Running MARSSIM

[mdpiper]

@alimaye writes:

Hi Mark, I'm writing with a question about running a model through CSDMS. I came across some of the helpful tutorials you authored on the website. I'd like to run the model MARSSIM, along the lines described in this tutorial: https://csdms.colorado.edu/wiki/CMT_Tutorial_Marssim In the last few weeks Lynn McCready and colleagues have set me up with CU login credentials and HPC account on blanca. I'm writing to check which interface I should use to run MARSSIM (i.e., CMT vs. WMT). I successfully logged into WMT but did not see a way to select the MARSSIM model. With CMT, the updated version of the GUI showed beach as the only login option, and the login failed (despite a VPN connection to colorado.edu). Thanks for your help. I'm excited to get started with these great modeling tools! Ajay

[mdpiper]

I spoke with @alimaye on the phone & explained that CMT no longer exists, and that there is no MARSSIM component in WMT. I'll try to build MARSSIM on Blanca, which should meet his needs.

[mdpiper]

We also need to remove obsolete pages like https://csdms.colorado.edu/wiki/CMT_Tutorial_Marssim from the CSDMS wiki. This is #2.

[mdpiper]

@alimaye I installed MARSSIM on blanca in /pl/active/csdms (the CSDMS Petalibrary). Once on a blanca compute node, you'll need to add this path to your PATH variable to run it:

PATH=/pl/active/csdms/local/bin:$PATH

Also load the gcc module to supply the Fortran shared library:

module load gcc

To check that MARSSIM works, I downloaded the Callisto example from the MARSSIM model page to /pl/active/csdms/scratch/Callisto. I found that had to change two files from the example (just uppercasing the names) to get the model to run:

cp marssim.prm MARSSIM.PRM
cp inelev.dat INELEV.DAT

In the Callisto directory, I ran MARSSIM with

run_marssim >& log &

All you really need is run_marssim, but it prints to the console on each update, so I redirected that info to log.

Good luck! Let me know how it goes.

[alimaye]

@mdpiper I got to the point of running the simulation with run_marssim, however the command was not found. Perhaps I do not have the proper permissions? I added the path per the instructions, but cannot see run_marssim

[mdpiper]

@alimaye Could you please copy/paste the command and error message?

[alimaye]

@mdpiper
[ajli7272@bnode0316 inputFiles]$ echo $PATH /pl/active/csdms/local/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin [ajli7272@bnode0316 inputFiles]$ run_marssim bash: run_marssim: command not found

[mdpiper]

@alimaye I see that the permissions on /pl/active/csdms are restricted:

[mapi8461@bnode0316 csdms]$ ls -ld /pl/active/csdms/
drwxrws--- 10 huttone huttonegrp 9 Mar 27 12:19 /pl/active/csdms/

I think this may be the problem. Can you cd to this directory? (My hunch is no.)

@mcflugen Could you please chmod +rx this directory? I don't have permissions to do so.

[alimaye]

Correct, I cannot cd to /pl/active/csdms/

[mcflugen]

@mdpiper I've changed the permissions on /pl/active/csdms.

$ ls -ld /pl/active/csdms/
drwxrwsr-x. 10 huttone huttonegrp 9 Mar 27 12:19 /pl/active/csdms/

Does that do the trick?

[alimaye]

Thanks @mcflugen @mdpiper now looking for the fortran library:

$ /pl/active/csdms/local/bin/run_marssim /pl/active/csdms/local/bin/run_marssim: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

[mdpiper]

@alimaye You'll have to load a compiler module that supplies the Fortran library. I built MARSSIM with gcc, but I think intel would also work.

$ module load gcc

I'll update the instructions upthread for posterity, as well.

[alimaye]

Got it - up and running!