Autodeploy to dockerhub using github action (#205)

* Create deploy_dockerhub.yml

* Build image from HEAD

* Explicitly enable oversubscription since we are using OpenMPI

.github/workflows/deploy_dockerhub.yml

@@ -0,0 +1,18 @@
+# https://github.com/marketplace/actions/publish-docker
+name: Deploy to dockerhub
+on: [push]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
+    - name: Publish to Registry
+      uses: elgohr/[email protected]
+      with:
+        name: dweindl/parpe
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: container/charliecloud/parpe_base/
+        dockerfile: Dockerfile
+        tag_names: true

container/charliecloud/parpe_base/install.sh

@@ -96,19 +96,20 @@ apt-get install -q -y git
 #echo "================= Adding awscli 1.14.64 ============"
 #sudo pip install -q 'awscli==1.14.64'
 
-#echo "================= parPE requirements ============"
-apt-get install gfortran libmpich-dev libatlas-base-dev libboost-all-dev libhdf5-dev cmake libceres-dev coinor-libipopt-dev swig3.0 python3-venv hdf5-tools libpython-dev
+echo "================= parPE requirements ============"
+# using openmpi coming with libboost-all-dev instead of libmpich-dev
+apt-get install gfortran libatlas-base-dev libboost-all-dev libhdf5-dev cmake libceres-dev coinor-libipopt-dev swig3.0 python3-venv hdf5-tools libpython-dev
 # for setuptools to find:
 ln -s /usr/bin/swig3.0 /usr/bin/swig
 python3 -m pip install --upgrade pip
 pip3 install -U setuptools pkgconfig wheel
 
 # echo "================= Intalling Shippable CLIs ================="
-# 
+#
 # git clone https://github.com/Shippable/node.git nodeRepo
 # ./nodeRepo/shipctl/x86_64/Ubuntu_16.04/install.sh
 # rm -rf nodeRepo
-# 
+#
 # echo "Installed Shippable CLIs successfully"
 # echo "-------------------------------------"
 

container/charliecloud/parpe_base/install_parpe.sh

@@ -3,10 +3,10 @@ set -e
 
 cd
 
-# Clone clean repository
-git clone --single-branch --branch feature_charlie --depth=1 https://github.com/ICB-DCM/parPE.git
+# unpack git archive
+mkdir parPE && cd parPE
+tar -xzf /u18/parpe.tar.gz
 
-cd parPE
 export PARPE_BASE=$(pwd)
 
 # Build dependencies
@@ -36,6 +36,7 @@ CC=mpicc CXX=mpiCC cmake \
       -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
       -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
       -DBUILD_TESTS=ON \
+      "-DTESTS_MPIEXEC_COMMAND=mpiexec;--allow-run-as-root;-n;4;--oversubscribe" \
       ..
 make -j12 VERBOSE=1
 

doc/parpe_with_charliecloud.md

@@ -21,6 +21,7 @@ This will create the parPE base image *from parPE from github*
 (takes about 10'):
 
     cd container/charliecloud/parpe_base
+    git archive -v -o parpe.tar.gz --format=tar.gz HEAD
     ch-build -t parpe .
 
 Export image to charliecloud archive in the current directory: