The E3SM model can be run within the E3SM Singularity container. This page describes how to install Singularity, build or download the E3SM container, and run the E3SM model within the container.
Install Singularity
Install Singularity as described at Singularity Installation.
Download the E3SM container
The latest version of the E3SM container can be downloaded from e3sm.sif. If you would like to build the container with some changes, the E3SM Singularity definition file is available at e3sm.def. To build the container, run:
sudo singularity build e3sm.sif e3sm.def
Run the E3SM developer tests
Download the E3SM source
git clone -b maint-1.2 --recursive git@github.com:E3SM-Project/E3SM.git
Modify cime/config/e3sm/machines/config_machines.xml, so a value of the NODENAME_REGEX
element of the linux-generic
machine is singularity
. Remove openmpi
from MPILIBS
:
<MPILIBS>mpich</MPILIBS>
Specify GMAKE command above the GMAKE_J element:
<GMAKE>make</GMAKE> <GMAKE_J>4</GMAKE_J>
Define also environment variables:
<environment_variables> <env name="E3SM_SRCROOT">$SRCROOT</env> </environment_variables> <environment_variables mpilib="mpi-serial"> <env name="NETCDF_PATH">/usr/local/packages/netcdf-serial</env> <env name="PATH">/usr/local/packages/hdf5-1.10.6-serial/bin:/usr/local/packages/netcdf-serial/bin:$ENV{PATH}</env> <env name="LD_LIBRARY_PATH">/usr/local/packages/szip-2.1.1/lib:/usr/local/packages/hdf5-1.10.6-serial/lib:/usr/local/packages/netcdf-serial/lib</env> </environment_variables> <environment_variables mpilib="!mpi-serial"> <env name="NETCDF_PATH">/usr/local/packages/netcdf-parallel</env> <env name="PNETCDF_PATH">/usr/local/packages/pnetcdf-1.12.1</env> <env name="PATH">/usr/local/packages/mpich-3.3.2/bin:/usr/local/packages/hdf5-1.10.6-parallel/bin:/usr/local/packages/netcdf-parallel/bin:/usr/local/packages/pnetcdf-1.12.1/bin:$ENV{PATH}</env> <env name="LD_LIBRARY_PATH">/usr/local/packages/mpich-3.3.2/lib:/usr/local/packages/szip-2.1.1/lib:/usr/local/packages/hdf5-1.10.6-parallel/lib:/usr/local/packages/netcdf-parallel/lib:/usr/local/packages/pnetcdf-1.12.1/lib</env> </environment_variables>
Then add options -lblas -llapack
to a linker in cime/config/e3sm/machines/config_compilers.xml:
<compiler COMPILER="gnu" MACH="linux-generic"> <NETCDF_PATH> $(NETCDF_PATH)</NETCDF_PATH> <PNETCDF_PATH> $(PNETCDF_PATH)</PNETCDF_PATH> <ADD_SLIBS> $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -lblas -llapack</ADD_SLIBS> </compiler>
At this point you can run the container
mkdir $HOME/projects
singularity shell -B $HOME/projects e3sm.sif
Singularity> cd <E3SM_SRC_DIR>/cime/scripts
Singularity> ./create_test e3sm_developer
The developer test creates and runs 36 cases. To create a new case separately and run it, for example A_WCYCL1850 with ultra low resolution:
Singularity> ./create_newcase --case master.A_WCYCL1850.ne4_oQU240.baseline —-compset A_WCYCL1850 —-res ne4_oQU240
Singularity> cd master.A_WCYCL1850.ne4_oQU240.baseline
Singularity> ./case.setup
Singularity> ./case.build
Singularity> ./case.submit
For more details on how to create a new case and run it, please refer to E3SM Quick Start.