fix docker & ccache

.travis.yml

@@ -65,12 +65,12 @@ matrix:
    # +boost +itk -hdf5 +swig
    env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
  # docker
- #- os: linux
- #  # +armadillo +boost +fftw3 +hdf5 +siemens_to_ismrmrd +swig
- #  env: DOCKER_BUILD=1
- #- os: linux
- #  # +DEVEL +armadillo +boost +fftw3 +hdf5 +siemens_to_ismrmrd +swig
- #  env: DOCKER_BUILD=DEVEL
+ - os: linux
+   # +ace +armadillo +boost +fftw3 +hdf5 +itk +siemens_to_ismrmrd +swig
+   env: DOCKER_BUILD=1
+ - os: linux
+   # +DEVEL +ace +armadillo +boost +fftw3 +hdf5 +itk +siemens_to_ismrmrd +swig
+   env: DOCKER_BUILD=DEVEL
 
 env:
  global:
@@ -219,19 +219,13 @@ before_install:
  - $PY_EXE --version
  - $PY_EXE -m pip --version
  - $PY_EXE -m pip freeze
- # ccache compiler override
- - ln -s "$(which ccache)" g++
- - ln -s "$(which ccache)" g++-6
- - ln -s "$(which ccache)" g++-7
- - ln -s "$(which ccache)" gcc
- - ln -s "$(which ccache)" gcc-6
- - ln -s "$(which ccache)" gcc-7
  - export PATH="$PWD:$PATH"
  - popd
  # N.B.: don't put into build matrix to allow caching.
  - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER"
+ - BUILD_FLAGS="$BUILD_FLAGS -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache"
  - cmake --version
- 
+
 install:
  - |
     if [[ -n "$DOCKER_BUILD" ]]; then
@@ -268,7 +262,7 @@ install:
         $PY_EXE -m pip install --user --only-binary=numpy,scipy,matplotlib numpy scipy matplotlib
         cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
         # Job may timeout (>50min) if no ccache, otherwise should be <1min:
-        make 
+        make
         mv INSTALL/share/gadgetron/config/gadgetron.xml.example INSTALL/share/gadgetron/config/gadgetron.xml
       ) || travis_terminate 1
       source $PWD/INSTALL/bin/env_ccppetmr.sh

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:16.04 as base
+FROM ubuntu:18.04 as base
 LABEL \
   author.name="Casper da Costa-Luis"          \
   [email protected]        \
@@ -76,9 +76,12 @@ COPY user_sirf-ubuntu.sh .
 COPY devel/.ccache/ /opt/ccache/
 RUN ccache -o cache_dir=/opt/ccache
 ARG BUILD_FLAGS="\
-  -DCMAKE_BUILD_TYPE=Release -DBUILD_STIR_WITH_OPENMP=ON \
-  -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON \
-  -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON"
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache\
+ -DCMAKE_BUILD_TYPE=Release\
+ -DBUILD_STIR_WITH_OPENMP=ON -DUSE_SYSTEM_ACE=ON\
+ -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON\
+ -DUSE_SYSTEM_HDF5=ON -DUSE_ITK=ON -DBUILD_siemens_to_ismrmrd=ON\
+ -DUSE_SYSTEM_SWIG=ON"
 ARG EXTRA_BUILD_FLAGS=""
 RUN bash user_sirf-ubuntu.sh
 RUN rm user_sirf-ubuntu.sh

docker/build_gadgetron-ubuntu.sh

@@ -1,16 +1,23 @@
 #!/usr/bin/env bash
 set -ev
 # Gadgetron
+# from https://github.com/gadgetron/gadgetron/blob/master/docker/base/ubuntu_1804/Dockerfile#L8
 apt-get update -qq
 apt-get install -yq --no-install-recommends \
-  h5utils              \
-  liblapack-dev        \
-  libace-dev
-# Not required (yet) by SIRF
-# libxml2-dev
-# libxslt-dev
-# python-h5py
-# python-libxml2
-# python-psutil
-# libplplot-dev
+  libhdf5-serial-dev     \
+  libboost-all-dev       \
+  libfftw3-dev           \
+  h5utils                \
+  jq                     \
+  hdf5-tools             \
+  libatlas-base-dev      \
+  libxml2-dev            \
+  libfreetype6-dev       \
+  libxslt-dev            \
+  libarmadillo-dev       \
+  libace-dev             \
+  liblapack-dev          \
+  liblapacke-dev         \
+  libplplot-dev          \
+  libdcmtk-dev
 apt-get clean

docker/build_system-ubuntu.sh

@@ -3,15 +3,11 @@ set -ev
 # SIRF external dependencies
 apt-get update -qq
 apt-get install -yq --no-install-recommends \
-  hdf5-tools           \
   hdfview              \
-  libarmadillo-dev     \
   libboost-all-dev     \
-  libfftw3-dev         \
   libgtest-dev         \
-  libhdf5-serial-dev   \
-  libplplot-dev        \
-  libxml2-dev          \
-  libxslt-dev          \
   swig
 apt-get clean
+
+# Not required (yet) by SIRF
+# libopenblas-dev

docker/devel/test.sh

@@ -19,11 +19,12 @@ GCONFIG=./INSTALL/share/gadgetron/config/gadgetron.xml
 [ -f "$GCONFIG" ] || cp "$GCONFIG".example "$GCONFIG"
 ./INSTALL/bin/gadgetron >& gadgetron.log&
 
-# print for debugging
-[ "$DEBUG" != 0 ] && cat builds/SIRF/build/CMakeCache.txt
 ctest -VV
 ret=$?
+kill -n 15 $(pidof gadgetron)
+
 # print for debugging
+[ "$DEBUG" != 0 ] && cat builds/SIRF/build/CMakeCache.txt
 [ "$DEBUG" != 0 ] && cat builds/SIRF/build/Testing/Temporary/LastTest.log
 # may exceed 4MB travis log limit
 [ "$DEBUG" != 0 ] && cat gadgetron.log

docker/docker-compose.yml

@@ -29,5 +29,5 @@ services:
    context: .
    target: core
    cache_from:
-    - ubuntu:16.04
+    - ubuntu:18.04
     - ccppetmr/sirf:core

docker/user_python-ubuntu.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-set -ev
 [ -f .bashrc ] && . .bashrc
+set -ev
 INSTALL_DIR="${1:-/opt/pyvenv}"
 PYTHON="${2:-miniconda}"
 
@@ -13,8 +13,8 @@ miniconda)
   rm miniconda.sh
   source "$INSTALL_DIR"/bin/activate
   conda config --add channels conda-forge
-  conda update -c conda-forge -y conda
-  conda update -c conda-forge -y --all
+  # https://github.com/conda/conda/issues/6030
+  #conda update -c conda-forge -y conda
   ;;
 *python*)
   # virtualenv

docker/user_sirf-ubuntu.sh

@@ -1,9 +1,10 @@
 #!/usr/bin/env bash
-set -ev
 [ -f .bashrc ] && . .bashrc
+set -ev
 # SIRF
-git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master /opt/SIRF-SuperBuild
+git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b docker /opt/SIRF-SuperBuild
 pushd /opt/SIRF-SuperBuild
+echo $BUILD_FLAGS $EXTRA_BUILD_FLAGS
 cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
 make -j 2