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Update boost and deal ii libraries, and an error #263

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2 changes: 1 addition & 1 deletion cmake/SetupTPLs.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ endif()

#### deal.II #################################################################
if(ENABLE_DEAL_II)
find_package(deal.II 8.4 REQUIRED PATHS ${DEAL_II_DIR})
find_package(deal.II 9.0.0 REQUIRED PATHS ${DEAL_II_DIR})
add_definitions(-DWITH_DEAL_II)
# If deal.II was configured in DebugRelease mode, then if Cap was configured
# in Debug mode, we link against the Debug version of deal.II. IF Cap was
Expand Down
13 changes: 7 additions & 6 deletions cpp/source/utils.cc
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Expand Up @@ -18,12 +18,6 @@ template std::map<std::string, double> to_map(std::string const &s);
template std::map<std::string, std::string> to_map(std::string const &s);
template std::map<std::string, bool> to_map(std::string const &s);

template std::vector<unsigned int> to_vector(std::string const &s);
template std::vector<int> to_vector(std::string const &s);
template std::vector<float> to_vector(std::string const &s);
template std::vector<double> to_vector(std::string const &s);
template std::vector<std::string> to_vector(std::string const &s);
template std::vector<bool> to_vector(std::string const &s);
#ifdef WITH_DEAL_II
template <>
std::vector<dealii::types::material_id> to_vector(std::string const &s)
Expand All @@ -41,6 +35,13 @@ std::vector<dealii::types::material_id> to_vector(std::string const &s)
}
#endif

template std::vector<unsigned int> to_vector(std::string const &s);
template std::vector<int> to_vector(std::string const &s);
template std::vector<float> to_vector(std::string const &s);
template std::vector<double> to_vector(std::string const &s);
template std::vector<std::string> to_vector(std::string const &s);
template std::vector<bool> to_vector(std::string const &s);

template std::string to_string(std::vector<int> const &v);
template std::string to_string(std::vector<unsigned int> const &v);
template std::string to_string(std::vector<float> const &v);
Expand Down
64 changes: 49 additions & 15 deletions docker/Dockerfile_stack
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Expand Up @@ -8,7 +8,6 @@ RUN apt-get update && apt-get install -y \
gfortran \
wget \
git \
cmake \
lcov \
valgrind \
cppcheck \
Expand All @@ -21,7 +20,6 @@ RUN apt-get update && apt-get install -y \
libbz2-dev \
libatlas-base-dev \
zlib1g-dev \
libopenmpi-dev \
libhdf5-dev \
python3.5-dev \
python3-tk \
Expand All @@ -45,13 +43,51 @@ RUN mkdir -p ${PREFIX} && \
mkdir build && \
mkdir install

# Install CMake
RUN export CMAKE_VERSION=3.12.1 && \
export CMAKE_VERSION_SHORT=3.12 && \
export CMAKE_URL=https://cmake.org/files/v${CMAKE_VERSION_SHORT}/cmake-${CMAKE_VERSION}-Linux-x86_64.sh && \
export CMAKE_SCRIPT=cmake-${CMAKE_VERSION}-Linux-x86_64.sh && \
export CMAKE_PREFIX=/opt/cmake/${CMAKE_VERSION_SHORT} && \
wget --quiet ${CMAKE_URL} --output-document=${CMAKE_SCRIPT} && \
mkdir -p ${CMAKE_PREFIX} && \
sh ${CMAKE_SCRIPT} --skip-license --prefix=${CMAKE_PREFIX} && \
rm ${CMAKE_SCRIPT}
ENV PATH=/opt/cmake/3.12/bin:$PATH

# Install OpenMPI
RUN export OPENMPI_VERSION=2.1.3 && \
export OPENMPI_VERSION_SHORT=2.1 && \
export OPENMPI_SHA1=e24502c7075c8e8f6de028a6aedecf7a6d2d0bb7 && \
export OPENMPI_URL=https://www.open-mpi.org/software/ompi/v${OPENMPI_VERSION_SHORT}/downloads/openmpi-${OPENMPI_VERSION}.tar.bz2 && \
export OPENMPI_ARCHIVE=${PREFIX}/archive/openmpi-${OPENMPI_VERSION}.tar.bz2 && \
export OPENMPI_SOURCE_DIR=${PREFIX}/source/openmpi/${OPENMPI_VERSION} && \
export OPENMPI_BUILD_DIR=${PREFIX}/build/openmpi/${OPENMPI_VERSION} && \
export OPENMPI_INSTALL_DIR=/opt/openmpi/${OPENMPI_VERSION_SHORT} && \
wget --quiet ${OPENMPI_URL} --output-document=${OPENMPI_ARCHIVE} && \
echo "${OPENMPI_SHA1} ${OPENMPI_ARCHIVE}" | sha1sum -c && \
mkdir -p ${OPENMPI_SOURCE_DIR} && \
tar -xf ${OPENMPI_ARCHIVE} -C ${OPENMPI_SOURCE_DIR} --strip-components=1 && \
mkdir -p ${OPENMPI_BUILD_DIR} && \
cd ${OPENMPI_BUILD_DIR} && \
${OPENMPI_SOURCE_DIR}/configure --prefix=${OPENMPI_INSTALL_DIR} && \
make -j${NPROC} install && \
rm -rf ${OPENMPI_ARCHIVE} && \
rm -rf ${OPENMPI_BUILD_DIR} && \
rm -rf ${OPENMPI_SOURCE_DIR}

ENV MPI_DIR=/opt/openmpi/2.1
# Put OPENMPI_DIR at the end of the path so that /ust/local/bin/mpiexec will
# overwrite it
ENV PATH=$PATH:${MPI_DIR}/bin

# install boost
RUN export BOOST_URL=http://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.bz2 && \
export BOOST_SHA256=beae2529f759f6b3bf3f4969a19c2e9d6f0c503edcb2de4a61d1428519fcb3b0 && \
export BOOST_ARCHIVE=${PREFIX}/archive/boost_1_63_0.tar.bz2 && \
export BOOST_SOURCE_DIR=${PREFIX}/source/boost/1.63.0 && \
export BOOST_BUILD_DIR=${PREFIX}/build/boost/1.63.0 && \
export BOOST_INSTALL_DIR=/opt/boost/1.63.0 && \
RUN export BOOST_URL=http://sourceforge.net/projects/boost/files/boost/1.68.0/boost_1_68_0.tar.bz2 && \
export BOOST_SHA256=7f6130bc3cf65f56a618888ce9d5ea704fa10b462be126ad053e80e553d6d8b7 && \
export BOOST_ARCHIVE=${PREFIX}/archive/boost_1_68_0.tar.bz2 && \
export BOOST_SOURCE_DIR=${PREFIX}/source/boost/1.68.0 && \
export BOOST_BUILD_DIR=${PREFIX}/build/boost/1.68.0 && \
export BOOST_INSTALL_DIR=/opt/boost/1.68.0 && \
wget --quiet ${BOOST_URL} --output-document=${BOOST_ARCHIVE} && \
echo "${BOOST_SHA256} ${BOOST_ARCHIVE}" | sha256sum -c && \
mkdir -p ${BOOST_SOURCE_DIR} && \
Expand All @@ -66,12 +102,13 @@ RUN export BOOST_URL=http://sourceforge.net/projects/boost/files/boost/1.63.0/bo
link=shared \
variant=release \
--build-dir=${BOOST_BUILD_DIR} \
hardcode-dll-paths=true dll-path=${BOOST_INSTALL_DIR}/lib \
&& \
rm -rf ${BOOST_ARCHIVE} && \
rm -rf ${BOOST_BUILD_DIR} && \
rm -rf ${BOOST_SOURCE_DIR}

ENV BOOST_DIR=/opt/boost/1.63.0
ENV BOOST_DIR=/opt/boost/1.68.0
#ENV LD_LIBRARY_PATH=${BOOST_DIR}/lib:${LD_LIBRARY_PATH}

# install TRILINOS
Expand Down Expand Up @@ -146,9 +183,9 @@ RUN export P4EST_VERSION=1.1 &&\
ENV P4EST_DIR=/opt/p4est/1.1

# install dealii
RUN export DEAL_II_VERSION=8.5.1 && \
RUN export DEAL_II_VERSION=9.0.0 && \
export DEAL_II_URL=https://github.com/dealii/dealii/releases/download/v${DEAL_II_VERSION}/dealii-${DEAL_II_VERSION}.tar.gz && \
export DEAL_II_SHA1=fe8e4748c1d9650487fb5145429a58e8509de276 && \
export DEAL_II_SHA1=820bf3961a6d840ee27cf0456d38d6dbd05e1565 && \
export DEAL_II_ARCHIVE=${PREFIX}/archive/dealii-${DEAL_II_VERSION}.tar.gz && \
export DEAL_II_SOURCE_DIR=${PREFIX}/source/dealii/${DEAL_II_VERSION} && \
export DEAL_II_BUILD_DIR=${PREFIX}/build/dealii/${DEAL_II_VERSION} && \
Expand All @@ -164,9 +201,6 @@ RUN export DEAL_II_VERSION=8.5.1 && \
-D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
-D DEAL_II_WITH_MPI=ON \
-D DEAL_II_WITH_CXX11=ON \
-D CMAKE_Fortran_COMPILER=mpifort \
-D CMAKE_CXX_COMPILER=mpicxx \
-D CMAKE_C_COMPILER=mpicc \
-D BOOST_DIR=${BOOST_DIR} \
-D P4EST_DIR=${P4EST_DIR} \
-D TRILINOS_DIR=${TRILINOS_DIR} \
Expand All @@ -176,7 +210,7 @@ RUN export DEAL_II_VERSION=8.5.1 && \
rm -rf ${DEAL_II_BUILD_DIR} && \
rm -rf ${DEAL_II_SOURCE_DIR}

ENV DEAL_II_DIR=/opt/dealii/8.5.1
ENV DEAL_II_DIR=/opt/dealii/9.0.0

ENV LD_LIBRARY_PATH=${LAPACK_DIR}/lib:${LD_LIBRARY_PATH}

Expand Down