[Debichem-devel] request for building beta release of GROMACS 2018
Andreas Tille
andreas at an3as.eu
Wed Dec 13 10:58:10 UTC 2017
Hi Mark,
thanks for your valuable feedback. I'd like to leave the implementation
for Nicolas who is way more involved in the packaging. Feel free to
ping me in case Nicolas might remain overworked to continue what I've
started. In any case I would love if Nicolas had a final view on the
packaging instead of pushing the upload myself without his confirmation.
Kind regards
Andreas.
On Wed, Dec 13, 2017 at 01:23:00AM +0000, Mark Abraham wrote:
> Hi Andreas,
>
> On Tue, Dec 12, 2017 at 11:36 PM Andreas Tille <andreas at an3as.eu> wrote:
>
> > Hi Mark and Nicolas,
> >
> > On Tue, Dec 12, 2017 at 04:51:47AM +0000, Mark Abraham wrote:
> > > Hi Debichem team, particularly Nicolas Breen,
> > >
> > > I'm the development manager for GROMACS, which you guys kindly package
> > and
> > > have given us some great feedback about. We've just released our second
> > > beta tarball for our 2018 release, and we'd love to find out early if
> > > there's any problems building or running the code. Is there anything I
> > can
> > > do to help get that process started? I note that the system has detected
> > > that we made our 2018-beta1 a few weeks back, but 2018-beta2 will be
> > > available when it next runs.
> >
> > As promised I have moved the gromacs packaging from SVN to Git[1].
> > Since the above new version seems to be our new target I imported this
> > as well and adapted the patches to the new upstream version (Nicolas,
> > please double check).
> >
> > Unfortunately when trying to build I get two test failures:
> >
> > ...
> >
> > Test project /build/gromacs-2018~beta2/build/mpich
> > Start 1: TestUtilsUnitTests
> > 1/24 Test #1: TestUtilsUnitTests ............... Passed 0.03 sec
> > Start 2: TestUtilsMpiUnitTests
> > 2/24 Test #2: TestUtilsMpiUnitTests ............***Failed 0.03 sec
> > --------------------------------------------------------------------------
> > The value of the MCA parameter "plm_rsh_agent" was set to a path
> > that could not be found:
> >
> > plm_rsh_agent: ssh : rsh
> >
> > Please either unset the parameter, or check that the path is correct
> > --------------------------------------------------------------------------
> >
> > Start 3: MdlibUnitTest
> > 3/24 Test #3: MdlibUnitTest .................... Passed 0.01 sec
> > Start 4: AppliedForcesUnitTest
> > 4/24 Test #4: AppliedForcesUnitTest ............ Passed 0.01 sec
> > Start 5: ListedForcesTest
> > 5/24 Test #5: ListedForcesTest ................. Passed 0.01 sec
> > Start 6: CommandLineUnitTests
> > 6/24 Test #6: CommandLineUnitTests ............. Passed 0.02 sec
> > Start 7: EwaldUnitTests
> > 7/24 Test #7: EwaldUnitTests ................... Passed 0.17 sec
> > Start 8: FFTUnitTests
> > 8/24 Test #8: FFTUnitTests ..................... Passed 0.05 sec
> > Start 9: GpuUtilsUnitTests
> > 9/24 Test #9: GpuUtilsUnitTests ................ Passed 0.01 sec
> > Start 10: HardwareUnitTests
> > 10/24 Test #10: HardwareUnitTests ................ Passed 0.02 sec
> > Start 11: MathUnitTests
> > 11/24 Test #11: MathUnitTests .................... Passed 0.00 sec
> > Start 12: MdrunUtilityUnitTests
> > 12/24 Test #12: MdrunUtilityUnitTests ............ Passed 0.01 sec
> > Start 13: MdrunUtilityMpiUnitTests
> > 13/24 Test #13: MdrunUtilityMpiUnitTests .........***Failed 0.01 sec
> > --------------------------------------------------------------------------
> > The value of the MCA parameter "plm_rsh_agent" was set to a path
> > that could not be found:
> >
> > plm_rsh_agent: ssh : rsh
> >
> > Please either unset the parameter, or check that the path is correct
> > --------------------------------------------------------------------------
> > ...
> > 24/24 Test #24: CompatibilityHelpersTests ........ Passed 0.00 sec
> >
> > 92% tests passed, 2 tests failed out of 24
> >
> > Label Time Summary:
> > GTest = 0.60 sec (24 tests)
> > MpiTest = 0.04 sec (2 tests)
> > UnitTest = 0.60 sec (24 tests)
> >
> > Total Test time (real) = 0.62 sec
> >
> > The following tests FAILED:
> > 2 - TestUtilsMpiUnitTests (Failed)
> > 13 - MdrunUtilityMpiUnitTests (Failed)
> >
> >
> > For your reference I have commited a copy of the full build log in
> > branch logs[2]. I admit the said error somehow rings a bell and I have
> > seen this in some other Debian Science package. It smells like this
> > bug[3] and thus I'll add openssh-client to Build-Depends and try
> > rebuilding.
> >
>
> Indeed, that is a useful step, despite the fact that it exposes a further
> issue that when ctest tries to launch these tests with multiple ranks, only
> one gets launched.
>
> When we register these tests that fail, we do so in a way that
> * gives them the MpiTest label within CTest (so that is a way for you to
> disable running them, if you run ctest manually rather than "make test" -
> but I haven't yet found the DebiChem build recipe for GROMACS to make a
> concrete suggestion), and
> * uses the machinery in our cmake/gmxManageMpi.cmake to find an mpirun and
> call it with multiple ranks - it's not necessary for the node running the
> test to have a network, or even a network interface, but the MPI runtime
> (e.g. openmpi-bin or mpich-bin) needs to (be able to) be configured to
> start more than one rank
>
> Skipping those tests is quite reasonable - the role of
> TestUtilsMpiUnitTests is to serve as a sentinel for exactly these kinds of
> infrastructure setup issues, and the role of MdrunUtilityMpiUnitTests is to
> test our functionality for handling thread affinity in an MPI context. We'd
> be interested to know that the latter pass on interesting hardware, but it
> isn't worth much work unless there's others who need the ability to run an
> MPI process with multiple ranks as part of their test process.
>
> Digging through that has exposed a bug in our handling of other MPI tests,
> which I will fix, so thanks for that. (MdrunMpiTests should be failing in
> the same way.)
>
> Minor suggestions:
> * setting "export GTEST_COLOR=no" will make the failures a little more
> readable because they won't have ascii color codes in them
> * cmake -DGMX_X11=on is reasonable for the non-MPI builds (but is off by
> our default); turning X11 off support makes good sense for the MPI builds,
> particularly with -DGMX_BUILD_MDRUN_ONLY=on; currently the MPI builds turn
> it on and then off, which works OK but is potentially a problem
> * using ctest -V would help troubleshoot aspects of these MPI tests (if we
> continue to test them) by hopefully letting us see the full command line in
> the log
>
> Mark
>
> Just to let you know about the status of the SVN-Git migration +
> > upgrade.
> >
> > Kind regards
> >
> > Andreas.
> >
> >
> > [1] https://anonscm.debian.org/git/debichem/packages/gromacs.git
> > [2]
> > https://anonscm.debian.org/cgit/debichem/packages/gromacs.git/tree/gromacs_2018~beta2-1_amd64.build?h=logs&id=05b0694d8a5deaf36460fa021752c58e1a0b1cd8
> > [3] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=882603
> >
> > --
> > http://fam-tille.de
> >
--
http://fam-tille.de
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