[gmx-users] Gromacs 2016: Installation proceeds without errors but binaries are not generated

[Justin Lemkul]

On 9/9/16 6:00 AM, Thereza Soares wrote:
> Hi All,
>
> I have compiled the latest Gromacs 2016 on my computer which runs OS X v.10.11.6, using CMake v.3.6.2 and gcc v.6.2.0. I have followed the “Quick and dirty installation” steps using “sudo cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gmx-2016 -DCMAKE_BUILD_TYPE=Debug"
>
> It all goes well, without any error messages (including make check whose output is below). However, no binaries are generated except for files GMXRC, GMXRC.zsh, gmx-completion-gmx.bash, GMXRC.bash, demux.pl, gmx-completion.bash, GMXRC.csh, xplor2gmx.pl. I experienced the same issue with a few other versions of Gromacs v5.0. However, the binaries are generated when I compile different versions of Gromacs 4.0 (I am currently using Gromacs 4.6.7.
>
> It would be great if someone has experienced the same issue and could advise me on how to solve it.
>

There is no issue.  As you see, all of your tests passed.  There is only one 
binary - it is called "gmx" and this has been the case for some time (started in 
5.0 with symlinks to the normal tools, since 5.1 there is only gmx).  Please 
consult the release notes for changes in syntax and some tool names.  I updated 
my tutorials a long time ago to reflect the change, as well.

-Justin

> Cheers,
>
> Th.
>
> [100%] Running all tests
> Test project /usr/local/gromacs-2016/build
>       Start  1: TestUtilsUnitTests
>  1/27 Test  #1: TestUtilsUnitTests ...............   Passed    0.03 sec
>       Start  2: MdlibUnitTest
>  2/27 Test  #2: MdlibUnitTest ....................   Passed    0.02 sec
>       Start  3: CommandLineUnitTests
>  3/27 Test  #3: CommandLineUnitTests .............   Passed    0.03 sec
>       Start  4: FFTUnitTests
>  4/27 Test  #4: FFTUnitTests .....................   Passed    0.08 sec
>       Start  5: HardwareUnitTests
>  5/27 Test  #5: HardwareUnitTests ................   Passed    0.01 sec
>       Start  6: MathUnitTests
>  6/27 Test  #6: MathUnitTests ....................   Passed    0.02 sec
>       Start  7: OnlineHelpUnitTests
>  7/27 Test  #7: OnlineHelpUnitTests ..............   Passed    0.02 sec
>       Start  8: OptionsUnitTests
>  8/27 Test  #8: OptionsUnitTests .................   Passed    0.03 sec
>       Start  9: RandomUnitTests
>  9/27 Test  #9: RandomUnitTests ..................   Passed    0.04 sec
>       Start 10: UtilityUnitTests
> 10/27 Test #10: UtilityUnitTests .................   Passed    0.04 sec
>       Start 11: FileIOTests
> 11/27 Test #11: FileIOTests ......................   Passed    0.03 sec
>       Start 12: PullTest
> 12/27 Test #12: PullTest .........................   Passed    0.02 sec
>       Start 13: SimdUnitTests
> 13/27 Test #13: SimdUnitTests ....................   Passed    0.11 sec
>       Start 14: LegacyToolsTests
> 14/27 Test #14: LegacyToolsTests .................   Passed    0.05 sec
>       Start 15: GmxPreprocessTests
> 15/27 Test #15: GmxPreprocessTests ...............   Passed    0.17 sec
>       Start 16: CorrelationsTest
> 16/27 Test #16: CorrelationsTest .................   Passed    0.14 sec
>       Start 17: AnalysisDataUnitTests
> 17/27 Test #17: AnalysisDataUnitTests ............   Passed    0.07 sec
>       Start 18: SelectionUnitTests
> 18/27 Test #18: SelectionUnitTests ...............   Passed    0.29 sec
>       Start 19: TrajectoryAnalysisUnitTests
> 19/27 Test #19: TrajectoryAnalysisUnitTests ......   Passed    0.74 sec
>       Start 20: MdrunTests
> 20/27 Test #20: MdrunTests .......................   Passed    6.55 sec
>       Start 21: MdrunMpiTests
> 21/27 Test #21: MdrunMpiTests ....................   Passed    0.04 sec
>       Start 22: regressiontests/simple
> 22/27 Test #22: regressiontests/simple ...........   Passed    1.65 sec
>       Start 23: regressiontests/complex
> grep "Test  #5" *
> 23/27 Test #23: regressiontests/complex ..........   Passed   41.76 sec
>       Start 24: regressiontests/kernel
> 24/27 Test #24: regressiontests/kernel ...........   Passed   26.90 sec
>       Start 25: regressiontests/freeenergy
> 25/27 Test #25: regressiontests/freeenergy .......   Passed   22.79 sec
>       Start 26: regressiontests/pdb2gmx
> 26/27 Test #26: regressiontests/pdb2gmx ..........   Passed   19.98 sec
>       Start 27: regressiontests/rotation
> 27/27 Test #27: regressiontests/rotation .........   Passed    2.37 sec
>
> 100% tests passed, 0 tests failed out of 27
>
> Label Time Summary:
> GTest                 =   1.89 sec (18 tests)
> IntegrationTest       =   6.60 sec (2 tests)
> MpiIntegrationTest    =   0.04 sec (1 test)
> UnitTest              =   1.89 sec (18 tests)
>
> Total Test time (real) = 124.01 sec
> [100%] Built target run-ctest
> Scanning dependencies of target check
> [100%] Built target check
>
> Thereza A. Soares
> Visiting Professor
> Umea Centre for Microbial Research - UCMR
> Umeå University
> theso0011 at ad.umu.se
> http://www.ucmr.umu.se/about-ucmr/ucmr-organization.html
>
>
> Professor Thereza A. Soares
> Head of the Graduate Program in Chemistry
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Av. Jornalista Anibal Fernandes, s/nº
> Cidade Universitária 50740-560
> Recife, PE, Brazil
> tel: +558121268440
> fax: +558121268442
> thereza.soares at ufpe.br
> http://dqfnet.ufpe.br/biomat/
>
> ____________________________
> Per Angusta Ad Augusta
>

-- 
==================================================

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

==================================================