From a2f7248bb6e24039c6d735e9bd54c8107eba0926 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 2 May 2024 14:22:27 -0600 Subject: [PATCH 1/4] Add missing packages for JEDI CI overlay to configs/containers/specs/jedi-ci.yaml --- configs/containers/specs/jedi-ci.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/configs/containers/specs/jedi-ci.yaml b/configs/containers/specs/jedi-ci.yaml index 38ebe9324..a1c3394d4 100644 --- a/configs/containers/specs/jedi-ci.yaml +++ b/configs/containers/specs/jedi-ci.yaml @@ -2,7 +2,7 @@ specs: [base-env@1.0.0, jedi-base-env@1.0.0, ewok-env@1.0.0, jedi-fv3-env@1.0.0, jedi-mpas-env@1.0.0, bacio@2.4.1, bison@3.8.2, bufr@12.0.1, ecbuild@3.7.2, eccodes@2.33.0, ecflow@5, eckit@1.24.5, ecmwf-atlas@0.36.0 +fckit +trans +tesselation +fftw, fiat@1.2.0, ectrans@1.2.0 +fftw, - eigen@3.4.0, fckit@0.11.0, fms@release-jcsda, g2@3.4.9, g2tmpl@1.10.2, gftl-shared@1.6.1, + eigen@3.4.0, fckit@0.11.0, fms@2023.04, g2@3.4.9, g2tmpl@1.10.2, gftl-shared@1.6.1, gsibec@1.2.1, hdf@4.2.15, hdf5@1.14.3, ip@5.0.0, jasper@2.0.32, jedi-cmake@1.4.0, libpng@1.6.37, nccmp@1.9.0.1, netcdf-c@4.9.2, netcdf-cxx4@4.3.1, netcdf-fortran@4.6.1, nlohmann-json@3.10.5, nlohmann-json-schema-validator@2.1.0, @@ -11,7 +11,9 @@ py-pandas@1.5.3, py-pip, py-pyyaml@6.0, py-scipy@1.11.4, py-shapely@1.8.0, py-xarray@2023.7.0, sp@2.5.0, udunits@2.2.28, w3emc@2.10.0, nco@5.1.6, esmf@8.6.0, mapl@2.40.3, zlib-ng@2.1.5, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port, - awscli-v2@2.13.22, py-globus-cli@3.16.0] + awscli-v2@2.13.22, py-globus-cli@3.16.0, + # Added for new CI system 2024/04/30 + py-ansi2html@1.6.0, py-pygithub@2.1.1, jq@1.6 ] # Notes: # 1. Don't build CRTM by default so that it gets built in the JEDI bundles # 2. Comment out for now until build problems are solved From 9143bcb6d629cf01785a9cc72294cbfbed457fe5 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 2 May 2024 14:23:11 -0600 Subject: [PATCH 2/4] Switch FMS in jedi-fv3-env from fms@release-jcsda to fms@2023.04+pic --- spack-ext/repos/spack-stack/packages/jedi-fv3-env/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spack-ext/repos/spack-stack/packages/jedi-fv3-env/package.py b/spack-ext/repos/spack-stack/packages/jedi-fv3-env/package.py index 8b18ec6bd..49567ca7a 100644 --- a/spack-ext/repos/spack-stack/packages/jedi-fv3-env/package.py +++ b/spack-ext/repos/spack-stack/packages/jedi-fv3-env/package.py @@ -17,6 +17,6 @@ class JediFv3Env(BundlePackage): version("1.0.0") depends_on("jedi-base-env", type="run") - depends_on("fms@release-jcsda", type="run") + depends_on("fms@2023.04+pic", type="run") # There is no need for install() since there is no code. From 29c7ee8ef70620156f7f60d0bca4f174fbee42ec Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 2 May 2024 14:23:30 -0600 Subject: [PATCH 3/4] Switch FMS in gmao-swell-env from fms@release-jcsda to fms@2023.04+pic --- spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py b/spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py index 31824eb8d..fb0d4b67a 100644 --- a/spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py +++ b/spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py @@ -24,7 +24,7 @@ class GmaoSwellEnv(BundlePackage): depends_on("crtm@v2.4-jedi.2", type="run") # Additional dependencies for JEDI used by swell - depends_on("fms@release-jcsda", type="run") + depends_on("fms@2023.04+pic", type="run") depends_on("nco", type="run") # GEOS From 3ad6d8a303481bfb1a715ba2e23bf384dfb20abb Mon Sep 17 00:00:00 2001 From: Evan Parker Date: Tue, 7 May 2024 16:18:48 -0600 Subject: [PATCH 4/4] add python3-nacl as external package in intel-impi --- configs/containers/docker-ubuntu-intel-impi.yaml | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/configs/containers/docker-ubuntu-intel-impi.yaml b/configs/containers/docker-ubuntu-intel-impi.yaml index ac8c160f1..67a5a7830 100644 --- a/configs/containers/docker-ubuntu-intel-impi.yaml +++ b/configs/containers/docker-ubuntu-intel-impi.yaml @@ -75,6 +75,11 @@ spack: externals: - spec: mysql@8.0.32 prefix: /usr + py-pynacl: + buildable: false + externals: + - spec: py-pynacl@1.5.0 + prefix: /usr/lib/python3/dist-packages/nacl # Turn off crypt, because libxcrypt doesn't # build with Intel. python: @@ -180,7 +185,8 @@ spack: wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null && \ echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list && \ apt update && \ - apt install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2022.1.0 intel-oneapi-compiler-fortran-2022.1.0 intel-oneapi-mkl-devel-2022.1.0 intel-oneapi-mpi-devel-2021.6.0 -y + apt install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2022.1.0 intel-oneapi-compiler-fortran-2022.1.0 intel-oneapi-mkl-devel-2022.1.0 intel-oneapi-mpi-devel-2021.6.0 python3-nacl -y && \ + rm -rf /var/lib/apt/lists/* pre_final: | # Set environment variables for installing tzdata ENV DEBIAN_FRONTEND=noninteractive @@ -199,7 +205,8 @@ spack: wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null && \ echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list && \ apt update && \ - apt install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2022.1.0 intel-oneapi-compiler-fortran-2022.1.0 intel-oneapi-mkl-devel-2022.1.0 intel-oneapi-mpi-devel-2021.6.0 -y + apt install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2022.1.0 intel-oneapi-compiler-fortran-2022.1.0 intel-oneapi-mkl-devel-2022.1.0 intel-oneapi-mpi-devel-2021.6.0 -y && \ + rm -rf /var/lib/apt/lists/* # Copy spack find output from builder COPY --from=builder /root/spack_find.out /root/spack_find.out # Make a non-root user:nonroot / group:nonroot for running MPI