diff --git a/create_user_and_lanes.sh b/create_lanes.sh similarity index 67% copy from create_user_and_lanes.sh copy to create_lanes.sh index 9f8dfe3..fc84fc3 100755 --- a/create_user_and_lanes.sh +++ b/create_lanes.sh @@ -1,143 +1,122 @@ #!/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 \"${user_name}\" --password \"\"" - echo "================================================================================" - echo "================================================================================" - echo "" -fi - -${install_path}/cryosparc_master/bin/cryosparcm.sh stop +#${install_path}/cryosparc_master/bin/cryosparcm.sh stop diff --git a/create_user_and_lanes.sh b/create_reserved_lanes.sh similarity index 60% copy from create_user_and_lanes.sh copy to create_reserved_lanes.sh index 9f8dfe3..816c836 100755 --- a/create_user_and_lanes.sh +++ b/create_reserved_lanes.sh @@ -1,143 +1,119 @@ #!/bin/bash set -euo pipefail # Script made from the page # https://docs.ycrc.yale.edu/clusters-at-yale/guides/cryosparc/ script_path=$(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 +read -p "Enter group account at SCITAS: " hpc_account +read -p "Enter reservation name: " reservation_name # 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) +cd ${install_path}/site_configs -mail=$(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 +for _account in $hpc_account; 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} + _worker_name=${HOSTNAME}-${_account}-reserved max_wall=$(sacctmgr show assoc where account=${_account} format=MaxWall -P | grep -v MaxWall | head -1) - for mem in 90 180 360 720; do + for mem in 90; 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 --time 3-00:00:00 #SBATCH -o {{ job_dir_abs }}/slurm.out #SBATCH -e {{ job_dir_abs }}/slurm.err #SBATCH -A ${_account} +#SBATCH --reservation $reservation_name module load gcc cuda/11.0.2 python mkdir -p /tmp/${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 \"${user_name}\" --password \"\"" - echo "================================================================================" - echo "================================================================================" - echo "" -fi - -${install_path}/cryosparc_master/bin/cryosparcm.sh stop diff --git a/create_user.sh b/create_user.sh new file mode 100755 index 0000000..a16f6db --- /dev/null +++ b/create_user.sh @@ -0,0 +1,85 @@ +#!/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 "${script_path}" && pwd) # absolutized and normalized + +install_path="$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 first name: " firstname +read -p "Enter your last name: " lastname +read -p "Enter your email address: " mail +read -p "Enter user name for the account: " user_name +read -p "Enter password for the 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 + +#${install_path}/cryosparc_master/bin/cryosparcm.sh stop diff --git a/cryosparc_install.sh b/cryosparc_install.sh index 1f7980a..9d9fac0 100755 --- a/cryosparc_install.sh +++ b/cryosparc_install.sh @@ -1,128 +1,141 @@ #!/bin/bash set -euo pipefail # Script made from the page # https://docs.ycrc.yale.edu/clusters-at-yale/guides/cryosparc/ script_path=$(dirname "$0") # relative script_path=$(cd "${script_path}" && pwd) # absolutized and normalized license_id= +port_number= install_path="$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 the port number: " port_number # 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${license_id}" == "x" ]; then echo "[Error] No license id was provided" >&2 usage exit 2 fi +if [ "x${port_number}" == "x" ]; then + echo "[Error] No part number 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" >> ${cryosparc_worker_path}/config.sh fi +set +u +if [ "x${port_number}" != "x" ]; then + sed -i -e 's/export CRYOSPARC_BASE_PORT.*$/export CRYOSPARC_BASE_PORT='$port_number'/g' ${cryosparc_master_path}/config.sh +fi +set -u + cp ${script_path}/cryosparcm.sh ${install_path}/cryosparc_master/bin -${script_path}/create_user_and_lanes.sh -p ${install_path} diff --git a/cryosparcm.sh b/cryosparcm.sh index 6c298ec..a03d44b 100755 --- a/cryosparcm.sh +++ b/cryosparcm.sh @@ -1,84 +1,84 @@ #!/usr/bin/env bash set -euo pipefail install_path="$HOME"/cryosparc # Usage usage () { echo "$0 -p -P command" echo "Usage:" echo " command : command to pass to cryosparcm (start|stop)" echo " -p install path : prefix for installation [${install_path}] " echo " -P base_port : base port [39000] " echo " -v : be verbose" echo " -h : print this notice" echo "" } set +u if [ "x$1" = "x" ]; then usage exit 1 fi set -u # Parse options while getopts ":P:p:h" opt; do case $opt in p) install_path="${OPTARG}" ;; P) cryosparcm_port="${OPTARG}" ;; h) usage OPTIND=1 exit 0 ;; \?) echo "Invalid option: -$OPTARG" >&2 usage OPTIND=1 exit 1 ;; :) echo "Option -$OPTARG requires an argument." >&2 usage OPTIND=1 exit 1 ;; esac done shift $((OPTIND-1)) OPTIND=1 command=$1 shift -module load gcc cuda python +module load gcc cuda/11.0.2 python export PATH=${install_path}/cryosparc_master/bin:$PATH cryosparcm_path="$(which cryosparcm 2> /dev/null)" base_dir=$(dirname "$(dirname "${cryosparcm_path}")") master_host=$(hostname) cp $base_dir/config.sh $base_dir/config.sh.bak sed -i -e 's/export CRYOSPARC_MASTER_HOSTNAME.*$/export CRYOSPARC_MASTER_HOSTNAME=\"'"$master_host"'\"/g' $base_dir/config.sh sed -i -e 's/export CRYOSPARC_HOSTNAME_CHECK.*$/export CRYOSPARC_HOSTNAME_CHECK=\"'"$master_host"'\"/g' $base_dir/config.sh set +u if [ "x${cryosparcm_port}" != "x" ]; then sed -i -e 's/export CRYOSPARC_BASE_PORT.*$/export CRYOSPARC_BASE_PORT='$cryosparcm_port'/g' $base_dir/config.sh fi set -u source $base_dir/config.sh ${cryosparcm_path} $command $* | sed -e 's/'$(hostname --fqdn)'/'${master_host}'.epfl.ch/' if [[ $command =~ '.*start' ]]; then ${cryosparcm_path} status fi diff --git a/create_user_and_lanes.sh b/generate_user_and_lanes.backup similarity index 100% rename from create_user_and_lanes.sh rename to generate_user_and_lanes.backup