Merge pull request #3 from scottwittenburg/some-docker-fixes

WIP: Some docker fixes

README.md

@@ -1,10 +1,10 @@
 # HPCCloud Services
 
-### Goal
+## Goal
 
 Streamline a test deployment environment.
 
-## Running it
+### Running it
 
 ```
 git clone https://github.com/Kitware/hpccloud-services.git
@@ -26,4 +26,16 @@ If you want to stop the services you can run the command
 docker-compose down
 ```
 
+### Running w/ GPU accleration
+
+In order to run compute and visualize containers which can utilize the GPU on your system:
+
+```
+docker-compose -f docker-compose.yml -f docker-compose-nvidia.yml up -d
+```
+
+This will apply the service overrides found in `docker-compose-nvidia.yml`, which make use of the `nvidia` container runtime.
+
+### Development workflow
+
 [Developent workflow][dev_workflow.md] has more complete instructions on troubleshooting and manual testing.

ansible/ansible.cfg

@@ -1,3 +1,4 @@
 [defaults]
 host_key_checking = False
-library=~/.ansible/roles/girder.girder/library
+library=~/.ansible/roles/girder.girder/library
+remote_tmp=/tmp

ansible/dev.yml

@@ -1,8 +1,6 @@
 
 - hosts: girder_setup
-  vars:
-    ansible_python_interpreter: "/usr/local/bin/python"
   connection: local
   roles:
     - role: girder
-  tags: girder_setup
+  tags: girder_setup

ansible/host_vars/compute

@@ -2,4 +2,4 @@ ansible_connection: ssh
 ansible_user: demo
 ansible_ssh_pass: letmein
 ansible_ssh_extra_args: '-o StrictHostKeyChecking=no'
-ansible_python_interpreter: /usr/local/bin/python
+ansible_python_interpreter: /usr/bin/python3

ansible/host_vars/localhost

@@ -1,8 +1,9 @@
+ansible_python_interpreter: "/usr/local/bin/python"
 dev: yes
 girder_host: girder
 girder_port: 8080
 girder_api_root: '/api/v1'
 girder_scheme: 'http'
 hpccloud_password: letmein
 cumulus_password: letmein
-demo_password: letmein
+demo_password: letmein

ansible/host_vars/visualize

@@ -2,4 +2,4 @@ ansible_connection: ssh
 ansible_user: demo
 ansible_ssh_pass: letmein
 ansible_ssh_extra_args: '-o StrictHostKeyChecking=no'
-ansible_python_interpreter: /usr/local/bin/python
+ansible_python_interpreter: /usr/bin/python3

docker-compose-nvidia.yml

@@ -0,0 +1,39 @@
+# Go back to an older compose format version due to a bug
+# where 'runtime' is available in version 2.3 but not 3
+#   https://github.com/docker/compose/issues/6239
+version: '2.3'
+services:
+
+  compute:
+    image: kitware/hpccloud:nvidia-compute-pyfr
+    build:
+      context: .
+      dockerfile: docker/compute-pyfr/Dockerfile
+      args:
+        - BASE_IMG=kitware/hpccloud:nvidia-sge-ssh
+    hostname: compute
+    runtime: nvidia
+    volumes:
+     - scratch.hc:/scratch
+    networks:
+      - hc
+    ports:
+      - "2201:22"
+
+  visualize:
+    image: kitware/hpccloud:visualize-egl
+    build:
+      context: .
+      dockerfile: docker/visualize-egl/Dockerfile
+      args:
+        - PARAVIEW_TAG=v5.6.1
+        - SUPERBUILD_TAG=v5.6.1
+    hostname: visualize
+    runtime: nvidia
+    volumes:
+     - scratch.hc:/scratch
+    networks:
+      - hc
+    ports:
+      - "2202:22"
+      - "9090:9090"

docker-compose.yml

@@ -1,4 +1,7 @@
-version: '3'
+# Go back to an older compose format version due to a bug
+# where 'runtime' is available in version 2.3 but not 3
+#   https://github.com/docker/compose/issues/6239
+version: '2.3'
 services:
   mongodb:
     image: mongo:3.6

docker/ansible/Dockerfile

@@ -1,12 +1,14 @@
 FROM python:3.6-slim
 
-RUN apt-get update && apt-get -y install \
-  git \
-  sshpass
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        git \
+        openssh-client \
+        sshpass && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
-
-RUN pip install ansible && \
-  pip install girder_client
+RUN pip3 install ansible \
+                 girder_client
 
 COPY ./ansible /ansible
 
@@ -16,7 +18,4 @@ RUN cd /ansible && \
 COPY ./docker/ansible/entrypoint.sh /entrypoint.sh
 COPY ./docker/ansible/wait-for-it.sh /wait-for-it.sh
 
-
 ENTRYPOINT ["/wait-for-it.sh", "-t", "30", "girder:8080",  "--", "/entrypoint.sh"]
-
-RUN apt-get clean && rm -rf /var/lib/apt/lists/*

docker/ansible/entrypoint.sh

@@ -1,3 +1,3 @@
 #!/bin/sh
 cd /ansible
-ansible-playbook -i inventory/localhost dev.yml
+ansible-playbook -i inventory/localhost dev.yml

docker/bionic-python/Dockerfile

@@ -1,21 +1,38 @@
 # Docker file for 18.04 Ubuntu with 3.6 Python
+#
+# To replace basic Ubuntu image with one ready for NVidia egl
+# builds, specify the BASE_IMAGE build argument when building:
+#
+#   docker build --build-arg BASE_IMAGE=nvidia/opengl:1.0-glvnd-devel-ubuntu18.04 -t kitware/hpccloud:nvidia-bionic-python .
+#
 
-ARG UBUNTU_VERSION=18.04
-ARG PYTHON_VERSION=3.6
+ARG BASE_IMAGE=ubuntu:18.04
 
-FROM ubuntu:${UBUNTU_VERSION}
+FROM ${BASE_IMAGE}
 
 LABEL maintainer="patrick.oleary@kitware.com" \
       version="1.0"
 
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    git \
+    locales \
+    python3.6 \
+    python3-dev \
+    python3-setuptools \
+    python3-pip && \
+    update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && \
+    locale-gen en_US.UTF-8 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
 # Add LANG default to en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
 ENV LANG en_US.UTF-8
+ENV LC_ALL en_US.UTF-8
 
-FROM python:${PYTHON_VERSION}
-
-RUN pip install supervisor && \
+RUN pip3 install supervisor && \
     mkdir /var/log/supervisor && \
     chmod 0777 /var/log/supervisor
 
 # overwrite this with 'CMD []' in a dependent Dockerfile
-CMD ["/bin/bash"]
+CMD ["/bin/bash"]

docker/celery-parflow/Dockerfile

@@ -6,22 +6,22 @@ LABEL maintainer="patrick.oleary@kitware.com" \
       parflow.version="master"
 
 RUN apt-get update && \
-    apt-get install -y build-essential \
-                       gcc-6 \
-                       g++-6 \
-                       g++-6-multilib \
-                       gfortran-6 \
-                       libopenblas-dev \
-                       liblapack-dev \
-                       openssh-client \
-                       openssh-server \
-                       openmpi-bin \
-                       libopenmpi-dev \
-                       cmake \
-                       --no-install-recommends && \
+    apt-get install -y --no-install-recommends \
+        gcc-6 \
+        g++-6 \
+        g++-6-multilib \
+        gfortran-6 \
+        libopenblas-dev \
+        liblapack-dev \
+        openssh-client \
+        openssh-server \
+        openmpi-bin \
+        libopenmpi-dev \
+        cmake && \
     update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 60 \
                         --slave /usr/bin/g++ g++ /usr/bin/g++-6 \
-                        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-6
+                        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-6 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Allow root to mpiexec (not in current openmpi version for Ubuntu 18.04)
 #ENV OMPI_ALLOW_RUN_AS_ROOT=1
@@ -72,4 +72,4 @@ RUN git clone https://gitlab.kitware.com/parflow/parflow.git parflow && \
     cd /
 
 # Allow root to run mpiexec (kludge)
-COPY ./docker/celery-parflow/run /parflow/bin/run
+COPY ./docker/celery-parflow/run /parflow/bin/run

docker/celery-pyfr/Dockerfile

@@ -6,26 +6,26 @@ LABEL maintainer="patrick.oleary@kitware.com" \
       pyfr.version="1.8.0"
 
 RUN apt-get update && \
-    apt-get install -y build-essential \
-                       gcc-6 \
-                       g++-6 \
-                       g++-6-multilib \
-                       gfortran-6 \
-                       libopenblas-dev \
-                       liblapack-dev \
-                       openssh-client \
-                       openssh-server \
-                       openmpi-bin \
-                       libopenmpi-dev \
-                       libhdf5-dev \
-                       libmetis-dev \
-                       strace \
-                       unzip \
-                       wget \
-                       --no-install-recommends && \
+    apt-get install -y --no-install-recommends \
+        gcc-6 \
+        g++-6 \
+        g++-6-multilib \
+        gfortran-6 \
+        libopenblas-dev \
+        liblapack-dev \
+        openssh-client \
+        openssh-server \
+        openmpi-bin \
+        libopenmpi-dev \
+        libhdf5-dev \
+        libmetis-dev \
+        strace \
+        unzip \
+        wget && \
     update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 60 \
                         --slave /usr/bin/g++ g++ /usr/bin/g++-6 \
                         --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-6 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* && \
     pip3 install appdirs \
                  numpy \
                  pytools \
@@ -43,5 +43,3 @@ RUN wget -q -O PyFR-1.8.0.zip http://www.pyfr.org/download/PyFR-1.8.0.zip && \
     cd /
 
 RUN chown -R celery  /PyFR-1.8.0
-
-RUN apt-get clean && rm -rf /var/lib/apt/lists/*

docker/celery/Dockerfile

@@ -1,4 +1,5 @@
-FROM kitware/hpccloud:bionic-python
+ARG BASE_IMAGE=kitware/hpccloud:bionic-python
+FROM ${BASE_IMAGE}
 
 LABEL maintainer="patrick.oleary@kitware.com" \
       version="1.0"
@@ -10,9 +11,9 @@ RUN git clone https://github.com/Kitware/cumulus.git /cumulus && \
   cd /cumulus && \
   # git checkout v1.0.0 && \
   cd / && \
-  pip install --no-cache-dir -r /cumulus/requirements.txt && \
-  pip install --no-cache-dir -e /cumulus && \
-  pip install --no-cache-dir girder
+  pip3 install --no-cache-dir -r /cumulus/requirements.txt && \
+  pip3 install --no-cache-dir -e /cumulus && \
+  pip3 install --no-cache-dir girder
 
 # TEMP cumulus fix - requirements.txt needs to be updated for AWS, in progress.
 # COPY ./cumulus/cumulus/girderclient.py /cumulus/cumulus/girderclient.py

docker/compute-parflow/Dockerfile

@@ -1,28 +1,30 @@
 # Docker file for compute Parflow
 
-FROM kitware/hpccloud:sge-ssh
+ARG BASE_IMAGE=kitware/hpccloud:sge-ssh
+
+FROM ${BASE_IMAGE}
 LABEL maintainer="patrick.oleary@kitware.com" \
       version="1.0" \
       parflow.version="master"
 
 RUN apt-get update && \
-    apt-get install -y build-essential \
-                       gcc-6 \
-                       g++-6 \
-                       g++-6-multilib \
-                       gfortran-6 \
-                       openmpi-bin \
-                       libopenmpi-dev \
-                       git \
-                       curl \
-                       cmake \
-                       strace \
-                       unzip \
-                       wget \
-                       --no-install-recommends && \
+    apt-get install -y --no-install-recommends \
+        gcc-6 \
+        g++-6 \
+        g++-6-multilib \
+        gfortran-6 \
+        openmpi-bin \
+        libopenmpi-dev \
+        git \
+        curl \
+        cmake \
+        strace \
+        unzip \
+        wget && \
     update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 60 \
                         --slave /usr/bin/g++ g++ /usr/bin/g++-6 \
-                        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-6
+                        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-6 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Allow root to mpiexec (not in current openmpi version for Ubuntu 18.04)
 #ENV OMPI_ALLOW_RUN_AS_ROOT=1
@@ -74,5 +76,3 @@ RUN git clone https://gitlab.kitware.com/parflow/parflow.git parflow && \
 
 # Allow root to run mpiexec (kludge)
 COPY ./docker/celery-parflow/run /parflow/bin/run
-
-RUN apt-get clean && rm -rf /var/lib/apt/lists/*