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make_ilamb_venv.sh
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make_ilamb_venv.sh
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#!/usr/bin/env bash
# from theh stack overflow to parse yaml
function parse_yaml {
local prefix=$2
local s='[[:space:]]*' w='[a-zA-Z0-9_]*' fs=$(echo @|tr @ '\034')
sed -ne "s|^\($s\):|\1|" \
-e "s|^\($s\)\($w\)$s:$s[\"']\(.*\)[\"']$s\$|\1$fs\2$fs\3|p" \
-e "s|^\($s\)\($w\)$s:$s\(.*\)$s\$|\1$fs\2$fs\3|p" $1 |
awk -F$fs '{
indent = length($1)/2;
vname[indent] = $2;
for (i in vname) {if (i > indent) {delete vname[i]}}
if (length($3) > 0) {
vn=""; for (i=0; i<indent; i++) {vn=(vn)(vname[i])("_")}
printf("%s%s%s=\"%s\"\n", "'$prefix'",vn, $2, $3);
}
}'
}
ilamb_venv_yml=ilamb-venv.yml
if [ $HOSTNAME ]; then
host=$HOSTNAME
fi
if [ $HOST ]; then
host=$HOST
fi
echo $host
groups=`groups`
case $host in
titan*)
useconda=True
module load python_anaconda/2.7.14-anaconda2-5.1.0
ilamb_venv_dir=/lustre/atlas1/cli106/world-shared/mxu/ilamb_venv
;;
rhea*)
useconda=True
module load python_anaconda2/5.1.0
ilamb_venv_dir=/lustre/atlas1/cli106/world-shared/mxu/ilamb_venv
;;
cori*)
useconda=True
module load python/2.7-anaconda-4.4
case $groups in
*acme*)
ilamb_venv_dir=/global/project/projectdirs/acme/minxu/ilamb-venv ;;
*m2467*)
ilamb_venv_dir=/global/project/projectdirs/m2467/prj_minxu/ilamb-venv ;;
*m1006*)
ilamb_venv_dir=/global/project/projectdirs/m1006/minxu/ilamb-venv ;;
*)
echo "your group do not have ilamb venv" ;;
esac
fxmpi4py=True
conda_mpi4py=${ilamb_venv_dir}/ilamb-venv-py27/lib/python2.7/conda_mpi4py
cray1_mpi4py=/global/common/edison/software/python/2.7-anaconda-4.4/lib/python2.7/site-packages/mpi4py-2.0.0-py2.7.egg-info
cray2_mpi4py=/global/common/edison/software/python/2.7-anaconda-4.4/lib/python2.7/site-packages/mpi4py
;;
edison*)
useconda=True
module load python/2.7-anaconda-4.4
case $groups in
*acme*)
ilamb_venv_dir=/global/project/projectdirs/acme/minxu/ilamb-venv ;;
*m2467*)
ilamb_venv_dir=/global/project/projectdirs/m2467/prj_minxu/ilamb-venv ;;
*m1006*)
ilamb_venv_dir=/global/project/projectdirs/m1006/minxu/ilamb-venv ;;
*)
echo "your group do not have ilamb venv";;
esac
fxmpi4py=True
conda_mpi4py=${ilamb_venv_dir}/ilamb-venv-py27/lib/python2.7/conda_mpi4py
cray1_mpi4py=/global/common/edison/software/python/2.7-anaconda-4.4/lib/python2.7/site-packages/mpi4py-2.0.0-py2.7.egg-info
cray2_mpi4py=/global/common/edison/software/python/2.7-anaconda-4.4/lib/python2.7/site-packages/mpi4py
;;
or-condo*)
useconda=True
module load anaconda2/4.4.0
ilamb_venv_dir=/lustre/or-hydra/cades-ccsi/e4x/ilamb_venv/
;;
*)
usepyenv=True
echo "Please set up ilamb_venv_dir and ilamb_venv_yml first"
;;
esac
if [ -d ${ilamb_venv_dir} ]; then
echo "Instaling ILAMB venv into the directory: ${ilamb_venv_dir}"
else
echo "Make the ILAMB venv directory in: ${ilamb_venv_dir}"
mkdir -p ${ilamb_venv_dir}
fi
if [ -f ${ilamb_venv_yml} ]; then
eval $(parse_yaml ${ilamb_venv_yml} "CONF_")
else
echo "Please provide the env file"
exit -1
fi
if [ x$useconda = 'xTrue' ]; then
export CONDA_ENVS_PATH=${ilamb_venv_dir}
export CONDA_PKGS_DIRS=${ilamb_venv_dir}/.pkgs
conda env create -f ilamb-venv.yml
mkdir -p ${ilamb_venv_dir}/${CONF_name}/etc/conda/activate.d
mkdir -p ${ilamb_venv_dir}/${CONF_name}/etc/conda/deactivate.d
touch ${ilamb_venv_dir}/${CONF_name}/etc/conda/activate.d/env_var.sh
touch ${ilamb_venv_dir}/${CONF_name}/etc/conda/deactivate.d/env_var.sh
echo "export ILAMB_VENV_DIR=${ilamb_venv_dir}" >> ${ilamb_venv_dir}/$CONF_name/etc/conda/activate.d/env_var.sh
echo "unset ILAMB_VENV_DIR" >> ${ilamb_venv_dir}/$CONF_name/etc/conda/deactivate.d/env_var.sh
# fix mpi4py error
if [ x$fxmpi4py = 'xTrue' ]; then
mkdir -p ${conda_mpi4py}
/bin/mv ${ilamb_venv_dir}/ilamb-venv-py27/lib/python2.7/site-packages/mpi4py-* ${conda_mpi4py}
/bin/mv ${ilamb_venv_dir}/ilamb-venv-py27/lib/python2.7/site-packages/mpi4py ${conda_mpi4py}
ln -sf ${cray1_mpi4py} ${ilamb_venv_dir}/ilamb-venv-py27/lib/python2.7/site-packages/
ln -sf ${cray2_mpi4py} ${ilamb_venv_dir}/ilamb-venv-py27/lib/python2.7/site-packages/
cp -f ilamb-run-ser-sample ${ilamb_venv_dir}/ilamb-venv-py27/bin
fi
# install ilamb
else
pip install virtualenv --user
$PYTHONUSERBASE/bin/virtualenv $ilamb_venv_dir/ilamb-venv-py27
fi
#source activate