Merge pull request #5 from casperdcl/jupyterhub_env

jupyterhub builds

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "jupyterhub/docker-stacks"]
+	path = jupyterhub/docker-stacks
+	url = https://github.com/jupyter/docker-stacks

jupyterhub/Dockerfile

@@ -1,10 +1,11 @@
+# syntax=docker/dockerfile:1
 ARG BASE_IMAGE=nvidia/cuda:11.7.1-cudnn8-devel-ubuntu22.04
 # paskino/jupyter   datascience-notebook-cuda11
 FROM ${BASE_IMAGE} as base
 
 # Make sure the image has the same libraries as the standard SIRF docker image
 # Add to the docker image the appropriate stuff
-user root
+USER root
 COPY --chown=jovyan:users docker/build_essential-ubuntu.sh docker/build_gadgetron-ubuntu.sh docker/build_system-ubuntu.sh docker/install-sirf-exercises-dep.py ./scripts/
 RUN bash ./scripts/build_essential-ubuntu.sh &&\
     bash ./scripts/build_gadgetron-ubuntu.sh &&\
@@ -14,10 +15,10 @@ RUN bash ./scripts/build_essential-ubuntu.sh &&\
 # https://docs.docker.com/develop/develop-images/multistage-build/#use-an-external-image-as-a-stage
 # not documented in https://docs.docker.com/engine/reference/builder/#copy
 # FROM --from=nginx:latest /etc/nginx/nginx.conf /nginx.conf
-COPY --from=synerbi/sirf:sirf-core /opt/SIRF-SuperBuild/INSTALL/ /opt/SIRF-SuperBuild/INSTALL
-COPY --from=synerbi/sirf:sirf-core /opt/SIRF-SuperBuild/sources/SIRF/ /opt/SIRF-SuperBuild/sources/SIRF/
+COPY --from=synerbi/sirf:latest --link /opt/SIRF-SuperBuild/INSTALL/ /opt/SIRF-SuperBuild/INSTALL
+COPY --from=synerbi/sirf:latest --link /opt/SIRF-SuperBuild/sources/SIRF/ /opt/SIRF-SuperBuild/sources/SIRF/
 
-from base as jup
+FROM base AS jup
 # remove the SIRF-Exercises and CIL-Demos that get installed by user_service-ubuntu.sh
 USER jovyan
 ARG NB_USER="jovyan"
@@ -44,7 +45,7 @@ RUN mamba env update -n base -f docker/requirements.yml &&\
 # Switch back to jovyan to avoid accidental container runs as root
 # From https://github.com/paskino/SIRF-SuperBuild/blob/301c2274621e4729cadbd2a1705d8c4d9e3b7e50/docker/Dockerfile#L212-L219
 # Set environment variables for SIRF
-USER jovyan 
+USER jovyan
 COPY docker/.bashrc /home/jovyan
 ENV PATH "/opt/conda/bin:/opt/SIRF-SuperBuild/INSTALL/bin:$PATH"
 ENV LD_LIBRARY_PATH "/opt/SIRF-SuperBuild/INSTALL/lib:/opt/SIRF-SuperBuild/INSTALL/lib64:$LD_LIBRARY_PATH"
@@ -55,8 +56,10 @@ ENV SIRF_PATH "/opt/SIRF-SuperBuild/sources/SIRF"
 #Suppress output from Gadgetron which gives some problems on notebooks (QUIERO)
 ENV GADGETRON_LOG_MASK ""
 RUN echo $PATH
+USER root
+RUN echo "export OMP_NUM_THREADS=\$(python -c 'import multiprocessing as mc; print(mc.cpu_count() // 2)')" > /usr/local/bin/before-notebook.d/omp_num_threads.sh
 
-# switch back to 
+# switch back to
 USER jovyan
 
-#/opt/SIRF-SuperBuild/INSTALL/lib:/opt/SIRF-SuperBuild/INSTALL/lib64:/usr/local/nvidia/lib:/usr/local/nvidia/lib64::/opt/conda/lib
+#/opt/SIRF-SuperBuild/INSTALL/lib:/opt/SIRF-SuperBuild/INSTALL/lib64:/usr/local/nvidia/lib:/usr/local/nvidia/lib64::/opt/conda/lib

jupyterhub/build_docker_stacks.sh

@@ -1,9 +1,10 @@
-# /bin/bash
+#!/usr/bin/env bash
+set -exuo pipefail
 
-set -ex
-pushd ../../docker-stacks/images/docker-stacks-foundation
+git submodule update --init --recursive
+pushd $(dirname "$0")/docker-stacks/images/docker-stacks-foundation
 # docker-stacks-foundations
-docker build --build-arg PYTHON_VERSION=3.9 --build-arg ROOT_CONTAINER=nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04 -t paskino/jupyter:docker-stacks-foundation-cuda11-cudnn8-runtime-ubuntu22.04 .
+docker build --build-arg PYTHON_VERSION=3.9 --build-arg BASE_CONTAINER=nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04 -t paskino/jupyter:docker-stacks-foundation-cuda11-cudnn8-runtime-ubuntu22.04 .
 
 # base notebook
 cd ../base-notebook
@@ -26,3 +27,4 @@ docker build --build-arg BASE_CONTAINER=paskino/jupyter:scipy-notebook-cuda11-cu
 
 popd
 
+docker build --build-arg BASE_IMAGE=paskino/jupyter:datascience-notebook-cuda11-cudnn8-runtime-ubuntu22.04 -t paskino/jupyter:sirf -f jupyterhub/Dockerfile .