|
|
| Line 210: |
Line 210: |
|
| |
|
| You also need some restarts to run the model. For Fortuna at "b" resolution you can copy a set (valid nominally at 20071001) from /discover/nobackup/pcolarco/restart0/fortuna/b72. You can just copy these files into your experiment directory, but what I like to is make a "restart0" directory in my EXPDIR and copy the files there, and then copy back up to the EXPDIR. | | You also need some restarts to run the model. For Fortuna at "b" resolution you can copy a set (valid nominally at 20071001) from /discover/nobackup/pcolarco/restart0/fortuna/b72. You can just copy these files into your experiment directory, but what I like to is make a "restart0" directory in my EXPDIR and copy the files there, and then copy back up to the EXPDIR. |
|
| |
| === Populate the Experiment Directory ===
| |
| At the beginning of the experiment, the experiment directory will contain a few things:
| |
|
| |
| # Resource Files
| |
| # Restart Files
| |
| # The GEOSgcm.x executable (the model itself)
| |
|
| |
| I've provided a sample experiment directory (/discover/nobackup/colarco/dragnet). There are a number of files that end in ".rc". These are the ''resource files''. Copy these to your experiment directory.
| |
|
| |
| I've prepared a set of restarts based on a previous GEOS-5 run that will serve for this example. You can find these files in /discover/nobackup/colarco/restart0/b72/. Copy all the "*rst" files to your experiment directory, e.g.,
| |
| % cp /discover/nobackup/colarco/restart0/b72/*rst /discover/nobackup/colarco/dragnet
| |
|
| |
| Finally, copy your GEOSgcm.x executable from wherever you built the model to your experiment directory, e.g.,
| |
| % cp /discover/nobackup/colarco/GEOSagcm/Linux/bin/GEOSgcm.x /discover/nobackup/colarco/dragnet
| |
|
| |
| There's one other file you need: in my experiment directory find a file called ''cap_restart''. Copy this over to your experiment directory. Take a look at this file. It has one line with two numbers:
| |
| 20021001 210000
| |
| These are the YYYYMMDD and HHMMSS timestamp I am using to start the model run. Note that I choose these dates to correspond to the date at which the restarts I gave you are valid.
| |
|
| |
| I haven't told you anything much about the resource files. Suffice to say for now that this group I am providing here will differ from the resource files in your source code collection. I've modified these to run aerosols and use aerosol source files that will work for the time period we will simulate.
| |
|
| |
| === Populate the Home Directory ===
| |
| Now go into your home directory and copy the contents of my sample into yours:
| |
| % cd /home/USERNAME/geos5/YOUR_EXPID
| |
| % cp /home/colarco/geos5/dragnet/* .
| |
|
| |
| There are several files here:
| |
| AGCM.tmpl
| |
| CAP.tmpl
| |
| HISTORY.tmpl
| |
| gcm_run.j
| |
| gcm_post.j
| |
| gcm_post.script
| |
| gcm_regress.j
| |
|
| |
| For the moment, we don't need to do anything to AGCM.tmpl or CAP.tmpl. They are filled in with information from the run script and written as AGCM.rc and CAP.rc in your experiment directory. (As a rule, if you have AGCM.rc and CAP.rc and HISTORY.rc in your experiment directory, you might want to remove them before starting an experiment so that you know you are using the *.tmpl files from your home directory.)
| |
|
| |
| We have to make several edits to the remaining files. In particular, we need to change the group ID code used to charge your jobs to PBS, we need to change the experiment ID to match the ID you've chosen for your experiment, and we need to modify various path variables to point to your user ID (not mine!). You can accomplish these changes by using ''grep'' on the files. For example, look for instances of my group ID ''r0605'':
| |
| % grep r0605 *
| |
| on these files find the following:
| |
| gcm_post.j:#PBS -W group_list=r0605
| |
| gcm_regress.j:#PBS -W group_list=r0605
| |
| gcm_run.j:#PBS -W group_list=r0605
| |
| Unless you have permission to charge to r0605 you need to change these numbers. Use your favorite editor to do this. Recall, to find your group ID, use ''getsponsor''.
| |
|
| |
| Here's the result of grepping on my username:
| |
| % grep colarco *
| |
| AGCM.tmpl:#REPLAY_FILE: /discover/nobackup/colarco/replay_b/winds/b5_merrasc_jan92.ana.eta.%y4%m2%d2_%h2z.hdf
| |
| gcm_post.j:setenv GEOSUTIL /home/colarco/GEOS_Util
| |
| gcm_post.j:setenv SOURCE /discover/nobackup/colarco/$EXPID
| |
| gcm_post.j:setenv ARCHIVE /archive/u/colarco/GEOS5.0/$EXPID
| |
| gcm_post.j:setenv HOMDIR /home/colarco/geos5/$EXPID
| |
| gcm_regress.j:setenv GEOSUTIL /home/colarco/GEOS_Util
| |
| gcm_regress.j:setenv EXPDIR /discover/nobackup/colarco/$EXPID
| |
| gcm_regress.j:setenv HOMDIR /home/colarco/geos5/$EXPID
| |
| gcm_run.j:setenv GEOSUTIL /home/colarco/GEOS_Util
| |
| gcm_run.j:setenv EXPDIR /discover/nobackup/colarco/$EXPID
| |
| gcm_run.j:setenv HOMDIR /home/colarco/geos5/$EXPID
| |
| gcm_run.j:/bin/ln -s /discover/nobackup/colarco/SST/dataoceanfile_MERRA_sst_1971-current.${OGCM_IM}x${OGCM_JM}.LE sst.data
| |
| gcm_run.j:/bin/ln -s /discover/nobackup/colarco/SST/dataoceanfile_MERRA_ice_temperature_1971-current.${OGCM_IM}x${OGCM_JM}.LE sstsi.data
| |
| gcm_run.j:/bin/ln -s /discover/nobackup/colarco/SST/dataoceanfile_MERRA_fraci_1971-current.${OGCM_IM}x${OGCM_JM}.LE fraci.data
| |
| Ignore the entry in AGCM.tmpl for now, it's been commented out. Ignore also the last three entries (pertaining to the location of the SST files); for whatever reason there were incompatible SST files on '''discover''' and these were copied by hand over from '''palm'''. For now, we'll use these. All the other instances of username "colarco" should be modified.
| |
|
| |
| Finally, here's the results of grepping on my experiment ID:
| |
| % grep dragnet *
| |
| gcm_post.j:setenv EXPID dragnet
| |
| gcm_regress.j:#PBS -N dragnet
| |
| gcm_regress.j:setenv EXPID dragnet
| |
| gcm_run.j:#PBS -N dragnet
| |
| gcm_run.j:setenv EXPID dragnet
| |
| HISTORY.tmpl:EXPID: dragnet
| |
| Your should change all instances of '''dragnet''' here to reflect your user ID. Note that lines that look like ''#PBS -N dragnet'' are really just the name of the experiment that PBS queueing system reports. This does not have to replicate your experiment ID at all; it is merely a string that helps you identify your job running in PBS.
| |
|
| |
|
| |
|
| === Run the Simulation === | | === Run the Simulation === |
| At this point we're ready to take a crack at running the model. Go into your experiment home directory (e.g., /home/colarco/geos5/dragnet). You can start the model job by issuing: | | At this point we're ready to take a crack at running the model. Go into your experiment HOMEDIR. You can start the model job by issuing: |
| % qsub gcm_run.j | | % qsub gcm_run.j (or qsub gcm_run.1) |
| And check the progress by issuing: | | And check the progress by issuing: |
| % qstat | grep YOUR_USERNAME | | % qstat | grep YOUR_USERNAME |