[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
>> >>
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>> >>
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>> >>
>> > --
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>> >
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>> >
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