subject:"Re\: \[gmx\-users\] Install Gromacs on VirtualBox"

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-07 Thread Szilárd Páll

Hi,

Unfortunately that does not tell much (at least not without a backtrace).
You can e.g. run the regressiontests to see whether mdrun does start at all
(or just run "gmx mdrun" manually).

--
Szilárd

On Tue, Oct 6, 2015 at 4:06 PM, Simon Dürr 
wrote:

> 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 :
> > 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 
> > 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 :
> >> > 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.du...@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 :
> >> >> > Hi,
> >> >> >
> >> >> > Can you share the CPUID flags shown in /proc/cpuinfo?
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Szilárd
> >> >> >
> >> >> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr <
> >> simon.du...@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:
>

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-06 Thread Simon Dürr

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 :
> 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 
> 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 :
>> > 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 > >
>> > 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 :
>> >> > Hi,
>> >> >
>> >> > Can you share the CPUID flags shown in /proc/cpuinfo?
>> >> >
>> >> >
>> >> > --
>> >> > Szilárd
>> >> >
>> >> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr <
>> simon.du...@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

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-05 Thread Szilárd Páll

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 
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 :
> > 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  >
> > 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 :
> >> > Hi,
> >> >
> >> > Can you share the CPUID flags shown in /proc/cpuinfo?
> >> >
> >> >
> >> > --
> >> > Szilárd
> >> >
> >> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr <
> simon.du...@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:
> >> >>

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-03 Thread Simon Dürr

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 :
> 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 
> 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 :
>> > Hi,
>> >
>> > Can you share the CPUID flags shown in /proc/cpuinfo?
>> >
>> >
>> > --
>> > Szilárd
>> >
>> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr 
>> > 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 -

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-02 Thread Szilárd Páll

Hi,

Can you share the CPUID flags shown in /proc/cpuinfo?


--
Szilárd

On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr 
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 :
> > 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 
> > 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)
> >>

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-02 Thread Szilárd Páll

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 
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 :
> > Hi,
> >
> > Can you share the CPUID flags shown in /proc/cpuinfo?
> >
> >
> > --
> > Szilárd
> >
> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr 
> > 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 :
> >> > My guess is that you need to turn off RDTSCP:
> >> >
> >>
>

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-02 Thread Simon Dürr

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 :
> Hi,
>
> Can you share the CPUID flags shown in /proc/cpuinfo?
>
>
> --
> Szilárd
>
> On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr 
> 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 :
>> > 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 
>> > 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
>> >>

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-01 Thread Szilárd Páll

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 
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-requ...@gromacs.org.
>
-- 
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* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-01 Thread Simon Dürr

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 :
> 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 
> 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

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

Re: [gmx-users] Install Gromacs on VirtualBox

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