GEOS-5

Ganymed 3.0 Quick Start: Difference between revisions

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This page describes the minimum steps required to build and run GEOS-5 Ganymed 1.0 on NCCS discover and NAS pleiades.  '''You should successfully complete the steps in these instructions before doing anything more complicated.  Also, it is helpful to read this page in its entirety before starting.'''   
This page describes the minimum steps required to build and run GEOS-5 Ganymed 3.0 on NCCS discover and NAS pleiades.  '''You should successfully complete the steps in these instructions before doing anything more complicated.  Also, it is helpful to read this page in its entirety before starting.'''   


'''Back to [[GEOS-5 Documentation for Ganymed 1.0]]'''
'''Back to [[GEOS-5 Documentation for Ganymed 3.0]]'''


== How to Obtain GEOS-5 and Compile Source Code ==
== How to Obtain GEOS-5 and Compile Source Code ==
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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 Ganymed-1_0_p7 -d Ganymed-1_0_p7 Ganymed
  cvs co -r Ganymed-3_0_p1 -d Ganymed-3_0_p1 Ganymed




This should check out the latest stable version of the model from the repository and create a directory called <code>Ganymed-1_0</code>.
This should check out the latest stable version of the model from the repository and create a directory called <code>Ganymed-3_0_p1</code>.


=== Compiling the Model ===
=== Compiling the Model ===


<code>cd</code> into <code>Ganymed-1_0/src</code> and <code>source</code> the file called <code>g5_modules</code>:
<code>cd</code> into <code>Ganymed-3_0_p1/src</code> and <code>source</code> the file called <code>g5_modules</code>:


  source g5_modules
  source g5_modules
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  Currently Loaded Modulefiles:
  Currently Loaded Modulefiles:
   1) comp/intel-11.0.083                     3) lib/mkl-10.0.3.020
   1) comp/intel-11.0.083                       3) lib/mkl-10.0.3.020
   2) mpi/impi-3.2.2.006                      4) other/SIVO-PyD/spd_1.6.0_gcc-4.3.4-sp1
   2) other/mpi/mvapich2-1.8.1/intel-11.0.083  4) other/SIVO-PyD/spd_1.6.0_gcc-4.3.4-sp1
 


If this all worked, then type:
If this all worked, then type:
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  gmake install
  gmake install


This will build the model.  It will take about 40 minutes.  If this works, it should create a directory under <code>Ganymed-1_0</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>Ganymed-3_0_p1</code> called <code>Linux/bin</code>.  In here you should find the executable: <code>GEOSgcm.x</code> .


== Setting up a Run ==
== Setting up a Run ==
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Then, log into  '''dirac''' and cut and paste the contents of the <code>id_rsa.pub</code> and <code>id_dsa.pub</code> files on '''discover''' into the  <code>~/.ssh/authorized_keys</code> file on  '''dirac'''.  Problems with <code>ssh</code> should be referred to NCCS support.
Then, log into  '''dirac''' and cut and paste the contents of the <code>id_rsa.pub</code> and <code>id_dsa.pub</code> files on '''discover''' into the  <code>~/.ssh/authorized_keys</code> file on  '''dirac'''.  Problems with <code>ssh</code> should be referred to NCCS support.


To set the model up to run, cd to <code>Ganymed-1_0/src/Applications/GEOSgcm_App</code> and run:
To set the model up to run, cd to <code>Ganymed-3_0_p1/src/Applications/GEOSgcm_App</code> and run:


  ./gcm_setup
  ./gcm_setup
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Spaces are ok here.  It will also ask you for the atmospheric model resolution, expecting the code for one of the displayed resolutions.  
Spaces are ok here.  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:
Enter the Atmospheric Horizontal Resolution code:
-----------------------------------------------------------
              b --  2  deg   
      Lat/Lon                    Cubed-Sphere
              c --  1  deg   
-----------------------------------------------------------
              d -- 1/2 deg   
    b --  2  deg               c48  -- 2  deg
              e -- 1/4 deg   
    c --  1  deg               c90 --  1  deg
              o --  other 
    d -- 1/2 deg               c180 -- 1/2 deg (56-km)
 
    e -- 1/4 deg (35-km)        c360 -- 1/4  deg (28-km)  
For your first time out you will probably want to enter <code>b</code> (corresponding to ~2 degree resolution).  Then it asks you which dynamical core to use:
                                c720 -- 1/8 deg (14-km)
 
                                c1440 - 1/16 deg ( 7-km)
Enter the Dynamical Core to use:  FV (Lat-Lon), FV3 (Cubed-Sphere)
 
For your first time out you will probably want to enter <code>c48</code> (corresponding to ~2 degree resolution with the cubed sphere).  On the next seven questions, hit enter to accept the default:
Enter <code>FV</code> for lat-lon.  On the next seven questions, hit enter to accept the default:
   
   
  Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE)
  Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE)
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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''.  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 sometimes provided with a set of restarts, but if not you can create it: 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.  If you need an arbitrary set of restarts, you can copy them from <code>/archive/u/aeichman/restarts/Ganymed-1_0/</code>, where they are indexed by resolution and date.  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.
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/Ganymed-3_0/C48/19800101/</code>, containing 2-degree cubed sphere restarts from Jan. 1, 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.


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.  An alternative way to stop the run is by commenting out the line <code> if ( $capdate < $enddate ) qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted, or rename the script file, or kill the job (described below).  
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.  An alternative way to stop the run is by commenting out the line <code> if ( $capdate < $enddate ) qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted, or rename the script file, or kill the job (described below).  
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The contents of the output files (including which variables get saved) may be configured in the  <code>''HOMEDIR''/HISTORY.rc</code> -- a good description of this file may be found at http://modelingguru.nasa.gov/clearspace/docs/DOC-1190 .
The contents of the output files (including which variables get saved) may be configured in the  <code>''HOMEDIR''/HISTORY.rc</code> -- a good description of this file may be found at http://modelingguru.nasa.gov/clearspace/docs/DOC-1190 .


'''Back to [[GEOS-5 Documentation for Ganymed 1.0]]'''
'''Back to [[GEOS-5 Documentation for Ganymed 3.0]]'''
Retrieved from "https://geos5.org/wiki/index.php?title=Ganymed_3.0_Quick_Start"