Gromacs 2018 and pytest low-performance custom plugin to control -nt #102

ianmkenney · 2017-01-27T16:02:40Z

~~Include Gromacs 2016 in tests (fixes #96)~~

EDIT: We use Gromacs 2018 (see PR #127 and discussion in #130 ). This PR contains experimental pytest plugin to provide the pytest --low-performance flag and code to explicitly set the number of threads for gmx mdrun in the tests.

codecov-io · 2017-01-27T16:15:44Z

Codecov Report

Merging #102 into develop will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop     #102   +/-   ##
========================================
  Coverage    48.54%   48.54%           
========================================
  Files           24       24           
  Lines         4837     4837           
  Branches       733      733           
========================================
  Hits          2348     2348           
+ Misses        2331     2330    -1     
- Partials       158      159    +1

Impacted Files	Coverage Δ
gromacs/utilities.py	`53.52% <0%> (ø)`	⬆️

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orbeckst · 2017-02-01T21:43:55Z

Similar problem with maxthreads as in Becksteinlab/MDPOW#77 ?

orbeckst · 2017-02-01T21:44:32Z

Can you enable full output so that we can see if this is again a problem with the number of threads? We probably need to explicitly restrict number of threads to 2 again...

orbeckst · 2017-05-10T01:26:16Z

@ianmkenney can you have a look again, please?

I would like this to work.

orbeckst · 2017-05-12T07:42:13Z

What is pytest-gmx and where is it used?

ianmkenney · 2017-05-12T15:11:50Z

I'm attempting to build a plugin for pytest that will make our tests a little more manageable. Setting the number of threads from the command line rather than hard coded into the tests themselves would be much more convenient since when we run local tests we would rather use a larger number of threads. For now I just added a low performance flag to pytest that, if provided, will set nt=2. Just an playing around with the idea, as it could still be useful in future projects. You can find it in my repos.

…

On May 12, 2017, at 12:42 AM, Oliver Beckstein ***@***.***> wrote: What is pytest-gmx and where is it used? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

orbeckst · 2017-05-12T20:21:40Z

@ianmkenney can you move the repo to Becksteinlab so that all the GW-related things are together?

orbeckst · 2018-04-29T18:11:53Z

Rebased against develop but there are problems in the tests

2016 test times out
5.1.2 test (and the 4.6.7 test) have an error in test_mdrun() with the wrong number of arguments and sort is not an attribute of DataFrame

orbeckst · 2018-04-30T09:15:56Z

rebased against develop (the errors in test_mdrun were fixed)

orbeckst · 2018-05-02T00:10:33Z

Btw, locally, the tests pass just fine with 2016.5.

orbeckst · 2018-05-02T00:34:31Z

Good and bad news:

Good: for the first time, all Gromacs 2016 tests run (probably due to using --low-performance, i.e., setting gmx mdrun -nt 2 instead of letting Gromacs choose the number of threads).
Bad: tests still fail
- Gromacs 2016 tests (However, my local version of Gromacs 2016.5 passes the tests just fine.)
  - pdb2gmx generates a system with a non-integer charge (?!?!?!?!) – maybe check the occupancy fields of the PDB file. pdb2gmx complains about a few of them.
  - cg minimization fails with a constraint problem
- Gromacs 4.6.7 tests: tests that used to pass, fail now:
  - cg energy minimization fails (not sure why)

orbeckst · 2018-07-31T01:21:45Z

I rebased against develop (with #127 merged) and force pushed.

The new low_performance fixture (from https://github.com/ianmkenney/pytest-gmx was not applied in derived classes. Fixed by removing superfluous methods that just called the superclass method. Also added a comment to the test that includes the low_performance fixture.

- fix #137 - use code from https://github.com/ianmkenney/pytest-gmx

orbeckst · 2018-08-02T23:02:47Z

This looks good, and the run time of the mdrun tests decreased from ~20s to ~4s by setting -nt 2. Will merge.

- Gromacs 2018 insists on -r for grompp, earlier uses the structure as default - required to make more Gromacs 2018 tests pass

- makes 2018 tests pass - small code cleanup in tests/top/top.py

- Gromacs 2018 on Python 2.7 passes all tests - fix #96 - Python 3.6 tests may fail (see issue #132) - updated CHANGES

needed so that it can be used with all fixtures

- test does not always hit the convergence criterion and then errors; this seems stochastic (eg depends on architecture); rerun the test with a much higher tolerance once this happens and hope for the best - use the low_performance fixture to set nt=2 for test_setup.py

ianmkenney added enhancement tests labels Jan 27, 2017

ianmkenney force-pushed the enable-gromacs-2016 branch from 718c7e1 to 9343a3f Compare February 3, 2017 22:34

orbeckst removed the enhancement label May 10, 2017

orbeckst force-pushed the enable-gromacs-2016 branch from bb4ccb6 to 753e3f9 Compare April 28, 2018 01:29

orbeckst force-pushed the enable-gromacs-2016 branch 2 times, most recently from 01e4bff to 1ebb7d7 Compare April 30, 2018 09:15

orbeckst force-pushed the enable-gromacs-2016 branch from 010ee7c to 2a7651d Compare May 2, 2018 00:39

This was referenced May 8, 2018

use Bioconda gromacs packages for testing #129

Closed

test Gromacs 2018 #96

Closed

orbeckst changed the title ~~Enable Gromacs 2016 in testing~~ Gromacs 2016 and pytest low-performance custom plugin to control -nt May 16, 2018

orbeckst force-pushed the enable-gromacs-2016 branch from 2a7651d to b9c8d1b Compare July 31, 2018 01:21

orbeckst mentioned this pull request Aug 2, 2018

make pytest-gmx a local plugin #137

Closed

ianmkenney and others added 5 commits August 2, 2018 14:32

set nt=2

dbe41c2

Added pytest-gmx installation through github

1868baa

Added low performance fixture

37ca2de

travis: run pytest --low-performance and show timing

343e5b0

orbeckst force-pushed the enable-gromacs-2016 branch from b9c8d1b to 343e5b0 Compare August 2, 2018 21:35

add pytest --low-performance option as local plugin

72f1ac5

- fix #137 - use code from https://github.com/ianmkenney/pytest-gmx

orbeckst force-pushed the enable-gromacs-2016 branch from 48586b9 to 72f1ac5 Compare August 2, 2018 22:02

orbeckst changed the title ~~Gromacs 2016 and pytest low-performance custom plugin to control -nt~~ Gromacs 2018 and pytest low-performance custom plugin to control -nt Aug 2, 2018

orbeckst force-pushed the enable-gromacs-2016 branch from 2f4b440 to 41724a1 Compare August 2, 2018 23:30

travis: mark Gromacs 2018 and Python 3 as allowed failure for right now

905f091

orbeckst force-pushed the enable-gromacs-2016 branch from 41724a1 to 905f091 Compare August 2, 2018 23:33

orbeckst added 3 commits August 2, 2018 16:55

setup.energy_minimize: always provide structure for -r restraints

552a841

- Gromacs 2018 insists on -r for grompp, earlier uses the structure as default - required to make more Gromacs 2018 tests pass

top tests: use maxwarn=1 for critical grompp

372bffd

- makes 2018 tests pass - small code cleanup in tests/top/top.py

require Gromacs 2018 / Python 2.7 tests to pass

f9e0dde

- Gromacs 2018 on Python 2.7 passes all tests - fix #96 - Python 3.6 tests may fail (see issue #132) - updated CHANGES

orbeckst force-pushed the enable-gromacs-2016 branch from 121db79 to f9e0dde Compare August 3, 2018 00:33

orbeckst added 2 commits August 2, 2018 17:55

make low_performance session-scoped

5c0c81a

needed so that it can be used with all fixtures

orbeckst self-assigned this Aug 3, 2018

orbeckst merged commit 6b87aa8 into develop Aug 3, 2018

orbeckst deleted the enable-gromacs-2016 branch August 3, 2018 01:03

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Gromacs 2018 and pytest low-performance custom plugin to control -nt #102

Gromacs 2018 and pytest low-performance custom plugin to control -nt #102

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Gromacs 2018 and pytest low-performance custom plugin to control -nt #102

Gromacs 2018 and pytest low-performance custom plugin to control -nt #102

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