Merge pull request #46 from PawseySC/nektar

Adding nektar application

applications/nektar/buildnektar.dockerfile

@@ -0,0 +1,65 @@
+# This recipe uses ubuntu as a base and 
+# adds minimal packages with apt-get
+# adds spack and the default base image is 
+# set to build on top of the pawsey provided mpich image
+
+ARG BASE_IMAGE="quay.io/pawsey/spack:0.20.0-mpich-lustre"
+FROM ${BASE_IMAGE}
+
+WORKDIR /
+RUN echo "Building nektar dependencies" \
+    && /usr/bin/spack/spack install -j16 \
+    [email protected]+cxx+fortran+hl~ipo~java+mpi+shared+szip~threadsafe+tools api=v110 build_type=Release \
+    && /usr/bin/spack/spack install -j16 [email protected] +atomic+chrono~clanglibcpp \  
+        +container~context~contract~coroutine\
+        ~date_time~debug+exception~fiber+filesystem~graph~graph_parallel~icu+iostreams~json~locale~log+math+mpi+multithreaded\
+        ~nowide~numpy+pic+program_options~python~random+regex+serialization+shared~signals~singlethreaded~stacktrace+system\
+        ~taggedlayout~test+thread~timer~type_erasure~versionedlayout~wave \
+    && /usr/bin/spack/spack install --reuse -j16 [email protected]~complex metis parmetis \
+    && /usr/bin/spack/spack install -j16 --reuse --only dependencies \
+        nektar+arpack+mpi+hdf5+fftw+scotch \
+    && echo "Done "
+
+# these are the arguments to get nektar to work 
+# for silly reasons, there is no include of blas and lapack headers
+# so it is easier to just have netkar build it's own version
+# the build is also quite bad and not including appropriate headers
+# for libraries and so needs to have the cmake files patched 
+ARG NEKTAR_VERSION=v5.5.0
+ARG NEKTAR_CMAKE_ARGS="-DNEKTAR_USE_MPI=ON -DNEKTAR_USE_ARPACK=ON -DNEKTAR_USE_FFTW=ON \
+-DNEKTAR_USE_HDF5=ON -DNEKTAR_USE_METIS=ON -DNEKTAR_USE_SCOTCH=ON -DNEKTAR_BUILD_PYTHON=OFF \
+-DNEKTAR_USE_PETSC=ON \
+-DTHIRDPARTY_BUILD_ARPACK=OFF -DTHIRDPARTY_BUILD_BLAS_LAPACK=ON -DTHIRDPARTY_BUILD_BOOST=OFF \
+-DTHIRDPARTY_BUILD_FFTW=OFF -DTHIRDPARTY_BUILD_HDF5=OFF -DTHIRDPARTY_BUILD_METIS=OFF -DTHIRDPARTY_BUILD_SCOTCH=OFF \
+-DTHIRDPARTY_BUILD_PETSC=OFF \
+-DCMAKE_INSTALL_PREFIX=/usr/"
+RUN echo "Building nektar" \
+    && mkdir -p /opt/nektar && cd /opt/nektar \
+    && . /root/spack/spack/share/spack/setup-env.sh \
+    # store the spack script and also edit it so it sets the LD_LIBARARY_PATH
+    && spack load --sh arpack-ng petsc [email protected] metis parmetis fftw scotch [email protected] cmake \
+        > /opt/nektar/set_spack_env.sh \
+    && grep "export PATH=" /opt/nektar/set_spack_env.sh | sed "s:export PATH=:export LD_LIBRARY_PATH=:g" | sed "s;/bin:;/lib:;g" >> /opt/nektar/set_spack_env.sh \
+    && . /opt/nektar/set_spack_env.sh \
+    && git clone http://gitlab.nektar.info/nektar/nektar nektar++ \
+    && cd nektar++ && git fetch --tags && git checkout ${NEKTAR_VERSION} \
+    # remove non-functioning findHDF5 and use inbuilt one \
+    && rm cmake/FindHDF5.cmake \
+    # update the include path for metis \
+    && sed -i "s:TARGET_LINK_LIBRARIES(SpatialDomains LINK_PRIVATE \${METIS_LIBRARY}):TARGET_LINK_LIBRARIES(SpatialDomains LINK_PRIVATE \${METIS_LIBRARY})\n    TARGET_INCLUDE_DIRECTORIES(SpatialDomains PRIVATE \${METIS_INCLUDE_DIR}):g" library/SpatialDomains/CMakeLists.txt \
+    && mkdir -p build && cd build \ 
+    && cmake ${NEKTAR_CMAKE_ARGS} ../ \
+    && make -j8 && make install \
+    && echo "Done "
+
+RUN rm -rf /opt/nektar/nektar++
+RUN mkdir -p /.singularity.d/env/
+RUN echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\${PETSC_DIR}/lib/" >> /opt/nektar/set_spack_env.sh \
+    && echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\${BOOST_ROOT}/lib/" >> /opt/nektar/set_spack_env.sh \
+    && echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/usr/lib64/:/usr/lib64/netkar++/" >> /opt/nektar/set_spack_env.sh \
+    && cat /opt/nektar/set_spack_env.sh >> /.singularity.d/env/91-environment.sh 
+
+# and copy the recipe into the docker recipes directory
+RUN mkdir -p /opt/docker-recipes/
+COPY buildnektar.dockerfile /opt/docker-recipes/
+