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cryosparc_install.sh
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Tue, Jul 22, 17:20

cryosparc_install.sh
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#!/bin/bash
set -euo pipefail
# Script made from the page
# https://docs.ycrc.yale.edu/clusters-at-yale/guides/cryosparc/
license_id=
install_path="$HOME"/cryosparc
cryosparc_passwd=Password123
# set up some more paths
db_path=${install_path}/database
worker_path=${install_path}/cryosparc2_worker
# Usage
usage () {
echo "Usage:"
echo " -l license_id : License ID"
echo " -p install path : prefix for installation [${install_path}] "
echo " -v : be verbose"
echo " -h : print this notice"
echo ""
}
VERBOSE=false
# Parse options
while getopts ":l:p:vh" opt; do
case $opt in
l)
license_id="${OPTARG}"
;;
p)
install_path="${OPTARG}"
;;
v)
VERBOSE=true
;;
h)
usage
OPTIND=1
exit 0
;;
\?)
echo "Invalid option: -$OPTARG" >&2
usage
OPTIND=1
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
usage
OPTIND=1
exit 1
;;
esac
done
# Reset OPTIND to allow the next invocation to work
OPTIND=1
message() {
if $VERBOSE
then
echo "${1}"
fi
}
if [ "x${license_id}" == "x" ]; then
echo "[Error] No license id was provided" >&2
usage
exit 2
fi
message "[Info] Preparing the install path and dowloading cryosparc_master and cryosparc_worker"
# go get the installers
mkdir -p $install_path
cd $install_path
# Download master
curl -sL -C - -\# https://get.cryosparc.com/download/master-latest/$license_id -o cryosparc2_master.tar.gz
# Download worker
curl -sL -C - -\# https://get.cryosparc.com/download/worker-latest/$license_id -o cryosparc2_worker.tar.gz
message "[Info] Expanding tarballs"
tar -xf cryosparc2_master.tar.gz
tar -xf cryosparc2_worker.tar.gz
module load gcc cuda python
message "[Info] Installing master"
cd ${install_path}/cryosparc_master
./install.sh --license $license_id --hostname $(hostname) --dbpath $db_path --yes
set +u
source ~/.bashrc
set -u
message "[Info] Installing worker"
cd ${install_path}/cryosparc_worker
./install.sh --license $license_id --cudapath $CUDA_HOME --yes
set +u
source ~/.bashrc
set -u
message "[Info] Creating worker configs"
cryosparc_master_path=${install_path}/cryosparc_master
if [ $(grep -c "export PATH" ${cryosparc_master_path}/config.sh) -eq 0 ]; then
echo "export PATH=${cryosparc_master_path}/bin:\$PATH" >> ${cryosparc_master_path}/config.sh
fi
if [ $(grep -q "export CRYOSPARC_HOSTNAME_CHECK" ${cryosparc_master_path}/config.sh) -eq 0 ]; then
echo "export CRYOSPARC_HOSTNAME_CHECK=${master_host}" >> ${cryosparc_master_path}/config.sh
fi
mkdir -p ${install_path}/site_configs && cd ${install_path}/site_configs
cat << EOF > cluster_info.json
{
"name" : "farnam",
"worker_bin_path" : "${install_path}/cryosparc2_worker/bin/cryosparcw",
"cache_path" : "/tmp/{{ cryosparc_username }}/cryosparc_cache",
"send_cmd_tpl" : "{{ command }}",
"qsub_cmd_tpl" : "sbatch {{ script_path_abs }}",
"qstat_cmd_tpl" : "squeue -j {{ cluster_job_id }}",
"qdel_cmd_tpl" : "scancel {{ cluster_job_id }}",
"qinfo_cmd_tpl" : "sinfo"
}
EOF
cat << EOF > cluster_script.sh
#!/bin/bash -l
#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
#SBATCH -c {{ num_cpu }}
#SBATCH --gres:gpu={{ num_gpu }}
#SBATCH --mem={{ (ram_gb*1024)|int }}
#SBATCH -o {{ job_dir_abs }}
#SBATCH -e {{ job_dir_abs }}
module load gcc cuda python
ln -sf \${TMPDIR} /tmp/${USER}/cryosparc2_cache
{{ run_cmd }}
EOF

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