Update spack submodule from spack/develop as of 2024/01/26 #977

climbfuji · 2024-01-29T22:33:41Z

Summary

Required updates in spack-stack for JCSDA/spack#401 (merge spack/develop as of 2024/01/26 into jcsda_emc_spack_stack). Unpin some package versions that we don't really care about (i.e. take the latest as long as it works for us).

Reviewers: Some core spack functionality changed that we use in our spack extension, therefore please take a close look at spack-ext/lib/*.

Testing

CI
Build complete spack-stack unified-dev environment on @climbfuji's macOS Monterey with [email protected] and [email protected]. Build and run a c12 GEOS-GCM test case!
Build JEDI-Skylab on @climbfuji's macOS Monterey with [email protected] and [email protected] and run small tests
Test on Discover Intel with GEOS and JEDI-Skylab
Test on Discover GNU with GEOS and JEDI-Skylab
- GEOS doesn't run - presumably due to a too old GNU compiler? Issue recorded here: GEOS-GCM on Discover with GNU - segfault in yafyaml #985
- Issues running skylab-trace-gas experiment unrelated to this PR (reported with spack-stack-1.6.0 since last week), other Skylab experiments tested ran fine
Test on AWS ParallelCluster GNU with GEOS and JEDI-Skylab
Test on AWS ParallelCluster Intel with GEOS and JEDI-Skylab
- GEOS skipped because of known problems of running GEOS with Intel on AWS ParallelCluster
- JEDI-Skylab works
Test on Gaea with UFS WM (@AlexanderRichert-NOAA)

Applications affected

All

Systems affected

Potentially all (although the changes are small) - but check in particular chained environments when using our spack stack create env --upstream functionality.

Dependencies

waiting on Merge spack/develop as of 2024/01/26 into jcsda_emc_spack_stack spack#401

Issue(s) addressed

This is the last part of compiling JEDI+GEOS with spack-stack (i.e. not using Baselibs) on more than just Discover. This PR resolves https://github.com/JCSDA-internal/AOP23/issues/33.

It also closes #918, because the update of eccodes to version 2.33.0 is done in this PR (and the update from spack develop brings the new version to our fork).

Checklist

This PR addresses one issue/problem/enhancement, or has a very good reason for not doing so.
These changes have been tested on the affected systems and applications.
All dependency PRs/issues have been resolved and this PR can be merged.

…d testing

…c/source/NewSiteConfigs.rst

…eature/update_spack_from_dev_20240126

…ommented-out version before merging, after extensive testing

…ck-stack/stack/stack_env.py

…eature/update_spack_from_dev_20240126

…s_*.yaml

…eature/update_spack_from_dev_20240126

…es.yaml, no longer exists

climbfuji

Self-review

configs/common/packages.yaml

climbfuji · 2024-01-31T18:53:37Z

spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py

@@ -271,7 +271,8 @@ def write(self):
            os.makedirs(env_pkgs_path, exist_ok=False)
            with open(os.path.join(env_repo_path, "repo.yaml"), "w") as f:
                f.write("repo:\n  namespace: envrepo")
-            repo_paths = spack.config.get("repos", scope=spack.config.default_list_scope())
+            # DH* ???
+            repo_paths = spack.config.get("repos", scope=None) # scope=spack.config.default_list_scope())


I think this works - need to test chained environments (use spack stack create env --upstream ...).

This looks okay (remember to test with --modify-pkg option). Just using repo_paths = spack.config.get("repos") with no scope argument seems to give the right behavior when I tested it just now.

Then let me change it to that, thanks!

Done in 05d44b4 - CI does test chained environments, so we will see.

.github/workflows/macos-ci-x86_64.yaml

climbfuji · 2024-02-07T14:39:22Z

configs/common/modules_lmod.yaml

@@ -285,5 +285,3 @@ modules:
      - PKG_CONFIG_PATH
      lib64/pkgconfig:
      - PKG_CONFIG_PATH
-      '':
-      - CMAKE_PREFIX_PATH


This was a duplicate, spack sets this variable automatically

climbfuji · 2024-02-07T14:39:26Z

configs/common/modules_tcl.yaml

@@ -284,5 +284,3 @@ modules:
      - PKG_CONFIG_PATH
      lib64/pkgconfig:
      - PKG_CONFIG_PATH
-      '':


srherbener

I am building unified-env on my arm64 based Mac, and when I ran the list of spack find commands, I got this in my site/packages.yaml file:

python:
     externals:
     - spec: [email protected]+bz2+crypt+ctypes+dbm+lzma+nis+pyexpat~pythoncmd+readline+sqlite3+ssl+t    ix+tkinter+uuid+zlib
       prefix: /usr

It didn't impact the python spec/requirement in that after concretizing spack decided to build [email protected] with no duplicates of the python spec. However, when I commented out the above section from the site/packages.yaml file, the spec for fms changed from 32-bit to 64-bit. Very strange, but I thought I would bring it to your attention in case it is of significance.

configs/common/packages.yaml

srherbener · 2024-02-07T16:07:23Z

doc/source/NewSiteConfigs.rst

@@ -249,7 +249,7 @@ Remember to activate the ``lua`` module environment and have MacTeX in your sear
   # Check your clang version then add it to your site compiler config.
   clang --version
   spack config add "packages:all:compiler:[apple-clang@YOUR-VERSION]"
-   spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+   spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"


This looks like a good update too. Perhaps this will help with the MacOS build issue #971?

.github/workflows/macos-ci-x86_64.yaml

climbfuji · 2024-02-07T16:44:43Z

I am building unified-env on my arm64 based Mac, and when I ran the list of spack find commands, I got this in my site/packages.yaml file:
python:
     externals:
     - spec: [email protected]+bz2+crypt+ctypes+dbm+lzma+nis+pyexpat~pythoncmd+readline+sqlite3+ssl+t    ix+tkinter+uuid+zlib
       prefix: /usr
It didn't impact the python spec/requirement in that after concretizing spack decided to build [email protected] with no duplicates of the python spec. However, when I commented out the above section from the site/packages.yaml file, the spec for fms changed from 32-bit to 64-bit. Very strange, but I thought I would bring it to your attention in case it is of significance.

We shouldn't be finding any external Python. If that's the case, then we need to exclude that from the spack external find command or ask spack external find to find explicitly listed packages only.

Regarding gettext, if you look further down in the CI script we still find it, but we need to use the full path to it on the Intel Macs. Otherwise, spack sanitizes the path because it thinks it is a system path. I think this only applies to the CI runner, though.

climbfuji · 2024-02-07T16:45:47Z

And as discussed yesterday, I've tested JEDI-Skylab with [email protected] extensively.

srherbener

Thanks for the quick responses. All looks good!

climbfuji · 2024-02-07T16:52:10Z

Thanks for the quick responses. All looks good!

Thanks for your review. I am going to add the --exclude python in the documentation and CI builds, because I am seeing external Python packages being found on new sites, too. Thanks for spotting that!

…Github CI scripts

climbfuji · 2024-02-07T16:54:27Z

Thanks for the quick responses. All looks good!

Thanks for your review. I am going to add the --exclude python in the documentation and CI builds, because I am seeing external Python packages being found on new sites, too. Thanks for spotting that!

Done in 0ade34d

…os)' in spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py

climbfuji · 2024-02-07T21:27:33Z

CI passed. I am going to merge this and then work on removing mysql from the default requirements on the HPCs and non-JCSDA user systems next.

climbfuji added 7 commits January 26, 2024 17:03

Update .gitmodules and submodule pointer for spack for code review an…

3066b6b

…d testing

For spack-ext/lib: env.env_file_config_scope_name() --> env.scope_name

2366a91

Update macOS site packages.yaml and corresponding documentation in do…

8987394

…c/source/NewSiteConfigs.rst

Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

f55f74c

…eature/update_spack_from_dev_20240126

Unpin many package versions in configs/common/packages.yaml; remove c…

7f4fb06

…ommented-out version before merging, after extensive testing

Replace default_list_scope() with None in spack-ext/lib/jcsda-emc/spa…

064ea42

…ck-stack/stack/stack_env.py

Update submodule pointer for spack

da87ff5

climbfuji mentioned this pull request Jan 29, 2024

Merge spack/develop as of 2024/01/26 into jcsda_emc_spack_stack JCSDA/spack#401

Merged

climbfuji self-assigned this Jan 29, 2024

climbfuji added the INFRA JEDI Infrastructure label Jan 29, 2024

climbfuji added 3 commits January 29, 2024 20:27

Update openmpi version for macOS CI runs

a521bd0

Skip external gettext for macOS CI

edc602a

Mark curl as non-buildable for Ubuntu CI to avoid duplicate packages

3e568fd

climbfuji changed the title ~~WIP Feature/update spack from dev 20240126~~ Update spack submodule from spack/develop as of 2024/01/26 Jan 31, 2024

climbfuji marked this pull request as ready for review January 31, 2024 18:53

climbfuji requested review from AlexanderRichert-NOAA, ulmononian and RatkoVasic-NOAA January 31, 2024 18:53

climbfuji mentioned this pull request Jan 31, 2024

Loading module py-gitpython AND py-cylc-uiserver AND py-cylc-rose after update from spack develop as of 2024/01/26 destroys macOS user environment #980

Closed

climbfuji added 8 commits February 1, 2024 08:44

Revert many updates to configs/common/packages.yaml

7bc5302

Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

11fdc06

…eature/update_spack_from_dev_20240126

Revert many more updates in .github, configs and doc

f57dd8c

Fix macOS Intel CI by adding gettext with correct (non-sys) path

60fa515

Avoid duplicate setting of CMAKE_PREFIX_PATH in configs/common/module…

3aa0f62

…s_*.yaml

Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

ff91325

…eature/update_spack_from_dev_20240126

Update submodule pointer for spack

5c94aba

Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

15f5dab

…eature/update_spack_from_dev_20240126

This was referenced Feb 6, 2024

Segfault in GEOS-GCM with Intel on AWS ParallelCluster #988

Closed

Upgrade the GSI to Spack-Stack version 1.6.0 NOAA-EMC/GSI#684

Merged

Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

8bd29c7

…eature/update_spack_from_dev_20240126

climbfuji added 2 commits February 6, 2024 20:33

Remove variant '+download_boost' for mysql from configs/common/packag…

0c40292

…es.yaml, no longer exists

Revert .gitmodules and update submodule pointer for spack

290ff2b

climbfuji commented Feb 7, 2024

View reviewed changes

climbfuji requested review from mathomp4 and srherbener February 7, 2024 14:41

srherbener reviewed Feb 7, 2024

View reviewed changes

srherbener approved these changes Feb 7, 2024

View reviewed changes

Add '--exclude python' to 'spack external find' in documentation and …

0ade34d

…Github CI scripts

climbfuji added 2 commits February 7, 2024 10:37

Update .github/workflows/macos-ci-x86_64.yaml

1247e9b

Change 'spack.config.get(repos, scope=None)' to 'spack.config.get(rep…

05d44b4

…os)' in spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py

ulmononian approved these changes Feb 7, 2024

View reviewed changes

climbfuji merged commit b7b36e0 into JCSDA:develop Feb 7, 2024
7 checks passed

climbfuji deleted the feature/update_spack_from_dev_20240126 branch February 7, 2024 21:29

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Update spack submodule from spack/develop as of 2024/01/26 #977

Update spack submodule from spack/develop as of 2024/01/26 #977

climbfuji commented Jan 29, 2024 •

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Update spack submodule from spack/develop as of 2024/01/26 #977

Update spack submodule from spack/develop as of 2024/01/26 #977

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climbfuji commented Jan 29, 2024 • edited Loading

Summary

Testing

Applications affected

Systems affected

Dependencies

Issue(s) addressed

Checklist

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climbfuji commented Feb 7, 2024

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