Installing Mars mesoscale model on spirit - Revision history

Emillour at 15:42, 28 May 2025

2025-05-28T15:42:38Z

2025-02-10T22:11:44Z

2024-05-15T13:37:10Z

‎Troubleshooting (in case this happens to you)

2024-04-08T05:52:53Z

2024-02-01T16:33:06Z

‎Run the full workflow GCM + initialization + mesoscale model

2024-01-30T16:25:25Z

‎Run the full workflow GCM + initialization + mesoscale model

2024-01-30T16:23:05Z

2024-01-30T16:03:46Z

2024-01-30T16:00:37Z

2024-01-30T15:54:56Z

@@ Line 152: / Line 152: @@
 squeue -u $USER
 </syntaxhighlight>
 === Extra technical stuff ===

@@ Line 112: / Line 112: @@
 <syntaxhighlight lang="Bash">
 ./mini_startbase.sh
 </syntaxhighlight>

@@ Line 97: / Line 97: @@
 === Troubleshooting (in case this happens to you) ===
-''Weird!'' fcm is not working interactively (this seems to happen if "." is in your PATH before "FCM_V1.2/bin") It only works if being declared in the environment file by adding
+If GCM compilation fails with error message "Can't locate Fcm/Config.pm in @INC (you may need to install the Fcm::Config module)", this is because "." is in your PATH before "FCM_V1.2/bin".
 <syntaxhighlight lang="Bash">
 declare -x PATH=/homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/code/LMDZ.COMMON/FCM_V1.2/bin/:$PATH
 </syntaxhighlight>
-then recompile the GCM compiling (which had failed previously) by doing
+or by removing the symbolic link to "fcm" in "/homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/code/LMDZ.COMMON/".
 <syntaxhighlight lang="Bash">
 cd /homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/
@@ Line 110: / Line 113: @@
 ./mini_startbase.sh
 </syntaxhighlight>
 === Extra technical stuff ===

@@ Line 97: / Line 97: @@
 === Troubleshooting (in case this happens to you) ===
-''Weird!'' fcm is not working interactively. It only works if being declared in the environment file by adding
+''Weird!'' fcm is not working interactively (this seems to happen if "." is in your PATH before "FCM_V1.2/bin") It only works if being declared in the environment file by adding
 <syntaxhighlight lang="Bash">
 declare -x PATH=/homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/code/LMDZ.COMMON/FCM_V1.2/bin/:$PATH

@@ Line 131: / Line 131: @@
 == Run the full workflow GCM + initialization + mesoscale model ==
-Have a look in the script named launch just for info or to change the number of processors or the step at which you start. Send the launch job to the cluster by typing (note that you can change the number of core to run with in the header of the script, e.g. ''#SBATCH --ntasks=24'' to use 24 cores)
+Have a look in the script named launch just for info or to change the number of processors or the step at which you start. Send the launch job to the cluster by typing (note that you can change the number of core to run with in the header of the script, e.g. ''#SBATCH --ntasks=24'' to use 24 cores, but this doesn't work for now...)
 <syntaxhighlight lang="Bash">
 sbatch launch
 </syntaxhighlight>
 You can check the status of the run by typing
 <syntaxhighlight lang="Bash">

@@ Line 36: / Line 36: @@
 </syntaxhighlight>
 at the beginning of the meso_install.sh script.
 === Extra technical details===

@@ Line 31: / Line 31: @@
 === Option 2 ===
-*If you prefer to not modify your .bashrc file, you should instead put all the lines in a "mesoscale.env" file and add a
+If you prefer to not modify your .bashrc file, you should instead put all the lines in a "mesoscale.env" file and add a
 <syntaxhighlight lang="bash">
 source mesoscale.env
@@ Line 88: / Line 88: @@
 </syntaxhighlight>
 ''Weird!'' fcm is not working interactively. It only works if being declared in the environment file by adding
 <syntaxhighlight lang="Bash">

@@ Line 1: / Line 1: @@
 == Set up environment ==
+=== Option 1 ===
 Add this in your ~/.bashrc then source the file
@@ Line 30: / Line 30: @@
 In the end, source the .bashrc file!
-=== Extra technical details===
+=== Option 2 ===
-* Note that you can decide to not modify your .bashrc file but instead put all the lines in a "mesoscale.env file and add a
+*If you prefer to not modify your .bashrc file, you should instead put all the lines in a "mesoscale.env" file and add a
 <syntaxhighlight lang="bash">
 source mesoscale.env
 </syntaxhighlight>
 at the beginning of the meso_install.sh script.
 * WRF needs a NETCDF environment variable where everything is in the same dir (Fortran and C stuff). If this is not available one needs to create a uniquer dire with links to all the C and Fortran stuff. NCDFLIB and NCDFINC are for the physics.
 * WHERE_MPI env variable is used by some scripts to make sure we use the right one

@@ Line 76: / Line 76: @@
 ./meso_install.sh -n DESCRIBE_YOUR_RESEARCH_PROJECT
 </syntaxhighlight>
 ''Special case'': In case you do not have a gitlab account, ask for an archive (tar.gz) of the code.