release/1.9.0: Pin py-numpy version to 1.26 for Orion Intel configuration #1482
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getting unwanted duplicate packages during concretize.
srherbener
requested review from
climbfuji,
AlexanderRichert-NOAA and
rickgrubin-noaa
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I don't know the list of all the platforms that would need an update like this so I have only added the one update for Orion, Intel. @climbfuji suggested updating intel and oneapi configs for all RDHPCS platforms. Please feel free to add to this PR with other configuration updates. |
climbfuji
approved these changes
Jan 29, 2025
climbfuji
changed the title
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@srherbener Ready to merge? |
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We can fill in the other site updates as part of the roll-out |
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Let's go ahead and merge this PR. It definitely fixes the concretize duplicated packages issue. I ran into a couple more problems trying to complete the spack-stack build (Orion, Intel), but I noticed that I'm out of sync with the release branch by several PR merges so the issues I ran into may have already been addressed. Thanks! |
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I don't expect the Intel compiler to be able to build the entire unified environment anymore. Time to move to oneapi 2024.2.1 and use icx + icpx + ifort .. |
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I will merge this right after #1486, no need to run CI tests if changing the Orion site config only. |
climbfuji
added a commit
that referenced
this pull request
Feb 4, 2025
…elop * Update .gitmodules and doc/source/conf.py for spack-stack release/1.9.0 * Avoid linking to libirc.so in spack (parallel-netcdf), turn off crypt variant for Python, and update Orion site config to fix tar issue (#1435) 1. Applications built with spack-stack packages esmf, parallelio, parallel-netcdf have libirc.so dynamically linked. Applications linked against libirc.so fail to start up. See Avoid linking to Intel's libirc.so library (aka bad configure script of package parallel-netcdf) #1436. The spack PR that is part of the suggested changes here fixes this by replacing libirc.so with libintlc.so in the parallel-netcdf build. See Bug fix in parallel-netcdf to avoid linking to libirc.so AND cherry-pick spack develop PR 48251 (conflict Intel Classic with [email protected]) spack#495. 2. Turn off crypt variant for Python; this variant leads to build errors with Intel in py-cryptography unless external curl and openssl are removed, which itself is problematic. 3. Add external wget on Orion, latest versions don't build with Intel on the machine. --------- Co-authored-by: Stephen Herbener <[email protected]> * Update ectrans from 1.2.0 to 1.5.0 in configs/common/packages.yaml (#1474) * Update .gitmodules and submodule pointer for spack for code review and testing * In spack-ext/lib/jcsda-emc/spack-stack/stack, update meta_modules.py and templates/{mpi,mpi.lua}: set compiler paths in MPI meta modules directly using SUBSTITUTES_SAVE, not using environment variables (#1479) * Revert .gitmodules and update submodule pointer for spack * release/1.9.0: Update instructions for setting up spack-stack with Nvidia compilers (#1462) This PR brings the Nvidia instructions a bit more up-to-date. On develop, the instructions only worked with Ubuntu 22.04 spack-stack 34bfda1 [email protected] With this PR, these constraints are updated to the slightly more recent Ubuntu 24.04 spack-stack 26901af [email protected] * For orion, intel config, pin py-numpy to version 1.26. This prevents (#1482) getting unwanted duplicate packages during concretize. * release/1.9.0: Add [email protected] to unified-dev and skylab-dev templates, bug fix in depencies for awscli-v2, bump wgrib2 to 3.5.0 and re-enable for all compilers (#1486) 1. Add [email protected] to templates skylab-dev and unified-dev (new version was added in recently merged PR Update crtm(-fix), wgrib2 spack#510) 2. Bump wgrib2 from 3.1.1 to 3.5.0 and re-enable for all compilers in spack-ext packages (new version was added in recently merged PR Update crtm(-fix), wgrib2 spack#510). Note. [email protected] doesn't compile on macOS with apple-clang (version 14.0.3 on the CI runner), see wgrib 3.5.0 does not compile with apple-clang 14.0.3 on macOS NOAA-EMC/wgrib2#312. But 3.4.0 does compile, thereforeuse this version on macOS only 3. Update spack submodule pointer for PR Update crtm(-fix), wgrib2 spack#510 and the changes in release/1.9.0: Fix bug in awcli-v2, add upper bound for py-cryptography spack#511 (fix upper bound for py-cryptography in awscli-v2) and release/1.9.0: Bug fix in wgrib2: apply '-Wno-error=implicit-function-declaration' for LLVM clang spack#513 (bug fix for wgrib2 with apple-clang) --------- Co-authored-by: Alex Richert <[email protected]> * Update .gitmodules and submodule pointer for spack for code review and testing * For release/1.9.0: cherry-pick `[email protected]: ~mpi` instead of `+mpi` from #1489 (#1491) In PR #1489 we are changing the requirements for py-netcdf4 from [email protected]: +mpi to [email protected]: ~mpi in configs/common/packages.yaml. This change is required to fix an error with py-netcdf4 on certain systems when built with +mpi. We used to build py-netcdf4 without mpi, but for a period this wasn't possible until we added a patch to disable the py-netcdf4 auto-detect parallel feature. That patch allows us to build py-netcdf4 ~mpi even if netcdf-c was built with +mpi. --------- Co-authored-by: Alex Richert <[email protected]> * Revert .gitmodules and update submodule pointer for spack --------- Co-authored-by: Stephen Herbener <[email protected]> Co-authored-by: Francois Hebert <[email protected]> Co-authored-by: Stephen Herbener <[email protected]> Co-authored-by: Alex Richert <[email protected]>
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Summary
This PR pins the Orion Intel version for py-numpy to 1.26. This prevents unwanted duplicate packages during the concretize step.
Testing
Applications affected
List all known applications (UFS WM, JEDI, SRW, etc.) intentionally or unintentionally affected by this PR.
UFS, JEDI, etc.
Systems affected
Orion, only for the Intel environment
Dependencies
None
Issue(s) addressed
Fixes #1477
Checklist