[gmx-users] Install Gromacs on VirtualBox

Szilárd Páll pall.szilard at gmail.com
Fri Oct 2 23:58:20 CEST 2015 

Should have asked for the CMakeCache file too, could you post that to a
file sharing service?

If you happen to have GMX_SIMD other than SSE2, that would explain the
issue - although I can't imagine why would the instruction set detection
fail.

Do you get an "illegal instruction" error if you e.g. try to run "gmx
-version" from the build tree?

Cheers,

--
Szilárd

On Fri, Oct 2, 2015 at 11:12 PM, Simon Dürr <simon.duerr at uni-konstanz.de>
wrote:

> Sure.
>
> >cat /proc/cpuinfo
> >
> > processor : 0
> > vendor_id : GenuineIntel
> > cpu family : 6
> > model : 69
> > model name : Intel(R) Core(TM) i7-4550U CPU @ 1.50GHz
> > stepping : 1
> > microcode : 0x19
> > cpu MHz : 2095.205
> > cache size : 6144 KB
> > physical id : 0
> > siblings : 1
> > core id : 0
> > cpu cores : 1
> > apicid : 0
> > initial apicid : 0
> > fdiv_bug : no
> > f00f_bug : no
> > coma_bug : no
> > fpu : yes
> > fpu_exception : yes
> > cpuid level : 5
> > wp : yes
> > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat
> pse36 clflush mmx fxsr sse sse2 rdtscp constant_tsc pni monitor ssse3
> > bugs :
> > bogomips : 4190.41
> > clflush size : 64
> > cache_alignment : 64
> > address sizes : 39 bits physical, 48 bits virtual
>
> Cheers,
> Simon
>
> 2015-10-02 5:36 GMT-04:00 Szilárd Páll <pall.szilard at gmail.com>:
> > Hi,
> >
> > Can you share the CPUID flags shown in /proc/cpuinfo?
> >
> >
> > --
> > Szilárd
> >
> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr <simon.duerr at uni-konstanz.de>
> > wrote:
> >
> >> I used this:
> >>
> >> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> >> -DGMX_USE_RDTSCP=OFF
> >>
> >> But Still:
> >> Test project /home/simon/gromacs-5.0.6/build
> >>       Start  1: TestUtilsUnitTests
> >>  1/15 Test  #1: TestUtilsUnitTests ...............***Exception:
> >> Illegal  0.29 sec
> >>
> >>       Start  2: PreprocessingTests
> >>  2/15 Test  #2: PreprocessingTests ...............***Exception:
> >> Illegal  0.23 sec
> >>
> >>       Start  3: CommandLineUnitTests
> >>  3/15 Test  #3: CommandLineUnitTests .............***Exception:
> >> Illegal  0.36 sec
> >>
> >>       Start  4: FFTUnitTests
> >>  4/15 Test  #4: FFTUnitTests .....................***Exception:
> >> Illegal  0.32 sec
> >>
> >>       Start  5: RandomUnitTests
> >>  5/15 Test  #5: RandomUnitTests ..................***Exception:
> >> Illegal  0.25 sec
> >>
> >>       Start  6: OnlineHelpUnitTests
> >>  6/15 Test  #6: OnlineHelpUnitTests ..............***Exception:
> >> Illegal  0.30 sec
> >>
> >>       Start  7: OptionsUnitTests
> >>  7/15 Test  #7: OptionsUnitTests .................***Exception:
> >> Illegal  0.31 sec
> >>
> >>       Start  8: UtilityUnitTests
> >>  8/15 Test  #8: UtilityUnitTests .................***Exception:
> >> Illegal  0.26 sec
> >>
> >>       Start  9: FileIOTests
> >>  9/15 Test  #9: FileIOTests ......................***Exception:
> >> Illegal  0.31 sec
> >>
> >>       Start 10: SimdUnitTests
> >> 10/15 Test #10: SimdUnitTests ....................***Exception:
> >> Illegal  0.30 sec
> >>
> >>       Start 11: LegacyToolsTests
> >> 11/15 Test #11: LegacyToolsTests .................***Exception:
> >> Illegal  0.30 sec
> >>
> >>       Start 12: AnalysisDataUnitTests
> >> 12/15 Test #12: AnalysisDataUnitTests ............***Exception:
> >> Illegal  0.23 sec
> >>
> >>       Start 13: SelectionUnitTests
> >> 13/15 Test #13: SelectionUnitTests ...............***Exception:
> >> Illegal  0.35 sec
> >>
> >>       Start 14: TrajectoryAnalysisUnitTests
> >> 14/15 Test #14: TrajectoryAnalysisUnitTests ......***Exception:
> >> Illegal  0.35 sec
> >>
> >>       Start 15: MdrunTests
> >> 15/15 Test #15: MdrunTests .......................***Exception:
> >> Illegal  0.28 sec
> >>
> >>
> >> 0% tests passed, 15 tests failed out of 15
> >>
> >> Label Time Summary:
> >> GTest              =   3.63 sec
> >> IntegrationTest    =   0.81 sec
> >> UnitTest           =   3.63 sec
> >>
> >> Total Test time (real) =   4.61 sec
> >>
> >>
> >> The following tests FAILED:
> >>  1 - TestUtilsUnitTests (ILLEGAL)
> >>  2 - PreprocessingTests (ILLEGAL)
> >>  3 - CommandLineUnitTests (ILLEGAL)
> >>  4 - FFTUnitTests (ILLEGAL)
> >>  5 - RandomUnitTests (ILLEGAL)
> >>  6 - OnlineHelpUnitTests (ILLEGAL)
> >>  7 - OptionsUnitTests (ILLEGAL)
> >>  8 - UtilityUnitTests (ILLEGAL)
> >>  9 - FileIOTests (ILLEGAL)
> >> 10 - SimdUnitTests (ILLEGAL)
> >> 11 - LegacyToolsTests (ILLEGAL)
> >> 12 - AnalysisDataUnitTests (ILLEGAL)
> >> 13 - SelectionUnitTests (ILLEGAL)
> >> 14 - TrajectoryAnalysisUnitTests (ILLEGAL)
> >> 15 - MdrunTests (ILLEGAL)
> >> 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
> >>
> >> 2015-10-01 11:00 GMT-04:00 Szilárd Páll <pall.szilard at gmail.com>:
> >> > My guess is that you need to turn off RDTSCP:
> >> >
> >>
> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#portability-aspects
> >> >
> >> >
> >> >
> >> > --
> >> > Szilárd
> >> >
> >> > On Thu, Oct 1, 2015 at 4:36 PM, Simon Dürr <
> simon.duerr at uni-konstanz.de>
> >> > wrote:
> >> >
> >> >> I have problems installing Gromacs on a VirtualBox machine.
> >> >>
> >> >> Stats of the System:
> >> >> Lubuntu 32bit, 14.04 LTS
> >> >> build-essential and cmake are installed.
> >> >>
> >> >> I follow the instructions:
> >> >> > tar xfz gromacs-5.0.6.tar.gz
> >> >> > cd gromacs-5.0.6
> >> >> > mkdir build
> >> >> > cd build
> >> >> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> >> >> > make
> >> >> > make check
> >> >> > sudo make install
> >> >> > source /usr/local/gromacs/bin/GMXRC
> >> >>
> >> >> However make check gives me the following errors and I can't figure
> out
> >> >> why.
> >> >> I can install Gromacs after and executing gmx "appname" works with no
> >> >> errors.
> >> >>
> >> >> Do you have ideas why?
> >> >>
> >> >> > 0% tests passed, 15 tests failed out of 15
> >> >> > Label Time Summary:
> >> >> > GTest              =   3.54 sec
> >> >> > IntegrationTest    =   0.88 sec
> >> >> > UnitTest           =   3.54 sec
> >> >> > Total Test time (real) =   4.58 sec
> >> >> > The following tests FAILED:
> >> >> >    1 - TestUtilsUnitTests (ILLEGAL)
> >> >> >    2 - PreprocessingTests (ILLEGAL)
> >> >> >    3 - CommandLineUnitTests (ILLEGAL)
> >> >> >    4 - FFTUnitTests (ILLEGAL)
> >> >> >    5 - RandomUnitTests (ILLEGAL)
> >> >> >    6 - OnlineHelpUnitTests (ILLEGAL)
> >> >> >    7 - OptionsUnitTests (ILLEGAL)
> >> >> >    8 - UtilityUnitTests (ILLEGAL)
> >> >> >    9 - FileIOTests (ILLEGAL)
> >> >> >   10 - SimdUnitTests (ILLEGAL)
> >> >> >   11 - LegacyToolsTests (ILLEGAL)
> >> >> >   12 - AnalysisDataUnitTests (ILLEGAL)
> >> >> >   13 - SelectionUnitTests (ILLEGAL)
> >> >> >   14 - TrajectoryAnalysisUnitTests (ILLEGAL)
> >> >> >   15 - MdrunTests (ILLEGAL)
> >> >> > 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
> >> >> --
> >> >> Gromacs Users mailing list
> >> >>
> >> >> * Please search the archive at
> >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> >> posting!
> >> >>
> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >>
> >> >> * For (un)subscribe requests visit
> >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >> >> send a mail to gmx-users-request at gromacs.org.
> >> >>
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
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>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>

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