[gmx-users] Install Gromacs on VirtualBox

Simon Dürr simon.duerr at uni-konstanz.de
Tue Oct 6 16:07:22 CEST 2015


Hi Szilard,

thanks for the help. Now only 1 of 15 tests fails.

> Label Time Summary:
> GTest              =   4.92 sec
> IntegrationTest    =   4.05 sec
> UnitTest           =   4.92 sec
> Total Test time (real) =   9.18 sec
> The following tests FAILED:
> 15 - MdrunTests (SEGFAULT)
> 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

See CMakeCache.txt here: http://pastebin.com/u4xwQcar

2015-10-05 11:29 GMT-04:00 Szilárd Páll <pall.szilard at gmail.com>:
> Oh, that was easy, should have asked about what the value of "GMX_SIMD" is
> in the CMake cache. Given that the GROMACS build system enabled AVX2 SIMD
> on your VM which seems to not support anything above SSE2, it's not a
> surprise that the first math instruction crashes the run.
>
> Immediate solution: set -DGMX_SIMD=SSE2 when configuring.
>
> Secondly: please open an issue on redmine.gromacs.org and briefly summarize
> what you described here (+ the VM setup you have) and attach the
> /proc/cpuinfo and CMakeCache.txt so we can have a look at why is the build
> system picking AVX2 even though the virtualized CPU does not support it.
>
> Thanks,
>
> --
> Szilárd
>
> On Sun, Oct 4, 2015 at 4:04 AM, Simon Dürr <simon.duerr at uni-konstanz.de>
> wrote:
>
>> After running make check I can install via sudo make install.
>> gmx --version returns:
>> http://pastebin.com/Gnx09wah
>>
>> The CMakeCache file is the following:
>> http://pastebin.com/9wb0e1tw
>>
>> Cheers,
>> Simon
>>
>> 2015-10-02 17:58 GMT-04:00 Szilárd Páll <pall.szilard at gmail.com>:
>> > 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!
>> >> >> >>
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>> >> >> >>
>> >> >> >> * For (un)subscribe requests visit
>> >> >> >>
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>> >> 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!
>> >> >> >
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>> or
>> >> >> send a mail to gmx-users-request at gromacs.org.
>> >> >> --
>> >> >> Gromacs Users mailing list
>> >> >>
>> >> >> * Please search the archive at
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>> >> >> posting!
>> >> >>
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>> >> >>
>> >> > --
>> >> > Gromacs Users mailing list
>> >> >
>> >> > * Please search the archive at
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>> >> posting!
>> >> >
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>> >>
>> >> * Please search the archive at
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>> >> posting!
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>> >>
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
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>> posting!
>> >
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>>
>> * Please search the archive at
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>> posting!
>>
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>>
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>>
> --
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>
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>
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