GEOS-5 Quick Start: Difference between revisions

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Copy the restart (initial condition) and ''cap_restart'' (t=t0) files into EXPDIR. Keep the "originals" handy since if the model crashes early in the run it might have renamed them. The model expects restarts to end in "rst" but produces them with the date at time appended to the filename, so you may have to rename them. The ''cap_restart'' file is simply one line of text with the format "YYYYMMDD HHMMSS". The boundary conditions/forcings are provided by symbolic links created by the run script.

The script you submit, ''gcm_run.j'', is in HOMEDIR. It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days between saving restarts, called segments) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time. END_DATE can be changed to your end date, or just left as is. Commenting out the ``qsub gcm_run.j'' at the end of the script will stop it, too. Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.

The script you submit, ''gcm_run.j'', is in HOMEDIR. It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days between saving restarts, called segments) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time. END_DATE can be changed to your end date, or just left as is. Commenting out the ''qsub gcm_run.j'' at the end of the script will stop it, too. Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.

Submit the job with ``qsub gcm_run.j''. You can keep track of it with qstat or ``qstat | grep USERNAME'', or stdout with ``tail -f /discovery/pbs_spool/JOBID.OU'', JOBID being returned by qsub and displayed with qstat. Jobs can be killed with ``qdel JOBID''. The stdout and stderr will be delivered as files to HOMEDIR at the end of a job.

Submit the job with ''qsub gcm_run.j''. You can keep track of it with qstat or ''qstat | grep USERNAME'', or stdout with ''tail -f /discovery/pbs_spool/JOBID.OU'', JOBID being returned by qsub and displayed with qstat. Jobs can be killed with ''qdel JOBID''. The stdout and stderr will be delivered as files to HOMEDIR at the end of a job.

During a normal run, the ''gcm_run.j'' script will run the model for the segment length (current default is 8 days). The model creates output files (with an ''nc4'' extension), also called collections (of output variables), in the ''EXPDIR/scratch'' directory. After each segment, the script moves the output to the ''EXPDIR/holding'' and spawns a post-processing batch job which partitions and moves the output files within the ''holding'' directory to their own distinct collection directory, which is again partitioned into the appropriate year and month. The post processing script then checks to

@@ Line 60: / Line 60: @@
 Copy the restart (initial condition) and ''cap_restart'' (t=t0) files into EXPDIR.   Keep the "originals" handy since if the model crashes early in the run it might have renamed them.  The model expects restarts to end in "rst" but produces them with the date at time appended to the filename, so you may have to rename them.   The ''cap_restart'' file is simply one line of text with the format "YYYYMMDD HHMMSS".  The boundary conditions/forcings are provided by symbolic links created by the run script.
-The script you submit, ''gcm_run.j'', is in HOMEDIR.  It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days between saving restarts, called segments) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  END_DATE can be changed to your end date, or just left as is.  Commenting out the ``qsub gcm_run.j'' at the end of the script will stop it, too.  Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.
+The script you submit, ''gcm_run.j'', is in HOMEDIR.  It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days between saving restarts, called segments) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  END_DATE can be changed to your end date, or just left as is.  Commenting out the ''qsub gcm_run.j'' at the end of the script will stop it, too.  Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.
-Submit the job with ``qsub gcm_run.j''.  You can keep track of it with qstat or ``qstat | grep USERNAME'', or stdout with ``tail -f /discovery/pbs_spool/JOBID.OU'', JOBID being returned by qsub and displayed with qstat.  Jobs can be killed with ``qdel JOBID''.  The stdout and stderr will be delivered as files to HOMEDIR at the end of a job.
+Submit the job with ''qsub gcm_run.j''.  You can keep track of it with qstat or ''qstat | grep USERNAME'', or stdout with ''tail -f /discovery/pbs_spool/JOBID.OU'', JOBID being returned by qsub and displayed with qstat.  Jobs can be killed with ''qdel JOBID''.  The stdout and stderr will be delivered as files to HOMEDIR at the end of a job.
 During a normal run, the ''gcm_run.j'' script will run the model for the segment length (current default is 8 days).  The model creates output files (with an ''nc4'' extension), also called collections (of output variables), in the ''EXPDIR/scratch'' directory.  After each segment, the script moves the output to the ''EXPDIR/holding'' and spawns a post-processing batch job which partitions and moves the output files  within the ''holding'' directory to their own distinct collection directory, which is again partitioned into the appropriate year and month.  The  post processing script then checks to