[gmx-users] Install Problem: make check, tests failed, incompatible library version

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 11 17:54:48 CEST 2016


Hi,

Something seems to be different between the environment when you configured
the build of GROMACS, and now, because different versions of
libxml2.2.dylib are being found.

Mark

On Mon, 8 Aug 2016 23:40 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/8/16 1:35 PM, Betty Wong wrote:
> > Hi,
> >
> > Posting again, hoping someone will help me! Much appreciated.
> >
> > I am trying to install Gromacs. (I believe that) I have successfully done
> > the following:
> >
> > tar xfz gromacs-5.1.3.tar.gz
> > cd gromacs-5.1.3
> > mkdir build
> > cd build
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > make
> >
> >
> > But when I get to make check, I get an error, I've copied and pasted only
> > one part of the what error output is.
> >  Start 20: MdrunMpiTests
> >
> > 20/26 Test #20: MdrunMpiTests ....................***Exception: Other
> 0.02
> > sec
> >
> > dyld: Library not loaded: libxml2.2.dylib
> >
> >   Referenced from: /Users/bwong/Desktop/gromacs-
> > 5.1.3/build/bin/mdrun-mpi-test
> >
> >   Reason: Incompatible library version: mdrun-mpi-test requires version
> > 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0
> >
>
> You need to upgrade to a newer version for this to work.
>
> -Justin
>
> > And if this helps as well:
> >
> > The following tests FAILED:
> >
> >   1 - TestUtilsUnitTests (OTHER_FAULT)
> >
> >   2 - GmxlibTests (OTHER_FAULT)
> >
> >   3 - MdlibUnitTest (OTHER_FAULT)
> >
> >   4 - CommandLineUnitTests (OTHER_FAULT)
> >
> >   5 - FFTUnitTests (OTHER_FAULT)
> >
> >   6 - MathUnitTests (OTHER_FAULT)
> >
> >   7 - RandomUnitTests (OTHER_FAULT)
> >
> >   8 - OnlineHelpUnitTests (OTHER_FAULT)
> >
> >   9 - OptionsUnitTests (OTHER_FAULT)
> >
> > 10 - UtilityUnitTests (OTHER_FAULT)
> >
> > 11 - FileIOTests (OTHER_FAULT)
> >
> > 12 - SimdUnitTests (OTHER_FAULT)
> >
> > 13 - LegacyToolsTests (OTHER_FAULT)
> >
> > 14 - GmxPreprocessTests (OTHER_FAULT)
> >
> > 15 - CorrelationsTest (OTHER_FAULT)
> >
> > 16 - AnalysisDataUnitTests (OTHER_FAULT)
> >
> > 17 - SelectionUnitTests (OTHER_FAULT)
> >
> > 18 - TrajectoryAnalysisUnitTests (OTHER_FAULT)
> >
> > 19 - MdrunTests (OTHER_FAULT)
> >
> > 20 - MdrunMpiTests (OTHER_FAULT)
> >
> > Errors while running CTest
> >
> > make[3]: *** [CMakeFiles/run-ctest] Error 8
> >
> > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
> >
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> >
> > make: *** [check] Error 2
> >
> > Any help? Not sure what the error is and how to fix. Thanks!
> >
> > Best,
> > Betty
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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