use `run_shell_cmd` in custom easyblock for ABAQUS by boegel · Pull Request #3414 · easybuilders/easybuild-easyblocks

boegel · 2024-08-16T16:30:48Z

No description provided.

…BAQUS easyblock, since spaces get replaced with [\s\n]+ by run_shell_cmd

boegel · 2024-08-20T19:58:27Z

Hitting an interesting problem when testing with ABAQUS-2022-hotfix-2214.eb.

At some point run_shell_cmd checks for question pattern matches in following end of stdout:

== 2024-08-20 21:10:00,492 run.py:270 DEBUG Found match for question pattern '\s*(?P<nr>[-0-9]+)[\s\n]+\[\*\][\s\n]+Isight[\s\w]*\n((?!Enter[\s\n]+selection[\s\n]+\(default:[\s\n]+Next\):\s*)(?!___)[\S[\s\n]+]*\n)*Enter[\s\n]+selection[\s\n]+\(default:[\s\n]+Next\):\s*$[\s\n]*$' at end of stdout: lished Products CAA API
  7 [*] Isight

Enter selection (default: Next):
 -1 Select All
  0 Select None
  1 [ ] NETVIBES Exalead CloudView
  2 [ ] EXALEAD Search for Documentation
  3 [ ] Extended Product Documentation
  4 [ ] FLEXnet License Server
  5 [*] SIMULIA Established Products
  6 [*] SIMULIA Established Products CAA API
  7 [ ] Isight

Enter selection (default: Next):
 -1 Select All
  0 Select None
  1 [ ] NETVIBES Exalead CloudView
  2 [ ] EXALEAD Search for Documentation
  3 [ ] Extended Product Documentation
  4 [ ] FLEXnet License Server
  5 [*] SIMULIA Established Products
  6 [*] SIMULIA Established Products CAA API
  7 [*] Isight

Enter selection (default: Next):
 -1 Select All
  0 Select None
  1 [ ] NETVIBES Exalead CloudView
  2 [ ] EXALEAD Search for Documentation
  3 [ ] Extended Product Documentation
  4 [ ] FLEXnet License Server
  5 [*] SIMULIA Established Products
  6 [*] SIMULIA Established Products CAA API
  7 [ ] Isight

Enter selection (default: Next):

The problem here is that "\[\*\] Isight" matches, even though it's not at the end of the output.
It should be matched once, to disable the installation of Isight.
But now we're going into an infinite enable/disable loop, because run_shell_cmd considers the full output, not just the last part of the output...

This probably indicates that another bug fix is required after easybuilders/easybuild-framework#4617, to only consider the new part of the output after a question has been answered?

…stallation command of ABAQUS, by using non-greedy matching (*?) in combination with negative lookahead (?!)

boegel · 2024-08-28T20:20:03Z

Problem with the tests has nothing to do with the changes to the ABAQUS easyblock, it's fallout from a change in framework that broke the easyblocks test suite (I'll get that fixed in a separate PR):

avoid suggesting that toolchainopts are supported for SYSTEM compiler, since they're not easybuild-framework#4585

edit: fixed by:

use non-system toolchain for testing --module-only for ELPA and FFTW easyblocks, since they rely on toolchain options like 'pic' being set #3425

…on commands executed by ABAQUS easyblock

boegel · 2024-08-28T20:31:35Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2022-hotfix-2214.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3515.doduo.os - Linux RHEL 8.8, x86_64, AMD EPYC 7552 48-Core Processor, Python 3.6.8
See https://gist.github.com/boegel/05fca2a4aafc3660f0ad6dd2878a33bc for a full test report.

Micket · 2024-08-28T21:03:09Z

Test report by @Micket

Overview of tested easyconfigs (in order)

FAIL (build issue) ABAQUS-2023-hotfix-2324.eb (partial log available at https://gist.github.com/Micket/e331163df66c00c9d5cb76c60bd9c33f)

Build succeeded for 0 out of 1 (1 easyconfigs in total)
alvis-skylake-build - Linux Rocky Linux 8.9, x86_64, Intel Xeon Processor (Skylake, IBRS, no TSX), Python 3.6.8
See https://gist.github.com/Micket/f15b99bfca3191a72ff3bdf981ea8e43 for a full test report.

Micket · 2024-08-28T22:05:03Z

Test report by @Micket

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2022-hotfix-2223.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
alvis-skylake-build - Linux Rocky Linux 8.9, x86_64, Intel Xeon Processor (Skylake, IBRS, no TSX), Python 3.6.8
See https://gist.github.com/Micket/cfd93697b9f9af61cecf227c8a8297be for a full test report.

branfosj · 2024-08-29T07:38:39Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2021.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/86fac84a70f2d1e356b660e403e9e471 for a full test report.

branfosj · 2024-08-29T07:53:48Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2024-hotfix-2405.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03b - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/61d9dbdfbb3d4090f27573ee2cf4b226 for a full test report.

Micket · 2024-08-29T08:35:28Z

Test report by @Micket

Overview of tested easyconfigs (in order)

FAIL (build issue) ABAQUS-2023-hotfix-2324.eb (partial log available at https://gist.github.com/Micket/f9d6796f8b8b7985d429b918ebd80690)

Build succeeded for 0 out of 1 (1 easyconfigs in total)
alvis-skylake-build - Linux Rocky Linux 8.9, x86_64, Intel Xeon Processor (Skylake, IBRS, no TSX), Python 3.6.8
See https://gist.github.com/Micket/c8ac16672d415e8d38dc0219e1503d03 for a full test report.

branfosj · 2024-08-29T09:02:10Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2023-hotfix-2314.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/98d04f891fa477887b8cf7c910f7b5c3 for a full test report.

branfosj · 2024-08-29T11:56:56Z

qa_timeout=100 is the default value. We should increase any that need increasing and remove the others.

…n installing on a sloooow filesystem

…syblocks into abaqus_run_shell_cmd

Micket

LGTM (I'm fine with 1000 everywhere. Probably overkill for many of these, but who knows, still isn't to terrible to wait out 1000 if there truly is some situation where it is broken)

boegel · 2024-08-29T13:02:57Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2022-hotfix-2214.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3515.doduo.os - Linux RHEL 8.8, x86_64, AMD EPYC 7552 48-Core Processor, Python 3.6.8
See https://gist.github.com/boegel/3d7362b49834df6f2a15c0cddbd27bb3 for a full test report.

branfosj · 2024-08-29T13:06:53Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2021.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/fda52432711b771d7164d3a2b418cb66 for a full test report.

branfosj · 2024-08-29T13:08:16Z

Going in, thanks @boegel!

branfosj · 2024-08-29T13:19:27Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2023-hotfix-2314.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/9eb9b2ac406667c4d67fc60126b140e5 for a full test report.

branfosj · 2024-08-29T13:21:23Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS ABAQUS-2024-hotfix-2405.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/deda4dc2ff7a74383102bc64a264b00c for a full test report.

use run_shell_cmd in custom easyblock for ABAQUS

305ce64

boegel added change EasyBuild-5.0 EasyBuild 5.0 labels Aug 16, 2024

boegel added this to the 5.0 milestone Aug 16, 2024

boegel marked this pull request as draft August 17, 2024 08:10

use \s rather than space in [ ] in part of question pattern used in A…

b7f6ca2

…BAQUS easyblock, since spaces get replaced with [\s\n]+ by run_shell_cmd

branfosj mentioned this pull request Aug 21, 2024

Replace run_cmd and run_cmd_qa with run_shell_cmd #3089

Closed

fix issues with regex patterns for questions raised in interactive in…

6472d46

…stallation command of ABAQUS, by using non-greedy matching (*?) in combination with negative lookahead (?!)

boegel marked this pull request as ready for review August 28, 2024 20:14

consistency use qa_wait_patterns for different interactive installati…

58599f7

…on commands executed by ABAQUS easyblock

boegel force-pushed the abaqus_run_shell_cmd branch from d0e941a to 58599f7 Compare August 28, 2024 20:20

boegel mentioned this pull request Aug 28, 2024

add check to make sure that easyblocks do not use run_cmd or run_cmd_qa #3426

Merged

Merge branch '5.0.x' into abaqus_run_shell_cmd

08f9d6a

branfosj reviewed Aug 29, 2024

View reviewed changes

Comment thread easybuild/easyblocks/a/abaqus.py Outdated

try increasing the qa timeout for the hotfix install

65f5f3b

boegel added 2 commits August 29, 2024 14:50

bump qa_timeout to 1000 in ABAQUS easyblock to take avoid trouble whe…

55d5f9a

…n installing on a sloooow filesystem

Merge branch 'abaqus_run_shell_cmd' of github.com:boegel/easybuild-ea…

d06d443

…syblocks into abaqus_run_shell_cmd

Micket approved these changes Aug 29, 2024

View reviewed changes

branfosj merged commit 068d8ea into easybuilders:5.0.x Aug 29, 2024

boegel deleted the abaqus_run_shell_cmd branch August 29, 2024 15:47

boegel mentioned this pull request Dec 18, 2024

Put our Python sitecustomize.py into the site-packages folder #3493

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boegel commented Aug 28, 2024 •

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