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generate_user_and_lanes.backup
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Wed, Apr 24, 09:52

generate_user_and_lanes.backup
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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 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
}
echo "[Info] Starting the master if needed"
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}"
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}
max_wall=$(sacctmgr show assoc where account=${_account} format=MaxWall -P | grep -v MaxWall | head -1)
for mem in 90 180 360 720; do
mkdir -p ${install_path}/site_configs/${_worker_name}_${mem}gb && cd ${install_path}/site_configs/${_worker_name}_${mem}gb
cat << EOF > cluster_info.json
{
"name": "${_worker_name}_${mem}gb",
"worker_bin_path": "${install_path}/cryosparc_worker/bin/cryosparcw",
"cache_path": "/tmp/{{ cryosparc_username }}/cryosparc_cache",
"cache_reserve_mb": 10000,
"cache_quota_mb": 1000000,
"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 ${mem}GB
#SBATCH --time ${max_wall}
#SBATCH -o {{ job_dir_abs }}/slurm.out
#SBATCH -e {{ job_dir_abs }}/slurm.err
#SBATCH -A ${_account}
module load gcc cuda/11.0.2 python
mkdir -p /tmp/${USER}
ln -sf \${TMPDIR} /tmp/${USER}/cryosparc_cache
{{ run_cmd }}
EOF
${install_path}/cryosparc_master/bin/cryosparcm cluster connect
done
fi
done
if [ "x$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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