Update spack stack setup-meta-modules to directly set compilers in MPI meta modules
#1479
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AlexanderRichert-NOAA
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Jan 28, 2025
…and templates/{mpi,mpi.lua}: set compiler paths in MPI meta modules directly using SUBSTITUTES_SAVE, not using environment variables
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@natalie-perlin Please test this, it should fix the |
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natalie-perlin
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Jan 29, 2025
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Confirming this worked OK!
Tested it on an older spack-stack-1.8.0 that had this problem. Replaced meta_modules.py by a new file to include the previous changes to the file. Added changed to mpi and mpi.lua. Then regenerated modulefiles for the meta-modules.
The problem no longer appears.
module use ~/spack-stack/spack-release-1.8.0/envs/ufs-srw-env/install/modulefiles/Core
module load stack-apple-clang/15.0.0
module load stack-openmpi/5.0.3
module load stack-openmpi/5.0.3
module unload stack-openmpi/5.0.3
No errors or warnings are reported. Approving, thank you!
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…and templates/{mpi,mpi.lua}: set compiler paths in MPI meta modules directly using SUBSTITUTES_SAVE, not using environment variables (JCSDA#1479)
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…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
In
spack-ext/lib/jcsda-emc/spack-stack/stack, updatemeta_modules.pyandtemplates/{mpi,mpi.lua}: set compiler paths in MPI meta modules directly usingSUBSTITUTES_SAVE, not using environment variables. This wasn't possible in the past, but whenSUBSTITUTES_SAVEwas introduced a few months back for an unrelated bug fix, that change could have been made as well.Testing
parallel-netcdf. Looked at the MPI meta module and verified theCC,CXX,FC,F77,F90variables are set correctly.Applications affected
All using MPI
Systems affected
All
Dependencies
n/a
Issue(s) addressed
Replaces #1465
Checklist
All dependency PRs/issues have been resolved and this PR can be merged.