Heracles 4.0 Quick Start: Difference between revisions
Created page with "This page describes the minimum steps required to build and run GEOS-5 Heracles 4.0 on NCCS discover and NAS pleiades. '''You should successfully complete the steps in these..." |
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where ''USERID'' is, of course, your repository username, which should be the same as your NASA and NCCS username. Then, issue the command: | where ''USERID'' is, of course, your repository username, which should be the same as your NASA and NCCS username. Then, issue the command: | ||
cvs co -r | cvs co -r Heracles-4_0 GEOSagcm | ||
This should check out the latest stable version of the model from the repository and create a directory called <code>GEOSagcm</code>. | This should check out the latest stable version of the model from the repository and create a directory called <code>GEOSagcm</code>. | ||
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First, you need to set <code>ESMADIR</code>. For example, if your <code>src/</code> directory is: | First, you need to set <code>ESMADIR</code>. For example, if your <code>src/</code> directory is: | ||
/discover/nobackup/mathomp4/Models/ | /discover/nobackup/mathomp4/Models/Heracles-4_0/GEOSagcm/src | ||
then you should set: | then you should set: | ||
setenv ESMADIR /discover/nobackup/mathomp4/Models/ | setenv ESMADIR /discover/nobackup/mathomp4/Models/Heracles-4_0/GEOSagcm | ||
Next, <code>cd</code> into <code>GEOSagcm/src</code> and <code>source</code> the file called <code>g5_modules</code>: | Next, <code>cd</code> into <code>GEOSagcm/src</code> and <code>source</code> the file called <code>g5_modules</code>: | ||
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Currently Loaded Modulefiles: | Currently Loaded Modulefiles: | ||
1) comp/intel-15.0.2.164 | |||
2) mpi/impi-5.0.3.048 | |||
3) lib/mkl-15.0.2.164 | |||
4) other/comp/gcc-4.6.3-sp1 | |||
5) other/SIVO-PyD/spd_1.20.0_gcc-4.6.3-sp1_mkl-15.0.0.090 | |||
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Enter a 1-line Experiment Description: | Enter a 1-line Experiment Description: | ||
Spaces are ok here. | Spaces are ok here. It will then ask for the source code version tag to associate with the model -- you should hit enter for the default: | ||
Enter the Atmospheric Horizontal Resolution code: | |||
Enter an Experiment Source Tag for History (Default: Heracles-4_0): | |||
Hit enter for the default to the next question: | |||
Do you wish to CLONE an old experiment? (Default: NO or FALSE) | |||
It will also ask you for the atmospheric model resolution, expecting the code for one of the displayed resolutions. | |||
Enter the Atmospheric Horizontal Resolution code: | |||
----------------------------------------------------------- | ----------------------------------------------------------- | ||
Lat/Lon Cubed-Sphere | Lat/Lon Cubed-Sphere | ||
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Hit ENTER to use Default Location: | Hit ENTER to use Default Location: | ||
---------------------------------- | ---------------------------------- | ||
Default: /discover/nobackup/''USER''/ | Default: /discover/nobackup/''USER''/GEOSagcm | ||
After these it will ask you for a group ID -- the default for this writer is g0620 (GMAO modeling group). Enter whatever is appropriate, as necessary. | After these it will ask you for a group ID -- the default for this writer is g0620 (GMAO modeling group). Enter whatever is appropriate, as necessary. | ||
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The script | The script will produce some messages and create an experiment directory (''EXPDIR'') in your space as <code>/discover/nobackup/''USERID''/''EXPID''</code>, which contains the files and sub-directories: | ||
*<code>AGCM.rc</code> -- resource file with specifications of boundary conditions, initial conditions, parameters, etc. | *<code>AGCM.rc</code> -- resource file with specifications of boundary conditions, initial conditions, parameters, etc. | ||
*<code>archive/</code> -- contains job script for archiving output | *<code>archive/</code> -- contains job script for archiving output | ||
*<code>CAP.rc</code> -- resource file with run job parameters | *<code>CAP.rc</code> -- resource file with run job parameters | ||
*<code>convert</code> -- contains job script that converts restarts (initial condition files) from older model versions | |||
*<code>ExtData.rc</code> -- sample resource file for external data, not used | *<code>ExtData.rc</code> -- sample resource file for external data, not used | ||
*<code>forecasts/</code> -- contains scripts used for data assimilation mode | *<code>forecasts/</code> -- contains scripts used for data assimilation mode | ||
*<code>fvcore_layout.rc</code> -- | |||
*<code>gcm_run.j</code> -- run script | *<code>gcm_run.j</code> -- run script | ||
*<code>GEOSgcm.x</code> -- model executable | *<code>GEOSgcm.x</code> -- model executable | ||
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*<code>RC/</code> -- contains resource files for various components of the model | *<code>RC/</code> -- contains resource files for various components of the model | ||
*<code>regress/</code> -- contains scripts for doing regression testing of model | *<code>regress/</code> -- contains scripts for doing regression testing of model | ||
*<code>src</code> -- directory with a tarball of the model version's source code | |||
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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. | 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''. You can get an arbitrary set of restarts by copying the contents of the directory <code>/archive/u/aeichman/restarts/ | Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. You can get an arbitrary set of restarts by copying the contents of the directory <code>/archive/u/aeichman/restarts/Heracles-4_0/c48/19800309</code>, containing 2-degree cubed sphere restarts from March 9, 1980, and their corresponding <code>cap_restart</code>. If you are unfamiliar with the way that the <code>/archive</code> filesystem works, keep in mind that a <code>cp</code> from there might appear to stall while the tape is loaded -- see the NCCS documentation for details. | ||
Submit the job with <code> | The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''. It should be ready to go as is. The parameter END_DATE in <code>CAP.rc</code> can be set to the date you want the run to stop. Submit the job with <code>sbatch gcm_run.j</code>. You can keep track of it with <code>qstat</code> or <code>qstat | grep ''USERID''</code>, or follow stdout with <code>tail -f ''EXPDIR''/slurm-''JOBID''.out</code>, ''JOBID'' being returned by <code>sbatch</code> and displayed with <code>qstat</code>. Jobs can be killed with <code>qdel ''JOBID''</code>. | ||
== Output and Plots == | == Output and Plots == | ||
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'''Back to [[GEOS-5 Documentation for Heracles 4.0]]''' | '''Back to [[GEOS-5 Documentation for Heracles 4.0]]''' | ||
Contact | Contact Matt Thompson at GMAO with questions and comments | ||