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429203f
Pin py-numpy to version 1 to avoid duplicate packages; update
climbfuji Jan 12, 2026
53ce67f
Update syntax for preferred compiler in configs/common/packages_{clan…
climbfuji Jan 12, 2026
c2d22f5
Remove external compiler runtime packages for tier 2 sites bounty and…
climbfuji Jan 12, 2026
05d4c75
Update submodule pointer for spack
climbfuji Jan 12, 2026
8b32c9e
Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…
climbfuji Jan 12, 2026
1d0ef40
Remove external/non-buildable runtime packages from .github/workflows…
climbfuji Jan 12, 2026
fd687ef
Set variants/versions for snappy and py-lxml in configs/common/packag…
climbfuji Jan 12, 2026
a22ae76
Attempt to fix spack-ext/lib/jcsda-emc/spack-stack/tests/test_setup_m…
climbfuji Jan 12, 2026
523380e
Update .github/workflows/ubuntu-ci-x86_64-*.yaml: remove old prefer s…
climbfuji Jan 13, 2026
afda902
configs/common/packages.yaml: set variant generator=make for libaec t…
climbfuji Jan 13, 2026
c9c5fab
configs/common/packages_*.yaml: Upde syntax for preferred compilers
climbfuji Jan 13, 2026
ce21e16
spack-ext/lib/jcsda-emc/spack-stack/stack/meta_modules.py: Update met…
climbfuji Jan 13, 2026
44bce84
Update spack-ext unit tests
climbfuji Jan 13, 2026
5b1f3ad
Update .gitmodules and submodule pointer for repos/builtin for code r…
climbfuji Jan 13, 2026
e0ce0fa
Bump bufr-query to 0.0.5
climbfuji Jan 13, 2026
7169e1e
Revert .gitmodules and update submodule pointer for repos/builtin
climbfuji Jan 14, 2026
75a0d1f
Remove all external compiler runtime packages from all site configs
climbfuji Jan 14, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/ubuntu-ci-x86_64-gnu.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ jobs:

# Set compiler and MPI specs
spack config add "packages:mpi:require:['openmpi@5.0.8']"
spack config add "packages:all:prefer:['%gcc']"
#spack config add "packages:all:prefer:['%gcc']"
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Suggested change
#spack config add "packages:all:prefer:['%gcc']"


# Add additional variants for MET packages, different from config/common/packages.yaml
spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"
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5 changes: 0 additions & 5 deletions .github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,6 @@
c: /opt/intel/oneapi/compiler/2024.2/bin/icx
cxx: /opt/intel/oneapi/compiler/2024.2/bin/icpx
fortran: /opt/intel/oneapi/compiler/2024.2/bin/ifx
intel-oneapi-runtime:
buildable: false
externals:
- spec: intel-oneapi-runtime@2024.2.0
prefix: /opt/intel/oneapi
intel-oneapi-mkl:
buildable: false
externals:
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2 changes: 1 addition & 1 deletion .github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ jobs:
# Set compiler and MPI specs
spack config add "packages:mpi:buildable:False"
spack config add "packages:mpi:require:['intel-oneapi-mpi@2021.13']"
spack config add "packages:all:prefer:['%oneapi']"
#spack config add "packages:all:prefer:['%oneapi']"
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Suggested change
#spack config add "packages:all:prefer:['%oneapi']"


# Add additional variants for MET packages, different from config/common/packages.yaml
spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"
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5 changes: 0 additions & 5 deletions .github/workflows/ubuntu-ci-x86_64-oneapi.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,6 @@
c: /opt/intel/oneapi/compiler/2024.2/bin/icx
cxx: /opt/intel/oneapi/compiler/2024.2/bin/icpx
fortran: /opt/intel/oneapi/compiler/2024.2/bin/ifort
intel-oneapi-runtime:
buildable: false
externals:
- spec: intel-oneapi-runtime@2024.2.0
prefix: /opt/intel/oneapi
intel-oneapi-mkl:
buildable: false
externals:
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2 changes: 1 addition & 1 deletion .github/workflows/ubuntu-ci-x86_64-oneapi.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ jobs:
# Set compiler and MPI specs
spack config add "packages:mpi:buildable:False"
spack config add "packages:mpi:require:['intel-oneapi-mpi@2021.13']"
spack config add "packages:all:prefer:['%oneapi']"
#spack config add "packages:all:prefer:['%oneapi']"
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Suggested change
#spack config add "packages:all:prefer:['%oneapi']"


# Add additional variants for MET packages, different from config/common/packages.yaml
spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"
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12 changes: 8 additions & 4 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
[submodule "spack"]
path = spack
url = https://github.com/jcsda/spack
branch = spack-stack-dev
#url = https://github.com/jcsda/spack
#branch = spack-stack-dev
url = https://github.com/climbfuji/spack
branch = feature/update_spack-stack-dev_from_develop
[submodule "repos/builtin"]
path = repos/builtin
url = https://github.com/jcsda/spack-packages
branch = spack-stack-dev
#url = https://github.com/jcsda/spack-packages
#branch = spack-stack-dev
url = https://github.com/climbfuji/spack-packages
branch = bugfix/pixman_meson_libpng
24 changes: 17 additions & 7 deletions configs/common/packages.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ packages:
- +python
bufr-query:
require:
- '@0.0.4'
- '@0.0.5'
- +python
cairo:
require:
Expand Down Expand Up @@ -199,6 +199,10 @@ packages:
landsfcutil:
require:
- '@2.4.2'
# https://github.com/JCSDA/spack-stack/actions/runs/20957699537/job/60226338267
libaec:
prefer:
- build_system=cmake generator=make
#libjpeg-turbo:
# require:
# - '@2.1.0'
Expand Down Expand Up @@ -347,6 +351,10 @@ packages:
py-hatchling:
require:
- '@1.27:'
# To avoid duplicate packages
py-lxml:
require:
- '@5.2.2'
# https://github.com/JCSDA/spack-stack/issues/1276
py-matplotlib:
require:
Expand All @@ -358,16 +366,14 @@ packages:
require:
- '@1.7.2'
- ~mpi
## To avoid duplicate packages
#py-numpy:
# require:
# - '@1.26'
# DH* 20250813
# To avoid duplicate packages
py-numpy:
require:
- '@1'
# To avoid duplicate packages
py-poetry-core:
require:
- '@1.7'
# *DH 20250813
# This version builds with Intel oneAPI compilers, newer versions don't
py-pyogrio:
require:
Expand Down Expand Up @@ -417,6 +423,10 @@ packages:
sigio:
require:
- '@2.3.3'
# To avoid duplicate packages
snappy:
require:
- +shared
sp:
require:
- '@2.5.0'
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20 changes: 0 additions & 20 deletions configs/common/packages_aocc.yaml.NOTYETUPDATED

This file was deleted.

19 changes: 0 additions & 19 deletions configs/common/packages_apple-clang.yaml.NOTYETUPDATED

This file was deleted.

11 changes: 9 additions & 2 deletions configs/common/packages_clang.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,14 @@
packages:
all:
# Compiler preferences
c:
prefer:
- '%clang'
- llvm
cxx:
prefer:
- llvm
fortran:
prefer:
- llvm
# Virtual provider settings
blas:
require: [openblas]
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11 changes: 9 additions & 2 deletions configs/common/packages_gcc.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,14 @@
packages:
all:
# Compiler preferences
c:
prefer:
- '%gcc'
- gcc
cxx:
prefer:
- gcc
fortran:
prefer:
- gcc
# Virtual provider settings
blas:
require: [openblas]
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50 changes: 0 additions & 50 deletions configs/common/packages_intel.yaml.NOTYETUPDATED

This file was deleted.

11 changes: 9 additions & 2 deletions configs/common/packages_oneapi.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,14 @@
packages:
all:
# Compiler preferences
c:
prefer:
- '%oneapi'
- intel-oneapi-compilers
cxx:
prefer:
- intel-oneapi-compilers
fortran:
prefer:
- intel-oneapi-compilers
# Virtual package settings
blas:
require: ['intel-oneapi-mkl']
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5 changes: 0 additions & 5 deletions configs/containers/docker-ubuntu-gcc-openmpi.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,11 +28,6 @@ spack:
c: /usr/bin/gcc
cxx: /usr/bin/g++
fortran: /usr/bin/gfortran
gcc-runtime:
buildable: false
externals:
- spec: gcc-runtime@13.3.0
prefix: /usr
mpi:
require: [openmpi@5.0.8]

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5 changes: 0 additions & 5 deletions configs/containers/docker-ubuntu-gcc11-openmpi.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -42,11 +42,6 @@ spack:
c: /usr/bin/gcc
cxx: /usr/bin/g++
fortran: /usr/bin/gfortran
gcc-runtime:
buildable: false
externals:
- spec: gcc-runtime@11.4.0
prefix: /usr
mpi:
require: [openmpi@5.0.8]

Expand Down
7 changes: 0 additions & 7 deletions configs/containers/docker-ubuntu-oneapi-impi.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -64,13 +64,6 @@ spack:
prefix: /opt/intel/oneapi
modules:
- tbb/2022.3
intel-oneapi-runtime:
buildable: false
externals:
- spec: intel-oneapi-runtime@2025.3.0
prefix: /opt/intel/oneapi
modules:
- compiler-rt/2025.3.0
mpi:
require: [intel-oneapi-mpi@2021.17]
mpich:
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5 changes: 0 additions & 5 deletions configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@ packages:
buildable: False
require:
- openmpi@4.1.8
gcc-runtime:
buildable: False
externals:
- spec: gcc-runtime@13.4.0%gcc@13.4.0
prefix: /gpfs/neptune/spack-stack/gcc-13.4.0
gcc:
buildable: False
externals:
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10 changes: 0 additions & 10 deletions configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@ packages:
buildable: false
require:
- intel-oneapi-mpi@2021.13
intel-oneapi-runtime:
buildable: false
externals:
- spec: intel-oneapi-runtime@2024.2.1
prefix: /cm/shared/apps/intel/oneapi-2024.2.1
intel-oneapi-compilers:
buildable: false
externals:
Expand All @@ -30,11 +25,6 @@ packages:
extra_rpaths:
- /cm/local/apps/gcc/11.2.0/lib64
- /cm/local/apps/gcc/11.2.0/lib
gcc-runtime:
buildable: false
externals:
- spec: gcc-runtime@11.2.0
prefix: /cm/local/apps/gcc/11.2.0
gcc:
buildable: false
externals:
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10 changes: 0 additions & 10 deletions configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@ packages:
buildable: false
require:
- intel-oneapi-mpi@2021.17
intel-oneapi-runtime:
buildable: false
externals:
- spec: intel-oneapi-runtime@2025.3.0
prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
intel-oneapi-compilers:
buildable: false
externals:
Expand All @@ -30,11 +25,6 @@ packages:
extra_rpaths:
- /cm/local/apps/gcc/11.2.0/lib64
- /cm/local/apps/gcc/11.2.0/lib
gcc-runtime:
buildable: false
externals:
- spec: gcc-runtime@11.2.0
prefix: /cm/local/apps/gcc/11.2.0
gcc:
buildable: false
externals:
Expand Down
5 changes: 0 additions & 5 deletions configs/sites/tier1/blueback/packages_gcc-13.3.0.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@ packages:
buildable: false
require:
- cray-mpich@8.1.32
gcc-runtime:
buildable: false
externals:
- spec: gcc-runtime@13.3.0
prefix: /usr
gcc:
buildable: false
externals:
Expand Down
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