{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 #17309

sassy-crick · 2023-02-13T11:03:42Z

(created using eb --new-pr)

Requires:

PR {vis}[GCCcore/11.3.0] motif v2.3.8 #17308

boegelbot · 2023-02-13T11:29:50Z

@sassy-crick: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/4162756804
Output from first failing test suite run:

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 326, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: motif/2.3.8-foss-2022a (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 313, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: motif/2.3.8-foss-2022a (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 853, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: motif/2.3.8-foss-2022a (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 16394 tests in 753.258s

FAILED (errors=3)
ERROR: Not all tests were successful

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Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

boegelbot · 2023-02-13T14:30:11Z

@sassy-crick: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/4164053635
Output from first failing test suite run:

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 326, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: motif/2.3.8-foss-2022a (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 313, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: motif/2.3.8-foss-2022a (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 853, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 278, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 216, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: motif/2.3.8-foss-2022a (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 16397 tests in 762.697s

FAILED (errors=3)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

sassy-crick · 2023-02-13T21:34:14Z

I mark that as Work In Progress as during the installation, some Python packages will be installed in the Python directory, both lib and bin! That messed up my Python install which I only found by chance. So I need to dig into that more.

…installed

sassy-crick · 2023-02-13T22:59:49Z

Hopefully fixed now, so WIP removed

…asyconfigs into 20230213110339_new_pr_AFNI23003

zao · 2023-02-17T20:38:46Z

Test report by @zao
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
eb-rocky9.zao.se - Linux Rocky Linux 9.1 (Blue Onyx), x86_64, AMD Ryzen 9 3900X 12-Core Processor, Python 3.9.14
See https://gist.github.com/29bd405e466e7d85a8f28fcca1f792e0 for a full test report.

verdurin · 2023-02-19T22:27:17Z

easybuild/easyconfigs/a/AFNI/AFNI-23.0.03-foss-2022a.eb

+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]


@sassy-crick wondering whether the buildopts from the previous versions are still needed?

@verdurin from what I could see it is not required any more:

[ 0%] Building C object src/CMakeFiles/pcor_objs.dir/configured_pcor/afni_pcor_byte.c.o cd /dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/src && /apps/sw-eb/software/GCCcore/11.3.0/bin/gcc -DDYNAMIC_suffix=\".so\" -DREPLACE_XT -DDTYPE=byte -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src/niml -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-build/nifti2 -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-src/nifti2 -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-build/znzlib -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-src/znzlib -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-build/nifticdf -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-src/nifticdf -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-build/niftilib -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/_deps/nifti_clib-src/niftilib -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/src/configured_pcor -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src/3DEdge/src -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src/f2c -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/src -I/dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src/rickr -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC -DUSE_TRACING -DHAVE_ZLIB -DREAD_WRITE_64 -DLINUX2 -O3 -DNDEBUG -fPIC -MD -MT src/CMakeFiles/pcor_objs.dir/configured_pcor/afni_pcor_byte.c.o -MF CMakeFiles/pcor_objs.dir/configured_pcor/afni_pcor_byte.c.o.d -o CMakeFiles/pcor_objs.dir/configured_pcor/afni_pcor_byte.c.o -c /dev/shm/jsassman/AFNI/23.0.03/foss-2022a/easybuild_obj/src/configured_pcor/afni_pcor_byte.c

That said, please feel free to test it to make sure nothing is slipping through. I don't know the program so I might get it wrong.

One thing which I cannot work out is I find two files in my local PYTHONPATH which should not be there:
afnipy.egg-link easy-install.pth
The content of them refers to the build directory. Do you or @zao have any idea if they are actually needed?

$ cat python3.10/site-packages/afnipy.egg-link /dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src/python_scripts $ cat python3.10/site-packages/easy-install.pth /dev/shm/jsassman/AFNI/23.0.03/foss-2022a/afni-AFNI_23.0.03/src/python_scripts

@zao would know much better than I would.

verdurin · 2023-02-19T22:47:11Z

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/2b54f0892a918fa2c228c64271462821 for a full test report.

tlangfor · 2023-04-21T18:17:24Z

@sassy-crick Have you fixed the issue of files being installed into Python's directories? I ran into this same issue when trying to build a 2020b version on my system.

sassy-crick · 2024-01-19T15:57:24Z

@tlangfor Apologies for all the delays, busy year.
I had another look at it and hopefully I finally nailed it. The install I tested is running the afni_system_check.py -check_all command fine, some warnings messages are due to missing data-directories which, from what I understand, users can download themselves.
Please try it out and see if that is all working for you now.
Also, please see the latest PR #19654 as well if that helps.

sassy-crick · 2024-01-19T16:07:33Z

FFmpeg downgraded to 4.4.2 so the checks are passed. Apparently there is also the 5.0.1 version. Please advise which one to use. Thanks

sassy-crick · 2024-01-19T18:05:59Z

@boegelbot please test @ generoso

boegelbot · 2024-01-19T18:10:10Z

@sassy-crick: Request for testing this PR well received on login1

PR test command 'EB_PR=17309 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_17309 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12674

Test results coming soon (I hope)...

- notification for comment with ID 1900861360 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 · 2024-01-19T18:20:57Z

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/boegelbot/d5da8746e18d942bac8395e618668179 for a full test report.

sassy-crick · 2024-04-03T22:12:19Z

Closed as PR #19654 is newer and just got merged.

adding easyconfigs: AFNI-23.0.03-foss-2022a.eb

08e4aa0

sassy-crick added the update label Feb 13, 2023

missing freeglut added

a4a5745

sassy-crick changed the title ~~{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4~~ {bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 WIP Feb 13, 2023

sassy-crick mentioned this pull request Feb 13, 2023

Could AFNI be compiled and installed through the source code? afni/afni#395

Open

Missing Python dependencies added to avoid them being downloaded and …

678f0b0

…installed

sassy-crick changed the title ~~{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 WIP~~ {bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 Feb 13, 2023

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

29b8544

…asyconfigs into 20230213110339_new_pr_AFNI23003

verdurin reviewed Feb 19, 2023

View reviewed changes

Installation cleaned up

84d0444

sassy-crick mentioned this pull request Jan 19, 2024

{bio}[foss/2023a] AFNI v24.0.02 #19654

Merged

1 task

FFmpeg downgraded to 4.4.2

3a43639

sassy-crick closed this Apr 3, 2024

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{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 #17309

{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 #17309

sassy-crick commented Feb 13, 2023 •

edited

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{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 #17309

{bio}[foss/2022a] AFNI v23.0.03 w/ Python 3.10.4 #17309

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sassy-crick commented Feb 13, 2023 • edited

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sassy-crick commented Feb 13, 2023 •

edited