Jupyterlab openmpp poc (#518)

* feat: install openmpp as jupyterlab service

* fix: generate dockerfiles

* chore: trigger auto-deploy

* fix: copy oms startup script

* fix: copy script in correct docker bit

* fix: make script executable

* fix: update openm version, fix config

* fix: sync issue

* fix: prepare openmpp config for prod deployment

* fix: move config to start-oms script

Makefile

@@ -46,6 +46,7 @@ DEFAULT_NB_PREFIX := /notebook/username/notebookname
 
 .PHONY: clean .output generate-dockerfiles
 
+
 clean:
 	rm -rf $(OUT) $(TMP)
 

docker-bits/6_jupyterlab.Dockerfile

@@ -121,6 +121,35 @@ RUN julia -e 'using Pkg; Pkg.add("LanguageServer")' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
 
+# OpenM install
+# Install OpenM++ MPI
+ARG OMPP_VERSION="1.15.4"
+# IMPORTANT: Don't forget to update the version number in the openmpp.desktop file!!
+ARG OMPP_PKG_DATE="20230803"
+ARG SHA256ompp=5da79984ef67ad16b3b7d429896b8a553930ca46a16079aaef24b3c9dc867956
+# OpenM++ environment settings
+ENV OMPP_INSTALL_DIR=/opt/openmpp/${OMPP_VERSION}
+
+# OpenM++ expects sqlite to be installed (not just libsqlite)
+RUN apt-get install --yes sqlite3 \
+    && wget -q https://github.com/openmpp/main/releases/download/v${OMPP_VERSION}/openmpp_debian_${OMPP_PKG_DATE}.tar.gz -O /tmp/ompp.tar.gz \
+    && echo "${SHA256ompp} /tmp/ompp.tar.gz" | sha256sum -c - \
+    && mkdir -p ${OMPP_INSTALL_DIR} \
+    && tar -xf /tmp/ompp.tar.gz -C ${OMPP_INSTALL_DIR} --strip-components=1
+
+# Customize and rebuild omp-ui for jupyter-ompp-proxy install
+# issue with making a relative publicPath https://github.com/quasarframework/quasar/issues/8513
+RUN sed -i -e 's/history/hash/' ${OMPP_INSTALL_DIR}/ompp-ui/quasar.conf.js \
+    && sed -i -e "s/OMS_URL:.*''/OMS_URL: '.'/" ${OMPP_INSTALL_DIR}/ompp-ui/quasar.conf.js \
+    && npm install --prefix ${OMPP_INSTALL_DIR}/ompp-ui \
+    && npm run build --prefix ${OMPP_INSTALL_DIR}/ompp-ui \
+    && rm -r ${OMPP_INSTALL_DIR}/html \
+    && mv ${OMPP_INSTALL_DIR}/ompp-ui/dist/spa ${OMPP_INSTALL_DIR}/html \
+    && fix-permissions ${OMPP_INSTALL_DIR}
+
+COPY jupyter-ompp-proxy/ /opt/jupyter-ompp-proxy/
+RUN pip install /opt/jupyter-ompp-proxy/
+
 # Solarized Theme and Cell Execution Time
 COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.json
 

docker-bits/∞_CMD.Dockerfile

@@ -6,6 +6,9 @@ EXPOSE 8888
 COPY start-custom.sh /usr/local/bin/
 COPY mc-tenant-wrapper.sh /usr/local/bin/mc
 COPY trino-wrapper.sh /usr/local/bin/trino
+COPY start-oms.sh /usr/local/bin/
+
+RUN chmod +x /usr/local/bin/start-oms.sh
 
 # Add --user to all pip install calls and point pip to Artifactory repository
 COPY pip.conf /tmp/pip.conf

docker-bits/∞_CMD_remote-desktop.Dockerfile

@@ -7,6 +7,7 @@ EXPOSE 8888
 COPY start-remote-desktop.sh /usr/local/bin/
 COPY mc-tenant-wrapper.sh /usr/local/bin/mc
 COPY trino-wrapper.sh /usr/local/bin/trino
+
 RUN chmod +x /usr/local/bin/trino
 RUN chsh -s /bin/bash $NB_USER
 

output/docker-stacks-datascience-notebook/Dockerfile

@@ -12,6 +12,9 @@ EXPOSE 8888
 COPY start-custom.sh /usr/local/bin/
 COPY mc-tenant-wrapper.sh /usr/local/bin/mc
 COPY trino-wrapper.sh /usr/local/bin/trino
+COPY start-oms.sh /usr/local/bin/
+
+RUN chmod +x /usr/local/bin/start-oms.sh
 
 # Add --user to all pip install calls and point pip to Artifactory repository
 COPY pip.conf /tmp/pip.conf

output/docker-stacks-datascience-notebook/jupyter-ompp-proxy/jupyter_ompp_proxy/__init__.py

@@ -0,0 +1,30 @@
+import os
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel("INFO")
+
+def setup_ompp():
+
+  def _get_cmd():
+
+    return [
+      "bash",
+      "-c",
+      "/usr/local/bin/start-oms.sh"
+    ]
+
+  def _rewrite_response(response):
+    if 'Location' in response.headers:
+      response.headers['Location'] = response.headers['Location'].replace('/SASStudio', os.environ.get('NB_PREFIX') + '/sasstudio/SASStudio')
+
+  return {
+    "command": _get_cmd,
+    "timeout": 60,
+    "port": 4040,
+    "launcher_entry": {
+      "title": "OpenM++",
+            "icon_path": os.path.join(os.getenv("OMPP_INSTALL_DIR", None), "html", "icons", "openmpp.svg"),
+    },
+    "rewrite_response": _rewrite_response,
+  }

output/docker-stacks-datascience-notebook/jupyter-ompp-proxy/setup.py

@@ -0,0 +1,23 @@
+import setuptools
+
+setuptools.setup(
+    name="jupyter-ompp-proxy",
+    version='0.0.1',
+    url="https://github.com/StatCan/jupyter-ompp-proxy",
+    author="Her Majesty The Queen In Right of Canada",
+    description="Jupyter extension to proxy OpenM++ webui",
+    packages=setuptools.find_packages(),
+	keywords=['SAS'],
+	classifiers=['Framework :: Jupyter'],
+    install_requires=[
+        'jupyter-server-proxy>=3.2.0'
+    ],
+    entry_points={
+        'jupyter_serverproxy_servers': [
+            'ompp = jupyter_ompp_proxy:setup_ompp'
+        ]
+    },
+    # package_data={
+    #     'jupyter_sasstudio_proxy': ['icons/sasstudio.svg'],
+    # },
+)

output/docker-stacks-datascience-notebook/start-custom.sh

@@ -151,6 +151,14 @@ if [[ "$KUBERNETES_SERVICE_HOST" =~ ".131." ]]; then
   conda config --add channels https://jfrog.aaw.cloud.statcan.ca/artifactory/api/conda/conda-pytorch-remote 
 fi
 
+# Copy default ompp models on first start up
+export OMS_MODELS_DIR="/home/jovyan/models"
+if [ ! -d "$OMS_MODELS_DIR" ]; then
+  echo "Creating ompp default model directory"
+  mkdir -p "$OMS_MODELS_DIR"
+  cp -r "$OMPP_INSTALL_DIR/models/." "$OMS_MODELS_DIR"
+fi
+
 echo "--------------------starting jupyter--------------------"
 
 /opt/conda/bin/jupyter server --notebook-dir=/home/${NB_USER} \

output/docker-stacks-datascience-notebook/start-oms.sh

@@ -0,0 +1,86 @@
+#!/usr/bin/env bash
+#
+# It does:
+#   ulimit -S -s 65536
+#   OM_ROOT=${OM_ROOT} bin/oms -oms.Listen http://localhost:${OMS_PORT} -oms.HomeDir models/home -oms.AllowDownload -oms.AllowUpload -oms.AllowMicrodata -oms.LogRequest
+#
+# Environment:
+#   OM_ROOT  - openM++ root folder, default: current directory
+#   OMS_PORT - oms web-service port to listen, default: 4040
+
+# set -e
+set -m
+
+# large models may require stack limit increase
+#
+ulimit -S -s 65536
+status=$?
+
+if [ $status -ne 0 ] ;
+then
+  echo "FAILED to set: ulimit -S -s 65536"
+  echo -n "Press Enter to exit..."
+  read any
+  exit $status
+fi
+
+# set openM++ root folder 
+#
+self=$(basename $0)
+
+OM_ROOT="$OMPP_INSTALL_DIR"
+
+[ "$OM_ROOT" != "$PWD" ] && pushd $OM_ROOT
+
+# allow to use $MODEL_NAME.ini file in UI for model run
+#
+export OM_CFG_INI_ALLOW=true
+export OM_CFG_INI_ANY_KEY=true
+export OMS_URL=${JUPYTER_SERVER_URL}ompp
+
+# OpenM++ default configuraton
+if [[ "$KUBERNETES_SERVICE_HOST" =~ ".131." ]]; then
+  #DEV
+  export OMS_MODEL_DIR=/home/jovyan/models
+  export OMS_HOME_DIR=/home/jovyan/
+else
+  if [ -d "/etc/protb" ]; then
+    export OMS_MODEL_DIR=/home/jovyan/buckets/aaw-protected-b/microsim/models
+    export OMS_HOME_DIR=/home/jovyan/buckets/aaw-protected-b/microsim/
+  else
+    export OMS_MODEL_DIR=/home/jovyan/buckets/aaw-unclassified/microsim/models
+    export OMS_HOME_DIR=/home/jovyan/buckets/aaw-unclassified/microsim/
+  fi
+fi
+
+# start oms web-service
+#
+[ -z "$OMS_PORT" ] && OMS_PORT=4040
+
+echo "OM_ROOT=$OM_ROOT"
+echo "OMS_PORT=$OMS_PORT"
+echo "OMS_URL=$OMS_URL"
+
+echo "OMS_MODEL_DIR=$OMS_MODEL_DIR"
+if [ ! -d $OMS_MODEL_DIR ]; then
+  mkdir -p $OMS_MODEL_DIR
+fi
+
+echo "OMS_HOME_DIR=$OMS_HOME_DIR"
+if [ ! -d $OMS_HOME_DIR ]; then
+  mkdir -p $OMS_HOME_DIR
+fi
+
+OM_ROOT=$OM_ROOT ./bin/oms -l localhost:${OMS_PORT} -oms.ModelDir ${OMS_MODEL_DIR} -oms.HomeDir ${OMS_HOME_DIR} -oms.AllowDownload -oms.AllowUpload -oms.AllowMicrodata -oms.LogRequest
+status=$?
+
+if [ $status -ne 0 ] ;
+then
+  [ $status -eq 130 ] && echo " oms web-service terminated by Ctrl+C"
+  [ $status -ne 130 ] && echo " FAILED to start oms web-service"
+fi
+
+echo "."
+echo -n "Press Enter to exit..."
+read any
+exit $status

output/jupyterlab-cpu/Dockerfile

@@ -291,6 +291,35 @@ RUN julia -e 'using Pkg; Pkg.add("LanguageServer")' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
 
+# OpenM install
+# Install OpenM++ MPI
+ARG OMPP_VERSION="1.15.4"
+# IMPORTANT: Don't forget to update the version number in the openmpp.desktop file!!
+ARG OMPP_PKG_DATE="20230803"
+ARG SHA256ompp=5da79984ef67ad16b3b7d429896b8a553930ca46a16079aaef24b3c9dc867956
+# OpenM++ environment settings
+ENV OMPP_INSTALL_DIR=/opt/openmpp/${OMPP_VERSION}
+
+# OpenM++ expects sqlite to be installed (not just libsqlite)
+RUN apt-get install --yes sqlite3 \
+    && wget -q https://github.com/openmpp/main/releases/download/v${OMPP_VERSION}/openmpp_debian_${OMPP_PKG_DATE}.tar.gz -O /tmp/ompp.tar.gz \
+    && echo "${SHA256ompp} /tmp/ompp.tar.gz" | sha256sum -c - \
+    && mkdir -p ${OMPP_INSTALL_DIR} \
+    && tar -xf /tmp/ompp.tar.gz -C ${OMPP_INSTALL_DIR} --strip-components=1
+
+# Customize and rebuild omp-ui for jupyter-ompp-proxy install
+# issue with making a relative publicPath https://github.com/quasarframework/quasar/issues/8513
+RUN sed -i -e 's/history/hash/' ${OMPP_INSTALL_DIR}/ompp-ui/quasar.conf.js \
+    && sed -i -e "s/OMS_URL:.*''/OMS_URL: '.'/" ${OMPP_INSTALL_DIR}/ompp-ui/quasar.conf.js \
+    && npm install --prefix ${OMPP_INSTALL_DIR}/ompp-ui \
+    && npm run build --prefix ${OMPP_INSTALL_DIR}/ompp-ui \
+    && rm -r ${OMPP_INSTALL_DIR}/html \
+    && mv ${OMPP_INSTALL_DIR}/ompp-ui/dist/spa ${OMPP_INSTALL_DIR}/html \
+    && fix-permissions ${OMPP_INSTALL_DIR}
+
+COPY jupyter-ompp-proxy/ /opt/jupyter-ompp-proxy/
+RUN pip install /opt/jupyter-ompp-proxy/
+
 # Solarized Theme and Cell Execution Time
 COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.json
 
@@ -365,6 +394,9 @@ EXPOSE 8888
 COPY start-custom.sh /usr/local/bin/
 COPY mc-tenant-wrapper.sh /usr/local/bin/mc
 COPY trino-wrapper.sh /usr/local/bin/trino
+COPY start-oms.sh /usr/local/bin/
+
+RUN chmod +x /usr/local/bin/start-oms.sh
 
 # Add --user to all pip install calls and point pip to Artifactory repository
 COPY pip.conf /tmp/pip.conf

output/jupyterlab-cpu/jupyter-ompp-proxy/jupyter_ompp_proxy/__init__.py

@@ -0,0 +1,30 @@
+import os
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel("INFO")
+
+def setup_ompp():
+
+  def _get_cmd():
+
+    return [
+      "bash",
+      "-c",
+      "/usr/local/bin/start-oms.sh"
+    ]
+
+  def _rewrite_response(response):
+    if 'Location' in response.headers:
+      response.headers['Location'] = response.headers['Location'].replace('/SASStudio', os.environ.get('NB_PREFIX') + '/sasstudio/SASStudio')
+
+  return {
+    "command": _get_cmd,
+    "timeout": 60,
+    "port": 4040,
+    "launcher_entry": {
+      "title": "OpenM++",
+            "icon_path": os.path.join(os.getenv("OMPP_INSTALL_DIR", None), "html", "icons", "openmpp.svg"),
+    },
+    "rewrite_response": _rewrite_response,
+  }

output/jupyterlab-cpu/jupyter-ompp-proxy/setup.py

@@ -0,0 +1,23 @@
+import setuptools
+
+setuptools.setup(
+    name="jupyter-ompp-proxy",
+    version='0.0.1',
+    url="https://github.com/StatCan/jupyter-ompp-proxy",
+    author="Her Majesty The Queen In Right of Canada",
+    description="Jupyter extension to proxy OpenM++ webui",
+    packages=setuptools.find_packages(),
+	keywords=['SAS'],
+	classifiers=['Framework :: Jupyter'],
+    install_requires=[
+        'jupyter-server-proxy>=3.2.0'
+    ],
+    entry_points={
+        'jupyter_serverproxy_servers': [
+            'ompp = jupyter_ompp_proxy:setup_ompp'
+        ]
+    },
+    # package_data={
+    #     'jupyter_sasstudio_proxy': ['icons/sasstudio.svg'],
+    # },
+)

output/jupyterlab-cpu/start-custom.sh

@@ -151,6 +151,14 @@ if [[ "$KUBERNETES_SERVICE_HOST" =~ ".131." ]]; then
   conda config --add channels https://jfrog.aaw.cloud.statcan.ca/artifactory/api/conda/conda-pytorch-remote 
 fi
 
+# Copy default ompp models on first start up
+export OMS_MODELS_DIR="/home/jovyan/models"
+if [ ! -d "$OMS_MODELS_DIR" ]; then
+  echo "Creating ompp default model directory"
+  mkdir -p "$OMS_MODELS_DIR"
+  cp -r "$OMPP_INSTALL_DIR/models/." "$OMS_MODELS_DIR"
+fi
+
 echo "--------------------starting jupyter--------------------"
 
 /opt/conda/bin/jupyter server --notebook-dir=/home/${NB_USER} \