remove singularity from vcell CI/CD (keep it in CLI/biosimulations)

virtualcell · Sep 26, 2024 · 8ebbdba · 8ebbdba
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commit 8ebbdba
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diff --git a/.github/workflows/CI-full.yml b/.github/workflows/CI-full.yml
@@ -94,34 +94,22 @@ jobs:
         java-version: '17'
         cache: 'maven'
 
-    - name: Install Singularity # to make singularity image for cluster
-      uses: eWaterCycle/setup-singularity@v6
-      with:
-        singularity-version: 3.7.1
     - name: build and publish all images
       shell: bash
       run: |
         cd docker/build
         sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
         docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
         ./build.sh all ${{ env.VCELL_REPO_NAMESPACE }} ${{ env.VCELL_TAG }}
-        cd singularity-vm
-        singularity remote login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} oras://ghcr.io
-    - name: tag as latest and push to registry  # (jcs) are explicit singularity push commands redundant? (see ./build.sh)
+
+    - name: tag as latest and push to registry
       shell: bash
       run: |
         for CONTAINER in vcell-api vcell-rest vcell-webapp-prod vcell-webapp-dev vcell-webapp-stage vcell-webapp-island vcell-batch vcell-opt vcell-clientgen vcell-data vcell-db vcell-mongo vcell-sched vcell-submit vcell-admin;\
-        do docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:latest;\
-        docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:${{ steps.version.outputs.tag }};\
-        docker push --all-tags ${VCELL_REPO_NAMESPACE}/$CONTAINER;\
+           do docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:latest;\
+           docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:${{ steps.version.outputs.tag }};\
+           docker push --all-tags ${VCELL_REPO_NAMESPACE}/$CONTAINER;\
         done
-        cd docker/build/singularity-vm
-        singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${VCELL_TAG}
-        singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${{ steps.version.outputs.tag }}
-        singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:latest
-        singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${VCELL_TAG}
-        singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${{ steps.version.outputs.tag }}
-        singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:latest
 
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v3

diff --git a/.github/workflows/site_deploy.yml b/.github/workflows/site_deploy.yml
@@ -182,20 +182,6 @@ jobs:
         ssh-keyscan $VCELL_MANAGER_NODE >> ~/.ssh/known_hosts
         cd docker/swarm
         scp ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/${VCELL_CONFIG_FILE_NAME} .
-    - name: install singularity
-      uses: eWaterCycle/setup-singularity@v6
-      with:
-        singularity-version: 3.7.1
-    - name: retrieve batch and opt singularity images
-      run: |
-        set -ux
-        cd docker/swarm
-        export BATCH_SINGULARITY_FILENAME=`cat $VCELL_CONFIG_FILE_NAME | grep VCELL_BATCH_SINGULARITY_FILENAME | cut -d"=" -f2`
-        export OPT_SINGULARITY_FILENAME=`cat $VCELL_CONFIG_FILE_NAME | grep VCELL_OPT_SINGULARITY_FILENAME | cut -d"=" -f2`
-        cd ../build/singularity-vm
-        singularity remote login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} oras://ghcr.io
-        singularity pull $BATCH_SINGULARITY_FILENAME oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
-        singularity pull $OPT_SINGULARITY_FILENAME   oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
     - name: setup java 17 with maven cache (for documentation build)
       uses: actions/setup-java@v4
       with:
@@ -207,16 +193,15 @@ jobs:
       run: |
         set -ux
         mvn clean install -DskipTests
-    - name: deploy installers and singularity to kubernetes site and web help to vcell.org
+    - name: deploy installers and web help to vcell.org
       run: |
         set -ux
         cd docker/swarm
         ssh -t ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE} sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
         if ${{ github.event.inputs.server_only != 'true' }}; then
-          # build and install the client installers, the singularity images, and the web help (kubernetes cluster deployments are separate)
+          # build and install the client installers, and the web help (kubernetes cluster deployments are separate)
           ./deploy-action-kubernetes.sh \
               --ssh-user ${{ secrets.CD_FULL_USER }} \
-              --install-singularity \
               --build-installers \
               --installer-deploy-dir $VCELL_INSTALLER_REMOTE_DIR \
               --webhelp-local-dir ../../vcell-client/target/classes/vcellDoc \
@@ -227,13 +212,6 @@ jobs:
           ssh ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE} \
             installer_deploy_dir=$VCELL_INSTALLER_REMOTE_DIR vcell_siteCamel=$VCELL_SITE_CAMEL vcell_version=$VCELL_VERSION vcell_build=$VCELL_BUILD \
             'bash -s' < link-installers.sh
-        else
-          # build and install only the singularity images (kubernetes cluster deployments are separate)
-          ./deploy-action-kubernetes.sh \
-              --ssh-user ${{ secrets.CD_FULL_USER }} \
-              --install-singularity  \
-              ${VCELL_MANAGER_NODE} \ 
-              ./${VCELL_CONFIG_FILE_NAME}
         fi
     - name: Capitalize first character of site name
       id: capitalize

diff --git a/docker/build/Dockerfile-submit-dev b/docker/build/Dockerfile-submit-dev
@@ -71,7 +71,6 @@ ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
     htc_vcellbatch_docker_name="htc-vcellbatch-docker-name-not-set" \
     htc_vcellbatch_solver_list="htc-vcellbatch-solver-list-not-set" \
     htc_vcellopt_docker_name="htc-vcellopt-docker-name-not-set" \
-    opt_singularity_imagefile=/path/to/external/opt/singularity_opt.img \
     batchhost="batch-host-not-set" \
     batchuser="batch-user-not-set" \
     slurm_cmd_sbatch=sbatch \

diff --git a/docker/swarm/deploy-action-kubernetes.sh b/docker/swarm/deploy-action-kubernetes.sh
@@ -3,7 +3,7 @@
 set -ux
 
 show_help() {
-	echo "Deploys vcell client installers, webhelp and singularity images for a Kubernetes deploy"
+	echo "Deploys vcell client installers and webhelp for a Kubernetes deploy"
 	echo ""
 	echo "usage: deploy-action-kubernetes.sh [OPTIONS] REQUIRED-ARGUMENTS"
 	echo ""
@@ -30,14 +30,11 @@ show_help() {
 	echo "    --webhelp-deploy-dir /remote/path/to/web/VCell_Help"
 	echo "                          directory for deployed html webhelp published on web server"
 	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/Alpha \\"
 	echo "   --webhelp_local_dir ../../vcell-client/target/classes/vcellDoc \\"
 	echo "   --webhelp_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/VCell_Tutorials/VCell_Help \\"
@@ -55,7 +52,6 @@ installer_deploy_dir=
 webhelp_local_dir=
 webhelp_deploy_dir=
 build_installers=false
-install_singularity=false
 while :; do
 	case $1 in
 		-h|--help)
@@ -78,9 +74,6 @@ while :; do
 			shift
 			webhelp_deploy_dir=$1
 			;;
-		--install-singularity)
-			install_singularity=true
-			;;
 		--build-installers)
 			build_installers=true
 			;;
@@ -106,50 +99,6 @@ local_config_file=$2
 vcell_siteCamel=$(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 "$local_config_file" | cut -d"=" -f2)
-
-
-#
-# install the singularity images on the cluster nodes
-#
-if [ "$install_singularity" == "true" ]; then
-
-	echo ""
-	pushd ../build/singularity-vm || (echo "pushd ../build/singularity-vm failed"; exit 1)
-	echo ""
-	echo "CURRENT DIRECTORY IS $PWD"
-
-	#
-	# get configuration from config file and load into current bash environment
-	#
-	echo ""
-
-	if [ ! -e "./${batch_singularity_filename}" ]; then
-		echo "failed to find local batch singularity image file $batch_singularity_filename in ./singularity-vm directory"
-		exit 1
-	fi
-
-	if ! scp "./${batch_singularity_filename}" "$ssh_user@$manager_node:${slurm_singularity_central_dir}"; then
-    echo "failed to copy batch singularity image to server"
-    exit 1
-  fi
-
-	if [ ! -e "./${opt_singularity_filename}" ]; then
-		echo "failed to find local opt singularity image file $opt_singularity_filename in ./singularity-vm directory"
-		exit 1
-	fi
-
-	if ! scp "./${opt_singularity_filename}" "$ssh_user@$manager_node:${slurm_singularity_central_dir}"; then
-	  echo "failed to copy opt singularity image to server"
-	  exit 1
-	fi
-
-	echo "popd"
-	popd || (echo "popd failed"; exit 1)
-fi
-
 
 #
 # if --build-installers, then generate client installers, placing then in ./generated_installers