Fix HDF5+mpi~fortran by s-sajid-ali · Pull Request #35400 · spack/spack

s-sajid-ali · 2023-02-08T17:04:01Z

Fixes #35377

spackbot-app · 2023-02-08T17:04:45Z

@byrnHDF can you review this PR?

This PR modifies the following package(s), for which you are listed as a maintainer:

hdf5

tldahlgren

LGTM

tldahlgren · 2023-02-10T22:48:23Z

@spackbot run pipeline

spackbot-app · 2023-02-10T22:48:30Z

I've started that pipeline for you!

hyoklee · 2023-02-13T16:23:14Z

@spackbot run pipeline

spackbot-app · 2023-02-13T16:23:23Z

I've started that pipeline for you!

s-sajid-ali · 2023-02-13T18:10:35Z

Pipeline errors seem to be related to WRF checksums that should have been fixed by #35401.

s-sajid-ali · 2023-02-14T18:01:44Z

@spackbot run pipeline

spackbot-app · 2023-02-14T18:01:51Z

I've started that pipeline for you!

s-sajid-ali · 2023-02-14T19:07:13Z

The latest pipeline still has wrf errors and an unrelated pfunit error.

spackbot-app · 2023-02-16T21:34:13Z

I've started that pipeline for you!

s-sajid-ali · 2023-02-17T18:10:49Z

@tldahlgren : Rebasing onto develop fixed the wrf errors, but now there are new errors pertaining to meson/py-docutils/parmets/vtk-m/.... While there are some build errors labelled as hdf5 build errors, the logs show that the errors occurred when building cmake (log).

tldahlgren · 2023-02-21T21:26:51Z

We're having problems with the pipeline builds. Hopefully this gets resolved soon as the ci/gitlab-ci checks are required.

s-sajid-ali · 2023-02-22T16:06:27Z

@spackbot run pipeline

spackbot-app · 2023-02-22T16:06:45Z

I've started that pipeline for you!

lrknox · 2023-02-22T20:25:50Z

We're having problems with the pipeline builds. Hopefully this gets resolved soon as the ci/gitlab-ci checks are required.

I saw this warning and error in an HDF5-1.14.0 build for

We're having problems with the pipeline builds. Hopefully this gets resolved soon as the ci/gitlab-ci checks are required.

I saw this warning and error in an HDF5 1.14.0 build for radius-aws-aarch64-build:
==> Warning: 'target=graviton2' is deprecated, use 'target=neoverse_n1' instead
==> Error: Unable to copy files (/tmp/root/spack-stage/spack-stage-hdf5-1.14.0-753ppmfvdqa6dcskvcahonprbmjp3ytj/spack-build-out.txt) to artifacts /builds/spack/spack/jobs_scratch_dir/logs due to exception: No such file or directory: '/tmp/root/spack-stage/spack-stage-hdf5-1.14.0-753ppmfvdqa6dcskvcahonprbmjp3ytj/spack-build-out.txt'

The warning message seems to appear in many of the failing builds in the pipeline. I also noticed in some recent builds on one of our local machines that spack install --keep-stage doesn't seem to be putting anything in the stage directory lately. I don't know what should be doen to change from graviton2 to neovers_n1, though.

s-sajid-ali · 2023-02-22T23:45:18Z

The issue with that particular CI run seems to be a build error for cmake : https://gitlab.spack.io/spack/spack/-/jobs/5732974#L220.

s-sajid-ali · 2023-03-08T15:29:38Z

Can this be merged now @alalazo / @eugeneswalker ?

alalazo · 2023-03-08T15:46:54Z

@s-sajid-ali I think this PR is just waiting for CI to finish successfully. Then it'll be auto-merged.

s-sajid-ali · 2023-03-08T15:53:05Z

@spackbot run pipeline

spackbot-app · 2023-03-08T15:53:15Z

I've started that pipeline for you!

alalazo · 2023-03-08T16:07:12Z

@s-sajid-ali Just so you know: by restarting an ongoing CI, you probably gained a longer waiting time 😬 (every pipeline that wasn't finished restarted the same builds from scratch).

s-sajid-ali · 2023-03-08T18:26:34Z

@alalazo Thanks for the information.

The new CI pipeline has errors for ml-linux-x86_64-cpu-pr-build/ml-linux-x86_64-cuda-pr-build , for py-tensorflow which seems unrelated to this PR. Is this a known issue?

tldahlgren · 2023-03-09T19:05:41Z

@spackbot run pipeline

spackbot-app · 2023-03-09T19:05:47Z

I've started that pipeline for you!

s-sajid-ali · 2023-03-10T17:26:21Z

@spackbot run pipeline

spackbot-app · 2023-03-10T17:26:28Z

I've started that pipeline for you!

s-sajid-ali · 2023-03-10T18:37:07Z

Current CI failures are (per this run):

e4s-power-pr-build:

h5bench/iygcoon 1.3 [email protected] linux-ubuntu20.04-ppc64le E4S Power
Reason:

  Created fresh repository.
  fatal: unable to access 'https://gitlab.spack.io/spack/spack.git/': Could not resolve host: gitlab.spack.io
  Uploading artifacts for failed job 00:02 
  Uploading artifacts...
  WARNING: jobs_scratch_dir/logs: no matching files   
  WARNING: jobs_scratch_dir/reproduction: no matching files 
  WARNING: jobs_scratch_dir/tests: no matching files 
  WARNING: jobs_scratch_dir/user_data: no matching files 
  ERROR: No files to upload                          
  Cleaning up project directory and file based variables 00:01
  ERROR: Job failed: exit code 1

warpx/yi62tyc 23.03 [email protected] linux-ubuntu20.04-ppc64le E4S Power
Reason: Same as above
dray/eg4gdf4 0.1.8 [email protected] linux-ubuntu20.04-ppc64le E4S Power
Reason: Same as above

ml-linux-x86_64-cpu-pr-build:

py-tensorflow/sbcleax 2.10.1 [email protected] linux-amzn2-x86_64_v3 Machine Learning
Reason:

# Configuration: 70d5859fdef852abbc7e778d3e97b9f1bece7a530d593fd25d634060c4c992fa
# Execution platform: @local_execution_config_platform//:platform
gcc: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 2342.864s, Critical Path: 334.01s
INFO: 9650 processes: 1140 internal, 8510 local.
FAILED: Build did NOT complete successfully

ml-linux-x86_64-cuda-pr-build:

py-tensorflow/7rm7vw4 2.10.1 [email protected] linux-amzn2-x86_64_v3 Machine Learning
Reason:

# Configuration: d236e8123202fbb1dc3edda1c1dfc704400c275ba451bbe641d3e897f49f1c21
# Execution platform: @local_execution_config_platform//:platform

 Server terminated abruptly (error code: 14, error message: 'Connection reset by peer', log file: '/tmp/spackq_v06wxb/b79c0385198eb909c6e134607174ccf8/server/jvm.out')

The py-tensorflow builds are being repeated in the CI after the first set of failures.

eugeneswalker · 2023-03-10T19:35:17Z

The power failures were a node issue, it has been fixed now. Re-running pipeline and they will finish: @spackbot run pipeline

spackbot-app · 2023-03-10T19:35:25Z

I've started that pipeline for you!

s-sajid-ali · 2023-03-10T21:36:08Z

Thanks @eugeneswalker !

The following failures with py-tensorflow remain ( from the latest run):

ml-linux-x86_64-cpu-pr-build:

py-tensorflow/sbcleax 2.10.1 [email protected] linux-amzn2-x86_64_v3 Machine Learning
Reason:

# Configuration: f8b41c6b368834d97a9badbd57c6bd2ce355775d99d313e59e55944349742ade
# Execution platform: @local_execution_config_platform//:platform
gcc: internal compiler error: Killed (program cc1plus) 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 2220.264s, Critical Path: 707.33s
INFO: 8251 processes: 1132 internal, 7119 local.
FAILED: Build did NOT complete successfully

ml-linux-x86_64-cuda-pr-build:

py-tensorflow/7rm7vw4 2.10.1 [email protected] linux-amzn2-x86_64_v3 Machine Learning
Reason:

# Configuration: 93b58564f565042f4c7209d19a3417f306b5df5b1d476b814880e5058b3e09e2
# Execution platform: @local_execution_config_platform//:platform
gcc: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 4797.839s, Critical Path: 771.12s
INFO: 29045 processes: 9590 internal, 19455 local.
FAILED: Build did NOT complete successfully

Pinging py-tensorflow maintainers regarding the CI failures: @adamjstewart / @aweits / @pradyunsg

kwryankrattiger · 2023-03-10T21:50:22Z

These should be fixed with #35996

s-sajid-ali · 2023-03-13T13:35:40Z

@spackbot run pipeline

spackbot-app · 2023-03-13T13:35:42Z

I'm sorry, gitlab does not have your latest revision yet, I can't run that pipeline for you right now.

One likely possibility is that your PR pipeline has been temporarily deferred, in which case, it is awaiting a develop pipeline, and will be run when that finishes.

Please check the gitlab commit status message to see if more information is available.

Details

pr head: a31d005, gitlab commit parents: ['a5b8066', 'a8bfb0f']

s-sajid-ali · 2023-03-14T21:02:10Z

@spackbot run pipeline

spackbot-app · 2023-03-14T21:02:16Z

I've started that pipeline for you!

* HDF5+mpi~fortran * fix style

ref. spack#35400

spackbot-app bot added the update-package label Feb 8, 2023

spackbot-app bot requested review from brtnfld, gheber, hyoklee, lkurz and lrknox February 8, 2023 17:04

byrnHDF previously approved these changes Feb 8, 2023

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hyoklee previously approved these changes Feb 8, 2023

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tldahlgren previously approved these changes Feb 8, 2023

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tldahlgren enabled auto-merge (squash) February 8, 2023 18:46

tldahlgren assigned hyoklee and tldahlgren Feb 8, 2023

lrknox previously approved these changes Feb 9, 2023

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tldahlgren assigned lrknox Feb 21, 2023

eugeneswalker approved these changes Mar 5, 2023

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lrknox approved these changes Mar 5, 2023

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tldahlgren assigned alalazo and eugeneswalker Mar 6, 2023

tldahlgren approved these changes Mar 6, 2023

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Merge branch 'develop' into sajid/hdf5_mpi_fortran

a8bfb0f

Merge branch 'develop' into sajid/hdf5_mpi_fortran

a31d005

tldahlgren merged commit 9a12540 into spack:develop Mar 14, 2023

s-sajid-ali deleted the sajid/hdf5_mpi_fortran branch March 15, 2023 16:44

cnegre pushed a commit to cnegre/spack that referenced this pull request Mar 20, 2023

Fix HDF5+mpi~fortran (spack#35400)

ba5952e

* HDF5+mpi~fortran * fix style

jmcarcell pushed a commit to key4hep/spack that referenced this pull request Apr 13, 2023

CI: Fix timeout for VisIt and ParaView (spack#35787)

c4be399

ref. spack#35400

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