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JEDI CI container specs update and FMS update for JEDI-FV3 #1099

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merged 6 commits into from
May 9, 2024
Merged

JEDI CI container specs update and FMS update for JEDI-FV3 #1099

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a2f7248
Add missing packages for JEDI CI overlay to configs/containers/specs/…
climbfuji May 2, 2024
9143bcb
Switch FMS in jedi-fv3-env from fms@release-jcsda to [email protected]+pic
climbfuji May 2, 2024
29c7ee8
Switch FMS in gmao-swell-env from fms@release-jcsda to [email protected]+pic
climbfuji May 2, 2024
4829f66
Merge branch 'develop' into feature/jedi_ci_container_and_fms_update_…
climbfuji May 7, 2024
3ad6d8a
add python3-nacl as external package in intel-impi
eap May 7, 2024
e64a316
Merge branch 'develop' into feature/jedi_ci_container_and_fms_update_…
climbfuji May 9, 2024
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11 changes: 9 additions & 2 deletions configs/containers/docker-ubuntu-intel-impi.yaml
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Expand Up @@ -75,6 +75,11 @@ spack:
externals:
- spec: [email protected]
prefix: /usr
py-pynacl:
buildable: false
externals:
- spec: [email protected]
prefix: /usr/lib/python3/dist-packages/nacl
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# Turn off crypt, because libxcrypt doesn't
# build with Intel.
python:
Expand Down Expand Up @@ -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/*
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@eap eap May 8, 2024 •
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Note I've added this rm command to each "RUN" directive with apt update since it reduces the layer size.

pre_final: |
# Set environment variables for installing tzdata
ENV DEBIAN_FRONTEND=noninteractive
Expand All @@ -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
Expand Down
6 changes: 4 additions & 2 deletions configs/containers/specs/jedi-ci.yaml
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Expand Up @@ -2,7 +2,7 @@
specs: [[email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected], [email protected], [email protected], ecflow@5,
[email protected], [email protected] +fckit +trans +tesselation +fftw, [email protected], [email protected] +fftw,
[email protected], [email protected], fms@release-jcsda, [email protected], [email protected], [email protected],
[email protected], [email protected], fms@2023.04, [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected],
Expand All @@ -11,7 +11,9 @@
[email protected], py-pip, [email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], shumlib@macos_clang_linux_intel_port,
[email protected], [email protected]]
[email protected], [email protected],
# Added for new CI system 2024/04/30
[email protected], [email protected], [email protected] ]
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nice

# 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
Expand Down
2 changes: 1 addition & 1 deletion spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py
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Expand Up @@ -24,7 +24,7 @@ class GmaoSwellEnv(BundlePackage):
depends_on("[email protected]", 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
Expand Down
2 changes: 1 addition & 1 deletion spack-ext/repos/spack-stack/packages/jedi-fv3-env/package.py
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Expand Up @@ -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.
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