Compiling

• General info on [[MOM6]]

Compiling on ARCHER2¶

Following the general instructions on the MOM6 wiki.

• Info on [[ARCHER2]]

Dataset downloads¶

Download datasets to ARCHER2 with

wget -r ftp://ftp.gfdl.noaa.gov/perm/Alistair.Adcroft/MOM6-testing/

unpack them, then link them with

cd MOM6-examples # navigate to base directory
ln -sf /path/to/downloaded/data .datasets

mkmf approach¶

Necessary for anything other than ocean-only configurations (ocean-only configurations can be built with the auto-configure approach, though I’ve not tried this on ARCHER2)

The compilation environment should be established with the following module calls:

module load PrgEnv-gnu  
module load cray-hdf5  
module load cray-netcdf  
module load cmake

Per the MOM6 wiki here, this can be included in a env file if desired, using

mkdir build
cat > build/env << EOFA
module load PrgEnv-gnu  
module load cray-hdf5  
module load cray-netcdf  
module load cmake
EOFA

and load these modules with source build/env.

mkmf template modifications¶

Compiling with mkmf requires the use of certain templates, found in src/mkmf/templates, for which we will use linux-gnu.md. A file containing the necessary modifications to this template can be found at /work/e786/shared/graemem/MOM6-examples/src/mkmf/templates/archer-gnu.mk.

The specific modifications are:

1. Set the compiler and library names to the default wrappers on ARCHER2 (see here). Do this on lines 8-11, which should now read:

############
# Commands Macros
FC = ftn
CC = cc
CXX = CC
LD = ftn $(MAIN_PROGRAM)

2. Add the following flags to the Fortran compiler flags (line 95):

-fallow-invalid-boz -fallow-argument-mismatch

Compile FMS¶

In creating the Makefile one additional flag is required: -DHAVE_GETTID. The set of commands now reads (pointing to the modified template file):

mkdir -p build/fms/
(cd build/fms; rm -f path_names; \
../../src/mkmf/bin/list_paths -l ../../src/FMS; \
../../src/mkmf/bin/mkmf -t ../../src/mkmf/templates/archer-gnu.mk -p libfms.a -c "-Duse_libMPI -Duse_netCDF -DHAVE_GETTID" path_names)

This generates the Makefile. Compile with:

(cd build/fms/; source ../env; make NETCDF=3 REPRO=1 libfms.a -j)

Compile MOM6¶

Generate the Makefile :

mkdir -p build/ocean_only/
(cd build/ocean_only/; rm -f path_names; \
../../src/mkmf/bin/list_paths -l ./ ../../src/MOM6/{config_src/infra/FMS1,config_src/memory/dynamic_symmetric,config_src/drivers/solo_driver,config_src/external,src/{*,*/*}}/ ; \
../../src/mkmf/bin/mkmf -t ../../src/mkmf/templates/archer-gnu.mk -o '-I../fms' -p MOM6 -l '-L../fms -lfms' path_names)

Compile with:

(cd build/ocean_only/; source ../env; make REPRO=1 MOM6 -j)

Compile MOM6-SIS2¶

Generate the Makefile:

mkdir -p build/ice_ocean_SIS2/
(cd build/ice_ocean_SIS2/; rm -f path_names; \
../../src/mkmf/bin/list_paths -l ./ ../../src/MOM6/config_src/{infra/FMS1,memory/dynamic_symmetric,drivers/FMS_cap,external} ../../src/SIS2/config_src/dynamic_symmetric ../../src/MOM6/src/{*,*/*}/ ../../src/{atmos_null,coupler,land_null,ice_param,icebergs/src,SIS2,FMS/coupler,FMS/include}/)
(cd build/ice_ocean_SIS2/; \
../../src/mkmf/bin/mkmf -t ../../src/mkmf/templates/archer-gnu.mk -o '-I../fms' -p MOM6 -l '-L../fms -lfms' -c '-Duse_AM3_physics -D_USE_LEGACY_LAND_' path_names )

Compile with:

(cd build/ice_ocean_SIS2/; source ../env; make REPRO=1 MOM6 -j)

Run a test¶

Just to check that the compilation has worked, run one of the test configurations via an interactive job. First, start the job:

salloc --nodes=8 --ntasks-per-node=128 --cpus-per-task=1 --time=00:20:00 --partition=standard --qos=short

Then, run the test:

cd ocean_only/double_gyre/
mkdir -p RESTART
srun -n 8 ../../build/ocean_only/MOM6

Compiling on a Mac¶

This information is derived from compiling the model on a 2018 MacBook Pro, running OSX 13.2 (Ventura).

autoconf approach¶

Detailed instructions here.

Preliminary steps:

1. Deactive any conda environment. Details of setting up an appropriate conda environment can be found here. For this set-up, I am installing everything in the native user environment (i.e. not conda). Note that you need to deactivate conda each time before you create the Makefile using autoconf, otherwise it will pick up some of the associated conda packages and lead to errors.

2. Set up environment, using homebrew to install required dependencies (see dependencies here):

brew install make
brew install gfortran
brew install mpich
brew install netcdf
brew install netcdf-fortran
brew install autoconf
brew install automake

(Ensure that command line tools (xcode) are up-to-date. I ran sudo xcode-select --install to ensure this was the case.)

Compile steps

1. Compile FMS

   1. Issue make -j in src/MOM6/ac/deps. This clones and compiles FMS and builds it in the local directory.

2. Create configuration script

   1. Issue autoreconf in src/MOM6/ac. Creates configure script in local directory.

3. Compile the model

   1. Create build directory (preferable to do this in MOM6-examples/build).

   2. Execute configure script (found in src/MOM6/src/ac) to create a Makefile.

   3. Issue make -j in build directory to compile.