From 42321ec31c68d6c4c07cbc3d195b14a2ff0fa2a1 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 3 Jun 2026 11:04:40 -0600 Subject: [PATCH 01/10] Remove gui variant from cube in repos/spack_stack/spack_repo/spack_stack/packages/dev_utils_env/package.py --- .gitmodules | 12 ++++++++---- repos/builtin | 2 +- .../spack_stack/packages/dev_utils_env/package.py | 2 +- spack | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-) diff --git a/.gitmodules b/.gitmodules index 2f6cb0566..4dbd9f15c 100644 --- a/.gitmodules +++ b/.gitmodules @@ -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/AlexanderHrabski-NOAA/spack + branch = update-spack-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 = feature/upd_spst_dev_from_upstream_20260602 diff --git a/repos/builtin b/repos/builtin index 6fd08efa4..d5f335345 160000 --- a/repos/builtin +++ b/repos/builtin @@ -1 +1 @@ -Subproject commit 6fd08efa4662fda2b4ef626cdc98c264d2dc05e5 +Subproject commit d5f3353458e195ca469f3c2aab921164dcbd2840 diff --git a/repos/spack_stack/spack_repo/spack_stack/packages/dev_utils_env/package.py b/repos/spack_stack/spack_repo/spack_stack/packages/dev_utils_env/package.py index 2e3911b54..0231146ea 100644 --- a/repos/spack_stack/spack_repo/spack_stack/packages/dev_utils_env/package.py +++ b/repos/spack_stack/spack_repo/spack_stack/packages/dev_utils_env/package.py @@ -31,7 +31,7 @@ class DevUtilsEnv(BundlePackage): # Scalasca/ScoreP depends_on("scalasca", when="+scalasca", type="run") - depends_on("cube +gui", when="+scalasca", type="run") + depends_on("cube", when="+scalasca", type="run") # Miscellaneous depends_on("cloc", type="run") diff --git a/spack b/spack index 324bf79a3..6fb75bd0c 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit 324bf79a31704dbc68fafc9e4a053aa4c60019ea +Subproject commit 6fb75bd0c607b5148c3a126301bc7a9e13b86b26 From d89808640bcfb67a83adec9e7032ffd91151ff3d Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 8 Jun 2026 10:03:06 -0600 Subject: [PATCH 02/10] Hard code old spack installer in configs/common/config.yaml --- configs/common/config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/configs/common/config.yaml b/configs/common/config.yaml index 178980d1c..856e36861 100644 --- a/configs/common/config.yaml +++ b/configs/common/config.yaml @@ -1,5 +1,9 @@ # Set package and module installation directories config: + # Old installer - needed for py-pynacl amongst others + # https://github.com/spack/spack-packages/issues/5106 + installer: old + install_hash_length: 7 install_tree: root: $env/install From ef0b2fb01e969272deefd5a36a272a6fd6668565 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Mon, 8 Jun 2026 10:03:25 -0600 Subject: [PATCH 03/10] Pin several older versions of Python packages in configs/common/packages.yaml --- configs/common/packages.yaml | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index bf657fb73..2463b7ceb 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -387,6 +387,10 @@ packages: py-cartopy: require: - +plotting + # See py-pycparser + py-click: + require: + - '@8.1.8' # Pin py-colorama to avoid duplicate packages, hopefully can be removed soon py-colorama: require: @@ -429,6 +433,15 @@ packages: py-poetry-core: require: - '@1.7' + # See py-pycparser + py-pooch: + require: + - '@1.7.0' + # Need older version of py-pycparser until we can update setuputils to >= 77 ? + # https://github.com/pydata/xarray/issues/10588 + py-pycparser: + require: + - '@2.21' # Need at least py-pygithub@2.7 for self-hosted runner management py-pygithub: require: @@ -437,6 +450,10 @@ packages: py-pyogrio: require: - '@0.9.0' + # See py-pycparser + py-pyparsing: + require: + - '@3.1.2' # To avoid duplicate packages py-python-dateutil: require: @@ -466,7 +483,7 @@ packages: # To avoid duplicate packages py-versioneer: require: - - '@0.29' + - '@=0.28' # On a per-site basis, either set qt to buildable: false # or add requirement to build with gcc for Intel oneAPI qt: From a979f56c93516adcc0b03c1c54aa4965cd7f5c9d Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 9 Jun 2026 06:01:08 -0600 Subject: [PATCH 04/10] Update submodule pointer for repos/builtin --- repos/builtin | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repos/builtin b/repos/builtin index 9505b9234..8635bd92b 160000 --- a/repos/builtin +++ b/repos/builtin @@ -1 +1 @@ -Subproject commit 9505b9234aad761da0800c7d5e35ba2c6e7301ec +Subproject commit 8635bd92bdb4493d87ee1de84b4e48fdd8cd0265 From 2f9aafeee32776742768ebfdd0dbb0f3106bb0b7 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 9 Jun 2026 06:04:12 -0600 Subject: [PATCH 05/10] Update configs/sites/tier1/atlantis/packages_*.yaml --- configs/sites/tier1/atlantis/packages_clang-22.1.0.yaml | 1 + configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml | 1 + configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml | 7 +++++++ configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml | 6 ++++++ 4 files changed, 15 insertions(+) diff --git a/configs/sites/tier1/atlantis/packages_clang-22.1.0.yaml b/configs/sites/tier1/atlantis/packages_clang-22.1.0.yaml index 71e1ffc18..e4d82ce5e 100644 --- a/configs/sites/tier1/atlantis/packages_clang-22.1.0.yaml +++ b/configs/sites/tier1/atlantis/packages_clang-22.1.0.yaml @@ -31,4 +31,5 @@ packages: - spec: openmpi@4.1.8 ~internal-hwloc +two_level_namespace prefix: /gpfs/neptune/spack-stack/openmpi-4.1.8/llvm-22.1.0 modules: + - llvm/22.1.0 - openmpi/4.1.8 diff --git a/configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml b/configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml index f679ce2bf..e2ad853d7 100644 --- a/configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml +++ b/configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml @@ -25,4 +25,5 @@ packages: - spec: openmpi@4.1.8 ~internal-hwloc +two_level_namespace prefix: /gpfs/neptune/spack-stack/openmpi-4.1.8/gcc-13.4.0 modules: + - gcc/13.4.0 - openmpi/4.1.8 diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml index 2399b9d46..eaeeabcca 100644 --- a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml +++ b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml @@ -47,6 +47,9 @@ packages: - spec: intel-oneapi-mpi@2021.13 prefix: /cm/shared/apps/intel/oneapi-2024.2.1 modules: + - intel-oneapi-2024.2.1 + - tbb/2021.13 + - compiler-rt/2024.2.1 - mpi/2021.13 - slurm intel-oneapi-mkl: @@ -54,3 +57,7 @@ packages: externals: - spec: intel-oneapi-mkl@2024.2 prefix: /cm/shared/apps/intel/oneapi-2024.2.1 + - intel-oneapi-2024.2.1 + - tbb/2021.13 + - compiler-rt/2024.2.1 + - mkl/2024.2 diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml index a284b3a2e..73d9d4dd1 100644 --- a/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml +++ b/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml @@ -47,6 +47,9 @@ packages: - spec: intel-oneapi-mpi@2021.17 prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0 modules: + - umf/1.0.2 + - tbb/2022.3 + - compiler-rt/2025.3.0 - mpi/2021.17 - slurm intel-oneapi-mkl: @@ -55,4 +58,7 @@ packages: - spec: intel-oneapi-mkl@2025.3 prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0 modules: + - umf/1.0.2 + - tbb/2022.3 + - compiler-rt/2025.3.0 - mkl/2025.3 From dd33ec6bc16b5063b9870a5fc480f92c2894370d Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 9 Jun 2026 06:10:10 -0600 Subject: [PATCH 06/10] Bug fix in configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml --- configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml index eaeeabcca..204dcedc0 100644 --- a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml +++ b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml @@ -57,6 +57,7 @@ packages: externals: - spec: intel-oneapi-mkl@2024.2 prefix: /cm/shared/apps/intel/oneapi-2024.2.1 + modules: - intel-oneapi-2024.2.1 - tbb/2021.13 - compiler-rt/2024.2.1 From 54ea8f119d6cc350afecddfbb7b0c414abd921da Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Tue, 9 Jun 2026 08:52:49 -0600 Subject: [PATCH 07/10] Pin py-sphinxcontrib-bibtex to 2.5.0 --- configs/common/packages.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index 2463b7ceb..d1bd0f998 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -471,6 +471,10 @@ packages: py-setuptools: require: - '@73.0.1' + # See py-pycparser + py-sphinxcontrib-bibtex: + require: + - '@2.5.0' py-torch: require: - +custom-protobuf From 31728d6b5ef3065debbe999d34564b44ac1f5ece Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 10 Jun 2026 21:17:49 -0600 Subject: [PATCH 08/10] Updates to build py-cylc-uiserver --- configs/common/packages.yaml | 22 ++++++++++--------- .../atlantis/packages_oneapi-2024.2.1.yaml | 5 ----- .../atlantis/packages_oneapi-2025.3.0.yaml | 5 ----- configs/templates/cylc-dev/spack.yaml | 6 ++--- repos/builtin | 2 +- 5 files changed, 16 insertions(+), 24 deletions(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index d1bd0f998..1d2aa0585 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -58,9 +58,6 @@ packages: require: - '@0.0.5' - +python - cairo: - require: - - +pic cdo: require: - ~openmp @@ -212,11 +209,12 @@ packages: require: - '@1.1.3' harfbuzz: + # cmake-based harfbuzz fails during build; autotools is only available + # for the deprecated @2.9.1 which doesn't compile against ICU >= 76 + # (-Werror=redundant-decls on u_strlen). Force meson. # cmake-based harfbuzz fails during build require: - - one_of: - - 'build_system=meson' - - 'build_system=autotools' + - 'build_system=meson' hdf: require: - '@4.2.15' @@ -399,10 +397,10 @@ packages: py-cryptography: require: - '@42' - # To avoid duplicate packages - py-flit-core: - require: - - '@3.8.0' + ## To avoid duplicate packages + #py-flit-core: + # require: + # - '@3.8.0' py-h5py: require: - ~mpi @@ -411,6 +409,10 @@ packages: py-hatchling: require: - '@1.27:' + ## See py-pycparser + #py-jsonschema: + # require: + # - '@4.17.3' # To avoid duplicate packages py-lxml: require: diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml index 204dcedc0..076758a36 100644 --- a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml +++ b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml @@ -57,8 +57,3 @@ packages: externals: - spec: intel-oneapi-mkl@2024.2 prefix: /cm/shared/apps/intel/oneapi-2024.2.1 - modules: - - intel-oneapi-2024.2.1 - - tbb/2021.13 - - compiler-rt/2024.2.1 - - mkl/2024.2 diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml index 73d9d4dd1..a24f655d1 100644 --- a/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml +++ b/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml @@ -57,8 +57,3 @@ packages: externals: - spec: intel-oneapi-mkl@2025.3 prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0 - modules: - - umf/1.0.2 - - tbb/2022.3 - - compiler-rt/2025.3.0 - - mkl/2025.3 diff --git a/configs/templates/cylc-dev/spack.yaml b/configs/templates/cylc-dev/spack.yaml index 342893872..b91ee0d9b 100644 --- a/configs/templates/cylc-dev/spack.yaml +++ b/configs/templates/cylc-dev/spack.yaml @@ -21,7 +21,7 @@ spack: include: [] specs: - - py-cylc-flow@8.4.2 - - py-cylc-rose@1.5.1 - - py-cylc-uiserver@1.6.1 + # These versions work with Python 3.11 + - py-cylc-flow@8.5.4 + - py-cylc-uiserver@1.7.1 - bats diff --git a/repos/builtin b/repos/builtin index 8635bd92b..f7e64f153 160000 --- a/repos/builtin +++ b/repos/builtin @@ -1 +1 @@ -Subproject commit 8635bd92bdb4493d87ee1de84b4e48fdd8cd0265 +Subproject commit f7e64f153f8ee868cfd34bbbb4d565358d6a1df1 From 41e5b03e26c2aeaf0e5b301a6724a05980c26c6a Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 11 Jun 2026 09:21:02 -0600 Subject: [PATCH 09/10] Build qt with gcc in CI workflows --- .github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg | 3 +++ .github/workflows/ubuntu-ci-x86_64-oneapi.cfg | 3 +++ 2 files changed, 6 insertions(+) diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg index 36af6d2ca..c69ab1160 100644 --- a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg +++ b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg @@ -17,3 +17,6 @@ externals: - spec: intel-oneapi-mpi@2021.13 prefix: /opt/intel/oneapi + qt: + require: + - '%c,cxx=gcc' diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg b/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg index dad047776..103f32006 100644 --- a/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg +++ b/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg @@ -17,3 +17,6 @@ externals: - spec: intel-oneapi-mpi@2021.13 prefix: /opt/intel/oneapi + qt: + require: + - '%c,cxx=gcc' From ebd3ef73c1c4d47ddfb22cc5eaa5bc1b5f9211c7 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Thu, 11 Jun 2026 15:07:54 -0600 Subject: [PATCH 10/10] Update submodule pointer for repos/builtin --- repos/builtin | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repos/builtin b/repos/builtin index f7e64f153..e3eaf3bd4 160000 --- a/repos/builtin +++ b/repos/builtin @@ -1 +1 @@ -Subproject commit f7e64f153f8ee868cfd34bbbb4d565358d6a1df1 +Subproject commit e3eaf3bd4b6877af120cbbf0ee1e8dd42045ff0b