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add Kubernetes deploy option to Github CD-sites action.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| #!/usr/bin/env bash | ||
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| set -ux | ||
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| show_help() { | ||
| echo "Deploys or updates a deployment of VCell on remote Kubernetes cluster" | ||
| echo "" | ||
| echo "usage: deploy-action-kubernetes.sh [OPTIONS] REQUIRED-ARGUMENTS" | ||
| echo "" | ||
| echo " REQUIRED-ARGUMENTS" | ||
| echo " manager-node any node for ssh access ( vcellapi-test.cam.uchc.edu )" | ||
| echo "" | ||
| echo " local-config-file local config file for setting environment" | ||
| echo "" | ||
| echo " [OPTIONS]" | ||
| echo " -h | --help show this message" | ||
| echo "" | ||
| echo " --ssh-user user user for ssh to node [defaults to current user id using whoami]" | ||
| echo " (user must have passwordless sudo for docker commands on manager-node)" | ||
| echo "" | ||
| echo " --build-installers optionally build client installers and place in ./generated_installers dir" | ||
| echo "" | ||
| echo " --installer-deploy-dir /path/to/installer/dir" | ||
| echo " directory for installers accessible to users" | ||
| echo " typically a web-accessible location to download the client installers for each platform" | ||
| echo "" | ||
| echo " --install-singularity optionally install batch and opt singularity images on each compute node in 'vcell' SLURM partition" | ||
| echo "" | ||
| echo "" | ||
| echo "example:" | ||
| echo "" | ||
| echo "deploy-action-kubernetes.sh \\" | ||
| echo " --ssh-user vcell \\" | ||
| echo " --install_singularity \\" | ||
| echo " --build_installers --installer_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/Test \\" | ||
| echo " vcellapi-test.cam.uchc.edu \\" | ||
| echo " ./server.config" | ||
| exit 1 | ||
| } | ||
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| if [[ $# -lt 6 ]]; then | ||
| show_help | ||
| fi | ||
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| ssh_user=$(whoami) | ||
| installer_deploy_dir= | ||
| build_installers=false | ||
| install_singularity=false | ||
| while :; do | ||
| case $1 in | ||
| -h|--help) | ||
| show_help | ||
| exit | ||
| ;; | ||
| --ssh-user) | ||
| shift | ||
| ssh_user=$1 | ||
| ;; | ||
| --installer-deploy-dir) | ||
| shift | ||
| installer_deploy_dir=$1 | ||
| ;; | ||
| --install-singularity) | ||
| install_singularity=true | ||
| ;; | ||
| --build-installers) | ||
| build_installers=true | ||
| ;; | ||
| -?*) | ||
| printf 'ERROR: Unknown option: %s\n' "$1" >&2 | ||
| echo "" | ||
| show_help | ||
| ;; | ||
| *) # Default case: No more options, so break out of the loop. | ||
| break | ||
| esac | ||
| shift | ||
| done | ||
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| if [[ $# -ne 6 ]] ; then | ||
| show_help | ||
| fi | ||
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| manager_node=$1 | ||
| local_config_file=$2 | ||
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| # get settings from config file | ||
| vcell_siteCamel=$(grep VCELL_SITE_CAMEL "$local_config_file" | cut -d"=" -f2) | ||
| vcell_version=$(grep VCELL_VERSION_NUMBER "$local_config_file" | cut -d"=" -f2) | ||
| vcell_build=$(grep VCELL_BUILD_NUMBER "$local_config_file" | cut -d"=" -f2) | ||
| batch_singularity_filename=$(grep VCELL_BATCH_SINGULARITY_FILENAME "$local_config_file" | cut -d"=" -f2) | ||
| opt_singularity_filename=$(grep VCELL_OPT_SINGULARITY_FILENAME "$local_config_file" | cut -d"=" -f2) | ||
| slurm_singularity_central_dir=$(grep VCELL_SLURM_CENTRAL_SINGULARITY_DIR "$local_config_file" | cut -d"=" -f2) | ||
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| # | ||
| # install the singularity images on the cluster nodes | ||
| # | ||
| if [ "$install_singularity" == "true" ]; then | ||
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| echo "" | ||
| pushd ../build/singularity-vm || (echo "pushd ../build/singularity-vm failed"; exit 1) | ||
| echo "" | ||
| echo "CURRENT DIRECTORY IS $PWD" | ||
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| # | ||
| # get configuration from config file and load into current bash environment | ||
| # | ||
| echo "" | ||
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| if [ ! -e "./${batch_singularity_filename}" ]; then | ||
| echo "failed to find local batch singularity image file $batch_singularity_filename in ./singularity-vm directory" | ||
| exit 1 | ||
| fi | ||
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| if ! scp "./${batch_singularity_filename}" "$ssh_user@$manager_node:${slurm_singularity_central_dir}"; then | ||
| echo "failed to copy batch singularity image to server" | ||
| exit 1 | ||
| fi | ||
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| if [ ! -e "./${opt_singularity_filename}" ]; then | ||
| echo "failed to find local opt singularity image file $opt_singularity_filename in ./singularity-vm directory" | ||
| exit 1 | ||
| fi | ||
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| if ! scp "./${opt_singularity_filename}" "$ssh_user@$manager_node:${slurm_singularity_central_dir}"; then | ||
| echo "failed to copy opt singularity image to server" | ||
| exit 1 | ||
| fi | ||
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| echo "popd" | ||
| popd || (echo "popd failed"; exit 1) | ||
| fi | ||
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| # | ||
| # if --build-installers, then generate client installers, placing then in ./generated_installers | ||
| # if --installer-deploy-dir, then also copy installers to $installer_deploy_dir | ||
| # *** unimplemented *** (if --link-installers, then also link installers to version independent installer names for each platform) | ||
| # | ||
| if [ "$build_installers" == "true" ]; then | ||
| # | ||
| # if --installer-deploy-dir, then copy the installers from ./generated_installers directory to the installer deploy directory | ||
| # | ||
| if [ ! -z "$installer_deploy_dir" ]; then | ||
| # vcell_siteCamel=Alpha | ||
| # vcell_version=7.0.0 | ||
| # vcell_build=19 | ||
| # version=7_0_0_19 | ||
| version=$(echo "${vcell_version}_${vcell_build}" | tr '.' _) | ||
| if ! scp "./generated_installers/VCell_${vcell_siteCamel}_windows-x64_${version}_64bit.exe" \ | ||
| "./generated_installers/VCell_${vcell_siteCamel}_unix_${version}_32bit.sh" \ | ||
| "./generated_installers/VCell_${vcell_siteCamel}_macos_${version}_64bit.dmg" \ | ||
| "./generated_installers/VCell_${vcell_siteCamel}_windows-x32_${version}_32bit.exe" \ | ||
| "./generated_installers/VCell_${vcell_siteCamel}_unix_${version}_64bit.sh" \ | ||
| "./generated_installers/updates.xml" \ | ||
| "./generated_installers/updates_linux32.xml" \ | ||
| "./generated_installers/updates_linux64.xml" \ | ||
| "./generated_installers/updates_mac64.xml" \ | ||
| "./generated_installers/updates_win32.xml" \ | ||
| "./generated_installers/updates_win64.xml" \ | ||
| "./generated_installers/output.txt" \ | ||
| "./generated_installers/md5sums" \ | ||
| "./generated_installers/sha256sums" \ | ||
| "$ssh_user@$manager_node:${installer_deploy_dir}"; | ||
| then | ||
| echo "failed to copy installers"; | ||
| exit 1; | ||
| fi | ||
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| fi | ||
| fi | ||
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| echo "exited normally" | ||
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| exit 0 |
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