PartMC-MOSAIC Installation on keeling
Zhonghua Zheng and Jeffrey Curtis (jcurtis2 at illinois.edu)
Last update: 2021/05/30
Prerequisites
Make sure you have access to keeling
Make sure you to have the permission to use the MOSAIC software
access keeling and prepare install
# from your local machine
$ ssh -y your_NetID@keeling7.earth.illinois.edu
# launch an interactive job
$ qsub -I -l select=1:ncpus=32 -l walltime=24:00:00
$ module load gnu/gnu-9.3.0
$ module load gnu/netcdf4-4.7.4-gnu-9.3.0
$ module load gnu/openmpi-3.1.6-gnu-9.3.0
$ export FC=gfortran
$ export CC=gcc
You can check if you have loaded successfully by typing
$ module list
You can check if you have set up FC
and CC
successfully by typing
$ which $FC
$ which $CC
build MOSAIC chemistry
$ cd your_path
$ tar -zxvf mosaic-2012-01-25.tar.gz
$ mv mosaic-2012-01-25 mosaic
$ cd your_path/mosaic
$ cp Makefile.local.gfortran Makefile.local
$ make
build PartMC-MOSAIC
step 1: download PartMC and set up
$ cd your_path
$ module load git # you may skip this if the command below works
$ git clone git@github.com:compdyn/partmc.git
$ cd partmc
$ mkdir build
$ cd build
$ export NETCDF_HOME=/sw/netcdf4-4.7.4-gnu-9.3.0
$ export MOSAIC_HOME=your_path/mosaic
$ ccmake ..
step 2: First, press “c”. Then press “e”, and type the following options
CMAKE_BUILD_TYPE: RELEASE
ENABLE_MOSAIC: ON
NETCDF_C_LIB:
/sw/netcdf4-4.7.4-gnu-9.3.0/lib/libnetcdf.so
NETCDF_FORTRAN_LIB:
/sw/netcdf4-4.7.4-gnu-9.3.0/lib/libnetcdff.so
NETCDF_INCLUDE_DIR:
/sw/netcdf4-4.7.4-gnu-9.3.0/include
step 3: press “c”, then “c” again, and “g”
step 4: compile and make sure you have all the test cases such as “test_mosaic_1” and “test_mosaic_2” passed.
make
make test