Update all the python packages on the jupyter notebooks as well as th…

…e dockerfile on the cuda layer

Remove jupyterlab-s3-browser from datascience notebook

Add skl2onnx, codeflare-sdk, pymongo, psycopg, mysql-connector-python, pyodbc python packages on the jupyter notebooks except minimal

Install unixODBC in favor of pyodbc package

Install cuda toolkit on c9s cuda base

Update runtimes' python packages

Upgrade packages on the ubi8 flavor of the notebooks

Move installation of usefull os packages like jq unixODBC postgreql git-lfs libsndfile on the base image

Upgrade packages on trustyAI ubi8

Add mongodb and mssql drivers on datascience notebook

Consider setuptool on the pipfiles of the notebooks

base/c9s-python-3.9/Pipfile

@@ -6,7 +6,9 @@ verify_ssl = true
 [dev-packages]
 
 [packages]
-wheel = "~=0.38.4"
+# Base packages
+wheel = "~=0.41.2"
+setuptools = "~=68.1.2"
 
 [requires]
 python_version = "3.9"

base/ubi8-python-3.8/Pipfile

@@ -6,7 +6,9 @@ verify_ssl = true
 [dev-packages]
 
 [packages]
-wheel = "~=0.38.4"
+# Base packages
+wheel = "~=0.41.2"
+setuptools = "~=68.1.2"
 
 [requires]
 python_version = "3.8"

base/ubi9-python-3.9/Pipfile

@@ -6,7 +6,9 @@ verify_ssl = true
 [dev-packages]
 
 [packages]
-wheel = "~=0.38.4"
+# Base packages
+wheel = "~=0.41.2"
+setuptools = "~=68.1.2"
 
 [requires]
 python_version = "3.9"

codeserver/c9s-python-3.9/Dockerfile

@@ -1,7 +1,7 @@
 ARG BASE_IMAGE
 FROM ${BASE_IMAGE}
 
-ARG CODESERVER_VERSION=v4.11.0
+ARG CODESERVER_VERSION=v4.16.1
 
 LABEL name="odh-notebook-code-server-c9s-python-3.9" \
       summary="Code Server (VS Code) image with python 3.9 based on CentOS Stream 9" \
@@ -22,8 +22,8 @@ RUN yum install -y "https://github.com/coder/code-server/releases/download/${COD
     yum -y clean all --enablerepo='*'
 
 # Install NGINX to proxy VSCode and pass probes check
-ENV NGINX_VERSION=1.20 \
-    NGINX_SHORT_VER=120 \
+ENV NGINX_VERSION=1.22 \
+    NGINX_SHORT_VER=122 \
     NGINX_CONFIGURATION_PATH=${APP_ROOT}/etc/nginx.d \
     NGINX_CONF_PATH=/etc/nginx/nginx.conf \
     NGINX_DEFAULT_CONF_PATH=${APP_ROOT}/etc/nginx.default.d \
@@ -34,7 +34,7 @@ ENV NGINX_VERSION=1.20 \
 
 # Modules does not exist
 RUN yum install -y https://download.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm && \
-    INSTALL_PKGS="nss_wrapper bind-utils gettext hostname nginx nginx-mod-stream nginx-mod-http-perl fcgiwrap initscripts chkconfig" && \
+    INSTALL_PKGS="bind-utils nginx nginx-mod-stream nginx-mod-http-perl fcgiwrap initscripts chkconfig" && \
     yum install -y --setopt=tsflags=nodocs $INSTALL_PKGS && \
     rpm -V $INSTALL_PKGS && \
     # spawn-fcgi is not in epel9 \
@@ -77,7 +77,6 @@ COPY nginx/serverconf/ /opt/app-root/etc/nginx.default.d/
 COPY nginx/httpconf/ /opt/app-root/etc/nginx.d/
 COPY nginx/api/ /opt/app-root/api/
 
-
 # Launcher
 COPY utils utils/
 COPY run-code-server.sh run-nginx.sh ./

codeserver/c9s-python-3.9/run-code-server.sh

@@ -8,10 +8,9 @@ source ${SCRIPT_DIR}/utils/*.sh
 run-nginx.sh &
 spawn-fcgi -s /var/run/fcgiwrap.socket -M 766 /usr/sbin/fcgiwrap 
 
-# Create .bashrc if not present
-if [ ! -f /opt/app-root/src/.bashrc ]
-then
-	touch /opt/app-root/src/.bashrc
+# Add .bashrc for custom promt if not present
+if [ ! -f "/opt/app-root/src/.bashrc" ]; then
+  echo 'PS1="\[\033[34;1m\][\$(pwd)]\[\033[0m\]\n\[\033[1;0m\]$ \[\033[0m\]"' > /opt/app-root/src/.bashrc
 fi
 
 # Initilize access logs for culling
@@ -23,4 +22,4 @@ start_process /usr/bin/code-server \
   --disable-telemetry \
   --auth none \
   --disable-update-check \
-  /opt/app-root/src
+  /opt/app-root/src

cuda/c9s-python-3.9/Dockerfile

@@ -17,7 +17,7 @@ USER 0
 WORKDIR /opt/app-root/bin
 
 ENV NVARCH x86_64
-ENV NVIDIA_REQUIRE_CUDA "cuda>=11.8 brand=tesla,driver>=450,driver<451 brand=tesla,driver>=470,driver<471 brand=unknown,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=geforce,driver>=470,driver<471 brand=geforcertx,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=titan,driver>=470,driver<471 brand=titanrtx,driver>=470,driver<471 brand=tesla,driver>=510,driver<511 brand=unknown,driver>=510,driver<511 brand=nvidia,driver>=510,driver<511 brand=nvidiartx,driver>=510,driver<511 brand=geforce,driver>=510,driver<511 brand=geforcertx,driver>=510,driver<511 brand=quadro,driver>=510,driver<511 brand=quadrortx,driver>=510,driver<511 brand=titan,driver>=510,driver<511 brand=titanrtx,driver>=510,driver<511 brand=tesla,driver>=515,driver<516 brand=unknown,driver>=515,driver<516 brand=nvidia,driver>=515,driver<516 brand=nvidiartx,driver>=515,driver<516 brand=geforce,driver>=515,driver<516 brand=geforcertx,driver>=515,driver<516 brand=quadro,driver>=515,driver<516 brand=quadrortx,driver>=515,driver<516 brand=titan,driver>=515,driver<516 brand=titanrtx,driver>=515,driver<516"
+ENV NVIDIA_REQUIRE_CUDA "cuda>=11.8 brand=tesla,driver>=450,driver<451 brand=tesla,driver>=470,driver<471 brand=unknown,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=geforce,driver>=470,driver<471 brand=geforcertx,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=titan,driver>=470,driver<471 brand=titanrtx,driver>=470,driver<471"
 ENV NV_CUDA_CUDART_VERSION 11.8.89-1
 
 COPY cuda.repo-x86_64 /etc/yum.repos.d/cuda.repo
@@ -103,7 +103,7 @@ ENV LIBRARY_PATH /usr/local/cuda/lib64/stubs
 
 # Install CUDA devel cudnn8 from:
 # https://gitlab.com/nvidia/container-images/cuda/-/blob/master/dist/11.8.0/ubi8/devel/cudnn8/Dockerfile
-ENV NV_CUDNN_VERSION 8.7.0.84-1
+ENV NV_CUDNN_VERSION 8.9.0.131-1
 ENV NV_CUDNN_PACKAGE libcudnn8-${NV_CUDNN_VERSION}.cuda11.8
 ENV NV_CUDNN_PACKAGE_DEV libcudnn8-devel-${NV_CUDNN_VERSION}.cuda11.8
 
@@ -115,9 +115,11 @@ RUN yum install -y \
     && yum clean all \
     && rm -rf /var/cache/yum/*
 
-# Install CUDA toolkit 11-8
+# Install CUDA toolkit 11.8
 RUN yum -y install cuda-toolkit-11-8 && \
-    yum -y clean all  --enablerepo='*'
+    yum -y clean all --enablerepo="*"
+
+# Set this flag so that libraries can find the location of CUDA
 ENV XLA_FLAGS=--xla_gpu_cuda_data_dir=/usr/local/cuda
 
 # Restore notebook user workspace

cuda/ubi9-python-3.9/Dockerfile

@@ -17,7 +17,7 @@ USER 0
 WORKDIR /opt/app-root/bin
 
 ENV NVARCH x86_64
-ENV NVIDIA_REQUIRE_CUDA "cuda>=11.8 brand=tesla,driver>=450,driver<451 brand=tesla,driver>=470,driver<471 brand=unknown,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=geforce,driver>=470,driver<471 brand=geforcertx,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=titan,driver>=470,driver<471 brand=titanrtx,driver>=470,driver<471 brand=tesla,driver>=510,driver<511 brand=unknown,driver>=510,driver<511 brand=nvidia,driver>=510,driver<511 brand=nvidiartx,driver>=510,driver<511 brand=geforce,driver>=510,driver<511 brand=geforcertx,driver>=510,driver<511 brand=quadro,driver>=510,driver<511 brand=quadrortx,driver>=510,driver<511 brand=titan,driver>=510,driver<511 brand=titanrtx,driver>=510,driver<511 brand=tesla,driver>=515,driver<516 brand=unknown,driver>=515,driver<516 brand=nvidia,driver>=515,driver<516 brand=nvidiartx,driver>=515,driver<516 brand=geforce,driver>=515,driver<516 brand=geforcertx,driver>=515,driver<516 brand=quadro,driver>=515,driver<516 brand=quadrortx,driver>=515,driver<516 brand=titan,driver>=515,driver<516 brand=titanrtx,driver>=515,driver<516"
+ENV NVIDIA_REQUIRE_CUDA "cuda>=11.8 brand=tesla,driver>=450,driver<451 brand=tesla,driver>=470,driver<471 brand=unknown,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=geforce,driver>=470,driver<471 brand=geforcertx,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=titan,driver>=470,driver<471 brand=titanrtx,driver>=470,driver<471"
 ENV NV_CUDA_CUDART_VERSION 11.8.89-1
 
 COPY cuda.repo-x86_64 /etc/yum.repos.d/cuda.repo
@@ -70,6 +70,9 @@ RUN yum install -y \
     && yum clean all \
     && rm -rf /var/cache/yum/*
 
+# Set this flag so that libraries can find the location of CUDA
+ENV XLA_FLAGS=--xla_gpu_cuda_data_dir=/usr/local/cuda
+
 # Install CUDA devel from:
 # https://gitlab.com/nvidia/container-images/cuda/-/blob/master/dist/11.8.0/ubi8/devel/Dockerfile
 ENV NV_CUDA_LIB_VERSION 11.8.0-1
@@ -103,7 +106,7 @@ ENV LIBRARY_PATH /usr/local/cuda/lib64/stubs
 
 # Install CUDA devel cudnn8 from:
 # https://gitlab.com/nvidia/container-images/cuda/-/blob/master/dist/11.8.0/ubi8/devel/cudnn8/Dockerfile
-ENV NV_CUDNN_VERSION 8.7.0.84-1
+ENV NV_CUDNN_VERSION 8.9.0.131-1
 ENV NV_CUDNN_PACKAGE libcudnn8-${NV_CUDNN_VERSION}.cuda11.8
 ENV NV_CUDNN_PACKAGE_DEV libcudnn8-devel-${NV_CUDNN_VERSION}.cuda11.8
 

jupyter/datascience/ubi8-python-3.8/Dockerfile

@@ -24,8 +24,25 @@ RUN echo "Installing softwares and packages" && \
 
 COPY utils ./utils/
 
+# OS Packages needs to be installed as root
 USER root
-RUN dnf install -y jq
+
+# Install usefull OS packages
+RUN dnf install -y jq unixODBC git-lfs libsndfile
+
+# Install MongoDB Client, We need a special repo for MongoDB as they do their own distribution
+COPY mongodb-org-6.0.repo-x86_64 /etc/yum.repos.d/mongodb-org-6.0.repo
+
+RUN dnf install -y mongocli
+
+# Install MSSQL Client, We need a special repo for MSSQL as they do their own distribution
+COPY mssql-2022.repo-x86_64 /etc/yum.repos.d/mssql-2022.repo
+
+RUN ACCEPT_EULA=Y dnf install -y mssql-tools18 unixODBC-devel
+
+ENV PATH="$PATH:/opt/mssql-tools18/bin"
+
+# Other apps and tools installed as default user
 USER 1001
 
 # setup path for runtime configuration
@@ -48,8 +65,6 @@ RUN mkdir /opt/app-root/runtimes && \
     jq '.properties.metadata.properties.runtime_type = input' $FILE_COMPONENT utils/component_runtime.json > "$tmp" && mv "$tmp" $FILE_COMPONENT && \
     jq '.properties.metadata.properties.runtime_type = input' $URL_COMPONENT utils/component_runtime.json > "$tmp" && mv "$tmp" $URL_COMPONENT && \
     sed -i "s/metadata.metadata.runtime_type/\"DATA_SCIENCE_PIPELINES\"/g" /opt/app-root/share/jupyter/labextensions/@elyra/pipeline-editor-extension/static/lib_index_js.*.js && \
-    # Explicitly enable jupyterlab_s3_browser plugin \
-    jupyter serverextension enable --py jupyterlab_s3_browser && \
     # Remove Elyra logo from JupyterLab because this is not a pure Elyra image \
     sed -i 's/widget\.id === \x27jp-MainLogo\x27/widget\.id === \x27jp-MainLogo\x27 \&\& false/' /opt/app-root/share/jupyter/labextensions/@elyra/theme-extension/static/lib_index_js.*.js && \
     # Replace Notebook's launcher, "(ipykernel)" with Python's version 3.x.y \

jupyter/datascience/ubi8-python-3.8/Pipfile

@@ -7,35 +7,42 @@ name = "pypi"
 
 [packages]
 # Datascience and useful extensions
-elyra-pipeline-editor-extension = "~=3.15.0"
-elyra-python-editor-extension = "~=3.15.0"
-elyra-code-snippet-extension = "~=3.15.0"
-kfp-tekton = "<1.6.0"
-
-boto3 = "~=1.26.69"
-jupyter-bokeh = "~=3.0.5"
+boto3 = "~=1.28.41"
 kafka-python = "~=2.0.2"
 matplotlib = "~=3.6.3"
-numpy = "~=1.24.1"
+numpy = "~=1.24.3"
 pandas = "~=1.5.3"
-plotly = "~=5.13.0"
-scikit-learn = "~=1.2.1"
+plotly = "~=5.16.1"
+scikit-learn = "~=1.3.0"
 scipy = "~=1.10.0"
-jupyterlab-lsp = "~=3.10.2"
-jupyterlab-widgets = "~=3.0.5"
-jupyter-resource-usage = "~=0.6.0"
-jupyterlab-s3-browser = "~=0.10.1"
+skl2onnx = "~=1.15.0"
+codeflare-sdk = "~=0.7.0"
+# DB connectors
+pymongo = "~=4.5.0"
+psycopg = "~=3.1.10"
+pyodbc = "~=4.0.39"
+mysql-connector-python = "~=8.0.33"
 
-# Parent image requirements to maintain cohesion
-jupyterlab = "~=3.5.3"
-jupyter-server = "~=2.1.0"
-jupyter-server-proxy = "~=3.2.2"
+# JupyterLab packages
+elyra-pipeline-editor-extension = ">=3.15.0"
+elyra-python-editor-extension = ">=3.15.0"
+elyra-code-snippet-extension = ">=3.15.0"
+kfp-tekton = "<1.6.0"
+jupyterlab = "~=3.6.5"
+jupyter-bokeh = "~=3.0.7"
+jupyter-server = "~=2.7.3"
+jupyter-server-proxy = "~=4.0.0"
 jupyter-server-terminals = "~=0.4.4"
-jupyterlab-git = "~=0.41.0"
-nbdime = "~=3.1.1"
-nbgitpuller = "~=1.1.1"
-# ---
-wheel = "~=0.38.4"
+jupyterlab-git = "~=0.42.0"
+jupyterlab-lsp = "~=4.2.0"
+jupyterlab-widgets = "~=3.0.8"
+jupyter-resource-usage = "~=0.6.0"
+nbdime = "~=3.2.1"
+nbgitpuller = "~=1.2.0"
+
+# Base packages
+wheel = "~=0.41.2"
+setuptools = "~=68.1.2"
 
 [requires]
 python_version = "3.8"