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Merge branch 'develop' into feature/update_derecho_jul2025
2 parents 7410ea5 + 0ba5216 commit 15297ed

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‎configs/common/packages.yaml‎

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@@ -171,6 +171,8 @@ packages:
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mapl:
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require: '@2.53 ~shared ~f2py'
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variants: '+pflogger'
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# Note: Please check the sites/tier1/nas/packages_gcc.yaml if
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# this is changed, as it has a custom variant combination
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met:
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require:
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- '@12.0.1'

‎configs/sites/tier1/gaea-c6/compilers.yaml‎

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compilers:
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- compiler:
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spec: [email protected]
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paths:
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cc: cc
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cxx: CC
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f77: ftn
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fc: ftn
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flags: {}
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operating_system: sles15
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target: x86_64
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modules:
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- PrgEnv-intel/8.6.0
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- intel/2024.2
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- craype/2.7.34
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- cray-libsci/24.11.0
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- libfabric/1.20.1
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environment:
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prepend_path:
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LD_LIBRARY_PATH: '/opt/cray/libfabric/1.20.1/lib64:/opt/cray/pe/libsci/24.07.0/INTEL/2023.2/x86_64/lib:/usr/lib64/gcc/x86_64-suse-linux/12:/opt/intel/oneapi/compiler/2024.2/lib'
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set:
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# OpenSUSE on Gaea C6 sets CONFIG_SITE so
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# Automake-based builds are installed in lib64
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# which confuses some packages.
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CONFIG_SITE: ''
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extra_rpaths:
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- /opt/intel/oneapi/compiler/2024.2/lib
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- compiler:
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spec: [email protected]
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paths:
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cxxflags: "-gxx-name=/usr/bin/g++-12 -gcc-name=/usr/bin/gcc-12 -static-libstdc++"
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fflags: "-gcc-name=/usr/bin/gcc-12"
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operating_system: sles15
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target: x86_64
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modules:
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- PrgEnv-intel/8.5.0
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- intel-classic/2023.2.0
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fc: /usr/bin/gfortran-12
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flags: {}
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operating_system: sles15
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target: x86_64
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modules:
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- PrgEnv-gnu/8.5.0
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- PrgEnv-gnu/8.6.0
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- gcc-native/12.3
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- craype/2.7.30
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- libfabric/1.20.1
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- craype/2.7.34
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- libfabric/1.20.1
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- cray-libsci/24.11.0
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- libfabric/1.20.1
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environment: {}
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extra_rpaths: []
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prepend_path:
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LD_LIBRARY_PATH: '/opt/cray/libfabric/1.20.1/lib64:/opt/cray/pe/libsci/24.07.0/INTEL/2023.2/x86_64/lib:/usr/lib64/gcc/x86_64-suse-linux/12:/opt/intel/oneapi/compiler/2024.2/lib'
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extra_rpaths:
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- /opt/intel/oneapi/compiler/2024.2/lib

‎configs/sites/tier1/gaea-c6/packages_gcc.yaml‎

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packages:
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all:
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compiler:: [[email protected]]
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providers:
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mpi:: [[email protected]]
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mpi:
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buildable: False
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cray-mpich:
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externals:
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- spec: [email protected]
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prefix: /opt/cray/pe/mpich/8.1.32/ofi/gnu/12.3
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modules:
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- craype-network-ofi
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- cray-mpich/8.1.32
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gcc-runtime:
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externals:
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- spec: [email protected]%[email protected]
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prefix: /usr

‎configs/sites/tier1/gaea-c6/packages_oneapi.yaml‎

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packages:
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all:
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compiler:: [[email protected], [email protected]]
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providers:
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mpi:: [[email protected]]
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### MPI, Python, MKL
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mpi:
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buildable: False
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cray-mpich:
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buildable: False
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externals:
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- spec: [email protected]%[email protected] ~wrappers
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prefix: /opt/cray/pe/mpich/8.1.32/ofi/intel/2022.1
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modules:
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- cray-mpich/8.1.32
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- craype-network-ofi
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intel-oneapi-runtime:
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buildable: False
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externals:
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- spec: [email protected]%[email protected]
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prefix: /opt/intel/oneapi/compiler/2024.2
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intel-oneapi-mkl:
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buildable: False
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externals:
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- spec: [email protected]%[email protected]
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prefix: /opt/intel/oneapi
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### Modification of common packages
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bison:
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require:
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- '%gcc'
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ectrans:
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require::
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- '@1.2.0 +mkl ~fftw'
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gsibec:
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require::
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- '@1.2.1 ~mkl'
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py-numpy:
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require::
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- '@1.26'
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- '^openblas'

‎configs/sites/tier1/hercules/packages_oneapi.yaml‎

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gsibec:
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require::
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- '@1.2.1 ~mkl'
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py-maturin:
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require:
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- '%gcc'
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py-numpy:
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require::
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- '@1.26'
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- '^openblas'
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py-scipy:
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require:
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'%gcc'
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zlib-ng:
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require:
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- '~shared'
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- '%gcc'

‎configs/sites/tier1/nas/README.md‎

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# How to build spack-stack at NAS
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## Generic
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```
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git clone --recursive https://github.com/JCSDA/spack-stack.git -b release/1.9.0 spack-stack-1.9.1
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```
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## oneapi
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```
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cd spack-stack-1.9.1
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. setup.sh
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spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas --compiler oneapi
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cd envs/ue-oneapi-2024.2.0
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spack env activate .
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spack concretize 2>&1 | tee log.concretize
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spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install
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```
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NOTE: You might need to run the `spack install` command multiple times because sometimes
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it just fails. But then you run it more and more and it will eventually succeed.
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```
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spack module tcl refresh -y
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spack stack setup-meta-modules
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spack env deactivate
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```
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## gcc
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```
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cd spack-stack-1.9.1
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. setup.sh
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spack stack create env --name ue-gcc-12.3.0 --template unified-dev --site nas --compiler gcc
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cd envs/ue-gcc-12.3.0
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spack env activate .
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spack concretize 2>&1 | tee log.concretize
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spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install
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```
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NOTE: You might need to run the `spack install` command multiple times because sometimes
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it just fails. But then you run it more and more and it will eventually succeed.
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```
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spack module tcl refresh -y
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spack stack setup-meta-modules
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spack env deactivate
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```

‎configs/sites/tier1/nas/compilers.yaml‎

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compilers:
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- compiler:
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spec: oneapi@=2024.2.0
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paths:
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cc: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/icx
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cxx: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/icpx
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f77: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/ifort
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fc: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/ifort
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flags: {}
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operating_system: rhel8
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target: x86_64
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modules:
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- comp-intel/2024.2.0-ifort
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environment:
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prepend_path:
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PATH: '/nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin'
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CPATH: '/nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/include'
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LD_LIBRARY_PATH: '/nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/lib/:/nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/lib64'
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set:
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MPI_COLL_REPRODUCIBLE: 'yes'
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MPI_MEMMAP_OFF: 'yes'
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MPI_XPMEM_ENABLED: 'yes'
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MPI_LAUNCH_TIMEOUT: '40'
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MPI_COMM_MAX: '1024'
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MPI_GROUP_MAX: '1024'
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MPI_BUFS_PER_PROC: '256'
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unset:
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- MPI_NUM_MEMORY_REGIONS
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- SUPPRESS_XPMEM_TRIM_THRESH
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- PMI_RANK
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extra_rpaths: []
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- compiler:
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spec: gcc@=12.3.0
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paths:
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cc: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/gcc
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cxx: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/g++
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f77: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/gfortran
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fc: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/gfortran
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flags: {}
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operating_system: rhel8
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target: x86_64
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modules:
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- comp-gcc/12.3.0-TOSS4
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environment:
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set:
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OMPI_MCA_mpi_preconnect_all: 1
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OMPI_MCA_coll_tuned_bcast_algorithm: 7
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OMPI_MCA_coll_tuned_scatter_algorithm: 2
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OMPI_MCA_coll_tuned_reduce_scatter_algorithm: 3
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OMPI_MCA_coll_tuned_allreduce_algorithm: 3
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OMPI_MCA_coll_tuned_allgather_algorithm: 4
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OMPI_MCA_coll_tuned_allgatherv_algorithm: 3
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OMPI_MCA_coll_tuned_gather_algorithm: 1
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OMPI_MCA_coll_tuned_barrier_algorithm: 0
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OMPI_MCA_coll_tuned_use_dynamic_rules: 1
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OMPI_MCA_sharedfp: '^lockedfile,individual'
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extra_rpaths: []

‎configs/sites/tier1/nas/config.yaml‎

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config:
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build_jobs: 6

‎configs/sites/tier1/nas/mirrors.yaml‎

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mirrors:
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local-source:
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fetch:
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url: file:///nobackup/gmao_SIteam/spack-stack/source-cache
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access_pair:
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- null
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- null
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access_token: null
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profile: null
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endpoint_url: null
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push:
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url: file:///nobackup/gmao_SIteam/spack-stack/source-cache
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access_pair:
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- null
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- null
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access_token: null
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profile: null
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endpoint_url: null

‎configs/sites/tier1/nas/modules.yaml‎

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modules:
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default:
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enable::
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- tcl
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tcl:
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include:
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# List of packages for which we need modules that are blacklisted by default
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- python

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