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Merge pull request #258 from xylar/add-aurora
Add support for Aurora
2 parents e624a55 + ace36ad commit 778c07b

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‎docs/developers_guide/quick_start.md‎

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@@ -62,10 +62,10 @@ process until your commit is successful. Some changes need to be made manually,
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such as inconsistent variable types. When this happens, you must update the
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file to `pre-commit`'s standards, and then attempt to re-commit the file.
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Internally, `pre-commit` uses [ruff](https://docs.astral.sh/ruff/) to check
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PEP8 compliance, as well as sort, check and format imports,
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[flynt](https://github.com/ikamensh/flynt) to change any format strings to
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f-strings, and [mypy](https://mypy-lang.org/) to check for consistent variable
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Internally, `pre-commit` uses [ruff](https://docs.astral.sh/ruff/) to check
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PEP8 compliance, as well as sort, check and format imports,
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[flynt](https://github.com/ikamensh/flynt) to change any format strings to
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f-strings, and [mypy](https://mypy-lang.org/) to check for consistent variable
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types. An example error might be:
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```bash
@@ -145,6 +145,7 @@ call `discover_machine()`. It will be recognized from the host name or the
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local environment:
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- andes
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- aurora
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- anvil
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- chicoma-cpu
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- chrysalis

‎mache/cime_machine_config/config_machines.xml‎

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‎mache/discover.py‎

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@@ -21,6 +21,8 @@ def discover_machine(quiet=False):
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machine = None
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machines_by_host_re = {
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r'^andes': 'andes',
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r'^aurora': 'aurora',
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r'^x\d{4}c\d{1}s\d{1}b0n0': 'aurora',
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r'^blueslogin': 'anvil',
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r'^b\d{3}': 'anvil',
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r'^ch-fe': 'chicoma-cpu',

‎mache/machines/aurora.cfg‎

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# Options related to deploying an e3sm-unified conda environment on supported
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# machines
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[e3sm_unified]
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# the unix group for permissions for the e3sm-unified conda environment
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group = E3SM_Dec
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# the compiler set to use for system libraries
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compiler = oneapi-ifx
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# the system MPI library
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mpi = mpich
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# the path to the directory where activation scripts, the base environment, and
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# system libraries will be deployed
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base_path = /lus/flare/projects/E3SM_Dec/soft/e3sm-unified
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# whether to use system modules for hdf5, netcdf-c, netcdf-fortran and pnetcdf
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# (spack modules are used otherwise)
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use_system_hdf5_netcdf = True
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# config options related to data needed by diagnostics software such as
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# e3sm_diags and MPAS-Analysis
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[diagnostics]
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# The base path to the diagnostics directory
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base_path = /lus/flare/projects/E3SM_Dec/diagnostics
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# the unix group for permissions for diagnostics
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group = E3SM_Dec
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# The parallel section describes options related to running jobs in parallel
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[parallel]
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# parallel system of execution: slurm, pbs or single_node
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system = pbs
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# whether to use mpirun or srun to run a task
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parallel_executable = mpirun
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# cores per node on the machine (with hyperthreading)
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cores_per_node = 208
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# account for running diagnostics jobs
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account = E3SM_Dec
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# queues (default is the first)
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queues = prod, debug
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# Config options related to spack environments
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[spack]
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# whether to load modules from the spack yaml file before loading the spack
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# environment
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modules_before = False
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# whether to load modules from the spack yaml file after loading the spack
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# environment
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modules_after = False
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# config options related to synchronizing files
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[sync]
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# the full hostname of the machine
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hostname = aurora.alcf.anl.gov

‎mache/spack/templates/aurora_oneapi-ifx_mpich.csh‎

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source /usr/share/lmod/lmod/init/csh
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module load \
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cmake/3.30.5 \
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oneapi/release/2025.0.5
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setenv LD_LIBRARY_PATH "/lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002/lib:/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002/lib:${LD_LIBRARY_PATH}"
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setenv PATH "/lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002/bin:/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002/bin:${PATH}"
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setenv FI_CXI_DEFAULT_CQ_SIZE "131072"
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setenv FI_CXI_CQ_FILL_PERCENT "20"
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setenv LIBOMPTARGET_DEBUG "0"
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setenv MPIR_CVAR_ENABLE_GPU "0"
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setenv GPU_TILE_COMPACT " "
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setenv RANKS_BIND "core"
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setenv KMP_AFFINITY "granularity=core,balanced"
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{%- if e3sm_hdf5_netcdf %}
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setenv NETCDF_PATH "/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002"
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setenv NETCDF_C_PATH "/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002"
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setenv NETCDF_FORTRAN_PATH "/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002"
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setenv PNETCDF_PATH "/lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002"
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{%- endif %}

‎mache/spack/templates/aurora_oneapi-ifx_mpich.sh‎

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source /usr/share/lmod/lmod/init/sh
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module load \
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cmake/3.30.5 \
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oneapi/release/2025.0.5
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export LD_LIBRARY_PATH="/lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002/lib:/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002/lib:${LD_LIBRARY_PATH}"
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export PATH="/lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002/bin:/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002/bin:${PATH}"
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export FI_CXI_DEFAULT_CQ_SIZE="131072"
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export FI_CXI_CQ_FILL_PERCENT="20"
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export LIBOMPTARGET_DEBUG="0"
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export MPIR_CVAR_ENABLE_GPU="0"
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export GPU_TILE_COMPACT=" "
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export RANKS_BIND="core"
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export KMP_AFFINITY="granularity=core,balanced"
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{%- if e3sm_hdf5_netcdf %}
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export NETCDF_PATH="/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002"
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export NETCDF_C_PATH="/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002"
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export NETCDF_FORTRAN_PATH="/lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002"
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export PNETCDF_PATH="/lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002"
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{%- endif %}

‎mache/spack/templates/aurora_oneapi-ifx_mpich.yaml‎

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{%- set compiler = "[email protected]" %}
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{%- set mpi = "[email protected]" %}
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spack:
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specs:
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- {{ mpi }}%{{ compiler }}
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{%- if e3sm_hdf5_netcdf %}
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- "hdf5%{{ compiler }}"
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- "netcdf-c%{{ compiler }}"
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- "netcdf-fortran%{{ compiler }}"
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- "parallel-netcdf%{{ compiler }}"
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{%- endif %}
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{%- for spec in specs %}
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- "{{ spec }}%{{ compiler }}"
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{%- endfor %}
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concretizer:
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unify: true
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packages:
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all:
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compiler: [{{ compiler }}]
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providers:
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mpi: [{{ mpi }}]
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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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buildable: false
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bzip2:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: false
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cmake:
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externals:
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- spec: [email protected]
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prefix: /opt/aurora/24.347.0/spack/unified/0.9.2/install/linux-sles15-x86_64/gcc-13.3.0/cmake-3.30.5-igar7ts
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buildable: false
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curl:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: false
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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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buildable: false
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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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buildable: false
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gmake:
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externals:
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- spec: [email protected]
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prefix: /opt/aurora/24.347.0/spack/unified/0.9.2/install/linux-sles15-x86_64/gcc-13.3.0/gmake-4.4.1-wza7sk4
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buildable: false
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libiconv:
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externals:
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- spec: [email protected]
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prefix: /opt/aurora/24.347.0/spack/unified/0.9.2/install/linux-sles15-x86_64/gcc-13.3.0/libiconv-1.17-jjpb4sl
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buildable: false
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libxml2:
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externals:
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- spec: [email protected]
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prefix: /opt/aurora/24.347.0/spack/unified/0.9.2/install/linux-sles15-x86_64/gcc-13.3.0/libxml2-2.13.5-jxhkqdj
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buildable: false
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openssl:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: false
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xz:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: false
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zlib:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: false
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perl:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: false
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oneapi:
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externals:
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- spec: {{ compiler }}
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modules:
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- oneapi/release/2025.0.5
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buildable: false
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gcc-runtime:
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externals:
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- spec: [email protected]
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prefix: /opt/aurora/24.347.0/spack/unified/0.9.2/install/linux-sles15-x86_64/gcc-13.3.0/gcc-runtime-13.3.0-ghotoln
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buildable: false
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mpich:
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externals:
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- spec: {{ mpi }}%{{ compiler }}
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prefix: /opt/aurora/24.347.0/spack/unified/0.9.2/install/linux-sles15-x86_64/oneapi-2025.0.5/mpich-develop-git.6037a7a-sxnhr7p
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buildable: false
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{%- if e3sm_hdf5_netcdf %}
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hdf5:
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externals:
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- spec: [email protected]+cxx+fortran+hl+mpi
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prefix: /lus/flare/projects/E3SM_Dec/soft/hdf5/1.14.5/oneapi.eng.2024.07.30.002/
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buildable: false
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netcdf-c:
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externals:
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- spec: [email protected]+mpi~parallel-netcdf
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prefix: /lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002
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buildable: false
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netcdf-fortran:
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externals:
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- spec: [email protected]
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prefix: /lus/flare/projects/E3SM_Dec/soft/netcdf/4.9.2c-4.6.1f/oneapi.eng.2024.07.30.002
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buildable: false
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parallel-netcdf:
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externals:
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- spec: [email protected]+cxx+fortran
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prefix: /lus/flare/projects/E3SM_Dec/soft/pnetcdf/1.14.0/oneapi.eng.2024.07.30.002
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buildable: false
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{%- endif %}
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compilers:
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- compiler:
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spec: {{ compiler }}
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paths:
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cc: /opt/aurora/24.347.0/oneapi/compiler/latest/bin/icx
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cxx: /opt/aurora/24.347.0/oneapi/compiler/latest/bin/icpx
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f77: /opt/aurora/24.347.0/oneapi/compiler/latest/bin/ifx
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fc: /opt/aurora/24.347.0/oneapi/compiler/latest/bin/ifx
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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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environment: {}
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extra_rpaths: []

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