1. General introduction
This wiki introduces the processes to run the Global Terrestrial Mercury Model (GTMM) coupled to the GEOS-Chem Hg simulation. Here I only introduce the content that is immediately related to set up a Hg/POPs simulation on the Harvard machine, as this is a work in progress.
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See other relevant wiki page for environment set-up scripts.
On odyssey, please always do work like this in an interactive session. To get an interactive session, enter command:
interactive 4 1 4000 240 test
The following might work with any compiler but has only been tested using the GEOS-Chem settings for the Intel comiler version 11, so do the following command:
load_if11
2 Obtain source code
2.1 Obtain
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GTMM/GEOS-Chem code
For users from the Harvard BGC group, a copy of the source code can be obtained from my home directory:
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Github link to follow when public version is complete.
2.2 Obtain GTMM data
Again, you can copy my version:
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This also contains a run directory for your pre-GEOS-Chem spin up.
3 Edit and compile GTMM code
3.1 Edit GTMM code
Edit the file YOUR_SOURCE_DIRECTORY/GTMM/defineConstants.F90 to point "filepath" and "outputpath" to the
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Note** you must also change "f_len" and "f_len_output" to match your defined paths (this silliness will be removed in the future).
3.2 Compile GTMM code
For now, GTMM must be compiled before GEOS-Chem to make its library available for the GEOS-Chem code. In the future, this will be built into the GEOS-Chem build sequence.
cd YOUR_SOURCE_DIRECTORY/GTMM
bash compile.sh
cp gtmm YOUR_GTMM_DIRECTORY/output/
3.3 Edit GEOS-Chem code
Until the GEOS-Chem build sequence is updated, edit the file YOUR_SOURCE_DIRECTORY/Makefile_header.mk
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GTMM_NEEDED :=1
3.4 Compile GEOS-Chem code
At this point the best way to proceed is to make a 4x5 degree Hg run directory using the GEOS-Chem unit tester.
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cd YOUR_RUN_DIRECTORY
make -j4 mpbuild
Note** if you did not use the unit tester to make your run directory, you will have to edit the path that "CODE_DIR" points to in YOUR_RUN_DIRECTORY/Makefile
If compilation completes normally, an executable "geos.mp" will be created.
4. Run the simulation
A quick guide for submitting and managing jobs on Odyssey is available here.
4.1 Run GTMM standalone (optional?)
If you need to do a spin up of GTMM uncoupled from GEOS-Chem, you can do this:
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When it's done, you can do the following to make GEOS-Chem happy:
cp HgPools HgPools.0
4.2 Run GEOS-Chem coupled to GTMM
An example runscript is available at /n/home02/thackray/gtmmrun/dorun.sh
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