GEOS-Chem High-Performance version (GCHP) (experimental)¶
We’ve successfully made GCHP running on the cloud. It is functioning correctly but there are several issues to be resolved:
- GCHP compiles with gfortran, but the overall performance is ~20% slower than with ifort. The major slow down comes from the new advection module (GFDL-FV3).
- The initial I/O takes a long time (does not affect long-term simulations).
- The data analysis pipeline is not fully documented. We do have some preliminary scripts to process and regrid cubed-sphere data, though.
- It is only set up to run in a single node, with at most 72 CPUs (c5.18xlarge).
Right now it is pretty good for learning and for small experiments. We will make a major update after the formal release of v11-02.
GCHP inside Singularity container¶
We will be using containers to run GCHP. It allows you to set up GCHP quickly on almost any machines, not just on Amazon cloud. You can adapt this guide for your own server.
The Singularity image for GCHP can be obtained from Singularity Hub, with the command:
$ singularity pull --name GCHP.simg shub://JiaweiZhuang/Singularity_GC
Launch from the AMI ID
ami-21f37a5e. This AMI is just to provide sample input data and pre-configured run directory. The software libraries will be provided by Singularity container.
The minimum hardware requirement is
r4.2xlarge with 8 CPUs and 60 GB memory. The minimum number of MPI processes for GCHP is 6 (one for each cubed-sphere panel). You can still start a GCHP simulation on an instance with <6 CPUs, but the program is likely to die somewhere.
After launching the instance and logging-in (username is
ubuntu), you should see:
$ ls gcdata GCHP GCHP.simg miniconda singularity
Run the container interactively by:
$ singularity shell GCHP.simg
If you just execute the container by
./GCHP.simg, it will print some instructions.
Go to the run directory and execute the pre-compiled executable:
$ cd ~/GCHP/gchp_standard $ mpirun -np 6 ./geos
To re-compile the model, for now you need to specify the code directory when starting the container:
$ SINGULARITYENV_GC_CODE_DIR=~/GCHP/Code.v11-02_gchp singularity shell GCHP.simg
Then re-compile the model in the run directory:
$ cd ~/GCHP/gchp_standard $ make compile_clean
For more information please see the official tutorial on GCHP wiki.