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Stephan Geuter

953 days ago
Unfiled. Edited by Hedwig , Stephan Geuter , Marianne Reddan 953 days ago
Marianne R
  • alias qrsh='qsub -q blanca-ics -I -vDISPLAY=blogin01:$VNCPORT.0 -lwalltime=43200'
Luke C
  • Note that there are newer versions for most of the software listed above that you should consider using.
NOTE: when I use qrsh  set up like this my job only lasts 24 hours for some reason. But if I type the same thing in the terminal, changing to VNCPORT to my vnc port my job lasts 7 days)
Stephan G --> interactive jobs should not run for more the 12/24hours
 
 
Marianne R walltime is the amount of time you can run a job on the cluster
default is 24 hours
max is 7 days aka 168 hours
you must specify your walltime if your jobs takes a long ass time to run, or it will stop early on you without warning
Marianne R
  • #PBS -l nodes=1:ppn=1,walltime=168:00:00 
Q: can insert that into a bash script? anywhere? just before the script call? or this has to go into qsub?
aren't hashtags comments in bash?
Stephan G A: You can either specify the PBS directive in your script (as with "#PBS -m ae") OR include it in the qsub command.
 
 
Stephan G
  •  This kind of loop will use a lot of resources at once - one core and lots of mem per job/subject. it may be more fair to bundle subjects and have each job run several subjects serially. Right now I only have a workaround where I  hardcode the number of subjects per job and have all subjects for one  job in a row in subs.txt.  I found that first PBS command is not  necessary. 
  • According to RC 4GB per core should not be exceeded in order to not crash a node. setting the SPM.stats.maxmem=2^33 allows for 8GB of RAM and the job may actually use more than 10GB on blanca. You want to then request 3-4 cores for your job to not use up the memory of other people.
 
  • #PBS -l nodes=1:ppn=1,walltime=24:00:00 # set the walltime, here 24hrs
  •     JOB=`qsub -q blanca-ics -m abe -N Big_run - <<EOJ # outer job description
  • #!/bin/bash
  • #PBS -l nodes=1:ppn=1,walltime=24:00:00 # set the walltime, here 24hrs
 
  • #PBS -m bea # Send Email on beginning completion and abortion
 
Hedwig More comments on submitting jobs on blanca:
  • you should not use more then 4GB RAM (? need to check that), to figure out how much you are using type: qstat -f JOBID | grep used.mem
  • use -vDISPLAY=blogin01:$PORT.0 if you use an interactive job (-I), this seems to speed up the display
  •  
 

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