Update spack-stack-dev from spack develop as of 2024/10/31 #482

climbfuji · 2024-11-01T00:27:57Z

Description

Update spack-stack-dev from spack develop as of 2024/10/31. The following files had merge conflicts that I needed to resolve and that I would like the reviewers to look at (there were a few more, but those I knew enough about to resolve with confidence):

        both modified:   .github/workflows/unit_tests.yaml
        both modified:   var/spack/repos/builtin/packages/fontconfig/package.py
        both modified:   var/spack/repos/builtin/packages/g2/package.py
        both modified:   var/spack/repos/builtin/packages/gdal/package.py
        both modified:   var/spack/repos/builtin/packages/gmake/package.py
        both modified:   var/spack/repos/builtin/packages/harfbuzz/package.py
        both modified:   var/spack/repos/builtin/packages/jasper/package.py
        both modified:   var/spack/repos/builtin/packages/landsfcutil/package.py
        both modified:   var/spack/repos/builtin/packages/libtirpc/package.py
        both modified:   var/spack/repos/builtin/packages/libxkbcommon/package.py
        both modified:   var/spack/repos/builtin/packages/openmpi/package.py
        both modified:   var/spack/repos/builtin/packages/pixman/package.py
        both modified:   var/spack/repos/builtin/packages/py-cffi/package.py
        both modified:   var/spack/repos/builtin/packages/py-metpy/package.py
        both modified:   var/spack/repos/builtin/packages/py-setuptools-rust/package.py
        both modified:   var/spack/repos/builtin/packages/qt/package.py
        both modified:   var/spack/repos/builtin/packages/sfcio/package.py
        both modified:   var/spack/repos/builtin/packages/sigio/package.py
        both modified:   var/spack/repos/builtin/packages/ufs-weather-model/package.py

Testing

Unit tests (GitHub actions) - note that I had to turn off the Windows Github actions tests, since they are written in a way that require the GitHub repo to be https://github.com/spack/spack
For testing with spack-stack, see Update spack-stack-dev from spack develop as of 2024/10/31 spack-stack#1363 (work in progress)

* CI: Add dynamic mapping section * Doc: Add documentation for dynamic mapping section * Add missing schema property * Fixes from review * query build fix up * add warning output for dynamic mapping request errors * Cleanup ci schema * Add more protections for disabling/mitigating bad endpoints for dynamic mapping * Remove references to "gantry" in the docs * Fixup rtd header * Add unit testing for dynamic-mapping section * Add arch to dynamic-mapping query string * Tests and cleanup schema

…6602) Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

* Add 0.9.14.1 and bound xarray version support * Fix bounds as per review

…nherited cmake (spack#47022)

Co-authored-by: Gava, Francesco <francesco.gava@mclaren.com> Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

* e4s external rocm ci: upgrade to v6.2.1 * use ghcr.io/spack/spack/ubuntu22.04-runner-amd64-gcc-11.4-rocm6.2.1:2024.10.08 * magma +rocm: add entry for v6.2.1

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>

* Updates Caliper recipe to build the new Python bindings * Implements setup_run_environment for Caliper to update PYTHONPATH

…k#47029) and add another backward compat bound for just 8.8

* e4s ci stacks: add fftx cpu, cuda, and rocm builds * disable fftx+rocm due to spack github issue spack#47034 * e4s oneapi: fftx has spack build error spack#47048

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

* voropp: migrate to cmake * lammps: update voropp dep

* Remove the implicit CORE-AVX512 since the CPU specific flags are added by the compiler wrappers. * Add `-i_use-path` to help `ifx` find `lld` even if `-gcc-name` is set in `ifx.cfg`. This file is written by `intel-oneapi-compilers` package to find the correct `gcc`. Not being able to find `ldd` is a bug in `ifx`. @rschon2 found this workaround.

…k#47023)

…#47065) Turns out `os=...` of the spec and `MACOSX_DEPLOYMENT_TARGET` are kept in sync, and the env variable is used to initialize `CMAKE_MACOSX_DEPLOYMENT_TARGET`. In bootstrap code we set the env variable, so these bits are redundant. --------- Co-authored-by: haampie <haampie@users.noreply.github.com>

…spack#47077)

Some unused methods in VTK-m resulted in compile errors. These were not discovered because many compilers ignore unused methods in templated classes, but the SYCL compiler for Aurora gave an error.

Co-authored-by: Peter Scheibel <scheibel1@llnl.gov>

Currently the order in which hooks are run is arbitrary. This can be fixed by sorted(list_modules(...)) but I think it is much more clear to just have a static list. Hooks are not extensible other than modifying Spack code, which means it's unlikely people maintain custom hooks since they'd have to fork Spack. And if they fork Spack, they might as well add an entry to the list when they're continuously rebasing.

* add verdict package Co-authored-by: becker33 <becker33@users.noreply.github.com> Co-authored-by: Alec Scott <scott112@llnl.gov>

caught by `prettier`

* mpidiff: new package * fix style with black * Add variants, docs, and examples variants. Remove options that are not really options in the build.

* optipng: add v0.7.8 * optipng: mv for_aarch64.patch for_aarch64_0.7.7.patch * optipng: add for_aarch64_0.7.8.patch * optipng: deprecate v0.7.7 * optipng: fix style

…pack#43517)

…ack#47343) Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

* py-ipympl: add v0.9.4 * Add node/npm dependencies at runtime * node-js: fix build with older GCC * Change CLANG flags too * Add supported compiler versions * Deprecate older version

…6576) * boost: boost.python does not support numpy@2 yet

…/update_from_spack_dev_20241031

…ge.py, var/spack/repos/builtin/packages/libxkbcommon/package.py, var/spack/repos/builtin/packages/openmpi/package.py

…and lib/spack/spack/compilers/oneapi.py: set correct version ranges

kwryankrattiger and others added 30 commits October 16, 2024 14:06

hermes: add more versions, variants and depend on hermes-shm (spack#4…

8d2a059

…6602) Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

py-cfgrib: add v0.9.14.1 (spack#46879)

f4a4acd

* Add 0.9.14.1 and bound xarray version support * Fix bounds as per review

librdkafka: added version 2.5.3 (spack#47009)

39063ba

gnuconfig: bump (spack#47020)

bfe434c

duckdb: install headers and libraries (spack#47015)

64a7525

cyrus-sasl: patch v2.1.27:2.1.28 for gcc-14 (spack#47019)

62fd5d1

openldap: add v2.6.8; conflict gcc@14: for older (spack#47024)

5d2c67e

updated package specs for rust; removed redundant dependency due to i…

7bddcd2

…nherited cmake (spack#47022)

dakota: add conflicts and additional flags (spack#42906)

b661acf

Co-authored-by: Gava, Francesco <francesco.gava@mclaren.com> Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

e4s external rocm ci: upgrade to v6.2.1 (spack#46871)

e4c2337

* e4s external rocm ci: upgrade to v6.2.1 * use ghcr.io/spack/spack/ubuntu22.04-runner-amd64-gcc-11.4-rocm6.2.1:2024.10.08 * magma +rocm: add entry for v6.2.1

isoquant: new package @3.6.1 (spack#47013)

178a8bb

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>

caliper: add +python variant with pybind11 bindings (spack#47031)

1eb2cb9

* Updates Caliper recipe to build the new Python bindings * Implements setup_run_environment for Caliper to update PYTHONPATH

curl: mbedtls 3.6.0 bound should be forward not backward compat (spac…

aa6caf9

…k#47029) and add another backward compat bound for just 8.8

freetype: prefer 2.13.2 due to interface change in 2.13.3 (spack#47021)

5f56eee

clingo: use CMAKE_OSX_DEPLOYMENT_TARGET instead of *flags (spack#47043)

adaa0a4

llvm-amdgpu and composable-kernel: fix build failures (spack#46891)

962262a

e4s ci stacks: add fftx cpu, cuda, and rocm builds (spack#47004)

7ecdc17

* e4s ci stacks: add fftx cpu, cuda, and rocm builds * disable fftx+rocm due to spack github issue spack#47034 * e4s oneapi: fftx has spack build error spack#47048

unrar: add v7.0.9 (spack#47036)

0a7533a

otf-cpt: add new package for OTF-CPT (spack#47042)

75c71f7

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

voropp: swich to cmake (spack#47039)

049ade0

* voropp: migrate to cmake * lammps: update voropp dep

AOCL: add v5.0 (spack#46964)

2da812c

Adds variant to toggle use of rdpmc due to icl-utk-edu/papi#238 (spac…

9ba7af4

…k#47023)

curl: add v8.10.1 (fix CVE) (spack#46960)

580cc3c

pika: Add minimum CMake version requirement when using CUDA and C++20 (…

49a8e84

…spack#47077)

vtk-m: Add sycl option to vtk-m package (spack#46996)

b9e0914

Some unused methods in VTK-m resulted in compile errors. These were not discovered because many compilers ignore unused methods in templated classes, but the SYCL compiler for Aurora gave an error.

Added heyoka versions 6.0.0 & 6.1.0 (spack#47074)

4432f5a

fix use of traceback.format_exception (spack#47080)

c6bfe7c

Co-authored-by: Peter Scheibel <scheibel1@llnl.gov>

haampie and others added 16 commits October 30, 2024 18:57

verdict: new package (spack#47333)

ce78e8a

* add verdict package Co-authored-by: becker33 <becker33@users.noreply.github.com> Co-authored-by: Alec Scott <scott112@llnl.gov>

Remove trailing spaces in default YAML files (spack#47328)

ec05855

caught by `prettier`

mpidiff: new package (spack#47335)

f809b56

* mpidiff: new package * fix style with black * Add variants, docs, and examples variants. Remove options that are not really options in the build.

Docs: remove reference to pyspack (spack#47346)

6ab92b1

vecgeom: new version 1.2.9 (spack#47306)

f003d8c

optipng: add v0.7.8 (spack#47311)

89d0215

* optipng: add v0.7.8 * optipng: mv for_aarch64.patch for_aarch64_0.7.7.patch * optipng: add for_aarch64_0.7.8.patch * optipng: deprecate v0.7.7 * optipng: fix style

minio: add v2024-10-13T13-34-11Z (spack#47303)

877930c

kokkos: add cmake_lang variant, require at least one active backend (s…

275339a

…pack#43517)

nalu-wind: put bounds on yaml-cpp versions. (spack#47341)

404b1c6

extrae: update checksums, fix build (-lintl), minor modernisation (sp…

a08b4ae

…ack#47343) Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

py-ipympl: add v0.9.4 (spack#47193)

ffde309

* py-ipympl: add v0.9.4 * Add node/npm dependencies at runtime * node-js: fix build with older GCC * Change CLANG flags too * Add supported compiler versions * Deprecate older version

salome,-med,-medcoupling: new versions, new/changed variants (spack#4…

0437c53

…6576) * boost: boost.python does not support numpy@2 yet

gsl: new version 2.8 (spack#47286)

c6a1ec9

Merge branch 'develop' of https://github.com/spack/spack into feature…

baa4000

…/update_from_spack_dev_20241031

Fix openmpi package recipe (two-level-namespace option)

ceb3b82

climbfuji self-assigned this Nov 1, 2024

climbfuji added 2 commits October 31, 2024 18:43

Fix style errors in var/spack/repos/builtin/packages/fontconfig/packa…

57a28cf

…ge.py, var/spack/repos/builtin/packages/libxkbcommon/package.py, var/spack/repos/builtin/packages/openmpi/package.py

Attempt to fix failing Windows unit tests in Github actions

fee35e5

srherbener mentioned this pull request Nov 1, 2024

openmpi: add two_level_namespace variant for MacOS spack/spack#47202

Open

climbfuji added 3 commits November 1, 2024 13:03

Fix merge conflict in lib/spack/spack/compilers/oneapi.py

b6b42d7

Fix merge conflict in .github/workflows/unit_tests.yaml

75c2f0f

Disable windows workflow for repos other than spack/spack

2f31a16

climbfuji changed the title ~~WIP Feature/update from spack dev 20241031~~ Update spack-stack-dev from spack develop as of 2024/10/31 Nov 4, 2024

climbfuji mentioned this pull request Nov 4, 2024

Update spack-stack-dev from spack develop as of 2024/10/31 JCSDA/spack-stack#1363

Draft

8 tasks

Bug fix for diab-disable flags in lib/spack/spack/compilers/intel.py …

7c25b42

…and lib/spack/spack/compilers/oneapi.py: set correct version ranges

climbfuji marked this pull request as ready for review November 5, 2024 19:35

climbfuji requested review from srherbener, RatkoVasic-NOAA and AlexanderRichert-NOAA November 5, 2024 19:35

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Update spack-stack-dev from spack develop as of 2024/10/31 #482

Update spack-stack-dev from spack develop as of 2024/10/31 #482

climbfuji commented Nov 1, 2024 •

edited

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Update spack-stack-dev from spack develop as of 2024/10/31 #482

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Update spack-stack-dev from spack develop as of 2024/10/31 #482

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climbfuji commented Nov 1, 2024 • edited Loading

Description

Testing

climbfuji commented Nov 1, 2024 •

edited

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