nbfix_symmetry - gromacs test skip by tjwatson-stx · Pull Request #1196 · ParmEd/ParmEd

tjwatson-stx · 2021-09-16T13:58:51Z

TL;DR - Test nbfix_symmetry uses a topology file from OpenFF, which, Gromacs
has. Without any of the Gromacs data paths, the test fails. With the
Gromacs data paths, the tests pass.

It might be that nbfix_symmetry has nothing to do with Gromacs, and a better "fix" would be using a topology file without the Gromacs dependency. I just don't know if that is the case.

Super long story -

No local GROMACS or system GROMACS, the test test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry fails

(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ env | grep GMX 
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ 
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ pytest test/test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry
====================================================================== test session starts =======================================================================
platform linux -- Python 3.7.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /projects2/insite/thomas.watson/Programs/ParmEd.stx
plugins: dependency-0.5.1
collected 1 item                                                                                                                                                 

test/test_parmed_parameterset.py F                                                                                                                         [100%]

============================================================================ FAILURES ============================================================================
______________________________________________________________ TestParameterSet.test_nbfix_symmetry ______________________________________________________________

self = <test_parmed_parameterset.TestParameterSet testMethod=test_nbfix_symmetry>

    def test_nbfix_symmetry(self):
        """ Tests that nbfixes are being added to each atom type """
>       struct = pmd.load_file(get_fn('2PPN_bulk.top'))

test/test_parmed_parameterset.py:84: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/home/thomas.watson/Programs/ParmEd/parmed/formats/registry.py:211: in load_file
    return cls(filename, *args, **kwargs)
/home/thomas.watson/Programs/ParmEd/parmed/gromacs/gromacstop.py:349: in __init__
    self.read(fname, defines, parametrize)
/home/thomas.watson/Programs/ParmEd/parmed/gromacs/gromacstop.py:386: in read
    for line in f:
/home/thomas.watson/Programs/ParmEd/parmed/gromacs/_gromacsfile.py:42: in __iter__
    for line in self._handle:
/home/thomas.watson/Programs/ParmEd/parmed/gromacs/_cpp.py:174: in __iter__
    self._ppcmdmap[cmd](self, args)
/home/thomas.watson/Programs/ParmEd/parmed/gromacs/_cpp.py:29: in wrapper
    return func(self, args)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <parmed.gromacs._cpp.CPreProcessor object at 0x7f9966aacc50>, args = '"oplsaa.ff/forcefield.itp"'

    @_strip_pp_comments
    def _pp_include(self, args):
        if self._satisfiedstack and not self._satisfiedstack[-1]:
            return
        # Locate the include file
        rematch = includere.match(args)
        if not rematch:
            raise PreProcessorError('Bad #include syntax')
        includefile = rematch.groups()[0]
        self.included_files.append(includefile)
        for folder in self._includes:
            testfile = path.join(folder, includefile)
            if path.isfile(testfile):
                break
        else:
            if self._notfound_fatal:
>               raise PreProcessorError(f'Could not find {includefile}')
E               parmed.exceptions.PreProcessorError: Could not find oplsaa.ff/forcefield.itp

/home/thomas.watson/Programs/ParmEd/parmed/gromacs/_cpp.py:283: PreProcessorError
==================================================================== short test summary info =====================================================================
FAILED test/test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry - parmed.exceptions.PreProcessorError: Could not find oplsaa.ff/forcefield.itp
======================================================================= 1 failed in 2.01s ========================================================================
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$

Using System GROMACS, the test test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry passes

(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ module load gromacs/2021.2
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ env | grep GMX 
GMXBIN=/software_common/gromacs_latest/2021.2/bin
GMXTOOLCHAINDIR=/software_common/gromacs_latest/2021.2/share/cmake
GMXDATA=/software_common/gromacs_latest/2021.2/share/gromacs
GMXLDLIB=/software_common/gromacs_latest/2021.2/lib
GMXMAN=/software_common/gromacs_latest/2021.2/share/man
GMXPREFIX=/software_common/gromacs_latest/2021.2
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ 
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ pytest test/test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry
====================================================================== test session starts =======================================================================
platform linux -- Python 3.7.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /projects2/insite/thomas.watson/Programs/ParmEd.stx
plugins: dependency-0.5.1
collected 1 item                                                                                                                                                 

test/test_parmed_parameterset.py .                                                                                                                         [100%]

======================================================================= 1 passed in 4.03s ========================================================================
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$

Purging the environment variables in the order https://parmed.github.io/ParmEd/html/gromacs.html to demonstrate the test fails.

(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ export GMXBIN=
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ export GMXDATA=
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ export PATH=/projects2/common/SOFTWARE/miniconda3/envs/apps3/bin:/projects2/insite/thomas.watson/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/thomas.watson/.dotnet/tools
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ pytest test/test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry
====================================================================== test session starts =======================================================================
platform linux -- Python 3.7.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /projects2/insite/thomas.watson/Programs/ParmEd.stx
plugins: dependency-0.5.1
collected 1 item                                                                                                                                                 

test/test_parmed_parameterset.py F                                                                                                                         [100%]

============================================================================ FAILURES ============================================================================
______________________________________________________________ TestParameterSet.test_nbfix_symmetry ______________________________________________________________

self = <test_parmed_parameterset.TestParameterSet testMethod=test_nbfix_symmetry>

    def test_nbfix_symmetry(self):
        """ Tests that nbfixes are being added to each atom type """
>       struct = pmd.load_file(get_fn('2PPN_bulk.top'))

With the skip unless

====================================================================== test session starts =======================================================================
platform linux -- Python 3.7.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /projects2/insite/thomas.watson/Programs/ParmEd.stx
plugins: dependency-0.5.1
collected 1 item                                                                                                                                                 

test/test_parmed_parameterset.py s                                                                                                                         [100%]

======================================================================= 1 skipped in 1.24s =======================================================================
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ module load gromacs/2021.2
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$ pytest test/test_parmed_parameterset.py::TestParameterSet::test_nbfix_symmetry
====================================================================== test session starts =======================================================================
platform linux -- Python 3.7.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /projects2/insite/thomas.watson/Programs/ParmEd.stx
plugins: dependency-0.5.1
collected 1 item                                                                                                                                                 

test/test_parmed_parameterset.py .                                                                                                                         [100%]

======================================================================= 1 passed in 3.84s ========================================================================
(apps3) [thomas.watson@stxfrontend001 ParmEd.stx](master)$

Test nbfix_symmetry uses a topology file from OpenFF, which, Gromacs has. Without any of the Gromacs data paths, the test fails. With the Gromacs data paths, the tests pass.

tjwatson-stx · 2021-09-16T14:01:52Z

Obviously, this PR can be closed if this is the garbage solution. Or I can collect and incorporate feedback.

nbfix_symmetry - gromacs test skip

c9a24e7

Test nbfix_symmetry uses a topology file from OpenFF, which, Gromacs has. Without any of the Gromacs data paths, the test fails. With the Gromacs data paths, the tests pass.

swails approved these changes Sep 30, 2021

View reviewed changes

swails merged commit 0f733a4 into ParmEd:master Sep 30, 2021

tjwatson-stx deleted the bug-maybe-test-nbfixsym-gromacs branch October 5, 2021 12:32

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nbfix_symmetry - gromacs test skip#1196

nbfix_symmetry - gromacs test skip#1196
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tjwatson-stx commented Sep 16, 2021

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tjwatson-stx commented Sep 16, 2021

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tjwatson-stx commented Sep 16, 2021

Super long story -

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tjwatson-stx commented Sep 16, 2021

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