diff --git a/docker/Dockerfile-fedora b/docker/Dockerfile-fedora index b4dee54..95487a3 100644 --- a/docker/Dockerfile-fedora +++ b/docker/Dockerfile-fedora @@ -13,6 +13,7 @@ RUN dnf -y install \ gdb \ git \ hdf5-mpich-devel \ + jq \ lapack-devel \ make \ mpich-devel \ diff --git a/docker/Dockerfile-ubuntu b/docker/Dockerfile-ubuntu index 2ac3dcb..45bb501 100644 --- a/docker/Dockerfile-ubuntu +++ b/docker/Dockerfile-ubuntu @@ -50,6 +50,7 @@ RUN apt-get update && \ python3 \ python3-dev \ pylint \ + python3-ase \ python3-coverage \ python3-dev \ python3-h5py \ @@ -60,6 +61,7 @@ RUN apt-get update && \ python3-nbconvert \ python3-numpy \ python3-numpydoc \ + python3-pandas \ python3-pint \ python3-pip \ python3-packaging \ @@ -110,15 +112,9 @@ RUN cd "${HOME}" && \ autopep8==2.1.0 \ pycodestyle==2.11.1 \ sphinx-toggleprompt==0.5.2 && \ - jupyter_config_root=$(jupyter --paths --json | jq ".config[0]") && \ - jupyter_config_root=${jupyter_config_root#\"} && \ - jupyter_config_root=${jupyter_config_root%\"} && \ - jupyter_kernels_root=$(jupyter --paths --json | jq ".data[0]")/kernels && \ - jupyter_kernels_root=${jupyter_kernels_root#\"} && \ - jupyter_kernels_root=${jupyter_kernels_root%\"} && \ - mkdir -p "${jupyter_config_root}" "${jupyter_kernels_root}" && \ + jupyter_config_root=$(jupyter --paths --json | jq -r ".config[0]") && \ + mkdir -p "${jupyter_config_root}" && \ mv "/tmp/jupyter_nbconvert_config.json" "${jupyter_config_root}/" && \ - ln -s "${VIRTUAL_ENV}/share/jupyter/kernels/python3" "${jupyter_kernels_root}/python3" && \ deactivate && \ mkdir -p "${HOME}/.local/bin" && \ mkdir -p "${HOME}/.local/etc/alternatives" && \ diff --git a/docker/install-kokkos.sh b/docker/install-kokkos.sh index 7774017..376d4ef 100644 --- a/docker/install-kokkos.sh +++ b/docker/install-kokkos.sh @@ -8,7 +8,7 @@ git clone -b 4.3.00 https://github.com/kokkos/kokkos cd kokkos/ mkdir build cd build/ -cmake .. -D Kokkos_ENABLE_CUDA=OFF -DKokkos_ENABLE_OPENMP=ON +cmake .. -D Kokkos_ENABLE_CUDA=OFF -DKokkos_ENABLE_OPENMP=ON -D CMAKE_POSITION_INDEPENDENT_CODE=ON make -j $(nproc) install cd rm -r /tmp/kokkos diff --git a/docker/install-scafacos.sh b/docker/install-scafacos.sh index 39ec66a..31f1c54 100755 --- a/docker/install-scafacos.sh +++ b/docker/install-scafacos.sh @@ -37,6 +37,9 @@ cd build --prefix=/usr/local make -j $(nproc) make install +# remove GCC version-specific library path to avoid library version mismatch at +# link or runtime when a different GCC version was used to compile client code +sed -i -r 's| -L/usr/lib/gcc/x86_64-linux-gnu/[0-9]+ | |' /usr/local/lib/pkgconfig/scafacos.pc cd rm -r /tmp/scafacos ldconfig diff --git a/docker/jupyter_nbconvert_config.json b/docker/jupyter_nbconvert_config.json index 51d0ec3..6cf8b7e 100644 --- a/docker/jupyter_nbconvert_config.json +++ b/docker/jupyter_nbconvert_config.json @@ -1,6 +1,6 @@ { "version": 1, - "Exporter": { + "HTMLExporter": { "require_js_url": "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js", "mathjax_url": "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS_CHTML-full,Safe" }