[gmx-users] Install Gromacs on VirtualBox
Szilárd Páll
pall.szilard at gmail.com
Wed Oct 7 15:50:00 CEST 2015
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 <simon.duerr at uni-konstanz.de>
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 <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!
> >> >> >> >>
> >> >> >> >> * 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-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
> >> >> >> >
> >> >> >> > * For (un)subscribe requests visit
> >> >> >> >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> 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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> >> >> >>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> 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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> 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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> 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
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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
> >>
> >> * For (un)subscribe requests visit
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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!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> --
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>
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