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Add NAS as tier1 site (#1708)
This PR adds NAS as a new site for spack-stack. These files were used to build spack-stack 1.9.0. The two stacks I was able to build are [email protected] with MPT and [email protected] with Open MPI. Note: For [email protected] I just could not build hdf-eos2 so I had to alter the met variants to skip that.
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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/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

‎configs/sites/tier1/nas/packages.yaml

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packages:
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all:
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target: [x86_64_v3]
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### Modification of common packages
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# Problems building shared hdf-eos2 with Intel, not needed
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hdf-eos2:
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variants: ~shared
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met:
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variants: +python +grib2 +graphics +lidar2nc +modis
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### All other external packages listed alphabetically
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automake:
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externals:
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- spec: [email protected]
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prefix: /usr
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binutils:
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externals:
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- spec: [email protected]~gold~headers
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prefix: /usr
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bison:
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externals:
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- spec: [email protected]
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prefix: /usr
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coreutils:
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externals:
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- spec: [email protected]
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prefix: /usr
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diffutils:
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externals:
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- spec: [email protected]
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prefix: /usr
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findutils:
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externals:
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- spec: [email protected]
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prefix: /usr
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flex:
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externals:
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- spec: [email protected]+lex
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prefix: /usr
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gawk:
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externals:
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- spec: [email protected]
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prefix: /usr
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git:
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externals:
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- spec: [email protected]~tcltk
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prefix: /usr
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gmake:
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externals:
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- spec: [email protected]
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prefix: /usr
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grep:
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externals:
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- spec: [email protected]
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prefix: /usr
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groff:
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externals:
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- spec: [email protected]
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prefix: /usr
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libtool:
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externals:
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- spec: [email protected]
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prefix: /usr
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m4:
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externals:
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- spec: [email protected]
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prefix: /usr
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perl:
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externals:
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- spec: [email protected]~cpanm+opcode+open+shared+threads
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prefix: /usr
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pkgconf:
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externals:
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- spec: [email protected]
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prefix: /usr
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sed:
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externals:
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- spec: [email protected]
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prefix: /usr
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subversion:
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externals:
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- spec: [email protected]
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prefix: /usr
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tar:
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externals:
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- spec: [email protected]
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prefix: /usr
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wget:
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externals:
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- spec: [email protected]
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prefix: /usr
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zlib:
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externals:
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- spec: [email protected]
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prefix: /usr

‎configs/sites/tier1/nas/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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openmpi:
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externals:
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- spec: [email protected]%gcc@=12.3.0~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath+lustre
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fabrics=ucx schedulers=tm
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prefix: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0
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environment:
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set:
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OPAL_PREFIX: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0
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UCX_MAX_EAGER_LANES: 1
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UCX_MAX_RNDV_LANES: 1
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OMPI_MCA_pml: ucx
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OMPI_MCA_btl: ^openib
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OMPI_MCA_oob_tcp_listen_mode: listen_thread
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OMPI_MCA_oob_tcp_if_include: ib0,ib1
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OMPI_MCA_btl_tcp_if_include: ib0,ib1
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OMPI_MCA_opal_warn_on_missing_libcuda: 0
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UCX_IB_SUBNET_PREFIX: fec0:0000:0000:0008
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OMPI_MCA_shmem_mmap_enable_nfs_warning: 0
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OPENMPI: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0
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prepend_path:
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PATH: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0/bin
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LIBRARY_PATH: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0/lib
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LD_LIBRARY_PATH: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0/lib
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CPATH: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0/include
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FPATH: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0/include
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MANPATH: /nobackup/gmao_SIteam/MPI/openmpi/4.1.8/gcc-12.3.0/share/man
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# MAT: I cannot figure out how to get hdf-eos2 to build with GCC on NAS
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# When I try, it dies with an error trying to *patch* the code!
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# This turns off the variants of met that need it
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met:
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variants::
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- '+python +grib2 +graphics'

‎configs/sites/tier1/nas/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:
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buildable: False
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mpt:
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externals:
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- spec: [email protected]%oneapi@=2024.2.0
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prefix: /nasa/hpe/mpt/2.30_rhel810
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intel-oneapi-mkl:
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externals:
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- spec: [email protected]%[email protected]
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prefix: /nobackup/gmao_SIteam/intel/oneapi

‎doc/source/PreConfiguredSites.rst

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| MSU +-----------------------+--------------------+--------------------------------------------------------+-----------------+
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| | Orion | oneAPI | ``/apps/contrib/spack-stack/`` | EPIC / JCSDA |
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+---------------------+-----------------------+--------------------+--------------------------------------------------------+-----------------+
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| NASA | Discover SCU17 | GCC, Intel | ``/gpfsm/dswdev/jcsda/spack-stack/scu17/`` | JCSDA |
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| | Discover SCU17 | GCC, Intel | ``/gpfsm/dswdev/jcsda/spack-stack/scu17/`` | JCSDA |
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| NASA +-----------------------+--------------------+--------------------------------------------------------+-----------------+
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| | NAS | GCC, Intel | ``/nobackup/gmao_SIteam/spack-stack/`` | GMAO |
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+---------------------+-----------------------+--------------------+--------------------------------------------------------+-----------------+
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| NCAR-Wyoming + Derecho | GCC, Intel | ``/glade/work/epicufsrt/contrib/spack-stack/derecho/`` | EPIC / JCSDA |
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+---------------------+-----------------------+--------------------+--------------------------------------------------------+-----------------+
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module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
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module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
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.. _Preconfigured_Sites_NAS:
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------------------------------
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NASA NAS
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------------------------------
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The following is required for building new spack environments with any supported compiler on this platform.
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.. code-block:: console
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module purge
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module use /nobackup/gmao_SIteam/modulefiles
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.. _Preconfigured_Sites_Narwhal:
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