From 085e508713f23725bc76d575414a711125fd35de Mon Sep 17 00:00:00 2001 From: cameronbook Date: Tue, 27 Sep 2022 16:41:08 +0000 Subject: [PATCH 01/61] Add ufs-wm-dev template to develop. --- configs/templates/ufs-wm-dev/spack.yaml | 44 +++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 configs/templates/ufs-wm-dev/spack.yaml diff --git a/configs/templates/ufs-wm-dev/spack.yaml b/configs/templates/ufs-wm-dev/spack.yaml new file mode 100644 index 000000000..838c5f71a --- /dev/null +++ b/configs/templates/ufs-wm-dev/spack.yaml @@ -0,0 +1,44 @@ +spack: + config: + install_tree: + root: $env/install + deprecated: true + modules: + default: + roots: + lmod: $env/install/modulefiles + tcl: $env/install/modulefiles + lmod: + projections: + parallelio: 'pio/{version}' + tcl: + projections: + parallelio: '{^mpi.name}/{^mpi.version}/{compiler.name}/{compiler.version}/pio/{version}' + + include: [] + + concretizer: + unify: when_possible + + specs: + - jasper@2.0.25 + - zlib@1.2.11 + - libpng@1.6.37 + - hdf5@1.10.6 + - netcdf-c@4.7.4 + - netcdf-fortran@4.5.4 + - parallelio@2.5.7 + - esmf@8.3.0b09 + - fms@2022.01 + - bacio@2.4.1 + - crtm@2.3.0 + - g2@3.4.5 + - g2tmpl@1.10.0 + - ip@3.3.3 + - sp@2.3.3 + - w3emc@2.9.2 + - gftl-shared@1.5.0 + - yafyaml@0.5.1 + - mapl@2.22.0 + + From 80307564bfd1b571bd1342887bc8211298ad44a9 Mon Sep 17 00:00:00 2001 From: cameronbook Date: Thu, 6 Oct 2022 21:33:43 +0000 Subject: [PATCH 02/61] Remove ufs-wm-dev template to get fork dev aligned with main dev. --- configs/templates/ufs-wm-dev/spack.yaml | 44 ------------------------- 1 file changed, 44 deletions(-) delete mode 100644 configs/templates/ufs-wm-dev/spack.yaml diff --git a/configs/templates/ufs-wm-dev/spack.yaml b/configs/templates/ufs-wm-dev/spack.yaml deleted file mode 100644 index 838c5f71a..000000000 --- a/configs/templates/ufs-wm-dev/spack.yaml +++ /dev/null @@ -1,44 +0,0 @@ -spack: - config: - install_tree: - root: $env/install - deprecated: true - modules: - default: - roots: - lmod: $env/install/modulefiles - tcl: $env/install/modulefiles - lmod: - projections: - parallelio: 'pio/{version}' - tcl: - projections: - parallelio: '{^mpi.name}/{^mpi.version}/{compiler.name}/{compiler.version}/pio/{version}' - - include: [] - - concretizer: - unify: when_possible - - specs: - - jasper@2.0.25 - - zlib@1.2.11 - - libpng@1.6.37 - - hdf5@1.10.6 - - netcdf-c@4.7.4 - - netcdf-fortran@4.5.4 - - parallelio@2.5.7 - - esmf@8.3.0b09 - - fms@2022.01 - - bacio@2.4.1 - - crtm@2.3.0 - - g2@3.4.5 - - g2tmpl@1.10.0 - - ip@3.3.3 - - sp@2.3.3 - - w3emc@2.9.2 - - gftl-shared@1.5.0 - - yafyaml@0.5.1 - - mapl@2.22.0 - - From ee8de7af5240b37527b73d4755312d1140f4d4c8 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 24 Jan 2023 17:19:10 -0700 Subject: [PATCH 03/61] Delete configs/common/packages.yaml and rename/update configs/templates/hpc-dev-v1 to configs/templates/unified-dev --- .gitmodules | 10 +- configs/common/modules.yaml | 12 +- configs/templates/hpc-dev-v1/spack.yaml | 243 ------------------ .../unified-dev/spack.yaml} | 60 +++-- spack | 2 +- 5 files changed, 54 insertions(+), 273 deletions(-) delete mode 100644 configs/templates/hpc-dev-v1/spack.yaml rename configs/{common/packages.yaml => templates/unified-dev/spack.yaml} (84%) diff --git a/.gitmodules b/.gitmodules index c92fbbc5e..2cf3483a5 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,9 +1,11 @@ [submodule "spack"] path = spack - #url = https://github.com/spack/spack - #branch = develop - url = https://github.com/NOAA-EMC/spack - branch = jcsda_emc_spack_stack + ##url = https://github.com/spack/spack + ##branch = develop + #url = https://github.com/NOAA-EMC/spack + #branch = jcsda_emc_spack_stack + url = https://github.com/climbfuji/spack + branch = feature/unified-env [submodule "doc/CMakeModules"] path = doc/CMakeModules url = https://github.com/noaa-emc/cmakemodules diff --git a/configs/common/modules.yaml b/configs/common/modules.yaml index c8677232e..9d9a19630 100644 --- a/configs/common/modules.yaml +++ b/configs/common/modules.yaml @@ -6,7 +6,7 @@ modules: arch_folder: false tcl: # Core compiler is a dummy that is not used to build the stack, do not change. - # Hopefully nobody is trying to build software with gcc-4.6 in 2022 ... + # Hopefully nobody is trying to build software with gcc-4.6 in 2023 ... core_compilers:: - gcc@4.6 projections: @@ -117,10 +117,10 @@ modules: suffixes: ^esmf@8.2.0~debug: 'esmf-8.2.0' ^esmf@8.2.0+debug: 'esmf-8.2.0-debug' - ^esmf@8.3.0b09~debug: 'esmf-8.3.0b09' - ^esmf@8.3.0b09+debug: 'esmf-8.3.0b09-debug' ^esmf@8.3.0~debug: 'esmf-8.3.0' ^esmf@8.3.0+debug: 'esmf-8.3.0-debug' + ^esmf@8.3.0b09~debug: 'esmf-8.3.0b09' + ^esmf@8.3.0b09+debug: 'esmf-8.3.0b09-debug' openmpi: environment: set: @@ -231,7 +231,7 @@ modules: lmod: # Core compiler is a dummy that is not used to build the stack, do not change. - # Hopefully nobody is trying to build software with gcc-4.6 in 2022 ... + # Hopefully nobody is trying to build software with gcc-4.6 in 2023 ... core_compilers:: - gcc@4.6 projections: @@ -340,10 +340,10 @@ modules: suffixes: ^esmf@8.2.0~debug: 'esmf-8.2.0' ^esmf@8.2.0+debug: 'esmf-8.2.0-debug' - ^esmf@8.3.0b09~debug: 'esmf-8.3.0b09' - ^esmf@8.3.0b09+debug: 'esmf-8.3.0b09-debug' ^esmf@8.3.0~debug: 'esmf-8.3.0' ^esmf@8.3.0+debug: 'esmf-8.3.0-debug' + ^esmf@8.3.0b09~debug: 'esmf-8.3.0b09' + ^esmf@8.3.0b09+debug: 'esmf-8.3.0b09-debug' openmpi: environment: set: diff --git a/configs/templates/hpc-dev-v1/spack.yaml b/configs/templates/hpc-dev-v1/spack.yaml deleted file mode 100644 index 7785298e9..000000000 --- a/configs/templates/hpc-dev-v1/spack.yaml +++ /dev/null @@ -1,243 +0,0 @@ -spack: - view: false - - include: [] - - concretizer: - unify: when_possible - - config: - install_tree: - root: $env/install - - modules: - default: - roots: - lmod: $env/install/modulefiles - tcl: $env/install/modulefiles - lmod: - core_specs: - - jedi-tools-env - - view: false - - packages: - bacio: - version: [2.4.1] - boost: - version: [1.78.0] - variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=14 visibility=hidden - bufr: - version: [11.7.1] - variants: +python - cmake: - version: [3.22.1] - crtm: - version: [2.3.0] - variants: +fix - ecbuild: - version: [3.6.5] - eccodes: - version: [2.27.0] - eckit: - version: [1.20.2] - variants: linalg=eigen,lapack compression=lz4,bzip2 - ecmwf-atlas: - version: [0.31.1] - variants: +fckit +trans - ectrans: - version: [1.2.0] - variants: ~enable_mkl - eigen: - version: [3.4.0] - esmf: - version: [8.3.0b09] - variants: ~xerces ~pnetcdf +pio - fckit: - version: [0.9.5] - variants: +eckit - fftw: - version: [3.3.10] - fiat: - version: [1.1.0] - fms: - version: [2022.04] - variants: +64bit +quad_precision +gfs_phys +openmp +fpic constants=GFS - g2: - version: [3.4.5] - g2c: - version: [1.6.4] - g2tmpl: - version: [1.10.0] - gfsio: - version: [1.4.1] - gftl-shared: - version: [1.5.0] - grib-util: - version: [1.2.3] - gsibec: - version: [1.0.6] - gsl-lite: - version: [0.37.0] - hdf: - version: [4.2.15] - variants: ~fortran ~netcdf - hdf5: - version: [1.12.1] - variants: +hl +fortran +mpi +threadsafe - ip: - version: [3.3.3] - ip2: - version: [1.1.2] - jasper: - version: [2.0.32] - jedi-cmake: - version: [1.4.0] - jpeg: - version: [9.1.0] - landsfcutil: - version: [2.4.1] - libjpeg-turbo: - version: [2.1.0] - libpng: - version: [1.6.37] - mapl: - version: [2.22.0] - met: - version: [10.1.1] - variants: +python +grib2 - metplus: - version: [4.1.1] - nco: - version: [5.0.6] - variants: ~doc - nemsio: - version: [2.5.2] - nemsiogfs: - version: [2.5.3] - nccmp: - version: [1.9.0.1] - ncio: - version: [1.1.2] - netcdf-c: - version: [4.8.1] - variants: +dap +mpi +parallel-netcdf - netcdf-cxx4: - version: [4.3.1] - netcdf-fortran: - version: [4.5.4] - nlohmann-json: - version: [3.10.5] - nlohmann-json-schema-validator: - version: [2.1.0] - odc: - version: [1.4.5] - variants: ~fortran - openblas: - version: [0.3.19] - variants: +noavx512 - parallelio: - version: [2.5.7] - variants: +pnetcdf - parallel-netcdf: - version: [1.12.2] - pkgconf: - buildable: False - prod-util: - version: [1.2.2] - proj: - version: [8.1.0] - variants: ~tiff - python: - version: [3.10.8] - py-cartopy: - variants: +plotting - py-click: - version: [8.0.3] - py-eccodes: - version: [1.4.2] - py-h5py: - version: [3.6.0] - py-netcdf4: - version: [1.5.3] - variants: +mpi - py-numpy: - version: [1.22.3] - variants: +blas +lapack - py-openpyxl: - version: [3.0.3] - py-pandas: - version: [1.4.0] - py-pybind11: - version: [2.8.1] - py-pycodestyle: - version: [2.8.0] - py-pygithub: - version: [1.55] - py-pygrib: - version: [2.1.4] - py-pyhdf: - version: [0.10.4] - py-pyproj: - version: [3.1.0] - py-python-dateutil: - version: [2.8.2] - #py-pythran: - # version: [0.11.0] - py-pyyaml: - version: [6.0] - py-scipy: - version: [1.9.3] - py-shapely: - version: [1.8.0] - sfcio: - version: [1.4.1] - shumlib: - version: [macos_clang_linux_intel_port] - sigio: - version: [2.3.2] - sp: - version: [2.3.3] - udunits: - version: [2.2.28] - upp: - version: [10.0.10] - w3emc: - version: [2.9.2] - w3nco: - version: [2.4.1] - wget: - version: [1.21.2] - wgrib2: - version: [2.0.8] - wrf-io: - version: [1.2.0] - yafyaml: - version: [0.5.1] - zlib: - version: [1.2.13] - - definitions: - - compilers: ['%gcc', '%intel'] - - packages: - - jedi-ewok-env@hpc-dev-v1 - - jedi-fv3-env@hpc-dev-v1 - - jedi-tools-env@hpc-dev-v1 - - jedi-ufs-env@hpc-dev-v1 - - jedi-um-env@hpc-dev-v1 - - global-workflow-env@hpc-dev-v1 - - ufs-weather-model-env@hpc-dev-v1 - - ufs-weather-model-env+debug@hpc-dev-v1 - - upp-env@hpc-dev-v1 - - ww3-env@hpc-dev-v1 - - gsi-env@hpc-dev-v1 - - ufs-utils-env@hpc-dev-v1 - - nceplibs-env@hpc-dev-v1 - - soca-env@hpc-dev-v1 - - specs: - - matrix: - - [$packages] - - [$compilers] - exclude: - - jedi-tools-env%intel diff --git a/configs/common/packages.yaml b/configs/templates/unified-dev/spack.yaml similarity index 84% rename from configs/common/packages.yaml rename to configs/templates/unified-dev/spack.yaml index cd444b980..2e139df34 100644 --- a/configs/common/packages.yaml +++ b/configs/templates/unified-dev/spack.yaml @@ -1,4 +1,10 @@ -# Pin versions and specs when building packages +spack: + concretizer: + unify: when_possible + + view: false + include: [] + packages: # all: @@ -18,8 +24,6 @@ # Attention - when updating also check orion site config boost: version: [1.78.0] - # Install only the minimum needed (JEDI packages need headers only, - # but ecflow needs several libraries) variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=14 visibility=hidden bufr: version: [11.7.1] @@ -34,15 +38,13 @@ # Attention - when updating also check the various jcsda-emc-bundles env packages crtm: version: [2.4.0] - diffutils: - version: [3.7] + variants: +fix ecbuild: version: [3.6.5] eccodes: version: [2.27.0] - #variants: +netcdf ecflow: - version: [5.8.3] + version: [5.8.4] variants: +ui eckit: version: [1.20.2] @@ -67,11 +69,6 @@ version: [3.3.10] fiat: version: [1.1.0] - findutils: - version: [4.8.0] - flex: - version: [2.6.4] - # Attention - when updating also check the various jcsda-emc-bundles env packages fms: version: [2022.04] variants: +64bit +quad_precision +gfs_phys +openmp +fpic constants=GFS @@ -80,7 +77,7 @@ g2c: version: [1.6.4] g2tmpl: - version: [1.10.0] + version: [1.10.2] gfsio: version: [1.4.1] gftl-shared: @@ -174,7 +171,6 @@ version: [1.2.2] proj: version: [8.1.0] - # don't really need tiff ... variants: ~tiff python: version: [3.10.8] @@ -196,11 +192,11 @@ version: [3.0.3] py-pandas: version: [1.4.0] - # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer - # versions of py-poetry-core when using external/homebrew Python as - # we do at the moment in spack-stack. - py-poetry-core: - version: [1.0.8] + ## To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer + ## versions of py-poetry-core when using external/homebrew Python as + ## we do at the moment in spack-stack. + #py-poetry-core: + # version: [1.0.8] py-pybind11: version: [2.8.1] py-pycodestyle: @@ -266,3 +262,29 @@ version: [0.5.1] zlib: version: [1.2.13] + + definitions: + - compilers: ['%apple-clang', '%gcc', '%intel'] + - packages: + - global-workflow-env@unified-dev + #- gsi-env@unified-dev + - jedi-ewok-env@unified-dev + - jedi-fv3-env@unified-dev + - jedi-tools-env@unified-dev + - jedi-ufs-env@unified-dev + - jedi-um-env@unified-dev + #- nceplibs-env@unified-dev + - soca-env@unified-dev + - ufs-srw-app-env@unified-dev + #- ufs-utils-env@unified-dev + - ufs-weather-model-env~debug@unified-dev + - ufs-weather-model-env+debug@unified-dev + #- upp-env@unified-dev + #- ww3-env@unified-dev + + specs: + - matrix: + - [$packages] + - [$compilers] + exclude: + - jedi-tools-env%intel diff --git a/spack b/spack index 0628e266b..37df3f1de 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit 0628e266b7f3c31381157792920938ba25a71751 +Subproject commit 37df3f1deb767def1884509c0e09c1f837a537f5 From 02761aec14d318e85bb9c9e77dfde64f44dec1ba Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 24 Jan 2023 17:23:30 -0700 Subject: [PATCH 04/61] Update configs/sites/orion/packages.yaml --- configs/sites/orion/packages.yaml | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/configs/sites/orion/packages.yaml b/configs/sites/orion/packages.yaml index 3128ea664..5725dfa59 100644 --- a/configs/sites/orion/packages.yaml +++ b/configs/sites/orion/packages.yaml @@ -1,10 +1,12 @@ packages: all: - compiler:: [intel@2022.0.2] + #compiler:: [intel@2022.0.2] #compiler:: [gcc@10.2.0] + compiler:: [intel@2022.0.2, gcc@10.2.0] providers: - mpi:: [intel-oneapi-mpi@2021.5.1] + #mpi:: [intel-oneapi-mpi@2021.5.1] #mpi:: [openmpi@4.0.4] + mpi:: [intel-oneapi-mpi@2021.5.1, openmpi@4.0.4] ### MPI, Python, MKL mpi: @@ -15,10 +17,10 @@ packages: prefix: /apps/intel-2022.1.2/intel-2022.1.2 modules: - impi/2022.1.2 - - spec: intel-oneapi-mpi@2021.2.0%intel@2021.2.0 - prefix: /apps/intel-2021.2/intel-2021.2 - modules: - - impi/2021.2 + # - spec: intel-oneapi-mpi@2021.2.0%intel@2021.2.0 + # prefix: /apps/intel-2021.2/intel-2021.2 + # modules: + # - impi/2021.2 #intel-oneapi-tbb: # externals: # - spec: intel-oneapi-tbb@2021.2.0%intel@2021.2.0 @@ -82,10 +84,6 @@ packages: prefix: /apps/cmake-3.22.1 modules: - cmake/3.22.1 - - spec: cmake@3.18.1 - prefix: /apps/cmake-3.18.1 - modules: - - cmake/3.18.1 cpio: externals: - spec: cpio@2.11 From 30d3dc160c2dfc6aa38d62d3de687d403153b76c Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 24 Jan 2023 20:30:18 -0700 Subject: [PATCH 05/61] Put pinning of py-poetry-core back in --- configs/templates/unified-dev/spack.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/configs/templates/unified-dev/spack.yaml b/configs/templates/unified-dev/spack.yaml index 2e139df34..dbb10e220 100644 --- a/configs/templates/unified-dev/spack.yaml +++ b/configs/templates/unified-dev/spack.yaml @@ -192,11 +192,11 @@ spack: version: [3.0.3] py-pandas: version: [1.4.0] - ## To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer - ## versions of py-poetry-core when using external/homebrew Python as - ## we do at the moment in spack-stack. - #py-poetry-core: - # version: [1.0.8] + # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer + # versions of py-poetry-core when using external/homebrew Python as + # we do at the moment in spack-stack. + py-poetry-core: + version: [1.0.8] py-pybind11: version: [2.8.1] py-pycodestyle: From 157e543cdbd4d707cea692543ae5bc4b33f154ba Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 25 Jan 2023 07:53:18 -0700 Subject: [PATCH 06/61] Update submodule pointer for spack --- spack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spack b/spack index 37df3f1de..fcbcd41a0 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit 37df3f1deb767def1884509c0e09c1f837a537f5 +Subproject commit fcbcd41a01223ab20f86d396ddcc372fefed1b63 From 25a6e5d374457bdaaef7f80b91ac66fefa839d1e Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 25 Jan 2023 08:49:48 -0700 Subject: [PATCH 07/61] Update submodule pointer for spack --- spack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spack b/spack index fcbcd41a0..7f49e4ff4 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit fcbcd41a01223ab20f86d396ddcc372fefed1b63 +Subproject commit 7f49e4ff411696aae5ffb8b87a43b9bf06c29663 From c8f030a6209e2f5cff80a210f9b5a461de95a8c7 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 26 Jan 2023 08:52:35 -0700 Subject: [PATCH 08/61] Restore configs/common/packages.yaml --- configs/common/packages.yaml | 257 ++++++++++++++++++++++ configs/templates/unified-dev/spack.yaml | 258 ----------------------- spack | 2 +- 3 files changed, 258 insertions(+), 259 deletions(-) create mode 100644 configs/common/packages.yaml diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml new file mode 100644 index 000000000..b4dcfdf45 --- /dev/null +++ b/configs/common/packages.yaml @@ -0,0 +1,257 @@ +packages: + # + all: + providers: + blas: [openblas] + fftw-api: [fftw] + gl: [opengl] + glu: [openglu] + jpeg: [libjpeg-turbo] + lapack: [openblas] + yacc: [bison] + # + bacio: + version: [2.4.1] + bison: + version: [3.8.2] + # Attention - when updating also check orion site config + boost: + version: [1.78.0] + variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=14 visibility=hidden + bufr: + version: [11.7.1] + variants: +python + # Newer versions of CDO require the C++-17 standard, which doesn't + # work with all compilers that are currently in use in spack-stack + cdo: + version: [2.0.5] + cmake: + version: [3.23.1] + variants: +ownlibs + # Attention - when updating also check the various jcsda-emc-bundles env packages + crtm: + version: [2.4.0] + variants: +fix + ecbuild: + version: [3.6.5] + eccodes: + version: [2.27.0] + ecflow: + version: [5.8.4] + variants: +ui + eckit: + version: [1.20.2] + variants: linalg=eigen,lapack compression=lz4,bzip2 + ecmwf-atlas: + version: [0.31.1] + variants: +fckit +trans + ectrans: + version: [1.2.0] + variants: ~enable_mkl + eigen: + version: [3.4.0] + # Attention - when updating the version also check the common modules.yaml + # config and update the projections for lmod/tcl + esmf: + version: [8.3.0b09] + variants: ~xerces ~pnetcdf +pio + fckit: + version: [0.9.5] + variants: +eckit + fftw: + version: [3.3.10] + fiat: + version: [1.1.0] + fms: + version: [2022.04] + variants: +64bit +quad_precision +gfs_phys +openmp +fpic constants=GFS + g2: + version: [3.4.5] + g2c: + version: [1.6.4] + g2tmpl: + version: [1.10.2] + gfsio: + version: [1.4.1] + gftl-shared: + version: [1.5.0] + #git-lfs: + # Assume git-lfs is provided, hard to install + # because of dependencies on go/go-bootstrap. + # Note: Uncommenting this entry will break + # the container builds. + #version: [2.11.0] + grib-util: + version: [1.2.3] + gsibec: + version: [1.0.6] + gsl-lite: + version: [0.37.0] + hdf: + version: [4.2.15] + variants: ~fortran ~netcdf + hdf5: + version: [1.12.1] + variants: +hl +fortran +mpi +threadsafe + ip: + version: [3.3.3] + ip2: + version: [1.1.2] + jasper: + version: [2.0.32] + jedi-cmake: + version: [1.4.0] + jpeg: + version: [9.1.0] + landsfcutil: + version: [2.4.1] + libjpeg-turbo: + version: [2.1.0] + libpng: + version: [1.6.37] + mapl: + version: [2.22.0] + met: + version: [10.1.1] + variants: +python +grib2 + metplus: + version: [4.1.1] + mpich: + variants: ~hwloc +two_level_namespace + nco: + version: [5.0.6] + variants: ~doc + # ncview - when adding information here, also check Orion + # and Discover site configs + nemsio: + version: [2.5.2] + nemsiogfs: + version: [2.5.3] + nccmp: + version: [1.9.0.1] + ncio: + version: [1.1.2] + netcdf-c: + version: [4.8.1] + variants: +dap +mpi +parallel-netcdf + netcdf-cxx4: + version: [4.3.1] + netcdf-fortran: + version: [4.5.4] + # ninja - when adding information here, also check Cheyenne + # and Discover site configs + nlohmann-json: + version: [3.10.5] + nlohmann-json-schema-validator: + version: [2.1.0] + odc: + version: [1.4.5] + variants: ~fortran + openblas: + version: [0.3.19] + variants: +noavx512 + openmpi: + variants: +internal-hwloc +two_level_namespace + parallelio: + version: [2.5.7] + variants: +pnetcdf + parallel-netcdf: + version: [1.12.2] + # Do not build pkgconf - https://github.com/NOAA-EMC/spack-stack/issues/123 + pkgconf: + buildable: False + prod-util: + version: [1.2.2] + proj: + version: [8.1.0] + variants: ~tiff + python: + version: [3.10.8] + py-cartopy: + variants: +plotting + py-click: + version: [8.0.3] + py-eccodes: + version: [1.4.2] + py-h5py: + version: [3.6.0] + py-netcdf4: + version: [1.5.3] + variants: +mpi + py-numpy: + version: [1.22.3] + variants: +blas +lapack + py-openpyxl: + version: [3.0.3] + py-pandas: + version: [1.4.0] + # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer + # versions of py-poetry-core when using external/homebrew Python as + # we do at the moment in spack-stack. + py-poetry-core: + version: [1.0.8] + py-pybind11: + version: [2.8.1] + py-pycodestyle: + version: [2.8.0] + py-pygithub: + version: [1.55] + py-pygrib: + version: [2.1.4] + py-pyhdf: + version: [0.10.4] + py-pyproj: + version: [3.1.0] + py-python-dateutil: + version: [2.8.2] + #py-pythran: + # # Earlier versions don't compile on macOS with llvm-clang/13.0.0 and Python/3.9 + # version: [0.11.0] + py-pyyaml: + version: [6.0] + py-scipy: + version: [1.9.3] + # Pin the py-setuptools version to avoid duplicate Python packages + py-setuptools: + version: [59.4.0] + # Pin the py-setuptools-scm version to avoid duplicate Python packages + py-setuptools-scm: + version: [7.0.5] + py-shapely: + version: [1.8.0] + qt: + version: [5.15.3] + sfcio: + version: [1.4.1] + shumlib: + version: [macos_clang_linux_intel_port] + sigio: + version: [2.3.2] + sp: + version: [2.3.3] + #texlive: + # Assume texlive is provided, hard to install + # because of its dependencies. Both Linux and + # macOS provide easy-to-install packages that + # can be added as external packages. + # Note: Uncommenting this entry will break + # the container builds. + #version: [2.11.0] + udunits: + version: [2.2.28] + upp: + version: [10.0.10] + w3emc: + version: [2.9.2] + w3nco: + version: [2.4.1] + wget: + version: [1.21.2] + wgrib2: + version: [2.0.8] + wrf-io: + version: [1.2.0] + yafyaml: + version: [0.5.1] + zlib: + version: [1.2.13] diff --git a/configs/templates/unified-dev/spack.yaml b/configs/templates/unified-dev/spack.yaml index dbb10e220..8c75d93cd 100644 --- a/configs/templates/unified-dev/spack.yaml +++ b/configs/templates/unified-dev/spack.yaml @@ -5,264 +5,6 @@ spack: view: false include: [] - packages: - # - all: - providers: - blas: [openblas] - fftw-api: [fftw] - gl: [opengl] - glu: [openglu] - jpeg: [libjpeg-turbo] - lapack: [openblas] - yacc: [bison] - # - bacio: - version: [2.4.1] - bison: - version: [3.8.2] - # Attention - when updating also check orion site config - boost: - version: [1.78.0] - variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=14 visibility=hidden - bufr: - version: [11.7.1] - variants: +python - # Newer versions of CDO require the C++-17 standard, which doesn't - # work with all compilers that are currently in use in spack-stack - cdo: - version: [2.0.5] - cmake: - version: [3.23.1] - variants: +ownlibs - # Attention - when updating also check the various jcsda-emc-bundles env packages - crtm: - version: [2.4.0] - variants: +fix - ecbuild: - version: [3.6.5] - eccodes: - version: [2.27.0] - ecflow: - version: [5.8.4] - variants: +ui - eckit: - version: [1.20.2] - variants: linalg=eigen,lapack compression=lz4,bzip2 - ecmwf-atlas: - version: [0.31.1] - variants: +fckit +trans - ectrans: - version: [1.2.0] - variants: ~enable_mkl - eigen: - version: [3.4.0] - # Attention - when updating the version also check the common modules.yaml - # config and update the projections for lmod/tcl - esmf: - version: [8.3.0b09] - variants: ~xerces ~pnetcdf +pio - fckit: - version: [0.9.5] - variants: +eckit - fftw: - version: [3.3.10] - fiat: - version: [1.1.0] - fms: - version: [2022.04] - variants: +64bit +quad_precision +gfs_phys +openmp +fpic constants=GFS - g2: - version: [3.4.5] - g2c: - version: [1.6.4] - g2tmpl: - version: [1.10.2] - gfsio: - version: [1.4.1] - gftl-shared: - version: [1.5.0] - #git-lfs: - # Assume git-lfs is provided, hard to install - # because of dependencies on go/go-bootstrap. - # Note: Uncommenting this entry will break - # the container builds. - #version: [2.11.0] - grib-util: - version: [1.2.3] - gsibec: - version: [1.0.6] - gsl-lite: - version: [0.37.0] - hdf: - version: [4.2.15] - variants: ~fortran ~netcdf - hdf5: - version: [1.12.1] - variants: +hl +fortran +mpi +threadsafe - ip: - version: [3.3.3] - ip2: - version: [1.1.2] - jasper: - version: [2.0.32] - jedi-cmake: - version: [1.4.0] - jpeg: - version: [9.1.0] - landsfcutil: - version: [2.4.1] - libjpeg-turbo: - version: [2.1.0] - libpng: - version: [1.6.37] - mapl: - version: [2.22.0] - met: - version: [10.1.1] - variants: +python +grib2 - metplus: - version: [4.1.1] - mpich: - variants: ~hwloc +two_level_namespace - nco: - version: [5.0.6] - variants: ~doc - # ncview - when adding information here, also check Orion - # and Discover site configs - nemsio: - version: [2.5.2] - nemsiogfs: - version: [2.5.3] - nccmp: - version: [1.9.0.1] - ncio: - version: [1.1.2] - netcdf-c: - version: [4.8.1] - variants: +dap +mpi +parallel-netcdf - netcdf-cxx4: - version: [4.3.1] - netcdf-fortran: - version: [4.5.4] - # ninja - when adding information here, also check Cheyenne - # and Discover site configs - nlohmann-json: - version: [3.10.5] - nlohmann-json-schema-validator: - version: [2.1.0] - odc: - version: [1.4.5] - variants: ~fortran - openblas: - version: [0.3.19] - variants: +noavx512 - openmpi: - variants: +internal-hwloc +two_level_namespace - parallelio: - version: [2.5.7] - variants: +pnetcdf - parallel-netcdf: - version: [1.12.2] - # Do not build pkgconf - https://github.com/NOAA-EMC/spack-stack/issues/123 - pkgconf: - buildable: False - prod-util: - version: [1.2.2] - proj: - version: [8.1.0] - variants: ~tiff - python: - version: [3.10.8] - py-cartopy: - variants: +plotting - py-click: - version: [8.0.3] - py-eccodes: - version: [1.4.2] - py-h5py: - version: [3.6.0] - py-netcdf4: - version: [1.5.3] - variants: +mpi - py-numpy: - version: [1.22.3] - variants: +blas +lapack - py-openpyxl: - version: [3.0.3] - py-pandas: - version: [1.4.0] - # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer - # versions of py-poetry-core when using external/homebrew Python as - # we do at the moment in spack-stack. - py-poetry-core: - version: [1.0.8] - py-pybind11: - version: [2.8.1] - py-pycodestyle: - version: [2.8.0] - py-pygithub: - version: [1.55] - py-pygrib: - version: [2.1.4] - py-pyhdf: - version: [0.10.4] - py-pyproj: - version: [3.1.0] - py-python-dateutil: - version: [2.8.2] - #py-pythran: - # # Earlier versions don't compile on macOS with llvm-clang/13.0.0 and Python/3.9 - # version: [0.11.0] - py-pyyaml: - version: [6.0] - py-scipy: - version: [1.9.3] - # Pin the py-setuptools version to avoid duplicate Python packages - py-setuptools: - version: [59.4.0] - # Pin the py-setuptools-scm version to avoid duplicate Python packages - py-setuptools-scm: - version: [7.0.5] - py-shapely: - version: [1.8.0] - qt: - version: [5.15.3] - sfcio: - version: [1.4.1] - shumlib: - version: [macos_clang_linux_intel_port] - sigio: - version: [2.3.2] - sp: - version: [2.3.3] - #texlive: - # Assume texlive is provided, hard to install - # because of its dependencies. Both Linux and - # macOS provide easy-to-install packages that - # can be added as external packages. - # Note: Uncommenting this entry will break - # the container builds. - #version: [2.11.0] - udunits: - version: [2.2.28] - upp: - version: [10.0.10] - w3emc: - version: [2.9.2] - w3nco: - version: [2.4.1] - wget: - version: [1.21.2] - wgrib2: - version: [2.0.8] - wrf-io: - version: [1.2.0] - yafyaml: - version: [0.5.1] - zlib: - version: [1.2.13] - definitions: - compilers: ['%apple-clang', '%gcc', '%intel'] - packages: diff --git a/spack b/spack index 7f49e4ff4..571bd8aaa 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit 7f49e4ff411696aae5ffb8b87a43b9bf06c29663 +Subproject commit 571bd8aaaa9b062317684ba2e78aad84cba15d7f From dacdfc6de380d6c848bc2c8c71434ab90a76093b Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 26 Jan 2023 08:54:13 -0700 Subject: [PATCH 09/61] Update CI to use unified-dev --- .github/workflows/macos-dom.yaml | 6 +++--- .github/workflows/macos.yaml | 2 +- .github/workflows/ubuntu.yaml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/macos-dom.yaml b/.github/workflows/macos-dom.yaml index b6bcb52c4..9a415b42f 100644 --- a/.github/workflows/macos-dom.yaml +++ b/.github/workflows/macos-dom.yaml @@ -13,7 +13,7 @@ on: template: description: 'Base spack.yaml template. Default is a complete JEDI-UFS environment.' required: true - default: 'skylab-dev' + default: 'unified-dev' specs: description: 'Which specs to add to the template. Default is none (empty string).' required: false @@ -38,8 +38,8 @@ jobs: - name: create-env run: | source ./setup.sh - spack stack create env --site macos.default --template ${{ inputs.template || 'skylab-dev' }} --name ${{ inputs.template || 'skylab-dev' }}.macos-dom - spack env activate -d envs/${{ inputs.template || 'skylab-dev' }}.macos-dom + spack stack create env --site macos.default --template ${{ inputs.template || 'unified-dev' }} --name ${{ inputs.template || 'unified-dev' }}.macos-dom + spack env activate -d envs/${{ inputs.template || 'unified-dev' }}.macos-dom spack add ${{ inputs.specs || '' }} spack external find diff --git a/.github/workflows/macos.yaml b/.github/workflows/macos.yaml index 90eee46a0..a6afe99fb 100644 --- a/.github/workflows/macos.yaml +++ b/.github/workflows/macos.yaml @@ -62,7 +62,7 @@ jobs: strategy: matrix: compiler-mpi: [ {compiler: apple-clang@13.0.0, mpi: openmpi@4.1.4} ] - template: [skylab-dev, ufs-weather-model, ufs-srw-dev] + template: [unified-dev] # [skylab-dev, ufs-weather-model, ufs-srw-dev] runs-on: macos-11 steps: diff --git a/.github/workflows/ubuntu.yaml b/.github/workflows/ubuntu.yaml index df48eea5b..c45fca33d 100644 --- a/.github/workflows/ubuntu.yaml +++ b/.github/workflows/ubuntu.yaml @@ -62,7 +62,7 @@ jobs: strategy: matrix: compiler-mpi: [ {compiler: intel@2021.8.0, mpi: intel-oneapi-mpi@2021.8.0}, {compiler: gcc@9.4.0, mpi: mvapich2@2.3.7}, {compiler: gcc@10.3.0, mpi: mpich@4.0.2} ] - template: [skylab-dev, ufs-weather-model, ufs-srw-dev] + template: [unified-dev] # [skylab-dev, ufs-weather-model, ufs-srw-dev] runs-on: ubuntu-20.04 steps: From b8047809d1ae4f05a14b9b743cab24b729db8ddf Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 30 Jan 2023 13:45:11 -0700 Subject: [PATCH 10/61] Revert indent changes in configs/common/packages.yaml --- configs/common/packages.yaml | 515 ++++++++++++++++++----------------- 1 file changed, 258 insertions(+), 257 deletions(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index b4dcfdf45..344fda727 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -1,257 +1,258 @@ -packages: - # - all: - providers: - blas: [openblas] - fftw-api: [fftw] - gl: [opengl] - glu: [openglu] - jpeg: [libjpeg-turbo] - lapack: [openblas] - yacc: [bison] - # - bacio: - version: [2.4.1] - bison: - version: [3.8.2] - # Attention - when updating also check orion site config - boost: - version: [1.78.0] - variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=14 visibility=hidden - bufr: - version: [11.7.1] - variants: +python - # Newer versions of CDO require the C++-17 standard, which doesn't - # work with all compilers that are currently in use in spack-stack - cdo: - version: [2.0.5] - cmake: - version: [3.23.1] - variants: +ownlibs - # Attention - when updating also check the various jcsda-emc-bundles env packages - crtm: - version: [2.4.0] - variants: +fix - ecbuild: - version: [3.6.5] - eccodes: - version: [2.27.0] - ecflow: - version: [5.8.4] - variants: +ui - eckit: - version: [1.20.2] - variants: linalg=eigen,lapack compression=lz4,bzip2 - ecmwf-atlas: - version: [0.31.1] - variants: +fckit +trans - ectrans: - version: [1.2.0] - variants: ~enable_mkl - eigen: - version: [3.4.0] - # Attention - when updating the version also check the common modules.yaml - # config and update the projections for lmod/tcl - esmf: - version: [8.3.0b09] - variants: ~xerces ~pnetcdf +pio - fckit: - version: [0.9.5] - variants: +eckit - fftw: - version: [3.3.10] - fiat: - version: [1.1.0] - fms: - version: [2022.04] - variants: +64bit +quad_precision +gfs_phys +openmp +fpic constants=GFS - g2: - version: [3.4.5] - g2c: - version: [1.6.4] - g2tmpl: - version: [1.10.2] - gfsio: - version: [1.4.1] - gftl-shared: - version: [1.5.0] - #git-lfs: - # Assume git-lfs is provided, hard to install - # because of dependencies on go/go-bootstrap. - # Note: Uncommenting this entry will break - # the container builds. - #version: [2.11.0] - grib-util: - version: [1.2.3] - gsibec: - version: [1.0.6] - gsl-lite: - version: [0.37.0] - hdf: - version: [4.2.15] - variants: ~fortran ~netcdf - hdf5: - version: [1.12.1] - variants: +hl +fortran +mpi +threadsafe - ip: - version: [3.3.3] - ip2: - version: [1.1.2] - jasper: - version: [2.0.32] - jedi-cmake: - version: [1.4.0] - jpeg: - version: [9.1.0] - landsfcutil: - version: [2.4.1] - libjpeg-turbo: - version: [2.1.0] - libpng: - version: [1.6.37] - mapl: - version: [2.22.0] - met: - version: [10.1.1] - variants: +python +grib2 - metplus: - version: [4.1.1] - mpich: - variants: ~hwloc +two_level_namespace - nco: - version: [5.0.6] - variants: ~doc - # ncview - when adding information here, also check Orion - # and Discover site configs - nemsio: - version: [2.5.2] - nemsiogfs: - version: [2.5.3] - nccmp: - version: [1.9.0.1] - ncio: - version: [1.1.2] - netcdf-c: - version: [4.8.1] - variants: +dap +mpi +parallel-netcdf - netcdf-cxx4: - version: [4.3.1] - netcdf-fortran: - version: [4.5.4] - # ninja - when adding information here, also check Cheyenne - # and Discover site configs - nlohmann-json: - version: [3.10.5] - nlohmann-json-schema-validator: - version: [2.1.0] - odc: - version: [1.4.5] - variants: ~fortran - openblas: - version: [0.3.19] - variants: +noavx512 - openmpi: - variants: +internal-hwloc +two_level_namespace - parallelio: - version: [2.5.7] - variants: +pnetcdf - parallel-netcdf: - version: [1.12.2] - # Do not build pkgconf - https://github.com/NOAA-EMC/spack-stack/issues/123 - pkgconf: - buildable: False - prod-util: - version: [1.2.2] - proj: - version: [8.1.0] - variants: ~tiff - python: - version: [3.10.8] - py-cartopy: - variants: +plotting - py-click: - version: [8.0.3] - py-eccodes: - version: [1.4.2] - py-h5py: - version: [3.6.0] - py-netcdf4: - version: [1.5.3] - variants: +mpi - py-numpy: - version: [1.22.3] - variants: +blas +lapack - py-openpyxl: - version: [3.0.3] - py-pandas: - version: [1.4.0] - # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer - # versions of py-poetry-core when using external/homebrew Python as - # we do at the moment in spack-stack. - py-poetry-core: - version: [1.0.8] - py-pybind11: - version: [2.8.1] - py-pycodestyle: - version: [2.8.0] - py-pygithub: - version: [1.55] - py-pygrib: - version: [2.1.4] - py-pyhdf: - version: [0.10.4] - py-pyproj: - version: [3.1.0] - py-python-dateutil: - version: [2.8.2] - #py-pythran: - # # Earlier versions don't compile on macOS with llvm-clang/13.0.0 and Python/3.9 - # version: [0.11.0] - py-pyyaml: - version: [6.0] - py-scipy: - version: [1.9.3] - # Pin the py-setuptools version to avoid duplicate Python packages - py-setuptools: - version: [59.4.0] - # Pin the py-setuptools-scm version to avoid duplicate Python packages - py-setuptools-scm: - version: [7.0.5] - py-shapely: - version: [1.8.0] - qt: - version: [5.15.3] - sfcio: - version: [1.4.1] - shumlib: - version: [macos_clang_linux_intel_port] - sigio: - version: [2.3.2] - sp: - version: [2.3.3] - #texlive: - # Assume texlive is provided, hard to install - # because of its dependencies. Both Linux and - # macOS provide easy-to-install packages that - # can be added as external packages. - # Note: Uncommenting this entry will break - # the container builds. - #version: [2.11.0] - udunits: - version: [2.2.28] - upp: - version: [10.0.10] - w3emc: - version: [2.9.2] - w3nco: - version: [2.4.1] - wget: - version: [1.21.2] - wgrib2: - version: [2.0.8] - wrf-io: - version: [1.2.0] - yafyaml: - version: [0.5.1] - zlib: - version: [1.2.13] +# Pin versions and specs when building packages + packages: + # + all: + providers: + blas: [openblas] + fftw-api: [fftw] + gl: [opengl] + glu: [openglu] + jpeg: [libjpeg-turbo] + lapack: [openblas] + yacc: [bison] + # + bacio: + version: [2.4.1] + bison: + version: [3.8.2] + # Attention - when updating also check orion site config + boost: + version: [1.78.0] + variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=14 visibility=hidden + bufr: + version: [11.7.1] + variants: +python + # Newer versions of CDO require the C++-17 standard, which doesn't + # work with all compilers that are currently in use in spack-stack + cdo: + version: [2.0.5] + cmake: + version: [3.23.1] + variants: +ownlibs + # Attention - when updating also check the various jcsda-emc-bundles env packages + crtm: + version: [2.4.0] + variants: +fix + ecbuild: + version: [3.6.5] + eccodes: + version: [2.27.0] + ecflow: + version: [5.8.4] + variants: +ui + eckit: + version: [1.20.2] + variants: linalg=eigen,lapack compression=lz4,bzip2 + ecmwf-atlas: + version: [0.31.1] + variants: +fckit +trans + ectrans: + version: [1.2.0] + variants: ~enable_mkl + eigen: + version: [3.4.0] + # Attention - when updating the version also check the common modules.yaml + # config and update the projections for lmod/tcl + esmf: + version: [8.3.0b09] + variants: ~xerces ~pnetcdf +pio + fckit: + version: [0.9.5] + variants: +eckit + fftw: + version: [3.3.10] + fiat: + version: [1.1.0] + fms: + version: [2022.04] + variants: +64bit +quad_precision +gfs_phys +openmp +fpic constants=GFS + g2: + version: [3.4.5] + g2c: + version: [1.6.4] + g2tmpl: + version: [1.10.2] + gfsio: + version: [1.4.1] + gftl-shared: + version: [1.5.0] + #git-lfs: + # Assume git-lfs is provided, hard to install + # because of dependencies on go/go-bootstrap. + # Note: Uncommenting this entry will break + # the container builds. + #version: [2.11.0] + grib-util: + version: [1.2.3] + gsibec: + version: [1.0.6] + gsl-lite: + version: [0.37.0] + hdf: + version: [4.2.15] + variants: ~fortran ~netcdf + hdf5: + version: [1.12.1] + variants: +hl +fortran +mpi +threadsafe + ip: + version: [3.3.3] + ip2: + version: [1.1.2] + jasper: + version: [2.0.32] + jedi-cmake: + version: [1.4.0] + jpeg: + version: [9.1.0] + landsfcutil: + version: [2.4.1] + libjpeg-turbo: + version: [2.1.0] + libpng: + version: [1.6.37] + mapl: + version: [2.22.0] + met: + version: [10.1.1] + variants: +python +grib2 + metplus: + version: [4.1.1] + mpich: + variants: ~hwloc +two_level_namespace + nco: + version: [5.0.6] + variants: ~doc + # ncview - when adding information here, also check Orion + # and Discover site configs + nemsio: + version: [2.5.2] + nemsiogfs: + version: [2.5.3] + nccmp: + version: [1.9.0.1] + ncio: + version: [1.1.2] + netcdf-c: + version: [4.8.1] + variants: +dap +mpi +parallel-netcdf + netcdf-cxx4: + version: [4.3.1] + netcdf-fortran: + version: [4.5.4] + # ninja - when adding information here, also check Cheyenne + # and Discover site configs + nlohmann-json: + version: [3.10.5] + nlohmann-json-schema-validator: + version: [2.1.0] + odc: + version: [1.4.5] + variants: ~fortran + openblas: + version: [0.3.19] + variants: +noavx512 + openmpi: + variants: +internal-hwloc +two_level_namespace + parallelio: + version: [2.5.7] + variants: +pnetcdf + parallel-netcdf: + version: [1.12.2] + # Do not build pkgconf - https://github.com/NOAA-EMC/spack-stack/issues/123 + pkgconf: + buildable: False + prod-util: + version: [1.2.2] + proj: + version: [8.1.0] + variants: ~tiff + python: + version: [3.10.8] + py-cartopy: + variants: +plotting + py-click: + version: [8.0.3] + py-eccodes: + version: [1.4.2] + py-h5py: + version: [3.6.0] + py-netcdf4: + version: [1.5.3] + variants: +mpi + py-numpy: + version: [1.22.3] + variants: +blas +lapack + py-openpyxl: + version: [3.0.3] + py-pandas: + version: [1.4.0] + # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer + # versions of py-poetry-core when using external/homebrew Python as + # we do at the moment in spack-stack. + py-poetry-core: + version: [1.0.8] + py-pybind11: + version: [2.8.1] + py-pycodestyle: + version: [2.8.0] + py-pygithub: + version: [1.55] + py-pygrib: + version: [2.1.4] + py-pyhdf: + version: [0.10.4] + py-pyproj: + version: [3.1.0] + py-python-dateutil: + version: [2.8.2] + #py-pythran: + # # Earlier versions don't compile on macOS with llvm-clang/13.0.0 and Python/3.9 + # version: [0.11.0] + py-pyyaml: + version: [6.0] + py-scipy: + version: [1.9.3] + # Pin the py-setuptools version to avoid duplicate Python packages + py-setuptools: + version: [59.4.0] + # Pin the py-setuptools-scm version to avoid duplicate Python packages + py-setuptools-scm: + version: [7.0.5] + py-shapely: + version: [1.8.0] + qt: + version: [5.15.3] + sfcio: + version: [1.4.1] + shumlib: + version: [macos_clang_linux_intel_port] + sigio: + version: [2.3.2] + sp: + version: [2.3.3] + #texlive: + # Assume texlive is provided, hard to install + # because of its dependencies. Both Linux and + # macOS provide easy-to-install packages that + # can be added as external packages. + # Note: Uncommenting this entry will break + # the container builds. + #version: [2.11.0] + udunits: + version: [2.2.28] + upp: + version: [10.0.10] + w3emc: + version: [2.9.2] + w3nco: + version: [2.4.1] + wget: + version: [1.21.2] + wgrib2: + version: [2.0.8] + wrf-io: + version: [1.2.0] + yafyaml: + version: [0.5.1] + zlib: + version: [1.2.13] From 63ebfeb31b43615cdb17dfb6f16dd9069fba908f Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 30 Jan 2023 14:05:21 -0700 Subject: [PATCH 11/61] [skip ci] Update versions of hdf5, netcdf-c, netcdf-fortran, parallelio in configs/common/packages.yaml --- configs/common/packages.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index 344fda727..62f6b0457 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -92,7 +92,7 @@ version: [4.2.15] variants: ~fortran ~netcdf hdf5: - version: [1.12.1] + version: [1.14.0] variants: +hl +fortran +mpi +threadsafe ip: version: [3.3.3] @@ -133,12 +133,12 @@ ncio: version: [1.1.2] netcdf-c: - version: [4.8.1] - variants: +dap +mpi +parallel-netcdf + version: [4.9.0] + variants: +dap +mpi ~parallel-netcdf netcdf-cxx4: version: [4.3.1] netcdf-fortran: - version: [4.5.4] + version: [4.6.0] # ninja - when adding information here, also check Cheyenne # and Discover site configs nlohmann-json: From b9d6c0668f6ac099a9faab4cb525a451b6e8ead8 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 30 Jan 2023 15:56:19 -0700 Subject: [PATCH 12/61] [skip ci] Update submodule pointer for spack --- spack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spack b/spack index 571bd8aaa..f71a88fec 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit 571bd8aaaa9b062317684ba2e78aad84cba15d7f +Subproject commit f71a88fec349c14c58acc648cb1ae212a2f96712 From bf386d304cef8b955fb1c2eb4c0ccd5d358c70a1 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 1 Feb 2023 10:49:49 -0700 Subject: [PATCH 13/61] Bump parallelio to 2.5.9 --- configs/common/packages.yaml | 2 +- spack | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index 62f6b0457..335959038 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -154,7 +154,7 @@ openmpi: variants: +internal-hwloc +two_level_namespace parallelio: - version: [2.5.7] + version: [2.5.9] variants: +pnetcdf parallel-netcdf: version: [1.12.2] diff --git a/spack b/spack index f71a88fec..55e2fa2e1 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit f71a88fec349c14c58acc648cb1ae212a2f96712 +Subproject commit 55e2fa2e17e448911eb995a5dfe384a196cc2a10 From a89a3ec126a107708cd5fc02148c44922250c856 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 1 Feb 2023 10:50:04 -0700 Subject: [PATCH 14/61] Add a known issue for macOS to documentation --- doc/source/KnownIssues.rst | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/doc/source/KnownIssues.rst b/doc/source/KnownIssues.rst index f15b9b467..2969da068 100644 --- a/doc/source/KnownIssues.rst +++ b/doc/source/KnownIssues.rst @@ -69,7 +69,7 @@ UW (Univ. of Wisconsin) S4 macOS ============================== -1. Error `invalid argument '-fgnu89-inline' not allowed with 'C++'` +1. Error ``invalid argument '-fgnu89-inline' not allowed with 'C++'`` This error occurs on macOS Monterey with ``mpich-3.4.3`` installed via Homebrew when trying to build the jedi bundles that use ``ecbuild``. The reason was that the C compiler flag ``-fgnu89-inline`` from ``/usr/local/Cellar/mpich/3.4.3/lib/pkgconfig/mpich.pc`` was added to the C++ compiler flags by ecbuild. The solution was to set ``CC=mpicc FC=mpif90 CXX=mpicxx`` when calling ``ecbuild`` for those bundles. Note that it is recommended to install ``mpich`` or ``openmpi`` with spack-stack, not with Homebrew. @@ -77,10 +77,17 @@ macOS This can happen when multiple versions of Python were installed with Homebrew and ``pip3``/``python3`` point to different versions. Run ``brew doctor`` and check if there are issues with Python not being properly linked. Follow the instructions given by ``brew``, if applicable. -3. Errors handling exceptions on macOS. A large number of errors related to handling exceptions thrown by applications was found when using default builds or Homebrew installations of ``mpich`` or ``openmpi``, which use flat namespaces. With our spack version, ``mpich`` and ``openmpi`` are installed with a ``+two_level_namespace`` option that fixes the problem. +3. Error ``AttributeError: Can't get attribute 'Mark' on Date: Wed, 1 Feb 2023 10:51:10 -0700 Subject: [PATCH 15/61] Add R2D2 mysql prerequisites to configs/common/packages.yaml --- configs/common/packages.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index 62f6b0457..43bef3819 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -119,6 +119,8 @@ version: [4.1.1] mpich: variants: ~hwloc +two_level_namespace + mysql: + buildable: False nco: version: [5.0.6] variants: ~doc @@ -176,6 +178,8 @@ version: [1.4.2] py-h5py: version: [3.6.0] + py-mysql-connector-python: + version: [8.0.13] py-netcdf4: version: [1.5.3] variants: +mpi From e6359d6a2954f6e3c19898e588aa59d561babb61 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 1 Feb 2023 10:51:36 -0700 Subject: [PATCH 16/61] Update .gitmodules and submodule pointer for spack for code review and testing --- .gitmodules | 2 +- spack | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitmodules b/.gitmodules index 2cf3483a5..e9387a057 100644 --- a/.gitmodules +++ b/.gitmodules @@ -5,7 +5,7 @@ #url = https://github.com/NOAA-EMC/spack #branch = jcsda_emc_spack_stack url = https://github.com/climbfuji/spack - branch = feature/unified-env + branch = feature/r2d2_mysql [submodule "doc/CMakeModules"] path = doc/CMakeModules url = https://github.com/noaa-emc/cmakemodules diff --git a/spack b/spack index f71a88fec..088fade99 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit f71a88fec349c14c58acc648cb1ae212a2f96712 +Subproject commit 088fade995d69993143711d2f15d561e7eb14c0e From d4065682b25a8debaa5b588c6a5eaa499c537f2a Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 1 Feb 2023 10:54:57 -0700 Subject: [PATCH 17/61] Try to update GitHub CI scripts and AWS parallelcluster documentation for mysql --- .github/actions/setup-os/action.yaml | 6 ++++++ .github/actions/setup-spack-stack/action.yaml | 3 +++ configs/sites/aws-pcluster/README.md | 3 +++ 3 files changed, 12 insertions(+) diff --git a/.github/actions/setup-os/action.yaml b/.github/actions/setup-os/action.yaml index 3fa808fce..4b7db2358 100644 --- a/.github/actions/setup-os/action.yaml +++ b/.github/actions/setup-os/action.yaml @@ -29,6 +29,9 @@ runs: # and also get rid of the macOS homebrew installation/package config sudo apt-get install qt5-default qttools5-dev-tools libqt5svg5-dev + # For R2D2 mysql backend + sudo apt-get install mysql-server + elif [[ "$RUNNER_OS" == "macOS" ]]; then brew install curl brew install git @@ -42,6 +45,9 @@ runs: brew install readline brew install wget + # For R2D2 mysql backend + brew install mysql + # Print version of xcode pkgutil --pkg-info=com.apple.pkg.CLTools_Executables diff --git a/.github/actions/setup-spack-stack/action.yaml b/.github/actions/setup-spack-stack/action.yaml index 604930279..17f075e23 100644 --- a/.github/actions/setup-spack-stack/action.yaml +++ b/.github/actions/setup-spack-stack/action.yaml @@ -147,6 +147,9 @@ runs: # Find homebrew qt@5 on macOS spack external find --path /usr/local/opt/qt@5 qt + # Find mysql server + spack external find mysql + # if [[ "$RUNNER_OS" == "Linux" ]]; then # spack external find curl # elif [[ "$RUNNER_OS" == "macOS" ]]; then diff --git a/configs/sites/aws-pcluster/README.md b/configs/sites/aws-pcluster/README.md index 081ae1337..dbdf0a0d8 100644 --- a/configs/sites/aws-pcluster/README.md +++ b/configs/sites/aws-pcluster/README.md @@ -42,6 +42,9 @@ apt install -y qt5-default apt install -y libqt5svg5-dev apt install -y qt5dxcb-plugin +# For R2D2 mysql backend, already installed +#apt install -y mysql-server + # Remove AWS openmpi apt remove -y openmpi40-aws From b24770548f01cb38633b6f22a62ce83be8dab161 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 1 Feb 2023 13:18:29 -0700 Subject: [PATCH 18/61] Debug CI --- .github/actions/setup-spack-stack/action.yaml | 2 +- configs/common/packages.yaml | 2 -- configs/sites/aws-pcluster/packages.yaml | 4 ++++ 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/actions/setup-spack-stack/action.yaml b/.github/actions/setup-spack-stack/action.yaml index 17f075e23..0c113ed0c 100644 --- a/.github/actions/setup-spack-stack/action.yaml +++ b/.github/actions/setup-spack-stack/action.yaml @@ -148,7 +148,7 @@ runs: spack external find --path /usr/local/opt/qt@5 qt # Find mysql server - spack external find mysql + spack external find --not-buildable mysql # if [[ "$RUNNER_OS" == "Linux" ]]; then # spack external find curl diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index 4326d56e7..1da38692d 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -119,8 +119,6 @@ version: [4.1.1] mpich: variants: ~hwloc +two_level_namespace - mysql: - buildable: False nco: version: [5.0.6] variants: ~doc diff --git a/configs/sites/aws-pcluster/packages.yaml b/configs/sites/aws-pcluster/packages.yaml index 10f5869f0..81862a5c6 100644 --- a/configs/sites/aws-pcluster/packages.yaml +++ b/configs/sites/aws-pcluster/packages.yaml @@ -91,6 +91,10 @@ packages: externals: - spec: m4@1.4.18 prefix: /usr + mysql: + externals: + - spec: mysql@8.0.30 + prefix: /usr openssh: externals: - spec: openssh@8.2p1 From 38802057fd2ca1cf453749fa754ca3709e80dd0d Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 1 Feb 2023 15:46:45 -0700 Subject: [PATCH 19/61] Update submodule pointer for spack --- spack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spack b/spack index 088fade99..2fcf1ca1a 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit 088fade995d69993143711d2f15d561e7eb14c0e +Subproject commit 2fcf1ca1a5ce4d503d3fe6dd5f0f8bc1a3e6697b From 603940dbb4c250ce9549b550ac4b3ac122180c45 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Fri, 3 Feb 2023 09:25:50 -0700 Subject: [PATCH 20/61] Add Orion Intel-18 config --- configs/sites/orion/compilers.yaml | 18 ++++++++++++++++++ configs/sites/orion/packages.yaml | 30 ++++++++---------------------- 2 files changed, 26 insertions(+), 22 deletions(-) diff --git a/configs/sites/orion/compilers.yaml b/configs/sites/orion/compilers.yaml index 39f646399..9abe2e487 100644 --- a/configs/sites/orion/compilers.yaml +++ b/configs/sites/orion/compilers.yaml @@ -17,6 +17,24 @@ compilers: LD_LIBRARY_PATH: '/apps/gcc-10.2.0/gcc-10.2.0/lib64:/apps/gcc-10.2.0/gcc-10.2.0/contrib/lib' CPATH: '/apps/gcc-10.2.0/gcc-10.2.0/include' extra_rpaths: [] +- compiler: + spec: intel@18.0.5 + paths: + cc: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icc + cxx: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icpc + f77: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/ifort + fc: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/ifort + flags: {} + operating_system: centos7 + target: x86_64 + modules: + - intel/2018.4 + environment: + prepend_path: + PATH: '/apps/gcc-10.2.0/gcc-10.2.0/bin' + LD_LIBRARY_PATH: '/apps/gcc-10.2.0/gcc-10.2.0/lib64:/apps/gcc-10.2.0/gcc-10.2.0/contrib/lib' + CPATH: '/apps/gcc-10.2.0/gcc-10.2.0/include' + extra_rpaths: [] - compiler: spec: gcc@10.2.0 paths: diff --git a/configs/sites/orion/packages.yaml b/configs/sites/orion/packages.yaml index 5725dfa59..95c6ceb9b 100644 --- a/configs/sites/orion/packages.yaml +++ b/configs/sites/orion/packages.yaml @@ -1,12 +1,8 @@ packages: all: - #compiler:: [intel@2022.0.2] - #compiler:: [gcc@10.2.0] - compiler:: [intel@2022.0.2, gcc@10.2.0] + compiler:: [intel@2022.0.2, intel@18.0.5, gcc@10.2.0] providers: - #mpi:: [intel-oneapi-mpi@2021.5.1] - #mpi:: [openmpi@4.0.4] - mpi:: [intel-oneapi-mpi@2021.5.1, openmpi@4.0.4] + mpi:: [intel-oneapi-mpi@2021.5.1, intel-mpi@2018.5.274, openmpi@4.0.4] ### MPI, Python, MKL mpi: @@ -17,22 +13,12 @@ packages: prefix: /apps/intel-2022.1.2/intel-2022.1.2 modules: - impi/2022.1.2 - # - spec: intel-oneapi-mpi@2021.2.0%intel@2021.2.0 - # prefix: /apps/intel-2021.2/intel-2021.2 - # modules: - # - impi/2021.2 - #intel-oneapi-tbb: - # externals: - # - spec: intel-oneapi-tbb@2021.2.0%intel@2021.2.0 - # prefix: /apps/intel-2021.2/intel-2021.2 - # modules: - # - intel/2021.2 - #intel-oneapi-mkl: - # externals: - # - spec: intel-oneapi-mkl@2021.2.0%intel@2021.2.0 - # prefix: /apps/intel-2021.2/intel-2021.2 - # modules: - # - intel/2021.2 + intel-mpi: + externals: + - spec: intel-mpi@2018.5.274%intel@18.0.5 + prefix: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/mpi + modules: + - impi/2018.4 openmpi: externals: - spec: openmpi@4.0.4%gcc@10.2.0~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath From 5f8e1084038ea2d402fc433037b492d5b2d56a90 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 6 Feb 2023 08:30:49 -0700 Subject: [PATCH 21/61] Attempt to fix CI tests --- .github/actions/setup-spack-stack/action.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/actions/setup-spack-stack/action.yaml b/.github/actions/setup-spack-stack/action.yaml index 0c113ed0c..ad0cdb0a4 100644 --- a/.github/actions/setup-spack-stack/action.yaml +++ b/.github/actions/setup-spack-stack/action.yaml @@ -174,6 +174,12 @@ runs: spack config add "packages:all:compiler:[${{ inputs.compiler }}]" # Set compiler as hard requirement for all packages spack config add "packages:all:require:one_of:['%${{ inputs.compiler }}']" + # Modify the compiler matrix definition + if [[ "$RUNNER_OS" == "macOS" ]]; then + sed -i "" "s/- compilers: ['%apple-clang', '%gcc', '%intel']/- compilers: ['%${{ inputs.compiler }}']/g" ${{ inputs.path }}/envs/${{ inputs.name }}/spack.yaml + else + sed -i "s/- compilers: ['%apple-clang', '%gcc', '%intel']/- compilers: ['%${{ inputs.compiler }}']/g" ${{ inputs.path }}/envs/${{ inputs.name }}/spack.yaml + fi if [[ "$RUNNER_OS" == "macOS" ]]; then # Turn of SSL for ecflow CI builds for now From 0f750d6c99e9d54a4a91be843887d13eb68c3da4 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 6 Feb 2023 08:45:11 -0700 Subject: [PATCH 22/61] Update documentation to - for now - manually adjust the compiler matrix --- .gitmodules | 10 ++++------ doc/source/Platforms.rst | 28 +++++++++++++++++++++------- doc/source/Quickstart.rst | 19 ++++++++++++++----- spack | 2 +- 4 files changed, 40 insertions(+), 19 deletions(-) diff --git a/.gitmodules b/.gitmodules index 2cf3483a5..c92fbbc5e 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,11 +1,9 @@ [submodule "spack"] path = spack - ##url = https://github.com/spack/spack - ##branch = develop - #url = https://github.com/NOAA-EMC/spack - #branch = jcsda_emc_spack_stack - url = https://github.com/climbfuji/spack - branch = feature/unified-env + #url = https://github.com/spack/spack + #branch = develop + url = https://github.com/NOAA-EMC/spack + branch = jcsda_emc_spack_stack [submodule "doc/CMakeModules"] path = doc/CMakeModules url = https://github.com/noaa-emc/cmakemodules diff --git a/doc/source/Platforms.rst b/doc/source/Platforms.rst index 40ca4739e..8fafc657f 100644 --- a/doc/source/Platforms.rst +++ b/doc/source/Platforms.rst @@ -661,7 +661,14 @@ Remember to activate the ``lua`` module environment and have MacTeX in your sear spack config add "packages:all:providers:mpi:[openmpi@4.1.4]" spack config add "packages:all:compiler:[apple-clang@13.1.6]" -7. Optionally, edit site config files and common config files, for example to remove duplicate versions of external packages that are unwanted, add specs in ``envs/jedi-ufs.mymacos/spack.yaml``, etc. +7. Edit the main config file for the environment and adjust the compiler matrix to match the compilers for macOS, as above: + +.. code-block:: console + + definitions: + - compilers: ['%apple-clang'] + +8. Edit site config files and common config files, for example to remove duplicate versions of external packages that are unwanted, add specs in ``envs/jedi-ufs.mymacos/spack.yaml``, etc. .. code-block:: console @@ -669,20 +676,20 @@ Remember to activate the ``lua`` module environment and have MacTeX in your sear vi envs/jedi-ufs.mymacos/common/*.yaml vi envs/jedi-ufs.mymacos/site/*.yaml -8. Process the specs and install +9. Process the specs and install .. code-block:: console spack concretize spack install [--verbose] [--fail-fast] -9. Create lmod module files +10. Create lmod module files .. code-block:: console spack module lmod refresh -10. Create meta-modules for compiler, mpi, python +11. Create meta-modules for compiler, mpi, python .. code-block:: console @@ -918,7 +925,14 @@ It is recommended to increase the stacksize limit by using ``ulimit -S -s unlimi spack config add "packages:all:providers:mpi:[mpich@4.0.2]" spack config add "packages:all:compiler:[gcc@11.2.0]" -7. Edit site config files and common config files, for example to remove duplicate versions of external packages that are unwanted, add specs in ``envs/jedi-ufs.mylinux/spack.yaml``, etc. +7. Edit the main config file for the environment and adjust the compiler matrix to match the compilers for Linux, as above: + +.. code-block:: console + + definitions: + - compilers: ['%gcc'] + +8. Edit site config files and common config files, for example to remove duplicate versions of external packages that are unwanted, add specs in ``envs/jedi-ufs.mylinux/spack.yaml``, etc. .. warning:: **Important:** Remove any external ``cmake@3.20`` package from ``envs/jedi-ufs.mylinux/site/packages.yaml``. It is in fact recommended to remove all versions of ``cmake`` up to ``3.20``. Further, on Red Hat/CentOS, remove any external curl that might have been found. @@ -929,14 +943,14 @@ It is recommended to increase the stacksize limit by using ``ulimit -S -s unlimi vi envs/jedi-ufs.mylinux/common/*.yaml vi envs/jedi-ufs.mylinux/site/*.yaml -8. Process the specs and install +9. Process the specs and install .. code-block:: console spack concretize spack install [--verbose] [--fail-fast] -9. Create tcl module files +10. Create tcl module files .. code-block:: console diff --git a/doc/source/Quickstart.rst b/doc/source/Quickstart.rst index 559e14451..b2c575d01 100644 --- a/doc/source/Quickstart.rst +++ b/doc/source/Quickstart.rst @@ -39,19 +39,28 @@ The following instructions install a new spack environment on a pre-configured s # Create a pre-configured Spack environment in envs/