[Debichem-devel] request for building beta release of GROMACS 2018

[Andreas Tille]

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.

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

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