       
     77$ ssh vip.rzg.mpg.de
     78# ----- working from vip.rzg.mpg.de, the file needs to be copied over to juropa
     79$ scp p'expt-number'.tbz juropa.fz-juelich.de:
     80$ ssh juropa.fz-juelich.de
     81# ----- now working from juropa, setup the job
     82$ mkdir -p $WORK/rzg0kpla/mwl/'expt-number'/jobs
     83$ cd $WORK/rzg0kpla/mwl/'expt-number'
     84$ tar jxf ~/p'expt-number'.tbz
     85# ------ submit them
     86$ for i in bbjob-{?,??}; { echo $i; msub $i; echo $i submitted; }
     87# ------ monitor the job:
     88$ showq -u rzg0kpla
     89# ------ when the job(s) is(are) done, make sure all completed
     90$ cd $WORK/rzg0kpla/mwl/'expt-number'
     91# ------ this will give you the number of jobs that should have been completed
     92$ echo exp*dat | wc -w
     93# ------- compare with the number run
     94$ cd jobs; echo mwl-* | wc -w
     95# ------- if they don't match, something didn't run & you'll have to dig further
     96# ------- now make sure all the jobs completed successfully
     97$ cd ~; perl bin/checkcomplete.pl 'expt-number' > runlog
     98# ------- an empty runlog file will mean they were all ok, otherwise it will contain a list of failed jobs, which should be investigated further
     99$ cat runlog
     100# ------- package and copy back the results
     101$ cd $WORK/rzg0kpla/mwl/'expt-number'
     102$ tar jcf ~/r'expt-number'.tbz jobs/mwl-*
     103$ scp ~/r'expt-number'.tbz myuser@bcf.uthscsa.edu:mwl/EXP2/exps/r'expt-number'.tbz
     104$ exit
     105# ------- now on vip.rzg
     106$ exit
     107# ------- now on bcf
     108$ cd $HOME/mwl/EXP2/exps/'expt-number'
     109$ tar jxf r'expt-number'.tbz
     110}}}
    72111
    73112= Viewing Results with us_viewmwl =