Axom: bring in changes from axom repo by white238 · Pull Request #32643 · spack/spack

white238 · 2022-09-13T21:43:17Z

It has been a while since I pulled in the updates from the Axom repo.

This mainly adds HIP support and uses a Spack's BLT instead of the internal submodule.

This also removes the the need to pull submodules with the source. The data submodule is particularly large.

white238 · 2022-09-13T22:03:23Z

@spackbot fix style

spackbot-app · 2022-09-13T22:04:01Z

Let me see if I can fix that for you!

spackbot-app · 2022-09-13T22:05:44Z

I was able to run spack style --fix for you!

spack style --fix

==> Running style checks on spack
  selected: isort, mypy, black, flake8
==> Modified files
  var/spack/repos/builtin/packages/axom/package.py
==> Running isort checks
  isort checks were clean
==> Running mypy checks
Success: no issues found in 558 source files
  mypy checks were clean
==> Running black checks
reformatted var/spack/repos/builtin/packages/axom/package.py
All done! ✨ 🍰 ✨
1 file reformatted.
  black checks were clean
==> Running flake8 checks
var/spack/repos/builtin/packages/axom/package.py:283: [E501] line too long (190 > 99 characters)
var/spack/repos/builtin/packages/axom/package.py:299: [E501] line too long (285 > 99 characters)
var/spack/repos/builtin/packages/axom/package.py:303: [E501] line too long (182 > 99 characters)
  flake8 found errors

Keep in mind that I cannot fix your flake8 or mypy errors, so if you have any you'll need to fix them and update the pull request. If I was able to push to your branch, if you make further changes you will need to pull from your updated branch before pushing again.

I've updated the branch with isort fixes.

tldahlgren

I have not reviewed the rest of this PR but the suggested change will at least help resolve the pipeline stack failures.

var/spack/repos/builtin/packages/axom/package.py

Co-authored-by: Tamara Dahlgren <[email protected]>

white238 · 2022-09-28T03:41:13Z

I have tested this in Axom's large set of specs across many LC machines. It should be ready to go.

tldahlgren

Other than my question and aversion to hard-coded paths, this LGTM.

@scheibelp Did you want to review this package, especially regarding the cray-specific changes?

var/spack/repos/builtin/packages/axom/package.py

white238 · 2022-10-03T19:11:20Z

Other than my question and aversion to hard-coded paths, this LGTM.

@scheibelp Did you want to review this package, especially regarding the cray-specific changes?

This has been addressed by just removing it

becker33 · 2022-10-03T19:12:45Z

var/spack/repos/builtin/packages/axom/package.py

    variant("tools", default=True, description="Build tools")

+    # Hard requirement after Axom 0.6.1
    variant("cpp14", default=True, description="Build with C++14 support")


We should make this variant only appear for axom@:0.6.0

variant("cpp14", default=True, when="@:0.6.0", ...)

doesn't need to be part of this PR

becker33 · 2022-10-03T19:16:27Z

var/spack/repos/builtin/packages/axom/package.py

            entries.append(cmake_cache_path("DEVTOOLS_ROOT", devtools_root))

-            # Only turn on clangformat support if devtools is on
+        if "+devtools" in spec and "toss_4" not in self._get_sys_type(spec):


Short term hack to support a problem specific to LC systems

* bring in changes from axom repo Co-authored-by: white238 <[email protected]> Co-authored-by: Tamara Dahlgren <[email protected]>

…(py-dendropy, py-phylophlan, py-pkgconfig) (#32936) * added metaphlan v4, cleaned up phylophlan * added iqtree2 * fixed phylophlan, builds now * changed config.yaml to default * fixed style * py-jsonschema: add 4.16.0 and new package py-hatch-fancy-pypi-readme (#32929) * acfl: add v22.1 (#32915) Co-authored-by: Annop Wongwathanarat <[email protected]> * Fixup errors introduced by Clingo Pr: (#32905) * re2c depends on cmake on Windows * Winbison properly added to bootstrap package search list * Set CMAKE_HIP_ARCHITECTURES with the value of amdgpu_target (#32901) * libtiff: default to +zlib+jpeg (#32945) * octave: add version 7.2.0 (#32943) * simgrid new releases (#32920) * [rocksdb] Added rtti variant (#32918) * rvs binary path updated for 5.2 rocm release (#32892) * Add checksum for py-pytest-runner 6.0.0 (#32957) * py-einops: add v0.5.0 (#32959) * Replace repo with the NVIDIA one (#32951) * Add checksum for py-tomli 2.0.1 (#32949) * QMCPACK: add @3.15.0 (#32931) * Tidied up configure arguments to use special spack autotools features. (#32930) * casper: old domain fell off, adding github repo (#32928) * unifyfs: pin mercury version; add boost variant (#32911) Mercury has a new version (v2.2) releasing soon that UnifyFS does not build with and hasn't been tested with. This pins UnifyFS to the last version of Mercury used/tested. Add a variant to avoid building/using boost Append -std=gnu99 to cflags if building with gcc@4. Needed for mochi-margo to compile * trilinos: constrain superlu-dist version (#32889) * trilinos: constrain superlu-dist version for 13.x * syntax * FEniCSx: Updates for 0.5.1 (#32665) * Updates for DOLFINx 0.5.1 and associated packages * xtensor needed on anything less than main * Switch back to Python 3.7 minimum. * Might be good to point out in our README how to fix Python version? * Fix basix, xtensor dep * Add numba feature * Fix checksum * Make slepc optional Co-authored-by: Tamara Dahlgren <[email protected]> * simgrid: add variant and remove flag (#32797) * simgrid: remove std c++11 flag * simgrid: add msg variant * Axom: bring in changes from axom repo (#32643) * bring in changes from axom repo Co-authored-by: white238 <[email protected]> Co-authored-by: Tamara Dahlgren <[email protected]> * Add checksum for py-pyparsing 3.0.9 (#32952) * rdma-core: fix syntax for external discoverability (#32962) * Add checksum for py-flatbuffers 2.0.7 (#32955) * amrex: add v22.10 (#32966) * Remove CMakePackage.define alias from most packages (#32950) * Bug fix for `ca-certificates-mozilla/package.py` to enable `spack install --source` (#32953) * made suggested changes to iqtree2, py-dendropy, py-metaphlan, and py-pkgconfig. Poetry install still broken * reverted py-pkgconfig deps to poetry-core * made iqtree2 less dedundant, changes to py-dendropy and py-pkgconfig deps Co-authored-by: Manuela Kuhn <[email protected]> Co-authored-by: Annop Wongwathanarat <[email protected]> Co-authored-by: Annop Wongwathanarat <[email protected]> Co-authored-by: John W. Parent <[email protected]> Co-authored-by: Auriane R <[email protected]> Co-authored-by: Adam J. Stewart <[email protected]> Co-authored-by: Kai Torben Ohlhus <[email protected]> Co-authored-by: Vinícius <[email protected]> Co-authored-by: Matthieu Dorier <[email protected]> Co-authored-by: renjithravindrankannath <[email protected]> Co-authored-by: iarspider <[email protected]> Co-authored-by: Paul R. C. Kent <[email protected]> Co-authored-by: Brian Van Essen <[email protected]> Co-authored-by: snehring <[email protected]> Co-authored-by: Cameron Stanavige <[email protected]> Co-authored-by: Cody Balos <[email protected]> Co-authored-by: Jack S. Hale <[email protected]> Co-authored-by: Tamara Dahlgren <[email protected]> Co-authored-by: Lucas Nesi <[email protected]> Co-authored-by: Chris White <[email protected]> Co-authored-by: white238 <[email protected]> Co-authored-by: Martin Pokorny <[email protected]> Co-authored-by: Weiqun Zhang <[email protected]> Co-authored-by: Massimiliano Culpo <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]>

spackbot-app bot added conflicts dependencies new-version update-package labels Sep 13, 2022

tldahlgren requested changes Sep 15, 2022

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var/spack/repos/builtin/packages/axom/package.py Outdated Show resolved Hide resolved

tldahlgren requested a review from scheibelp September 15, 2022 00:18

alalazo assigned scheibelp and tldahlgren Sep 20, 2022

white238 and others added 4 commits September 27, 2022 20:40

bring in changes from axom repo

47ce563

[@spackbot] updating style on behalf of white238

ed8dc3d

fix long lines

dcdc168

Update var/spack/repos/builtin/packages/axom/package.py

e2a3441

Co-authored-by: Tamara Dahlgren <[email protected]>

white238 force-pushed the task/white238/update_axom branch from 34df825 to e2a3441 Compare September 28, 2022 03:40

white238 added 2 commits September 27, 2022 22:11

guard path that may not exist

764dc1e

fix indentation

2d8b135

white238 requested a review from tldahlgren September 29, 2022 20:38

tldahlgren previously approved these changes Sep 29, 2022

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var/spack/repos/builtin/packages/axom/package.py Outdated Show resolved Hide resolved

var/spack/repos/builtin/packages/axom/package.py Outdated Show resolved Hide resolved

remove hardcoded crayftn

46f73e2

white238 dismissed tldahlgren’s stale review via 46f73e2 September 30, 2022 01:34

white238 added 3 commits September 29, 2022 18:38

remove extra format

de035b4

remove extra format

4eba30c

remove extra format

f72b554

Merge branch 'develop' into task/white238/update_axom

4778d6d

becker33 approved these changes Oct 3, 2022

View reviewed changes

becker33 enabled auto-merge (squash) October 3, 2022 19:20

tldahlgren assigned becker33 Oct 3, 2022

becker33 merged commit 9225f4f into develop Oct 3, 2022

becker33 deleted the task/white238/update_axom branch October 3, 2022 20:02

luke-dt pushed a commit to dantaslab/spack that referenced this pull request Oct 4, 2022

Axom: bring in changes from axom repo (spack#32643)

7efb9ea

* bring in changes from axom repo Co-authored-by: white238 <[email protected]> Co-authored-by: Tamara Dahlgren <[email protected]>

alalazo mentioned this pull request Feb 20, 2023

axom/conduit: allow use of hdf5+cxx+fortran #24459

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Axom: bring in changes from axom repo#32643

Axom: bring in changes from axom repo#32643
becker33 merged 11 commits intodevelopfrom
task/white238/update_axom

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