Changes between Version 2 and Version 3 of pace


Ignore:
Timestamp:
01/13/21 08:06:57 (4 years ago)
Author:
arobel
Comment:

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  • pace

    v2 v3  
    1616(a) To copy these files to your home directory, run the following commands:
    1717
    18 cd ~
    19 mkdir ISSM
    20 cd ISSM
    21 cp /storage/coda1/p-arobel3/0/shared/ISSM/ISSMintro/* .
     18cd ~[[BR]]
     19mkdir ISSM[[BR]]
     20cd ISSM[[BR]]
     21cp /storage/coda1/p-arobel3/0/shared/ISSM/ISSMintro/* .[[BR]]
    2222
    2323(b) Then to run the test script on PACE, run the following command:
    2424
    25 qsub batch_issm.pbs
     25qsub batch_issm.pbs [[BR]]
    2626
    2727(c) You can check the status of the run using the following command:
    2828
    29 qstat -u YOURPACEUSERNAME
     29qstat -u YOURPACEUSERNAME [[BR]]
    3030
    3131(d) An output text file should be created in the same directory as the batch file. You can have a quick look at the status of the run (which ISSM should output) using vi or less.
    … …  
    33332. For other non-test ISSM runs, the batch script should generally look like:<br />
    3434------
    35 #PBS -N JOBNAME <br />
    36 #PBS -A GT-arobel3-atlas<br />
    37 #PBS -o output.$PBS_JOBID<br />
    38 #PBS -j oe<br />
    39 #PBS -l nodes=NNODES:ppn=NPROC<br />
    40 #PBS -l walltime=DAYS:HOURS:MINS:00<br />
    41 <br />
    42 cd $PBS_O_WORKDIR<br />
    43 module purge<br />
    44 module load intel/19.0.3<br />
    45 module load issm/4.16<br />
    46 source $ISSMROOT/etc/environment.sh<br />
    47 <br />
    48 matlab -nodesktop -nosplash -r "NAMEOFSCRIPT; exit"<br />
     35#PBS -N JOBNAME [[BR]]
     36#PBS -A GT-arobel3-atlas[[BR]]
     37#PBS -o output.$PBS_JOBID[[BR]]
     38#PBS -j oe[[BR]]
     39#PBS -l nodes=NNODES:ppn=NPROC[[BR]]
     40#PBS -l walltime=DAYS:HOURS:MINS:00[[BR]]
     41
     42cd $PBS_O_WORKDIR[[BR]]
     43module purge[[BR]]
     44module load intel/19.0.3[[BR]]
     45module load issm/4.16[[BR]]
     46source $ISSMROOT/etc/environment.sh[[BR]]
     47
     48matlab -nodesktop -nosplash -r "NAMEOFSCRIPT; exit"[[BR]]
    4949------
    50 In this script, the only things that should be changed are lines 1, 5, 6, 14.<br />
    51 <br />
    52 (Line 1) JOBNAME is just the name of the job you pick (whatever you like) in the scheduler system.<br />
    53 <br />
    54 (Line 5) NNODES indicates the number of nodes and NPROC indicates the number of processors on each node to use. For very simple jobs, both can be 1. For more intensive jobs NNODES=1 and NPROC can be up to 28 (on the typical node architecture of phoenix). For very computationally intensive jobs, you can use more than one node, but talk to Alex first.<br />
    55 <br />
     50In this script, the only things that should be changed are lines 1, 5, 6, 14.[[BR]]
     51[[BR]]
     52(Line 1) JOBNAME is just the name of the job you pick (whatever you like) in the scheduler system.[[BR]]
     53[[BR]]
     54(Line 5) NNODES indicates the number of nodes and NPROC indicates the number of processors on each node to use. For very simple jobs, both can be 1. For more intensive jobs NNODES=1 and NPROC can be up to 28 (on the typical node architecture of phoenix). For very computationally intensive jobs, you can use more than one node, but talk to Alex first.[[BR]]
     55[[BR]]
    5656(Line 6) The maximum time to allocate for the job is specified here in units of DAYS:HOURS:MINS:00. The phoenix cluster has a maximum walltime of 21 days.<br />
    57 <br />
    58 (Line 14) NAMEOFSCRIPT is the file name of the MATLAB script that you are using to run ISSM.<br />
    59 <br />
     57[[BR]]
     58(Line 14) NAMEOFSCRIPT is the file name of the MATLAB script that you are using to run ISSM.[[BR]]
     59[[BR]]
    6060For more details on how to specify jobs on the PACE phoenix cluster see here: http://docs.pace.gatech.edu/phoenix_cluster/submit_jobs_phnx/
    6161