Changes between Version 6 and Version 7 of pace


Ignore:
Timestamp:
01/13/21 20:30:19 (4 years ago)
Author:
Mathieu Morlighem
Comment:

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  • pace

    v6 v7  
    44
    55== Running ISSM (Standard install) on PACE ==
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    87ISSM has been built on the PACE cluster at CODA as a module. This means that it is already "installed" and can be used by any PACE user without needing to configure anything (except what is needed for the specific simulation). A user with privileges in the eas-robel group can follow these directions:
    … …  
    1413(a) To copy these files to your home directory, run the following commands:
    1514
     15{{{
     16#!sh
    1617cd ~[[BR]]
    1718mkdir ISSM[[BR]]
    1819cd ISSM[[BR]]
    1920cp /storage/coda1/p-arobel3/0/shared/ISSM/ISSMintro/* .[[BR]]
     21}}}
    2022
    2123(b) Then to run the test script on PACE, run the following command:
    2224
     25{{{
     26#!sh
    2327qsub batch_issm.pbs [[BR]]
     28}}}
    2429
    2530(c) You can check the status of the run using the following command:
    2631
     32{{{
     33#!sh
    2734qstat -u YOURPACEUSERNAME [[BR]]
     35}}}
    2836
    2937(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.
    3038
    31392. For other non-test ISSM runs, the batch script should generally look like:
    32 ------
     40
     41{{{
     42#!sh
    3343#PBS -N JOBNAME [[BR]]
    3444#PBS -A GT-arobel3-atlas[[BR]]
    … …  
    4555
    4656matlab -nodesktop -nosplash -r "NAMEOFSCRIPT; exit"[[BR]]
    47 ------
     57}}}
     58
    4859In this script, the only things that should be changed are lines 1, 5, 6, 14.[[BR]]
    4960[[BR]]
    … …  
    65761. First, you must download or provide your own version of the source code in you local directory on PACE. You can do this using SVN run through a batch script, or simply by downloading the ISSM source to your personal machine (using the directions here: https://issm.jpl.nasa.gov/download/). In the Ice & Climate group shared directory, there is a build script (build-with-mvapich.sh), written by Dr. Fang Liu at PACE (who is the expert on all things related to ISSM builds on PACE) which can be used to build ISSM locally. Navigate into the "trunk" directory of the source code, then copy this build script from the shared directory:
    6677
     78{{{
     79#!sh
    6780cp /storage/coda1/p-arobel3/0/shared/ISSM/ISSMsrc/build-with-mvapich.sh .[[BR]]
     81}}}
    6882
    69832. The build script is organized into "batches". To build the packages and source code in the correct order, simply go through the build script and uncomment one batch at a time and then run the script (using the command ./build-with-mvapich.sh after uncommenting each batch individually).
    7084
    71853. Once you've successfully built ISSM, the batch script will look slightly different:
    72 ------
     86
     87{{{
     88#!sh
    7389#PBS -N JOBNAME [[BR]]
    7490#PBS -A GT-arobel3-atlas[[BR]]
    … …  
    87103
    88104matlab -nodesktop -nosplash -r "NAMEOFSCRIPT; exit"[[BR]]
    89 ------
     105}}}
    90106
    911074. If you are modifying source code and have previously built ISSM locally successfully, you should only need to run batch 6 which simply compiles the source code (and doesn't recompile all the dependencies).
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