Merge branch 'v1.3_cuda-10.2_ubuntu-18.04'

.build/Dockerfile

@@ -289,6 +289,107 @@ RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
 
 USER $NB_UID
 
+WORKDIR $HOME
+
+  ############################################################################
+  ################ Dependency: jupyter/datascience-notebook ##################
+  ############################################################################
+
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+LABEL maintainer="Jupyter Project <[email protected]>"
+
+# Set when building on Travis so that certain long-running build steps can
+# be skipped to shorten build time.
+ARG TEST_ONLY_BUILD
+
+# Fix DL4006
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+USER root
+
+# Julia installation
+# Default values can be overridden at build time
+# (ARGS are in lower case to distinguish them from ENV)
+# Check https://julialang.org/downloads/
+ARG julia_version="1.5.3"
+# SHA256 checksum
+ARG julia_checksum="f190c938dd6fed97021953240523c9db448ec0a6760b574afd4e9924ab5615f1"
+
+# R pre-requisites
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    fonts-dejavu \
+    gfortran \
+    gcc && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Julia dependencies
+# install Julia packages in /opt/julia instead of $HOME
+ENV JULIA_DEPOT_PATH=/opt/julia \
+    JULIA_PKGDIR=/opt/julia \
+    JULIA_VERSION="${julia_version}"
+
+WORKDIR /tmp
+
+# hadolint ignore=SC2046
+RUN mkdir "/opt/julia-${JULIA_VERSION}" && \
+    wget -q https://julialang-s3.julialang.org/bin/linux/x64/$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)"/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" && \
+    echo "${julia_checksum} *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
+    tar xzf "julia-${JULIA_VERSION}-linux-x86_64.tar.gz" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
+    rm "/tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz"
+RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
+
+# Show Julia where conda libraries are \
+RUN mkdir /etc/julia && \
+    echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
+    # Create JULIA_PKGDIR \
+    mkdir "${JULIA_PKGDIR}" && \
+    chown "${NB_USER}" "${JULIA_PKGDIR}" && \
+    fix-permissions "${JULIA_PKGDIR}"
+
+USER $NB_UID
+
+# R packages including IRKernel which gets installed globally.
+RUN conda install --quiet --yes \
+    'r-base=4.0.3'  \
+    'r-caret=6.0*' \
+    'r-crayon=1.4*' \
+    'r-devtools=2.3*' \
+    'r-forecast=8.13*' \ 
+    'r-hexbin=1.28*' \
+    'r-htmltools=0.5*' \
+    'r-htmlwidgets=1.5*' \ 
+    'r-irkernel=1.1*' \
+    'r-nycflights13=1.0*' \
+    'r-randomforest=4.6*' \
+    'r-rcurl=1.98*' \
+    'r-rmarkdown=2.6*' \
+    'r-rsqlite=2.2*' \
+    'r-shiny=1.6*' \
+    'r-tidyverse=1.3*' \
+    'rpy2=3.4*' && \
+    conda clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+# Add Julia packages. Only add HDF5 if this is not a test-only build since
+# it takes roughly half the entire build time of all of the images on Travis
+# to add this one package and often causes Travis to timeout.
+#
+# Install IJulia as jovyan and then move the kernelspec out
+# to the system share location. Avoids problems with runtime UID change not
+# taking effect properly on the .local folder in the jovyan home dir.
+RUN julia -e 'import Pkg; Pkg.update()' && \
+    (test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
+    julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
+    # move kernelspec out of home \
+    mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
+    chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
+    rm -rf "${HOME}/.local" && \
+    fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
+
 WORKDIR $HOME
 
 ############################################################################
@@ -303,13 +404,16 @@ RUN pip install --upgrade pip && \
     pip install --no-cache-dir "tensorflow==2.3.2" && \
     pip install --no-cache-dir keras
 
-# Install PyTorch with dependencies
+# Update cudatoolkit and install PyTorch with dependencies
 RUN conda install --quiet --yes \
     pyyaml mkl mkl-include setuptools cmake cffi typing
+# RUN conda install --quiet --yes \
+#    cudatoolkit=10.1 -c pytorch
 
 # Check compatibility here: https://pytorch.org/get-started/locally/
 # Installation via conda leads to errors installing cudatoolkit=10.2
-RUN pip install torch torchvision torchaudio torchviz
+RUN conda install pytorch torchvision torchaudio cudatoolkit=10.1 -c pytorch
+# RUN pip install torch torchvision torchaudio torchviz
 
 # Clean installation
 RUN conda clean --all -f -y && \
@@ -325,52 +429,13 @@ RUN apt-get update && \
 
 RUN git clone https://github.com/Syllo/nvtop.git /run/nvtop && \
     mkdir -p /run/nvtop/build && cd /run/nvtop/build && \
-    unlink cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True || : && \
-    unlink make || : && unlink make install || : && \
+    (cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True 2> /dev/null || echo "cmake was not successful") && \
+    (make 2> /dev/null || echo "make was not successful") && \
+    (make install 2> /dev/null || echo "make install was not successful") && \
     cd /tmp && rm -rf /tmp/nvtop
 
-USER $NB_UID
-
-  ############################################################################
-  ############################ Useful packages ###############################
-  ############################################################################
-
-LABEL authors="Christoph Schranz <[email protected]>, Mathematical Michael <[email protected]>"
-
-USER root
-
-RUN pip install --no-cache-dir ipyleaflet plotly>=4.14.3 "ipywidgets>=7.5"
-
-# Install important packages and Graphviz
-RUN set -ex \
- && buildDeps=' \
-    graphviz==0.11 \
-' \
- && apt-get update \
- && apt-get -y install htop apt-utils iputils-ping graphviz libgraphviz-dev openssh-client \
- && pip install --no-cache-dir $buildDeps
-
-# Install various extensions
-RUN fix-permissions $CONDA_DIR
-# jupyterlab/github Does not support jlab 3.x yet, install well maintained alternative instead.
-# RUN jupyter labextension install @jupyterlab/github
-RUN pip install jupyterlab-git
-RUN pip install jupyterlab-drawio
-RUN jupyter nbextension enable --py --sys-prefix ipyleaflet
-RUN jupyter labextension install jupyterlab-plotly
-RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager plotlywidget
-# RUN pip install --no-cache-dir jupyter-tabnine  --user && \
-#   jupyter nbextension install --py jupyter_tabnine --user && \
-#   jupyter nbextension enable --py jupyter_tabnine --user && \
-#   jupyter serverextension enable --py jupyter_tabnine --user
-RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
-  jupyter_nbextensions_configurator rise
-#  jupyter nbextension enable codefolding/main
-RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
-
 RUN fix-permissions /home/$NB_USER
 
-# Switch back to jovyan to avoid accidental container runs as root
 USER $NB_UID
 
 # Copy jupyter_notebook_config.json

docker-compose.yml

@@ -9,7 +9,7 @@ services:
             - capabilities:
               - gpu
     ports:
-      - 8849:8888
+      - 8848:8888
     volumes:
       - ./data:/home/jovyan/work
     environment: