[gmx-users] Install Gromacs on VirtualBox
Simon Dürr
simon.duerr at uni-konstanz.de
Sun Oct 4 04:05:06 CEST 2015
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
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>> >> >> posting!
>> >> >>
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>> >> >>
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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!
>> >> >
>> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> >
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>> >> 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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>> >>
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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!
>> >
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>> >
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>> --
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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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