Install the model components

The official repository of SKRIPS v2.0 is maintained on Github:

https://github.com/iurnus/scripps_kaust_model/releases/tag/v2.0

Now I am using the SDSC supercomputer COMET as an example. To install the SKRIPS model in the mead system (/cw3e/mead/projects/csg102/rus043/scripps_kaust_model/), we have to download the SKRIPS model and set up the bashrc file.

Install step 1.1: Download SKRIPS version from Github:

# I am using my work folder as an example
cd /cw3e/mead/projects/csg102/rus043/
wget https://github.com/iurnus/scripps_kaust_model/archive/v2.0.zip
unzip v2.0.zip
mv scripps_kaust_model-2.0 scripps_kaust_model
cd scripps_kaust_model
ls -l

You will see the following folders and files:

drwxr-sr-x  8 rus043 csg102 57344 Oct  4 10:56 coupler
drwxr-sr-x  4 rus043 csg102 57344 Oct  4 10:56 esmf_test_application
drwxr-sr-x  4 rus043 csg102 57344 Oct 11 14:05 installOption_OTH
drwxr-sr-x  6 rus043 csg102 57344 Oct 11 09:12 installOption_WRF
drwxr-sr-x  6 rus043 csg102 57344 Oct 10 23:39 installOption_WW3
drwxr-sr-x  2 rus043 csg102 57344 Oct  4 10:56 license_statements
-rw-r--r--  1 rus043 csg102  2597 Oct 11 11:03 README.md

Install step 1.2: Create a bashrc file for SKRIPS model:

cp ./installOption_OTH/bashrc_comet ~/.bashrc_skrips

Here I am copying the bashrc file that I used for COMET. There are also bashrc files for other machines that can be used in installOption_OTH folder.

Then, add the following line to ~/.bashrc file:

alias load_skrips="source ~/.bashrc_skrips"

Now activate the bashrc setups in the command line. Also, you need to activate the bachrc setups when you want to run SKRIPS model, otherwise the Linux system will not remember what you did:

load_skrips

After the bashrc file is successfully loaded. We get the following output:

Setting up the bashrc for SKRIPS model...
SKRIPS_DIR is: /cw3e/mead/projects/csg102/rus043/scripps_kaust_model/

In the ~/.bashrc_skrips file, we have:

module purge
module load intel
module load intelmpi
module load netcdf

# Location of the modules
export SKRIPS_DIR=/cw3e/mead/projects/csg102/rus043/scripps_kaust_model/
export ESMF_DIR=$SKRIPS_DIR/esmf/
export WRF_DIR=$SKRIPS_DIR/WRFV413_AO/
export MITGCM_DIR=$SKRIPS_DIR/MITgcm_c67m/
export WW3_DIR=$SKRIPS_WAVE_DIR/ww3_607/

# NETCDF and MPI
export NETCDF=/opt/netcdf/4.6.1/intel/intelmpi/
export NETCDF_DIR=/opt/netcdf/4.6.1/intel/intelmpi/
export NETCDF_INC=/opt/netcdf/4.6.1/intel/intelmpi/include/
export NETCDF_LIB=/opt/netcdf/4.6.1/intel/intelmpi/lib/
export SKRIPS_MPI_DIR=$MPIHOME
export SKRIPS_MPI_INC=$MPIHOME/include/
export SKRIPS_MPI_LIB=$MPIHOME/lib/

# For WW3
export WWATCH3_NETCDF=NC4
export NETCDF_CONFIG=$NETCDF_DIR/bin/nc-config
export PATH=$WW3_DIR/bin:${PATH}
export PATH=$WW3_DIR/exe:${PATH}

# For ESMF
export ESMF_OS=Linux
export ESMF_COMPILER=intel
export ESMF_COMM=intelmpi
export ESMF_OPENMP=OFF
export ESMF_LAPACK=internal
export ESMF_NETCDF=nc-config
export ESMF_BOPT=g
export ESMF_ABI=64
export ESMF_YAMLCPP=OFF
export ESMF_LIB=$ESMF_DIR/lib/lib$ESMF_BOPT/$ESMF_OS.$ESMF_COMPILER.$ESMF_ABI.$ESMF_COMM.default/
export ESMF_MOD=$ESMF_DIR/mod/mod$ESMF_BOPT/$ESMF_OS.$ESMF_COMPILER.$ESMF_ABI.$ESMF_COMM.default/
export ESMFMKFILE=$ESMF_LIB/esmf.mk

# Others
export SKRIPS_NETCDF_INCLUDE=-I`nc-config --includedir`
export SKRIPS_NETCDF_LIB=-L`nc-config --libdir`

export LD_LIBRARY_PATH=$NETCDF_LIB/${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=$SKRIPS_MPI_LIB/${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=$ESMF_LIB/${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}

When you want to install the SKRIPS model on another machine:

  1. Please make sure the paths for the model components, NETCDF, MPI, WW3, and ESMF are correct. The ESMF setups will be detailed in latter sections.

  2. WW3 is not necessary for running the coupled model.

  3. To install the coupled model on ring@ucsd, please use installOption_OTH/bashrc_ring.

  4. To install the coupled model on Shaheen, please use installOption_OTH/bashrc_shaheen.

Now we can start install the module components and the coupled model.