Merge pull request #8 from guimou/cuda-monai

Monai + Streamlit 1.10.0

.gitignore

@@ -5,7 +5,6 @@ node_modules/
 *.egg-info/
 .ipynb_checkpoints
 *.tsbuildinfo
-*.lock
 __pycache__
 
 # Ensure embedme does not run ont node_modules README.md files.

CHANGELOG.md

@@ -13,6 +13,18 @@ Nothing there!
 
 ### Added
 
+- New notebook image: CUDA 11.6.2 + Monai 0.9.0 + Streamlit 1.10.0 notebook (quay.io/guimou/s2i-monai-notebook:0.0.2)
+
+### Modified
+
+- Streamlit image updated to streamlit 1.10.0 - fixes #5
+- fix Streamlit launch scripts for directory context - fixes #6
+- new streamlit image: quay.io/guimou/s2i-generic-data-science-streamlit-notebook:0.0.7
+
+## [0.0.10] - 2022-06-22
+
+### Added
+
 - nbgitpuller added to Streamlit notebook (quay.io/guimou/s2i-generic-data-science-streamlit-notebook:0.0.6)
 
 ### Modified

monai-notebook/README.md

@@ -0,0 +1,16 @@
+# Monai Notebook
+
+Custom notebook based on RHODS standard data science notebook, adding:
+
+* CUDA, which is a requirement for Monai.
+
+* [Monai](https://monai.io/) ([Github repo](https://github.com/Project-MONAI))
+
+MONAI is a freely available, community-supported, PyTorch-based framework for deep learning in healthcare imaging. It provides domain-optimized foundational capabilities for developing healthcare imaging training workflows in a native PyTorch paradigm.
+Project MONAI also includes MONAI Label, an intelligent open source image labeling and learning tool that helps researchers and clinicians collaborate, create annotated datasets, and build AI models in a standardized MONAI paradigm.
+
+* [Streamlit](https://streamlit.io/) ([Github repo](https://github.com/streamlit/streamlit))
+
+Streamlit turns data scripts into shareable web apps in minutes.
+All in pure Python. No front‑end experience required.
+See [details on Streamlit implementation](../streamlit-notebook/README.md).

monai-notebook/container/3.9/root/opt/app-root/etc/generate_container_user

@@ -0,0 +1,19 @@
+# Set current user in nss_wrapper
+USER_ID=$(id -u)
+GROUP_ID=$(id -g)
+
+if [ x"$USER_ID" != x"0" -a x"$USER_ID" != x"1001" ]; then
+
+    NSS_WRAPPER_PASSWD=/opt/app-root/etc/passwd
+    NSS_WRAPPER_GROUP=/etc/group
+
+    cat /etc/passwd | sed -e 's/^default:/builder:/' > $NSS_WRAPPER_PASSWD
+
+    echo "default:x:${USER_ID}:${GROUP_ID}:Default Application User:${HOME}:/sbin/nologin" >> $NSS_WRAPPER_PASSWD
+
+    export NSS_WRAPPER_PASSWD
+    export NSS_WRAPPER_GROUP
+
+    LD_PRELOAD=libnss_wrapper.so
+    export LD_PRELOAD
+fi

monai-notebook/container/3.9/root/opt/app-root/etc/scl_enable

@@ -0,0 +1,9 @@
+# IMPORTANT: Do not add more content to this file unless you know what you are
+#            doing. This file is sourced everytime the shell session is opened.
+# This will make scl collection binaries work out of box.
+unset BASH_ENV PROMPT_COMMAND ENV
+if head "/etc/redhat-release" | grep -q "^CentOS Linux release 7" || \
+   head "/etc/redhat-release" | grep -q "^Red Hat Enterprise Linux\( Server\)\? release 7"; then
+    source scl_source enable httpd24 $NODEJS_SCL rh-python39
+fi
+source /opt/app-root/bin/activate

monai-notebook/container/3.9/s2i/bin/assemble

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+# Thoth patch already applied
+
+function is_django_installed() {
+  python -c "import django" &>/dev/null
+}
+
+function should_collectstatic() {
+  is_django_installed && [[ -z "$DISABLE_COLLECTSTATIC" ]]
+}
+
+function virtualenv_bin() {
+    # New versions of Python (>3.6) should use venv module
+    # from stdlib instead of virtualenv package
+    python3.9 -m venv $1
+}
+
+set -e
+
+shopt -s dotglob
+echo "---> Installing application source ..."
+mv /tmp/src/* "$HOME"
+
+# set permissions for any installed artifacts
+fix-permissions /opt/app-root -P
+
+if [[ ! -z "$UPGRADE_PIP_TO_LATEST" ]]; then
+  echo "---> Upgrading pip, setuptools and wheel to latest version ..."
+  if ! pip install -U pip setuptools wheel; then
+    echo "WARNING: Installation of the latest pip, setuptools and wheel failed, trying again from official PyPI with pip --isolated install"
+    pip install --isolated -U pip setuptools wheel
+  fi
+fi
+
+if [[ -z "$PIP_INDEX_URL" ]]; then
+  thamos install
+else
+  pip install -r requirements.txt
+fi
+
+if [[ ( -f setup.py || -f setup.cfg ) && -z "$DISABLE_SETUP_PY_PROCESSING" ]]; then
+  echo "---> Installing application ..."
+  pip install .
+fi
+
+if should_collectstatic; then
+  (
+    echo "---> Collecting Django static files ..."
+
+    APP_HOME=$(readlink -f "${APP_HOME:-.}")
+    # Change the working directory to APP_HOME
+    PYTHONPATH="$(pwd)${PYTHONPATH:+:$PYTHONPATH}"
+    cd "$APP_HOME"
+
+    # Look for 'manage.py' in the current directory
+    manage_file=./manage.py
+
+    if [[ ! -f "$manage_file" ]]; then
+      echo "WARNING: seems that you're using Django, but we could not find a 'manage.py' file."
+      echo "'manage.py collectstatic' ignored."
+      exit
+    fi
+
+    if ! python $manage_file collectstatic --dry-run --noinput &> /dev/null; then
+      echo "WARNING: could not run 'manage.py collectstatic'. To debug, run:"
+      echo "    $ python $manage_file collectstatic --noinput"
+      echo "Ignore this warning if you're not serving static files with Django."
+      exit
+    fi
+
+    python $manage_file collectstatic --noinput
+  )
+fi
+
+# set permissions for any installed artifacts
+fix-permissions /opt/app-root -P

monai-notebook/container/3.9/s2i/bin/init-wrapper

@@ -0,0 +1,18 @@
+#!/bin/sh
+
+# Overview of how this script works: http://veithen.io/2014/11/16/sigterm-propagation.html
+# Set a trap to kill the main app process when this
+# init script receives SIGTERM or SIGINT
+trap 'kill -s TERM $PID' TERM INT
+# Execute the main application in the background
+"$@" &
+PID=$!
+# wait command always terminates when trap is caught, even if the process hasn't finished yet
+wait $PID
+# Remove the trap and wait till the app process finishes completely
+trap - TERM INT
+# We wait again, since the first wait terminates when trap is caught
+wait $PID
+# Exit with the exit code of the app process
+STATUS=$?
+exit $STATUS

monai-notebook/container/3.9/s2i/bin/run

@@ -0,0 +1,142 @@
+#!/bin/bash
+source /opt/app-root/etc/generate_container_user
+
+set -e
+
+function is_gunicorn_installed() {
+  hash gunicorn &>/dev/null
+}
+
+function is_django_installed() {
+  python -c "import django" &>/dev/null
+}
+
+function should_migrate() {
+  is_django_installed && [[ -z "$DISABLE_MIGRATE" ]]
+}
+
+# Guess the number of workers according to the number of cores
+function get_default_web_concurrency() {
+  limit_vars=$(cgroup-limits)
+  local $limit_vars
+  if [ -z "${NUMBER_OF_CORES:-}" ]; then
+    echo 1
+    return
+  fi
+
+  local max=$((NUMBER_OF_CORES*2))
+  # Require at least 43 MiB and additional 40 MiB for every worker
+  local default=$(((${MEMORY_LIMIT_IN_BYTES:-MAX_MEMORY_LIMIT_IN_BYTES}/1024/1024 - 43) / 40))
+  default=$((default > max ? max : default))
+  default=$((default < 1 ? 1 : default))
+  # According to http://docs.gunicorn.org/en/stable/design.html#how-many-workers,
+  # 12 workers should be enough to handle hundreds or thousands requests per second
+  default=$((default > 12 ? 12 : default))
+  echo $default
+}
+
+function maybe_run_in_init_wrapper() {
+  if [[ -z "$ENABLE_INIT_WRAPPER" ]]; then
+    exec "$@"
+  else
+    exec $STI_SCRIPTS_PATH/init-wrapper "$@"
+  fi
+}
+
+APP_HOME=$(readlink -f "${APP_HOME:-.}")
+# Change the working directory to APP_HOME
+PYTHONPATH="$(pwd)${PYTHONPATH:+:$PYTHONPATH}"
+cd "$APP_HOME"
+
+if [ -z "$APP_SCRIPT" ] && [ -z "$APP_FILE" ] && [ -z "$APP_MODULE" ]; then
+  # Set default values for APP_SCRIPT and APP_FILE only when all three APP_
+  # variables are not defined by user. This prevents a situation when
+  # APP_MODULE is defined to app:application but the app.py file is found as the
+  # APP_FILE and then executed by Python instead of gunicorn.
+  APP_SCRIPT="app.sh"
+  APP_SCRIPT_DEFAULT=1
+  APP_FILE="app.py"
+  APP_FILE_DEFAULT=1
+fi
+
+if [ ! -z "$APP_SCRIPT" ]; then
+  if [[ -f "$APP_SCRIPT" ]]; then
+    echo "---> Running application from script ($APP_SCRIPT) ..."
+    if [[ "$APP_SCRIPT" != /* ]]; then
+      APP_SCRIPT="./$APP_SCRIPT"
+    fi
+    maybe_run_in_init_wrapper "$APP_SCRIPT"
+  elif [[ -z "$APP_SCRIPT_DEFAULT" ]]; then
+    echo "ERROR: file '$APP_SCRIPT' not found." && exit 1
+  fi
+fi
+
+if [ ! -z "$APP_FILE" ]; then
+  if [[ -f "$APP_FILE" ]]; then
+    echo "---> Running application from Python script ($APP_FILE) ..."
+    maybe_run_in_init_wrapper python "$APP_FILE"
+  elif [[ -z "$APP_FILE_DEFAULT" ]]; then
+    echo "ERROR: file '$APP_FILE' not found." && exit 1
+  fi
+fi
+
+# Look for 'manage.py' in the current directory
+manage_file=./manage.py
+
+if should_migrate; then
+  if [[ -f "$manage_file" ]]; then
+    echo "---> Migrating database ..."
+    python "$manage_file" migrate --noinput
+  else
+    echo "WARNING: seems that you're using Django, but we could not find a 'manage.py' file."
+    echo "Skipped 'python manage.py migrate'."
+  fi
+fi
+
+# If not set, use 8080 as the default port
+if [ -z "$PORT" ]; then
+  PORT=8080
+fi
+
+if is_gunicorn_installed; then
+  setup_py=$(find "$HOME" -maxdepth 2 -type f -name 'setup.py' -print -quit)
+  # Look for wsgi module in the current directory
+  if [[ -z "$APP_MODULE" && -f "./wsgi.py" ]]; then
+    APP_MODULE=wsgi
+  elif [[ -z "$APP_MODULE" && -f "$setup_py" ]]; then
+    APP_MODULE="$(python "$setup_py" --name)"
+  fi
+
+  if [[ "$APP_MODULE" ]]; then
+    export WEB_CONCURRENCY=${WEB_CONCURRENCY:-$(get_default_web_concurrency)}
+
+    # Default settings for gunicorn if none of the custom are set
+    if [ -z "$APP_CONFIG" ] && [ -z "$GUNICORN_CMD_ARGS" ]; then
+      GUNICORN_CMD_ARGS="--bind=0.0.0.0:$PORT --access-logfile=-"
+      gunicorn_settings_source="default"
+    else
+      gunicorn_settings_source="custom"
+    fi
+
+    # Gunicorn can read GUNICORN_CMD_ARGS as an env variable but because this is not
+    # supported in Gunicorn < 20 we still need for Python 2, we are using arguments directly.
+    echo "---> Serving application with gunicorn ($APP_MODULE) with $gunicorn_settings_source settings ..."
+    exec gunicorn "$APP_MODULE" $GUNICORN_CMD_ARGS --config "$APP_CONFIG"
+  fi
+fi
+
+if is_django_installed; then
+  if [[ -f "$manage_file" ]]; then
+    echo "---> Serving application with 'manage.py runserver 0.0.0.0:$PORT' ..."
+    echo "WARNING: this is NOT a recommended way to run you application in production!"
+    echo "Consider using gunicorn or some other production web server."
+    maybe_run_in_init_wrapper python "$manage_file" runserver 0.0.0.0:$PORT
+  else
+    echo "WARNING: seems that you're using Django, but we could not find a 'manage.py' file."
+    echo "Skipped 'python manage.py runserver'."
+  fi
+fi
+
+>&2 echo "ERROR: don't know how to run your application."
+>&2 echo "Please set either APP_MODULE, APP_FILE or APP_SCRIPT environment variables, or create a file 'app.py' to launch your application."
+exit 1

monai-notebook/container/3.9/s2i/bin/usage

@@ -0,0 +1,18 @@
+#!/bin/sh
+
+DISTRO=`cat /etc/*-release | grep ^ID= | grep -Po '".*?"' | tr -d '"'`
+NAMESPACE=centos
+[[ $DISTRO =~ rhel* ]] && NAMESPACE=rhscl
+
+cat <<EOF
+This is a S2I python-3.9 ${DISTRO} base image:
+There are multiple ways how to run the image, see documentation at:
+https://github.com/sclorg/s2i-python-container/blob/master/3.9/README.md
+
+To use it in Openshift, run:
+oc new-app python:3.9~https://github.com/sclorg/s2i-python-container.git --context-dir=3.9/test/setup-test-app/
+
+You can then run the resulting image via:
+oc get pods
+oc exec <pod> -- curl 127.0.0.1:8080
+EOF