Initial commit

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

LICENSE

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+MIT License
+
+Copyright (c) 2019 Gert-Jan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docker_templates/docker-compose_cpu.yml

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+version: "3"
+services:
+  compute:
+    image: {{IMAGE}}
+    ports:
+      - "8888:8888"
+      - "6006:6006"
+    volumes:  
+      - simplest-sync:/home/jovyan/work/:nocopy 
+    command: bash -c "cd /home/jovyan/work/ &&      
+                      python setup.py develop &&         
+                      jupyter lab --allow-root --NotebookApp.token=''"
+
+
+volumes:
+  simplest-sync:
+    external: true

docker_templates/docker-compose_gpu.yml

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+version: "3"
+  compute:
+    image: {{IMAGE}}
+    runtime: nvidia
+    ports:
+      - "8888:8888"
+      - "6006:6006"
+    volumes:  
+      - simplest-sync:/home/jovyan/work/:nocopy 
+    command: bash -c "cd /home/jovyan/work/ &&      
+                      python setup.py develop &&         
+                      jupyter lab --allow-root --NotebookApp.token=''"
+
+
+volumes:
+  simplest-sync:
+    external: true

docker_templates/docker-sync_template.yml

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+version: "2"
+
+syncs:
+  simplest-sync:
+    src: {{PROJECT_FOLDER}}

phimal-cpu/.docker-sync/daemon.log

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+          ok  Starting native_osx for sync simplest-sync
+          ok  simplest-sync container still running, restarting unison in container
+unison: stopped
+unison: started
+     success  Sync container started
+     success  Showing unison logs from your sync container: simplest-sync

phimal-cpu/Dockerfile

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+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+ARG BASE_CONTAINER=phimal/minimal
+FROM $BASE_CONTAINER
+
+LABEL maintainer="Gert-Jan Both"
+
+USER $NB_UID
+
+# Install Python 3 packages
+# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
+# use notebook-friendly backends in these images
+RUN conda install --quiet --yes \
+    'tensorflow=1.13.*' &&\
+    conda install --quiet --yes -c pytorch pytorch-cpu=1.1.* &&\
+    conda clean --all -f -y && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+USER root

phimal-gpu/Dockerfile

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+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+FROM phimal/minimal:v0.5
+
+LABEL maintainer="Gert-Jan Both"
+USER root
+
+# CUDA stuff.
+ENV CUDA_VERSION 10.0.130
+ENV CUDA_PKG_VERSION 10-0=$CUDA_VERSION-1
+ENV PATH /usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
+ENV LD_LIBRARY_PATH /usr/local/nvidia/lib:/usr/local/nvidia/lib64
+ENV NVIDIA_VISIBLE_DEVICES all
+ENV NVIDIA_DRIVER_CAPABILITIES compute,utility
+ENV NVIDIA_REQUIRE_CUDA "cuda>=10.0 brand=tesla,driver>=384,driver<385 brand=tesla,driver>=410,driver<411"
+ENV NCCL_VERSION 2.4.2
+ENV CUDNN_VERSION 7.5.1.10
+
+#Installing cuda
+RUN apt-get update && apt-get install -y --no-install-recommends gnupg2 curl ca-certificates && \
+    curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub | apt-key add - && \
+    echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" > /etc/apt/sources.list.d/cuda.list && \
+    echo "deb https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64 /" > /etc/apt/sources.list.d/nvidia-ml.list && \
+    apt-get purge --autoremove -y curl && \
+    rm -rf /var/lib/apt/lists/*
+
+# For libraries in the cuda-compat-* package: https://docs.nvidia.com/cuda/eula/index.html#attachment-a
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        cuda-cudart-$CUDA_PKG_VERSION \
+        cuda-compat-10-0 && \
+    ln -s cuda-10.0 /usr/local/cuda && \
+    rm -rf /var/lib/apt/lists/*
+
+# nvidia-container-runtime
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        cuda-libraries-$CUDA_PKG_VERSION \
+        cuda-nvtx-$CUDA_PKG_VERSION \
+        libnccl2=$NCCL_VERSION-1+cuda10.0 && \
+    apt-mark hold libnccl2 && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+            libcudnn7=$CUDNN_VERSION-1+cuda10.0 && \
+    apt-mark hold libcudnn7 && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Python 3 packages
+# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
+# use notebook-friendly backends in these images
+RUN pip install tensorflow-gpu==1.13.* &&\
+    conda install --quiet --yes -c pytorch pytorch=1.1.* &&\
+    conda clean --all -f -y && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+USER $NB_UID
+
+
+
+

phimal-minimal/.ipynb_checkpoints/Untitled-checkpoint.ipynb

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+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

phimal-minimal/Dockerfile

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+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+ARG BASE_CONTAINER=jupyter/base-notebook:python-3.7.3
+FROM $BASE_CONTAINER
+
+LABEL maintainer="Gert-Jan Both"
+
+USER root
+
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update && \
+    apt-get -y install gcc mono-mcs && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Python 3 packages
+# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
+# use notebook-friendly backends in these images
+RUN conda install --quiet --yes \
+    'pandas=0.24*' \
+    'matplotlib=3.0*' \
+    'seaborn=0.9*' \
+    'numpy=1.16.*' \
+    'setuptools=41.0.*' \
+    'git=2.20.*' && \
+    pip install jupyterlab-git &&\
+    conda remove --quiet --yes --force qt pyqt && \
+    conda clean --all -f -y && \
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager@^0.38.* && \
+    jupyter labextension install [email protected].* && \
+    jupyter labextension install @jupyterlab/[email protected].* && \
+    jupyter labextension install @jupyterlab/[email protected].* && \
+    jupyter serverextension enable --py jupyterlab_git &&\
+    npm cache clean --force && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    rm -rf /home/$NB_USER/.node-gyp && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Import matplotlib the first time to build the font cache.
+ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
+RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
+    fix-permissions /home/$NB_USER
+
+USER $NB_UID

start_notebook_cpu.sh

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+#!/bin/bash
+
+#First automatically find project directory
+cd ../
+projectdir=$(pwd)
+cd config/
+
+# Make docker-sync for project
+sed "s#{{PROJECT_FOLDER}}#$projectdir#g" docker_templates/docker-sync_template.yml > docker-sync.yml
+
+#Make docker-compose file dependent for cpu
+sed "s#{{IMAGE}}#phimal/cpu:latest#g" docker_templates/docker-compose_cpu.yml > docker-compose.yml
+
+# Run docker sync 
+sudo docker-sync-stack start

start_notebook_gpu.sh

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+#!/bin/bash
+
+#First automatically find project directory
+cd ../
+projectdir=$(pwd)
+cd config/
+
+# Make docker-sync for project
+sed "s#{{PROJECT_FOLDER}}#$projectdir#g" docker_templates/docker-sync_template.yml > docker-sync.yml
+
+#Make docker-compose file dependent for cpu
+sed "s#{{IMAGE}}#phimal/gpu:latest#g" docker_templates/docker-compose_template.yml > docker-compose.yml
+
+# Run docker sync 
+sudo docker-sync-stack start