Ganymed 1.0 Quick Start: Difference between revisions
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This will build the model. It will take about 40 minutes. If this works, it should create a directory under <code>GEOSagcm</code> called <code>Linux/bin</code>. In here you should find the executable: <code>GEOSgcm.x</code> . | This will build the model. It will take about 40 minutes. If this works, it should create a directory under <code>GEOSagcm</code> called <code>Linux/bin</code>. In here you should find the executable: <code>GEOSgcm.x</code> . | ||
== | == Setting up a Run == | ||
First of all, to run jobs on the cluster you will need to set up passwordless <code>ssh</code> (which operates within the cluster). To do so, run the following from your '''discover''' home directory: | First of all, to run jobs on the cluster you will need to set up passwordless <code>ssh</code> (which operates within the cluster). To do so, run the following from your '''discover''' home directory: | ||
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The script produces an experiment directory (''EXPDIR'') in your space as <code>/discover/nobackup/''USERID''/''EXPID''</code>, which contains, among other things, the sub-directories: | The script produces an experiment directory (''EXPDIR'') in your space as <code>/discover/nobackup/''USERID''/''EXPID''</code>, which contains, among other things, the sub-directories: | ||
*<code>post</code> (containing the | *<code>post</code> (containing the script and .rc file for post processing model output) | ||
*<code>archive</code> (containing an incomplete archiving job script) | *<code>archive</code> (containing an incomplete archiving job script) | ||
*<code>plot</code> (containing | *<code>plot</code> (containing plotting job script template and .rc file) | ||
The post-processing script will complete (i.e., add necessary commands to) the archiving and plotting scripts as it runs. The setup script that you ran also creates an experiment home directory (''HOMEDIR'') as <code>~''USERID''/geos5/''EXPID''</code> containing the run scripts and GEOS resource (<code>.rc</code>) files. | The post-processing script will complete (i.e., add necessary commands to) the archiving and plotting scripts as it runs. The setup script that you ran also creates an experiment home directory (''HOMEDIR'') as <code>~''USERID''/geos5/''EXPID''</code> containing the run scripts and GEOS resource (<code>.rc</code>) files. | ||
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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. | ||
== Running GEOS-5 == | |||
Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them. The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them back to ending in "rst". The <code>cap_restart</code> file is often provided with a set of restarts, but if not you can create it: is simply one line of text with the date of the restart files in the format ''<code>YYYYMMDD HHMMSS</code>'' (with a space). The boundary conditions/forcings are provided by symbolic links created by the run script. | Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them. The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them back to ending in "rst". The <code>cap_restart</code> file is often provided with a set of restarts, but if not you can create it: is simply one line of text with the date of the restart files in the format ''<code>YYYYMMDD HHMMSS</code>'' (with a space). The boundary conditions/forcings are provided by symbolic links created by the run script. | ||