GEOS-5 Quick Start: Difference between revisions

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where <code>.g5_modules</code> is simply a copy of the <code>g5_modules</code> that you ran earlier before compiling. The <code>umask 022</code> is not strictly necessary, but it will make the various files readable to others, which will facilitate data sharing and user support. Your home directory <code>~''USERID''</code> is also inaccessible to others by default; running <code>chmod 755 ~</code> is helpful.

Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them. The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them. The <code>cap_restart</code> file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS. The boundary conditions/forcings are provided by symbolic links created by the run script.

Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them. The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them. The <code>cap_restart</code> file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS. The boundary conditions/forcings are provided by symbolic links created by the run script. If you need an arbitrary set of restarts, you can copy them from <code>/discover/nobackup/aeichman/restarts/Fortuna-2_0/144x91</code>

The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''. It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time. Leave END_DATE alone in Fortuna 2.0 -- there is a bug that erroneously resubmits the script after this date. You can stop the run by commenting out the <code>qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted. Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.

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 where <code>.g5_modules</code> is simply a copy of the <code>g5_modules</code> that you ran earlier before compiling.  The <code>umask 022</code> is not strictly necessary, but it will make the various files readable to others, which will facilitate data sharing and user support.  Your home directory <code>~''USERID''</code> is also inaccessible to others by default; running <code>chmod 755 ~</code> is helpful.
-Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''.   Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them.  The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them.   The <code>cap_restart</code> file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS.  The boundary conditions/forcings are provided by symbolic links created by the run script.
+Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''.   Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them.  The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them.   The <code>cap_restart</code> file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS.  The boundary conditions/forcings are provided by symbolic links created by the run script.  If you need an arbitrary set of restarts, you can copy them from <code>/discover/nobackup/aeichman/restarts/Fortuna-2_0/144x91</code>
 The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''.  It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  Leave END_DATE alone in Fortuna 2.0 -- there is a bug that erroneously resubmits the script after this date.  You can stop the run by commenting out the <code>qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted.  Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.