1936980 – python-ase fails to build with Python 3.10: test runs until it timeouts

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Bug 1936980 - python-ase fails to build with Python 3.10: test runs until it timeouts

Summary: python-ase fails to build with Python 3.10: test runs until it timeouts

Keywords:
Status:	CLOSED RAWHIDE
Alias:	None
Product:	Fedora
Classification:	Fedora
Component:	python-ase
Sub Component:
Version:	rawhide
Hardware:	Unspecified
OS:	Unspecified
Priority:	unspecified
Severity:	unspecified
Target Milestone:	---
Assignee:	marcindulak
QA Contact:	Fedora Extras Quality Assurance
Docs Contact:
URL:
Whiteboard:
Depends On:
Blocks:	PYTHON3.10
TreeView+	depends on / blocked

Reported:	2021-03-09 15:32 UTC by Tomáš Hrnčiar
Modified:	2021-05-10 08:11 UTC (History)
CC List:	3 users (show)
Fixed In Version:
Doc Type:	If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed:	2021-05-10 08:11:40 UTC
Type:	Bug
Embargoed:
Dependent Products:

Attachments	(Terms of Use)

Description Tomáš Hrnčiar 2021-03-09 15:32:30 UTC

python-ase fails to build with Python 3.10.0a6.

+ python -m ase test --verbose
platform                 Linux-5.10.7-200.fc33.x86_64-x86_64-with-glibc2.33.9000
python-3.10.0a6          /builddir/build/BUILD/ase-3.19.1/bin/python
ase-3.19.1               /builddir/build/BUILD/ase-3.19.1/build/lib/ase/
numpy-1.20.1             /usr/lib64/python3.10/site-packages/numpy/
scipy-1.6.1              /usr/lib64/python3.10/site-packages/scipy/
test directory           /tmp/ase-test-9o229kqp
Enabled calculators:     emt
number of processes      2
time                     Mon Mar  8 07:32:08 2021

                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:32:08        4.035042*       1.1099
BFGSLineSearch:    1[  1] 07:32:08        3.945642*       0.4608
BFGSLineSearch:    2[  2] 07:32:08        3.932762*       0.1573
BFGSLineSearch:    3[  3] 07:32:08        3.931335*       0.0135
BFGSLineSearch:    4[  4] 07:32:08        3.931324*       0.0003
                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:32:08        4.035042*       1.1099
BFGSLineSearch:    1[  1] 07:32:08        3.945642*       0.4608
BFGSLineSearch:    2[  2] 07:32:08        3.932762*       0.1573
BFGSLineSearch:    3[  3] 07:32:08        3.931335*       0.0135
BFGSLineSearch:    4[  4] 07:32:08        3.931324*       0.0003
      Step     Time          Energy         fmax
BFGS:    0 07:32:08        7.561109       16.2844
[ 1.27279221  1.27279221  1.82868705] 3.9313244937607417
[ 1.78190909  1.27279221  1.82868705] 4.243308366017629
[ 2.29102597  1.27279221  1.82868705] 4.807729787580028
[ 2.80014285  1.27279221  1.82868705] 4.80772978758003
[ 3.30925974  1.27279221  1.82868705] 4.243308366017628
[ 3.81837662  1.27279221  1.82868705] 3.931324493760753
      Step     Time          Energy         fmax
BFGS:    0 07:32:08        4.807730        4.2279
BFGS:    1 07:32:08        4.666306        3.3810
BFGS:    1 07:32:08        6.522155       12.8277
BFGS:    2 07:32:09        4.552512        2.6100
BFGS:    3 07:32:09        4.465836        1.9212
BFGS:    2 07:32:09        5.585341        9.9352
BFGS:    4 07:32:09        4.404185        1.3138
BFGS:    3 07:32:09        4.813412        7.5171
BFGS:    5 07:32:10        4.364972        0.7860
BFGS:    4 07:32:10        4.198699        5.4974
BFGS:    6 07:32:10        4.345537        0.3450
BFGS:    5 07:32:10        3.721432        3.8142
BFGS:    7 07:32:10        4.342508        0.1578
BFGS:    8 07:32:11        4.343133        0.1610
BFGS:    6 07:32:11        3.361445        2.4200
BFGS:    9 07:32:11        4.344384        0.1647
BFGS:    7 07:32:11        3.107775        1.3197
BFGS:   10 07:32:11        4.347314        0.1607
BFGS:    8 07:32:12        2.946984        0.8860
BFGS:   11 07:32:12        4.351393        0.1566
BFGS:   12 07:32:12        4.354994        0.1975
BFGS:    9 07:32:12        2.845434        0.6057
BFGS:   13 07:32:12        4.357831        0.1843
BFGS:   14 07:32:12        4.359108        0.1324
BFGS:   15 07:32:12        4.359732        0.1311
BFGS:   16 07:32:12        4.359809        0.0818
BFGS:   10 07:32:13        2.780295        0.4077
BFGS:   17 07:32:13        4.360033        0.0373
[ 1.27279221  1.27279221  1.82868705] 3.9313244937607417
[ 1.7659821   1.27279221  1.96719791] 4.140682131847802
[ 2.27778754  1.27279221  2.08929688] 4.335185985903331
[ 2.55928154  1.27279221  2.10925228] 4.360032966541432
[ 3.31648802  1.27279221  1.9677217 ] 4.14528661924233
[ 3.81837662  1.27279221  1.82868705] 3.931324493760753
Writing vib.eq.pckl
Writing vib.4x-.pckl
Writing vib.4x+.pckl
Writing vib.4y-.pckl
Writing vib.4y+.pckl
Writing vib.4z-.pckl
Writing vib.4z+.pckl
[  81.26517153+0.j   81.26517153+0.j  144.81156978+0.j]
---------------------
  #    meV     cm^-1
---------------------
  0   10.1      81.3 
  1   10.1      81.3 
  2   18.0     144.8 
---------------------
Zero-point energy: 0.019 eV
[[  0.00000000e+00   0.00000000e+00   0.00000000e+00]
 [  0.00000000e+00   0.00000000e+00   0.00000000e+00]
 [  0.00000000e+00   0.00000000e+00   0.00000000e+00]
 [  0.00000000e+00   0.00000000e+00   0.00000000e+00]
 [  2.62872116e-16  -7.80344501e-16   9.62838138e-02]]
      Step     Time          Energy         fmax
BFGS:    0 07:32:13        7.561109       16.2844
BFGS:   11 07:32:13        2.737771        0.4945
BFGS:    1 07:32:13        6.529916       12.8222
BFGS:    2 07:32:13        5.596620        9.9131
BFGS:    3 07:32:13        4.821491        7.4731
BFGS:    4 07:32:13        4.201408        5.4334
BFGS:    5 07:32:13        3.719580        3.7361
BFGS:    6 07:32:14        3.357249        2.3349
BFGS:   12 07:32:14        2.708078        0.5541
BFGS:    7 07:32:14        3.095982        1.1971
BFGS:    8 07:32:14        2.930835        0.8017
BFGS:    9 07:32:14        2.834209        0.5393
BFGS:   10 07:32:14        2.775042        0.4266
BFGS:   11 07:32:14        2.735600        0.5573
BFGS:   13 07:32:14        2.685197        0.5318
BFGS:   12 07:32:14        2.706804        0.5780
BFGS:   13 07:32:14        2.683271        0.5199
BFGS:   14 07:32:14        2.660555        0.4011
BFGS:   15 07:32:14        2.635789        0.3528
BFGS:   14 07:32:14        2.664499        0.4471
BFGS:   16 07:32:14        2.610006        0.3677
BFGS:   17 07:32:14        2.590406        0.2977
BFGS:   18 07:32:14        2.576442        0.2116
BFGS:   19 07:32:14        2.563150        0.1527
BFGS:   20 07:32:14        2.554476        0.1167
BFGS:   15 07:32:14        2.641897        0.3138
BFGS:   21 07:32:14        2.550559        0.1197
BFGS:   22 07:32:14        2.547701        0.1107
BFGS:   23 07:32:15        2.544998        0.0910
BFGS:   24 07:32:15        2.542361        0.0717
BFGS:   25 07:32:15        2.540222        0.0512
BFGS:   26 07:32:15        2.539040        0.0446
BFGS:   16 07:32:15        2.616420        0.3685
      Step     Time          Energy         fmax
BFGS:    0 07:32:15        7.561109       16.2844
BFGS:    1 07:32:15        6.529916       12.8222
BFGS:    2 07:32:15        5.596620        9.9131
BFGS:    3 07:32:15        4.821491        7.4731
BFGS:   17 07:32:15        2.594181        0.3291
BFGS:    4 07:32:15        4.201408        5.4334
BFGS:    5 07:32:15        3.719580        3.7361
BFGS:    6 07:32:15        3.357249        2.3349
BFGS:    7 07:32:15        3.095982        1.1971
BFGS:   18 07:32:15        2.578841        0.2412
BFGS:    8 07:32:15        2.930835        0.8017
BFGS:    9 07:32:15        2.834209        0.5393
BFGS:   10 07:32:15        2.775042        0.4266
BFGS:   11 07:32:15        2.735600        0.5573
BFGS:   12 07:32:15        2.706804        0.5780
BFGS:   19 07:32:16        2.567436        0.1715
BFGS:   13 07:32:16        2.683271        0.5199
BFGS:   14 07:32:16        2.660555        0.4011
BFGS:   15 07:32:16        2.635789        0.3528
BFGS:   16 07:32:16        2.610006        0.3677
BFGS:   17 07:32:16        2.590406        0.2977
BFGS:   20 07:32:16        2.556763        0.1138
BFGS:   18 07:32:16        2.576442        0.2116
BFGS:   19 07:32:16        2.563150        0.1527
BFGS:   20 07:32:16        2.554476        0.1167
BFGS:   21 07:32:16        2.550559        0.1197
BFGS:   21 07:32:16        2.551125        0.1180
BFGS:   22 07:32:16        2.547701        0.1107
BFGS:   23 07:32:16        2.544998        0.0910
BFGS:   24 07:32:16        2.542361        0.0717
BFGS:   25 07:32:16        2.540222        0.0512
BFGS:   26 07:32:16        2.539040        0.0446
BFGS:   22 07:32:16        2.547981        0.1181
BFGS:   23 07:32:17        2.545184        0.1046
BFGS:   24 07:32:17        2.542562        0.0817
BFGS:   25 07:32:17        2.539999        0.0613
BFGS:   26 07:32:17        2.538145        0.0470
      Step     Time          Energy         fmax
BFGS:    0 07:32:18        7.561109       16.2844
BFGS:    1 07:32:18        6.522155       12.8277
BFGS:    2 07:32:18        5.585341        9.9352
BFGS:    3 07:32:19        4.813412        7.5171
BFGS:    4 07:32:19        4.198699        5.4974
BFGS:    5 07:32:19        3.721432        3.8142
BFGS:    6 07:32:20        3.361445        2.4200
BFGS:    7 07:32:20        3.107775        1.3197
BFGS:    8 07:32:20        2.946984        0.8860
BFGS:    9 07:32:20        2.845434        0.6057
BFGS:   10 07:32:21        2.780295        0.4077
BFGS:   11 07:32:21        2.737771        0.4945
BFGS:   12 07:32:21        2.708078        0.5541
                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:32:22        2.808888*       0.0775
BFGS:   13 07:32:22        2.685197        0.5318
BFGSLineSearch:    1[  1] 07:32:22        2.807165*       0.0281
2.06698194767
2.08219265984
2.07846096908
                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:32:22        3.148897*       3.2834
BFGSLineSearch:    1[  1] 07:32:22        2.784790*       0.9054
BFGSLineSearch:    2[  2] 07:32:22        2.697266*       0.2665
BFGSLineSearch:    3[  3] 07:32:22        2.685797*       0.1211
BFGS:   14 07:32:22        2.664499        0.4471
BFGSLineSearch:    4[  4] 07:32:22        2.682083*       0.0553
BFGSLineSearch:    5[  5] 07:32:22        2.681375*       0.0312
                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:32:22        2.797809*       0.7990
BFGSLineSearch:    1[  1] 07:32:22        2.732047*       0.4597
BFGS:   15 07:32:22        2.641897        0.3138
BFGSLineSearch:    2[  2] 07:32:22        2.702285*       0.2008
BFGSLineSearch:    3[  3] 07:32:22        2.694408*       0.1018
BFGSLineSearch:    4[  4] 07:32:22        2.689178*       0.0710
BFGSLineSearch:    5[  5] 07:32:22        2.686936*       0.0725
BFGSLineSearch:    6[  6] 07:32:22        2.684538*       0.0720
BFGS:   16 07:32:22        2.616420        0.3685
BFGSLineSearch:    7[  7] 07:32:22        2.683434*       0.0486
BFGS:   17 07:32:23        2.594181        0.3291
BFGS:   18 07:32:23        2.578841        0.2412
BFGS:   19 07:32:23        2.567436        0.1715
BFGS:   20 07:32:23        2.556763        0.1138
BFGS:   21 07:32:24        2.551125        0.1180
BFGS:   22 07:32:24        2.547981        0.1181
BFGS:   23 07:32:24        2.545184        0.1046
BFGS:   24 07:32:24        2.542562        0.0817
BFGS:   25 07:32:24        2.539999        0.0613
BFGS:   26 07:32:24        2.538145        0.0470
Relax initial image
      Step     Time          Energy         fmax
BFGS:    0 07:32:24        2.808888        0.0775
BFGS:    1 07:32:25        2.808490        0.0706
BFGS:    2 07:32:25        2.807016        0.0397
2.0644180317
2.08255862816
2.07846096908
      Step     Time          Energy         fmax
BFGS:    0 07:32:25        3.144034        3.2609
BFGS:    1 07:32:25        2.945854        2.2174
BFGS:    2 07:32:25        2.825127        1.4094
BFGS:    3 07:32:25        2.757236        0.7758
BFGS:    4 07:32:25        2.723413        0.4125
BFGS:    5 07:32:25        2.710171        0.3532
BFGS:    6 07:32:25        2.701193        0.2926
BFGS:    7 07:32:25        2.692812        0.2074
BFGS:    8 07:32:25        2.688386        0.1486
BFGS:    9 07:32:25        2.686206        0.0967
BFGS:   10 07:32:25        2.684995        0.0989
BFGS:   11 07:32:25        2.683638        0.0779
BFGS:   12 07:32:25        2.682493        0.0542
BFGS:   13 07:32:25        2.682009        0.0407
Relax final image
      Step     Time          Energy         fmax
BFGS:    0 07:32:25        2.800761        0.8179
BFGS:    1 07:32:25        2.787403        0.7717
BFGS:    2 07:32:25        2.751136        0.6100
BFGS:    3 07:32:25        2.727709        0.4382
BFGS:    4 07:32:25        2.715252        0.2637
BFGS:    5 07:32:25        2.709939        0.2702
BFGS:    6 07:32:25        2.704402        0.2514
BFGS:    7 07:32:25        2.697193        0.1612
BFGS:    8 07:32:25        2.694630        0.1661
BFGS:    9 07:32:25        2.693184        0.1433
BFGS:   10 07:32:25        2.691435        0.0977
Create neb with 2 intermediate steps
Optimize neb using a single calculator
      Step     Time          Energy         fmax
BFGS:    0 07:32:25        2.816674        1.1252
BFGS:    1 07:32:26        2.783238        0.8123
BFGS:    2 07:32:26        2.745925        0.1847
BFGS:    3 07:32:26        2.743388        0.1630
BFGS:    4 07:32:26        2.740057        0.1746
BFGS:    5 07:32:26        2.737313        0.1525
BFGS:    6 07:32:26        2.735809        0.1228
BFGS:    7 07:32:26        2.735129        0.0902
 !! Copr timeout => sending INT
Copr build error: Build failed

Last successful build of python-ase was with 5th alpha so it might be cause by some change included in 6th alpha.
You can find changelog here: https://docs.python.org/3.10/whatsnew/changelog.html#python-3-10-0-alpha-6 

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/%40python/python3.10/fedora-rawhide-x86_64/02025831-python-ase/

For all our attempts to build python-ase with Python 3.10, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.10/package/python-ase/

Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.10:
https://copr.fedorainfracloud.org/coprs/g/python/python3.10/

Let us know here if you have any questions.

Python 3.10 will be included in Fedora 35. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.10.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon.
We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 marcindulak 2021-05-09 16:35:09 UTC

Upstream notified about python 3.10 issues https://gitlab.com/ase/ase/-/issues/909

Comment 2 marcindulak 2021-05-10 08:11:40 UTC

Currently a new version of python-ase is in succeeded state
https://copr.fedorainfracloud.org/coprs/g/python/python3.10/build/2174556/

There was a certain flakiness in the copr runs from
https://copr.fedorainfracloud.org/coprs/g/python/python3.10/build/2101540/ failed
to
https://copr.fedorainfracloud.org/coprs/g/python/python3.10/build/2162346/ succeeded

Unfortunately the failed logs are not longer accessible and the name of the test which timeouts is not included in the bug report,
but looking at another run it seemed to be this test:

neb/test_Ag_Cu100.py::test_Ag_Cu100                 Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:54:40        4.035042*       1.1099
BFGSLineSearch:    1[  1] 07:54:40        3.945642*       0.4608
BFGSLineSearch:    2[  2] 07:54:40        3.932762*       0.1573
BFGSLineSearch:    3[  3] 07:54:40        3.931335*       0.0135
BFGSLineSearch:    4[  4] 07:54:40        3.931324*       0.0003
                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 07:54:40        4.035042*       1.1099
BFGSLineSearch:    1[  1] 07:54:40        3.945642*       0.4608
BFGSLineSearch:    2[  2] 07:54:40        3.932762*       0.1573
BFGSLineSearch:    3[  3] 07:54:40        3.931335*       0.0135
BFGSLineSearch:    4[  4] 07:54:40        3.931324*       0.0003
...

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