How to compile and run JEDI applications on Derecho computer?

JEDI
1

Since UCAR has upgraded their supercomputer from Cheyenne to Derecho, and Derecho doesn’t seem to provide certain environments or dependent libraries (e.g. atlas) to compile and run JEDI like Cheyenne did, does anyone know how to compile and run JEDI on Derecho? Or does anyone has such experience on Derecho? Or should I consider the Singularity container? Thanks,

2

Hi @lchen,

You should have very similar environments on Derecho (compared to Cheyenne) so the task of building JEDI should work in a similar fashion. Please check the documention links:

https://spack-stack.readthedocs.io/en/latest/PreConfiguredSites.html#ncar-wyoming-derecho

https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/using/running_skylab/running_skylab.html#build-jedi-bundle

Give the instructions in the above links a try, and we can help with further questions.

Thanks,

Steve

3

Hi @stephenh,

Thank you for the links. I am following the steps in the links, but still have some questions.
What I have done on Derecho:

export LMOD_TMOD_FIND_FIRST=yes
module load ncarenv/23.09
module use /glade/work/epicufsrt/contrib/spack-stack/derecho/modulefiles
module load ecflow/5.8.4

module use /glade/work/epicufsrt/contrib/spack-stack/derecho/spack-stack-1.7.0/envs/ue-intel/install/modulefiles/Core
module load stack-intel/2021.10.0
module load stack-cray-mpich/8.1.25
module load stack-python/3.10.13
module load jedi-fv3-env
module unload fms
module load fms/2023.04

#Build jedi-bundle
mkdir $JEDI_ROOT
cd $JEDI_ROOT
git clone GitHub - JCSDA/jedi-bundle: Bundle containing all the repositories that are needed to compile JEDI for use in Skylab

mkdir $JEDI_BUILD
cd $JEDI_BUILD
ecbuild $JEDI_SRC >& ecbuild.log &

But in ecbuild.log file, I found the following error messages:
Make Error at soca/mom6/CMakeLists.txt:28 (add_library):
** add_library cannot create target “mom6” because another target with the**
** same name already exists. The existing target is a shared library created**
** in source directory “/glade/work/hsiaof/jedi/jedi-bundle/mom6”. See**
** documentation for policy CMP0002 for more details.**

CMake Error at soca/mom6/CMakeLists.txt:41 (target_link_libraries):
** Attempt to add link library “NetCDF::NetCDF_C” to target “mom6” which is**
** not built in this directory.**

** This is allowed only when policy CMP0079 is set to NEW.**

5

Hi @gnosis83. I think you have a mis-match between the spack-stack version and the jedi-bundle version. You have loaded spack-stack-1.7.0 modules, and used the public jedi-bundle (git clone JCSDA/jedi-bundle). As I recall, the public jedi-bundle goes with the spack-stack-1.5.1 modules.

However, if you have access the the github jcsda-internal (private) organization, then you should be able to clone JCSDA-internal/jedi-bundle instead and use that with spack-stack-1.7.0.

Hope this helps!

Steve