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cryosparc_install.sh
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Wed, May 1, 04:43

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/
script_path=$(dirname "$0") # relative
script_path=$(cd "${script_path}" && pwd) # absolutized and normalized
license_id=
install_path="$HOME"/cryosparc
# set up some more paths
db_path=${install_path}/database
worker_path=${install_path}/cryosparc2_worker
# Usage
usage () {
echo "Usage:"
echo " -p install path : prefix for installation [${install_path}] "
echo " -v : be verbose"
echo " -h : print this notice"
echo ""
}
VERBOSE=false
read -p "Enter your license id: " license_id
read -p "Enter password for the user account to be created [leave empty to not create the initial account]: " password
# Parse options
while getopts ":p:vh" opt; do
case $opt in
p)
install_path="${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 purge
module load gcc cuda/11.0.2 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 -c "export CRYOSPARC_HOSTNAME_CHECK" ${cryosparc_master_path}/config.sh) -eq 0 ]; then
echo "export CRYOSPARC_HOSTNAME_CHECK=${HOSTNAME}" >> ${cryosparc_master_path}/config.sh
fi
cryosparc_worker_path=${install_path}/cryosparc_worker
if [ $(grep -c "export PATH" ${cryosparc_worker_path}/config.sh) -eq 0 ]; then
echo "export PATH=${cryosparc_worker_path}/bin:\$PATH" >> ${cryosparc_worker_path}/config.sh
fi
cp ${script_path}/cryosparcm.sh ${install_path}/cryosparc_master/bin
if [ $(${install_path}/cryosparc_master/bin/cryosparcm.sh status | grep -c "CryoSPARC is not running") -eq 1 ]; then
${install_path}/cryosparc_master/bin/cryosparcm.sh start
fi
user_name=$(whoami)
mail=$(ldapsearch -x -LLL -h scoldap.epfl.ch -b "o=epfl,c=ch" uid=${user_name} mail | grep mail | awk '{ print $2 }')
firstname=$(ldapsearch -x -LLL -h scoldap.epfl.ch -b "o=epfl,c=ch" uid=${user_name} givenName | grep givenName | awk '{ print $2 }')
lastname=$(ldapsearch -x -LLL -h scoldap.epfl.ch -b "o=epfl,c=ch" uid=${user_name} sn | grep sn | awk '{ print $2 }')
if [ "x$password" != "x" ]; then
${install_path}/cryosparc_master/bin/cryosparcm.sh createuser --email "${mail}" --firstname "${firstname}" --lastname "${lastname}" --username "${user_name}" --password "${password}"
echo "Initial account \"${user_name} - ${firstname} ${lastname} <${mail}>\" was created with the provided password"
fi
user_accounts=$(sacctmgr show assoc where user=${user_name} format=Account%100 -P | grep -v Account)
mkdir -p ${install_path}/site_configs && cd ${install_path}/site_configs
for _account in $user_accounts; do
if [ $(sacctmgr show assoc where account=${_account} format=ParentName%100 -P | grep -v "Par Name" | grep -c courses) -eq 0 ]; then
_worker_name=${HOSTNAME}-${_account}
mkdir -p ${install_path}/site_configs/${_worker_name} && cd ${install_path}/site_configs/${_worker_name}
cat << EOF > cluster_info.json
{
"name": "${_worker_name}",
"worker_bin_path": "${install_path}/cryosparc_worker/bin/cryosparcw",
"cache_path": "/tmp/{{ cryosparc_username }}/cryosparc_cache",
"cache_reserve_mb": "10000",
"cache_quota_mb": "null",
"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 -n {{ num_cpu }}
#SBATCH --gres gpu:{{ num_gpu }}
#SBATCH --mem {{ ram_gb|int }}GB
#SBATCH --time 48:0:0
#SBATCH -o {{ job_dir_abs }}/slurm.out
#SBATCH -e {{ job_dir_abs }}/slurm.err
#SBATCH -A ${_account}
module load gcc cuda/11.0.2 python
ln -sf \${TMPDIR} /tmp/${USER}/cryosparc2_cache
{{ run_cmd }}
EOF
${install_path}/cryosparc_master/bin/cryosparcm cluster connect
fi
done
if [ "x$password" = "x" ]; then
echo ""
echo "================================================================================"
echo "================================================================================"
echo " No password was given the initial account cannot be created"
echo " Create one using the following command:"
echo " ${install_path}/cryosparc_master/bin/cryosparcm.sh createuser --email \"${mail}\" --firstname \"${firstname}\" --lastname \"${lastname}\" --username \"${user_name}\" --password \"<password>\""
echo "================================================================================"
echo "================================================================================"
echo ""
fi
${install_path}/cryosparc_master/bin/cryosparcm.sh stop

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