[gmx-users] Install Gromacs on VirtualBox

Simon Dürr simon.duerr at uni-konstanz.de
Fri Oct 2 23:13:25 CEST 2015


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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>> >> 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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>> >
>> > * For (un)subscribe requests visit
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>> --
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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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>
> * 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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