Merge pull request #153 from ubccr/isc-hpc-updates

aebruno · web-flow · commit fa35052343a0 · 2023-04-19T09:06:50.000-04:00
First pass at updates for ISC HPC
diff --git a/.env b/.env
@@ -1,4 +1,5 @@
-HPCTS_VERSION="2022.07"
+HPCTS_VERSION="2023.05"
 SLURM_VERSION="21.08.8-2"
 MARIADB_VERSION=10.3
 MONGODB_VERSION=5.0
+COLDFRONT_RESTORE="true"
diff --git a/coldfront/Dockerfile b/coldfront/Dockerfile
@@ -13,6 +13,7 @@ RUN /build/install.sh && rm -rf /build
 COPY --chown=coldfront:coldfront local_settings.py /etc/coldfront/local_settings.py
 COPY --chown=coldfront:coldfront coldfront.env /etc/coldfront/coldfront.env
 COPY --chown=coldfront:coldfront checkdb.py /srv/www/checkdb.py
+COPY coldfront.dump /usr/share/coldfront/coldfront.dump
 COPY coldfront-nginx.conf /etc/nginx/conf.d/coldfront.conf
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
diff --git a/coldfront/coldfront.dump b/coldfront/coldfront.dump
diff --git a/coldfront/entrypoint.sh b/coldfront/entrypoint.sh
@@ -24,7 +24,7 @@ then
 
     if ! coldfront show_users_in_project_but_not_in_allocation &> /dev/null; then
         echo "-- Initializing coldfront database..."
-        coldfront initial_setup
+        coldfront initial_setup -f
 
         echo "-- Generating static css files..."
         coldfront collectstatic
@@ -34,6 +34,11 @@ then
                coldfront shell
     fi
 
+    if [ "$2" = "true" ]; then
+        echo "---> Restoring coldfront database..."
+        mysql --host mysql --user coldfrontapp --password=9obCuAphabeg coldfront < /usr/share/coldfront/coldfront.dump
+    fi
+
     echo "---> Starting nginx on coldfront..."
     /sbin/nginx
 
diff --git a/coldfront/install.sh b/coldfront/install.sh
@@ -11,8 +11,7 @@ ARCHTYPE=`uname -m`
 
 log_info "Installing required packages for coldfront.."
 dnf install -y \
-    python3 \
-    python3-devel \
+    python39-devel \
     memcached \
     nginx \
     openssl \
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -160,7 +160,7 @@ services:
       context: ./coldfront
       args:
         HPCTS_VERSION: $HPCTS_VERSION
-    command: ["serve"]
+    command: ["serve", $COLDFRONT_RESTORE]
     hostname: coldfront
     container_name: coldfront
     networks:
diff --git a/hpcts b/hpcts
@@ -10,10 +10,10 @@ log_warn() {
 
 start() {
     log_info "Fetching latest HPC Toolset Images.."
-    docker-compose pull
+    docker compose pull
 
     log_info "Starting HPC Toolset Cluster.."
-    docker-compose up -d --no-build
+    docker compose up -d --no-build
 
     log_info "Coldfront URL: https://localhost:2443"
     log_info "OnDemand URL: https://localhost:3443"
@@ -23,14 +23,14 @@ start() {
 
 stop() {
     log_info "Stopping HPC Toolset Cluster containers.."
-    docker-compose stop
+    docker compose stop
 }
 
 destroy() {
     log_info "Stopping and removing HPC Toolset Cluster containers and volumes.."
-    docker-compose stop && \
-    docker-compose rm -f -v && \
-    docker-compose down -v
+    docker compose stop && \
+    docker compose rm -f -v && \
+    docker compose down -v
 }
 
 cleanup() {
diff --git a/ondemand/Dockerfile b/ondemand/Dockerfile
@@ -1,9 +1,8 @@
 ARG HPCTS_VERSION=latest
 
 FROM --platform=linux/amd64 ubccr/hpcts:slurm-${HPCTS_VERSION} as stage-amd64
-RUN dnf install -y https://yum.osc.edu/ondemand/2.0/ondemand-release-web-2.0-1.noarch.rpm
+RUN dnf install -y https://yum.osc.edu/ondemand/3.0/ondemand-release-web-3.0-1.noarch.rpm
 RUN dnf install -y netcat ondemand ondemand-dex
-RUN sed -i 's/\-nohttpd//' /opt/ood/ondemand/root/usr/share/gems/2.7/ondemand/2.0.27/gems/ood_core-0.19.0/lib/ood_core/batch_connect/templates/vnc.rb
 
 FROM --platform=linux/arm64 ubccr/hpcts:slurm-${HPCTS_VERSION} as stage-arm64
 RUN dnf install -y file lsof sudo gcc gcc-c++ git \
@@ -16,7 +15,6 @@ COPY . /build
 RUN /build/install-dex-arm64.sh
 RUN /build/install-passenger-arm64.sh
 RUN /build/install-ood-arm64.sh
-RUN sed -i 's/\-nohttpd//' /usr/share/gems/gems/ood_core-0.19.0/lib/ood_core/batch_connect/templates/vnc.rb
 RUN rm -rf /build
 
 ARG TARGETARCH
@@ -35,6 +33,4 @@ COPY notebook_data /data/notebook_data
 COPY initializers/dashboard.rb /etc/ood/config/apps/dashboard/initializers/dashboard.rb
 COPY themes/hpc-coop /usr/share/ondemand-dex/web/themes/hpc-coop
 
-RUN sed -i '/  passenger_load_shell_envvars off;/a   passenger_preload_bundler on;' /opt/ood/nginx_stage/templates/pun.conf.erb
-
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
diff --git a/ondemand/cluster-config.yml b/ondemand/cluster-config.yml
@@ -13,7 +13,7 @@ v2:
     vnc:
       script_wrapper: |
         export PATH="/opt/TurboVNC/bin:$PATH"
-        export WEBSOCKIFY_CMD="/usr/bin/websockify"
+        export WEBSOCKIFY_CMD="/usr/local/bin/websockify"
         %s
   custom:
     xdmod:
diff --git a/ondemand/install-dex-arm64.sh b/ondemand/install-dex-arm64.sh
@@ -7,8 +7,8 @@ log_info() {
   printf "\n\e[0;35m $1\e[0m\n\n"
 }
 
-DEX_VERSION=${DEX_VERSION:-2.31.1}
-DEX_PATCH_VERSION=${DEX_PATCH_VERSION:-703e26bc109e86d00be22ef1803bdb96b2dc09e2}
+DEX_VERSION=${DEX_VERSION:-2.32.0}
+DEX_PATCH_VERSION=${DEX_PATCH_VERSION:-9366a1969bd656daa1df44e0bdd02f14437ed466}
 
 dnf install -y golang-bin
 log_info "Install dex ${DEX_VERSION}..."
diff --git a/ondemand/install-ood-arm64.sh b/ondemand/install-ood-arm64.sh
@@ -28,7 +28,7 @@ sh autogen.sh
 make && make install
 
 cd $BUILD_DIR
-OOD_VERSION='2.0.27'
+OOD_VERSION='3.0.0'
 wget "https://github.com/OSC/ondemand/archive/refs/tags/v$OOD_VERSION.tar.gz"
 tar -xf "v$OOD_VERSION.tar.gz"
 cd ondemand-$OOD_VERSION
diff --git a/ondemand/install.sh b/ondemand/install.sh
@@ -38,6 +38,7 @@ ssl:
 node_uri: "/node"
 rnode_uri: "/rnode"
 oidc_scope: "openid profile email groups"
+dex_uri: false
 dex:
   client_redirect_uris:
     - "https://localhost:4443/simplesaml/module.php/authoidcoauth2/linkback.php"
diff --git a/slurm/install.sh b/slurm/install.sh
@@ -8,14 +8,14 @@ log_info() {
 }
 
 SLURM_VERSION=${SLURM_VERSION:-21.08.8-2}
-WEBSOCKIFY_VERSION=${WEBSOCKIFY_VERSION:-0.8.0}
+WEBSOCKIFY_VERSION=${WEBSOCKIFY_VERSION:-0.11.0}
 ARCHTYPE=`uname -m`
 
 log_info "Installing required packages for building slurm.."
 curl -o /etc/yum.repos.d/turbovnc.repo https://turbovnc.org/pmwiki/uploads/Downloads/TurboVNC.repo
 dnf -y install dnf-plugins-core
 dnf -y config-manager --set-enabled powertools
-dnf -y module enable ruby:2.7 nodejs:12
+dnf -y module enable ruby:3.0 nodejs:14
 dnf install -y \
     @Development \
     munge \
@@ -33,21 +33,23 @@ dnf install -y \
     mariadb \
     turbovnc \
     mariadb-devel \
-    python3 \
+    python39 \
     python2-numpy \
     kitty-terminfo \
     stress
 
 log_info "Installing compute packages .."
 
+alternatives --set python3 /usr/bin/python3.9
+
 dnf groupinstall -y "Xfce"
 
 log_info "Compiling python-websockify version ${WEBSOCKIFY_VERSION}.."
 wget -O /tmp/websockify-${WEBSOCKIFY_VERSION}.tar.gz https://github.com/novnc/websockify/archive/refs/tags/v${WEBSOCKIFY_VERSION}.tar.gz
 pushd /tmp
 tar xzf websockify-${WEBSOCKIFY_VERSION}.tar.gz
 pushd websockify-${WEBSOCKIFY_VERSION}
-python2 setup.py install
+python3 setup.py install
 popd
 rm -rf /tmp/websockify*
 
@@ -109,7 +111,7 @@ sed -i 's#^LOCALHOSTNAME.*$#LOCALHOSTNAME   y   n   "/home/pcp/$(date +%Y)/$(dat
 log_info "Installing Jupyter.."
 python3 -m venv --without-pip --prompt jupyter/2.1.4 /usr/local/jupyter/2.1.4
 source /usr/local/jupyter/2.1.4/bin/activate
-curl https://bootstrap.pypa.io/pip/3.6/get-pip.py | python
+curl https://bootstrap.pypa.io/get-pip.py | python
 
 pip install jupyterlab==2.1.4 jupyter-console qtconsole ipywidgets plotly==4.8.2 pandas scikit-learn numpy
 deactivate
diff --git a/xdmod/install.sh b/xdmod/install.sh
@@ -19,8 +19,13 @@ ARCHTYPE=`uname -m`
 # needed for automated setup, not for supremm
 #------------------------
 
+dnf module -y reset nodejs
+dnf module -y install nodejs:16
+
 dnf install -y \
     expect \
+    python3-devel \
+    pcp-devel \
     python3-pexpect \
     php-pear \
     php-devel
@@ -37,10 +42,13 @@ dnf install -y \
 # be installed in the same container.  In a production deployment they may be installed
 # on separate hosts.
 #------------------------
-dnf install -y https://github.com/ubccr/xdmod/releases/download/v10.0.0-beta5-el8/xdmod-10.0.0-1.5.beta5.el8.noarch.rpm \
+dnf install -y https://github.com/ubccr/xdmod/releases/download/v10.0.2-beta1-el8/xdmod-10.0.2-1.0.el8.noarch.rpm \
                https://github.com/ubccr/xdmod-ondemand/releases/download/v10.0.0/xdmod-ondemand-10.0.0-1.0.beta1.el8.noarch.rpm \
                https://github.com/ubccr/xdmod/releases/download/v10.0.0-beta4-el8/xdmod-supremm-10.0.0-1.4.beta4.el8.noarch.rpm \
-               https://github.com/ubccr/supremm/releases/download/2.0.0-beta3/supremm-2.0.0-1.0_beta3.el8."$ARCHTYPE".rpm
+               https://github.com/ubccr/xdmod-appkernels/releases/download/v10.0.0/xdmod-appkernels-10.0.0-1.0.beta1.el8.noarch.rpm
+
+# supremm rpm has broken deps so we force install the rpm and install the deps via pip
+rpm --nodeps -ivh https://github.com/ubccr/supremm/releases/download/2.0.0-beta3/supremm-2.0.0-1.0_beta3.el8."$ARCHTYPE".rpm
 
 #------------------------
 # The Job Performance software uses MongoDB to store the job-level performance
@@ -53,14 +61,19 @@ dnf install -y \
     https://repo.mongodb.org/yum/redhat/8/mongodb-org/5.0/${ARCHTYPE}/RPMS/mongodb-org-shell-5.0.9-1.el8.${ARCHTYPE}.rpm
 
 
-
 #------------------------
 #
 #------------------------
 pecl install mongodb
 echo "extension=mongodb.so" >> /etc/php.d/40-mongodb.ini
 
-pip3 install pymongo==3.7.0 --upgrade
+# This is required because /usr/bin/supremm-setup uses the platform-python
+/usr/libexec/platform-python -m pip install pymongo==3.7.0 --upgrade
+/usr/libexec/platform-python -m pip install pytz
+/usr/libexec/platform-python -m pip install scipy
+/usr/libexec/platform-python -m pip install Cython
+/usr/libexec/platform-python -m pip install pcp
+/usr/libexec/platform-python -m pip install PyMySQL
 
 #------------------------
 # O/S package configuration.
diff --git a/xdmod/scripts/supremm.py b/xdmod/scripts/supremm.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/libexec/platform-python
 import pexpect
 import sys
 
diff --git a/xdmod/scripts/xdmod-setup-ondemand.tcl b/xdmod/scripts/xdmod-setup-ondemand.tcl
@@ -36,7 +36,7 @@ confirmFileWrite yes
 enterToContinue
 
 # Setup the OnDemand database
-selectMenuOption 10
+selectMenuOption 11
 
 selectMenuOption d
 
diff --git a/xdmod/scripts/xdmod-setup-supremm.tcl b/xdmod/scripts/xdmod-setup-supremm.tcl
@@ -19,7 +19,7 @@ source [file join [file dirname [info script]] helper-functions.tcl]
 set timeout 240
 spawn "xdmod-setup"
 
-selectMenuOption 9
+selectMenuOption 10
 
 selectMenuOption d
 answerQuestionAlt {DB Admin Username:} root

Original file line number	Diff line number	Diff line change
`@@ -7,8 +7,8 @@ log_info() {`
`7`	`7`	`printf "\n\e[0;35m $1\e[0m\n\n"`
`8`	`8`	`}`
`9`	`9`
`10`		`-DEX_VERSION=${DEX_VERSION:-2.31.1}`
`11`		`-DEX_PATCH_VERSION=${DEX_PATCH_VERSION:-703e26bc109e86d00be22ef1803bdb96b2dc09e2}`
	`10`	`+DEX_VERSION=${DEX_VERSION:-2.32.0}`
	`11`	`+DEX_PATCH_VERSION=${DEX_PATCH_VERSION:-9366a1969bd656daa1df44e0bdd02f14437ed466}`
`12`	`12`
`13`	`13`	`dnf install -y golang-bin`
`14`	`14`	`log_info "Install dex ${DEX_VERSION}..."`