GEOS-5 Checkout and Build Instructions (Fortuna): Difference between revisions
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These instructions presume checking out the PIESA group tag: '''AeroChem-Fortuna- | These instructions presume checking out the PIESA group tag: '''AeroChem-Fortuna-2_5-b23'''. | ||
== How to Check Out and Build the Code == | == How to Check Out and Build the Code == | ||
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Here, $CVSROOT specifies the CVS repository we'll be getting the code from, DIRECTORY is the name of the directory you would like to create to hold the code, MODULENAME is the particular module (set of code) we'll be checking out, and TAGNAME is a particular version of that module. Let's fill in the blanks: | Here, $CVSROOT specifies the CVS repository we'll be getting the code from, DIRECTORY is the name of the directory you would like to create to hold the code, MODULENAME is the particular module (set of code) we'll be checking out, and TAGNAME is a particular version of that module. Let's fill in the blanks: | ||
% cvs -d :ext:pcolarco@cvsacldirect:/cvsroot/esma co -d GEOSagcm -r AeroChem-Fortuna- | % cvs -d :ext:pcolarco@cvsacldirect:/cvsroot/esma co -d GEOSagcm -r AeroChem-Fortuna-2_5-b23 Fortuna | ||
So our module is ''Fortuna'' and the tag is ''AeroChem-Fortuna- | So our module is ''Fortuna'' and the tag is ''AeroChem-Fortuna-2_5-b23''. The code will check-out to a newly created directory call ''GEOSagcm''. Note that I substituted the shortcut ''co'' for ''checkout'' in the above command. | ||
The above command is generally valid. You ought to be able to execute it and checkout some code. If you don't have your ''ssh keys'' setup on '''cvsacl''' then you should be prompted for your '''cvsacl''' password. The assumption here is that your username on '''cvsacl''' is the same as on the machine you are checking the code out on. | The above command is generally valid. You ought to be able to execute it and checkout some code. If you don't have your ''ssh keys'' setup on '''cvsacl''' then you should be prompted for your '''cvsacl''' password. The assumption here is that your username on '''cvsacl''' is the same as on the machine you are checking the code out on. | ||
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If you set that up, you should be able now to type in: | If you set that up, you should be able now to type in: | ||
% cvs co -d GEOSagcm -r AeroChem-Fortuna- | % cvs co -d GEOSagcm -r AeroChem-Fortuna-2_5-b23 Fortuna | ||
and the code will check out. | and the code will check out. | ||
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The code builds faster in this instance, but be warned that without optimization any generated code will run very slowly. | The code builds faster in this instance, but be warned that without optimization any generated code will run very slowly. | ||
''NOTE: I don't find the parallel build to actually work at this point, so if the following fails I suggest just doing a gmake install --ed.'' | |||
A better way is to do a parallel build. To do this, start an interactive queue (on '''discover'''): | A better way is to do a parallel build. To do this, start an interactive queue (on '''discover'''): | ||
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'''CAP.rc''' | '''CAP.rc''' | ||
This file controls the timing of the model run. For example, you specify the END_DATE, the number of days to run per segment (JOB_SGMT) and the number of segments (NUM_SGMT). If you modify nothing else, the model would run until it reached END_DATE or had run for NUM_SGMT segments. Note that you might think that BEG_DATE specifies a beginning date for the model to run. It is set by default to BEG_DATE: 18910301 000000, which is probably before the period you want to simulate. The actual model start time is specified later when we set up your | This file controls the timing of the model run. For example, you specify the END_DATE, the number of days to run per segment (JOB_SGMT) and the number of segments (NUM_SGMT). If you modify nothing else, the model would run until it reached END_DATE or had run for NUM_SGMT segments. Note that you might think that BEG_DATE specifies a beginning date for the model to run. It is set by default to BEG_DATE: 18910301 000000, which is probably before the period you want to simulate. The actual model start time is specified later when we set up your EXP directory. | ||
'''gcm_run.j''' | '''gcm_run.j''' | ||
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This tag has successfully checked out, built, run, and archived results on NAS machine Pleiades. No modifications to scripts are needed, as the appropriate choices for that machine are handled in gcm_setup. | This tag has successfully checked out, built, run, and archived results on NAS machine Pleiades. No modifications to scripts are needed, as the appropriate choices for that machine are handled in gcm_setup. | ||
=== Setup the | === Setup the EXP directory === | ||
Now go to your | Now go to your EXP directory. | ||
You want to specify the model start time at this point. Create a file called ''cap_restart". The contents of the file should read: | You want to specify the model start time at this point. Create a file called ''cap_restart". The contents of the file should read: | ||
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You might want to edit the resource files in the RC sub-directory (e.g., '''GEOS_ChemGridComp.rc''' to turn on '''GOCART''' and '''Chem_Registry.rc''' to turn components on/off). | You might want to edit the resource files in the RC sub-directory (e.g., '''GEOS_ChemGridComp.rc''' to turn on '''GOCART''' and '''Chem_Registry.rc''' to turn components on/off). | ||
You also need some restarts to run the model. For Fortuna at "b" resolution you can copy a set (valid nominally at 20071231) from /discover/nobackup/ | You also need some restarts to run the model. For Fortuna at "b" resolution you can copy a set (valid nominally at 20071231) from /discover/nobackup/projects/gmao/iesa/aerosol/Data/restarts/Fortuna-2_5/b72/20071231/ (on pleiades: /nobackupp10/pcolarco/restart0/piesa/Fortuna-2_5/). You can just copy all the files *.rst into your experiment directory, but what I like to is make a "restart0" directory in my EXP directory and copy the files there, and then copy back up to the EXP directory. ***Note: For tags more recent than AeroChem-Fortuna-2_5-b7 bootstrap moist_import_rst by erasing this file from the restarts.*** | ||
=== Run the Simulation === | === Run the Simulation === | ||
At this point we're ready to take a crack at running the model. Go into your experiment | At this point we're ready to take a crack at running the model. Go into your experiment HOME directory. You can start the model job by issuing: | ||
% qsub gcm_run.j | % qsub gcm_run.j | ||
And check the progress by issuing: | And check the progress by issuing: | ||
% qstat | grep YOUR_USERNAME | % qstat | grep YOUR_USERNAME | ||