Before compiling, source the HPC environment file to load the correct modules and compilers. See the HPC environment section for details.

Source HPC environment — Betzy (NRIS/Sigma2)

source ${HOME}/NERSC-HYCOM-CICE/environment/betzy_env.sh

Source HPC environment — Olivia (NRIS/Sigma2)

source ${HOME}/NERSC-HYCOM-CICE/environment/olivia_env.sh

Note

Olivia support is a work in progress.

Compile MSCPROGS (libhycnersc.a)

Before compiling: source the HPC environment file to load the correct modules and compilers (see top of this page).

MSCPROGS provides libhycnersc.a, a shared library used by the MSCPROGS post-processing tools and also required when compiling HYCOM with the BGC module. It only needs to be rebuilt when the HPC modules are updated or the source code changes.

Create a symlink for your machine and compiler, then build and install:

cd ${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/src/Make.Inc
ln -sf make.betzy.ifort make.inc
cd ${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/src
gmake clean && gmake all && gmake install

After installation, libhycnersc.a is at:

${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/lib/libhycnersc.a

For more detail, see the MSCPROGS README.

Missing build directories (NERSC-HYCOM-CICE_BIORANv2 only)

If using the NERSC-HYCOM-CICE_BIORANv2 repository, create these missing directories before running gmake:

mkdir -p ${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/src/Average/TMP
mkdir -p ${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/src/Hycom_mean/TMP
mkdir -p ${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/src/Perturb_Forcing-2.2.98_TP5/TMP
mkdir -p ${HOME}/NERSC-HYCOM-CICE/hycom/MSCPROGS/src/Perturb_Parameter/TMP

BGC dependencies (FABM)

Before compiling: source the HPC environment file to load the correct modules and compilers (see top of this page).

Only needed when running with biogeochemical modules (ntracr > 0 in blkdat.input). FABM only needs to be rebuilt when the HPC modules are updated or the source code changes.

Note

BGC compilation also requires libhycnersc.a from MSCPROGS; see Compile MSCPROGS above.

Compile FABM (libfabm.a)

Configure and build inside a build/ directory within the FABM clone:

rm -rf ${HOME}/fabm/build
mkdir ${HOME}/fabm/build && cd ${HOME}/fabm/build
cmake ${HOME}/fabm \
    -DFABM_HOST=hycom \
    -DCMAKE_Fortran_COMPILER=ifort \
    -DFABM_INSTITUTES="ersem;nersc;gotm" \
    -DFABM_NERSC_BASE=${HOME}/nersc \
    -DFABM_ERSEM_BASE=${HOME}/ersem
make install

After installation, libfabm.a is at:

${HOME}/local/fabm/hycom/lib64/libfabm.a

Compile HYCOM-CICE

Before compiling: source the HPC environment file to load the correct modules and compilers (see top of this page).

Unlike the sections above, this step must be repeated for each new experiment.

Before running the compile script, check that the Makefile configuration symlink points to the correct HYCOM version. The symlink is at:

${HOME}/NERSC-HYCOM-CICE/hycom/RELO/config/Linux.betzy.ifort_cice

It must point to one of:

Target	Use when
Linux.betzy.ifort_cice.V22	HYCOM version 2.2 (default)
Linux.betzy.ifort_cice.V23	HYCOM version 2.3

Check and update the symlink if needed:

ls -la ${HOME}/NERSC-HYCOM-CICE/hycom/RELO/config/Linux.betzy.ifort_cice
# To switch to V23:
ln -sf Linux.betzy.ifort_cice.V23 \
    ${HOME}/NERSC-HYCOM-CICE/hycom/RELO/config/Linux.betzy.ifort_cice

Note

If compiling with the BGC module: ensure ntracr in blkdat.input is non-zero and copy the FABM configuration files and CICE namelist into the experiment directory before compiling:

CONFIGNAME=<CONFIGNAME>   # e.g. TP2a0.10
EXPT_ID=<EXPT_ID>         # e.g. 01.0

cd ${WORK}/${CONFIGNAME}/expt_${EXPT_ID}
cp /nird/datalake/NS9481K/shuang/TP2_setup/exp02.6_seaclim_ref/fabm.yaml .
cp /nird/datalake/NS9481K/shuang/TP2_setup/exp02.6_seaclim_ref/hycom_fabm.nml .
cp /nird/datalake/NS9481K/shuang/TP2_setup/exp02.6_seaclim_ref/ice_in .

Run the compile script from the experiment directory:

CONFIGNAME=<CONFIGNAME>   # e.g. TP2a0.10
EXPT_ID=<EXPT_ID>         # e.g. 01.0

cd ${WORK}/${CONFIGNAME}/expt_${EXPT_ID}
bash ${HOME}/NERSC-HYCOM-CICE/bin/compile_model.sh ifort -u

The script manages the build/ directory containing a per-experiment copy of the source:

• First compile (build/ does not exist): source is automatically synced from the repository.

• Recompile after repo changes (use -u): source is resynced from the repository, overwriting any local modifications in build/.

• Recompile without -u: uses whatever is currently in build/, preserving any local edits.

To start completely fresh, delete build/ before running the script:

rm -rf build

What compile_model.sh does behind the scenes

The script must be run from the experiment directory. It sources REGION.src and EXPT.src to read configuration, then proceeds in the following order:

1. Detect site and compiler: derives SITE from the hostname and constructs a MACROID (e.g. Linux.betzy.ifort) used to select the correct Makefile macros.

2. Resolve ESMF paths: sets ESMF_DIR, ESMF_MOD_DIR, and ESMF_LIB_DIR. If these are already set in the environment they are used as-is; otherwise the script uses hardcoded paths for known sites (Betzy, Fram) or exits with an error on unknown systems.

3. Select equation of state: reads SIGVER from EXPT.src and links the matching stmt_fns.h include file in the build directory. This must be consistent with thflag in blkdat.input (the script checks this and exits if they differ).

4. Sync source code: rsyncs HYCOM and CICE source from $NHCROOT/hycom/RELO/ into build/ on first run, or when -u is passed. Existing build/ directories are left untouched otherwise, preserving any local edits.

5. Apply feature flags: if a file named hycom_feature_flags exists in the experiment directory it is copied into the build directory and passed to the C preprocessor, allowing you to activate or deactivate specific HYCOM features.

6. Compile CICE: runs comp_ice.esmf with the grid dimensions read from blkdat.input. Only runs when iceflg=2 in blkdat.input.

7. Compile HYCOM-CICE: builds the final hycom_cice executable and links it against the CICE objects.

The executable hycom_cice is created inside build/ in a subdirectory whose name encodes the HYCOM version, equation-of-state terms, and thermodynamic flag, for example:

${WORK}/<CONFIGNAME>/expt_<EXPT_ID>/build/src_2.2.98ZA-07Tsig0-i-sm-sse_relo_mpi/hycom_cice

The version prefix changes with the Makefile symlink target (2.2.98 for V22, 2.3 for V23), and the 07Tsig0 part reflects the equation-of-state choice in EXPT.src.

Compile hycom_ALL

Before compiling: source the HPC environment file to load the correct modules and compilers (see top of this page).

hycom_ALL provides domain-independent pre/post processing utilities used to prepare external input files. Like MSCPROGS and FABM, it only needs to be compiled once per machine/compiler setup (not per experiment) or when the source code changes.

What hycom_ALL compiles and what it is used for

Make_all.com builds executables into several subdirectories:

Directory	Purpose
relax/	Generate relaxation climatologies (relaxi, relaxv, rmu, …)
topo/	Grid and bathymetry processing
archive/	Archive file conversion (archv2data2d, archt2archv, …)
force/	Atmospheric forcing file preparation
meanstd/	Compute mean and standard deviation fields
sample/	Sample model output at points or sections
subregion/	Extract subregions from model output
bin/	General utilities, including hycom_nest_dates (used for nesting)

All programs read regional.grid.b at runtime to get the grid dimensions for the domain being processed. The same executables work for any HYCOM configuration.

These utilities are called by setup and pre-processing scripts such as create_ref_case.sh (relaxation climatologies and MPI tile definition files) and nemo2hycom.sh (boundary and initial conditions from NEMO output). Recompilation is only needed when the HPC modules or compiler change.

cd ${HOME}/NERSC-HYCOM-CICE/hycom/hycom_ALL/hycom_2.2.72_ALL

Open Make_all.src in a text editor. Find the ARCH line and set it to your compiler:

setenv ARCH intelIFC

Then compile:

csh ./Make_clean.com
csh ./Make_all.com