{bio}[GCC/11.2.0] Raven v1.8.1 w/ Python 3.9.6 by ItIsI-Orient · Pull Request #15833 · easybuilders/easybuild-easyconfigs

ItIsI-Orient · 2022-07-08T12:05:06Z

(created using eb --new-pr)

boegel

@ItIsI-Orient The tests aren't happy because you should set download_dep_fail and use_pip via exts_default_options (as opposed to in the extension itself in exts_list), like so:

exts_default_options = {
    'download_dep_fail': True,
    'use_pip': True,
}

(that's just a style thing, functionally there's no difference)

…ding

ItIsI-Orient · 2022-07-18T14:31:58Z

Test report by @ItIsI-Orient
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3701.slaking.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 3.6.8
See https://gist.github.com/0e3296e4f9ee74dc5ba6142219dd4442 for a full test report.

bedroge · 2022-07-18T14:52:34Z

Test report by @bedroge
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.4
See https://gist.github.com/78b729178009076c6956e810e7133941 for a full test report.

bedroge · 2022-07-18T14:52:51Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
pg-interactive.hpc.rug.nl - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 3.6.8
See https://gist.github.com/33f962162202fdcf123c663958711b4a for a full test report.

bedroge · 2022-07-18T14:55:04Z

The installation of the Python extension fails on my Ubuntu system:

  [25/26] Linking CXX static library lib/libraven.a
  [26/26] Linking CXX shared module lib/ravenpy.cpython-310-x86_64-linux-gnu.so
  error: [Errno 2] No such file or directory: '/data/eb/tmp/eb-aklw6_1o/pip-req-build-6c3ee0ie/build/lib.linux-x86_64-3.9/ravenpy_build/lib/ravenpy.cpython-39-x86_64-linux-gnu.so'

It looks like it's somehow mixing up the Python versions from the OS (3.10) and the module (3.9)...

  -- Found PythonInterp: /usr/bin/python3.10 (found version "3.10.4")
  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so

bedroge · 2022-07-20T09:42:23Z

I've debugged this a bit more, and the issue seems to be caused by the way CMake is trying to find Python. This behavior has been changed in CMake 3.15: https://cmake.org/cmake/help/latest/policy/CMP0094.html#policy:CMP0094
With older versions/policies of CMake, it would just look for the newest Python it could find (and since my Ubuntu has Python 3.10, it prefers that one), with newer ones the location is preferred. We do use a newer CMake for this easyconfig, but because Raven's CMakeLists.txt has cmake_minimum_required(VERSION 3.11), it still falls back to the old policy. We can change this by either patching that line in CMakeLists.txt, or by explicitly enabling the new policy in setup.py; I'd prefer the latter. On top of that, we should also make sure that pybind uses CMake's FindPython functionality by setting PYBIND11_FINDPYTHON=ON.

Finally, I see that the installation pulls in some dependencies, see:
https://github.com/lbcb-sci/raven/blob/1.8.1/Raven.deps.cmake
It would be cleaner if we would list these as dependencies in the easyconfig. For most(/all?) of them, easyconfigs already seem to exist, they may only require a version bump.

ItIsI-Orient · 2022-07-20T13:15:19Z

Will take a look into that.

Also I am not sure how to enable the new policy in setup.py, could you point me in the right direction about solving this one?

boegel · 2022-08-08T13:36:52Z

Will take a look into that.

Also I am not sure how to enable the new policy in setup.py, could you point me in the right direction about solving this one?

@ItIsI-Orient Via -DPython3_FIND_STRATEGY I guess, see https://cmake.org/cmake/help/latest/policy/CMP0094.html ?

boegel · 2023-01-02T13:25:16Z

We fixed a very similar problem with the Python being used for VTK in #16741 via -DPython3_EXECUTABLE, which we should also use here (and actually everywhere where CMake is being used and Python is included as a dependency, so in the CMakeMake easyblock, but that's a big hammer...)

ItIsI-Orient · 2023-01-04T17:46:04Z

Test report by @ItIsI-Orient
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3703.slaking.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 3.6.8
See https://gist.github.com/89f3570fd5c99e45fc384ccf907537b7 for a full test report.

ItIsI-Orient · 2023-01-04T21:56:26Z

@bedroge Could you please test, whether the issue you had is resolved?

bedroge · 2023-01-05T12:29:40Z

Test report by @bedroge
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.6
See https://gist.github.com/206dd0cc6458400f3d2af95b759d14b0 for a full test report.

bedroge · 2023-01-05T12:31:07Z

This doesn't seem to solve the issue, as it's only passed to the build of Raven itself, while the issue pops up while RavenPy is being built. In order to pass it to that (CMake) build as well, I guess we have to modify the setup.py (e.g. using something like what I used in a previous suggestion here: #15833 (review)), which also calls cmake with some predefined arguments.

boegel · 2023-02-24T15:39:17Z

@boegelbot please test @ generoso

boegelbot · 2023-02-24T15:40:11Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=15833 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_15833 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10358

Test results coming soon (I hope)...

Details

- notification for comment with ID 1443865533 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegel · 2023-02-24T15:41:36Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3125.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/7c1b0a19f7e28bf2de4510f47adb7997 for a full test report.

boegelbot · 2023-02-24T15:42:38Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/0324f014d74381b5aa05bb00934e4c0a for a full test report.

boegel · 2023-02-24T16:30:09Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-02-24T16:32:08Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=15833 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_15833 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2255

Test results coming soon (I hope)...

Details

- notification for comment with ID 1443963056 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-02-24T16:33:04Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/987b445944ed55f5a8d4b8cbd2714493 for a full test report.

requested changes made

…asyconfigs into 20220708140501_new_pr_Raven181

bedroge · 2023-02-28T09:27:59Z

Test report by @bedroge
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.6
See https://gist.github.com/d0c9cb1ee0f20f8d7c3a953d93174ca6 for a full test report.

bedroge · 2023-02-28T09:37:57Z

@boegel looks like your raw string from commit 0678a00 broke things?

boegel · 2023-03-22T09:13:01Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-03-22T09:17:10Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=15833 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_15833 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2410

Test results coming soon (I hope)...

Details

- notification for comment with ID 1479164900 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-03-22T09:18:45Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/bd53821c5440f29074f10a5017677173 for a full test report.

boegel · 2023-03-22T09:22:28Z

@boegelbot please test @ generoso

boegel · 2023-03-22T09:24:23Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3133.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/acdb3455fc6d79d09e96b1e65a79b926 for a full test report.

boegelbot · 2023-03-22T09:25:13Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=15833 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_15833 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10540

Test results coming soon (I hope)...

Details

- notification for comment with ID 1479189975 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-03-22T09:27:44Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/5a1e2a033c4df58889057f5fab7236d0 for a full test report.

boegel

lgtm

boegel · 2023-03-22T10:03:01Z

Going in, thanks @ItIsI-Orient!

adding easyconfigs: Raven-1.8.1-GCC-11.2.0.eb

a7ac8d3

ItIsI-Orient mentioned this pull request Jul 8, 2022

Raven vscentrum/vsc-software-stack#6

Closed

3 tasks

Orient added 3 commits July 8, 2022 14:11

Fixed sanity_check_paths

4c1f146

Added new line to the end of file

50a3d6b

Added checksums

59e6754

easybuilders deleted a comment from boegelbot Jul 9, 2022

boegel added the new label Jul 9, 2022

boegel added this to the 4.x milestone Jul 9, 2022

boegel requested changes Jul 9, 2022

View reviewed changes

Orient added 2 commits July 12, 2022 17:00

Added exts_default_options

81692ca

Specified the maximum number of concurrent processes to use when buil…

ac94590

…ding

bedroge previously requested changes Jul 18, 2022

View reviewed changes

Comment thread easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb Outdated

Added sanity check for binary

f05a609

bedroge reviewed Jul 20, 2022

View reviewed changes

Comment thread easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb

ItIsI-Orient marked this pull request as draft August 9, 2022 08:44

easybuilders deleted a comment from boegelbot Jan 2, 2023

ItIsI-Orient marked this pull request as ready for review January 4, 2023 16:13

Fixed raven using highest version on Python found

5c71bb8

use better way to run 'pip check' in Raven easyconfig

438320f

use raw string in Raven easyconfig

0678a00

boegel previously approved these changes Feb 24, 2023

View reviewed changes

boegel modified the milestones: 4.x, next release (4.7.1?) Feb 24, 2023

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

f83198e

…asyconfigs into 20220708140501_new_pr_Raven181

boegel modified the milestones: next release (4.7.1), release after 4.7.1 Mar 17, 2023

fix preinstallopts for ravenpy extension in Raven easyconfig

0125ffc

boegel dismissed their stale review via 0125ffc March 22, 2023 09:11

boegel approved these changes Mar 22, 2023

View reviewed changes

boegel merged commit 9fd2699 into easybuilders:develop Mar 22, 2023

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