GEOS-5 Quick Start: Difference between revisions
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This section describes the minimum steps required to build and run GEOS-5 on discover. You should successfully complete the steps in these instructions before doing anything more complicated. | This section describes the minimum steps required to build and run GEOS-5 on discover. You should successfully complete the steps in these instructions before doing anything more complicated. | ||
== Checking Out and Compiling == | == Checking Out and Compiling GEOS-5 == | ||
The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on '''sourcemotel'''. The commands below assume that your shell is ''csh''. Since the scripts to build and run GEOS-5 tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell. If you prefer a different shell, it is easiest just to open a ''csh'' process to build the model and your experiment. | The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on '''sourcemotel'''. The commands below assume that your shell is ''csh''. Since the scripts to build and run GEOS-5 tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell. If you prefer a different shell, it is easiest just to open a ''csh'' process to build the model and your experiment. | ||
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This will build the model. It will take about 40 minutes. If this works, it should create a directory under ''GEOSagcm'' called ''Linux/bin''. In here you should find the executable: ''GEOSgcm.x'' . | This will build the model. It will take about 40 minutes. If this works, it should create a directory under ''GEOSagcm'' called ''Linux/bin''. In here you should find the executable: ''GEOSgcm.x'' . | ||
== Running GEOS-5 == | |||
Setting up to run: | Setting up to run: | ||
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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. | ||
== Output and Plots == | |||
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 | 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 | ||