oh that was simply solved by upgrading of G++ :) the only problem which remains is the missing of support of mu GPU :( That time I've tried to start simulation on simply 2 cores CPU + geforce 9500
>From md run I've obtained NOTE: Error occurred during GPU detection: CUDA driver version is insufficient for CUDA runtime version Can not use GPU acceleration, will fall back to CPU kernels. ED sampling will be performed! ED: Reading edi file new_a2a_pca_biased.edi ED: Note: Reference and average structure are composed of the same atom indices. ED: Found 1 ED group. Using 1 MPI thread Using 2 OpenMP threads No GPUs detected I've installed cuda-5.0 with driver NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29 00:05:49 PDT 2012 that system works fine with the recent nvidia GPU's but has no support for GeForce 9500. James 2013/1/24, James Starlight <jmsstarli...@gmail.com>: > After switching to gcc-4.6 I've obtained that error on the first step > of gromacs compilation > > [ 0%] Building NVCC (Device) object > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > gcc: error trying to exec 'cc1plus': execvp: No such file or directory > CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): > Error generating > > /home/own/distr/gromacs-4.6/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > > > make[2]: *** > [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] > Error 1 > make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 > make: *** [all] Error 2 > > > 2013/1/24, Szilárd Páll <szilard.p...@cbr.su.se>: >> Hi all, >> >> Let me clarify one thing: I highly doubt that the *gcc version* upgrade >> is >> what fixes your the issue, but rather the standard C++ library's version, >> as you can see the undefined symbols refer to "GLIBCXX_3.4.15". >> >> Of course, updating the compiler is a perfectly fine solution if you get >> the new (enough version of the) standard C++ library by doing so. >> >> Just wanted to clarify this for users bumping into this issue later. >> >> Cheers, >> >> -- >> Szilárd >> >> >> On Wed, Jan 23, 2013 at 5:47 PM, Ricardo <rsoa...@fcfrp.usp.br> wrote: >> >>> On 01/22/2013 06:02 PM, Christoph Junghans wrote: >>> >>>> Message: 5 >>>>> Date: Tue, 22 Jan 2013 19:42:01 +0100 >>>>> From: Szil?rd P?ll<szilard.p...@cbr.su.se> >>>>> Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on >>>>> Debian >>>>> To: Discussion list for GROMACS users<gmx-users@gromacs.org> >>>>> Message-ID: >>>>> >>>>> <CANnYEw5=t=25hnZPfHpdJot7=3YN**CU1AeGv7HCAc3mut_75w8Q@mail.** >>>>> gmail.com <3yncu1aegv7hcac3mut_75...@mail.gmail.com>> >>>>> Content-Type: text/plain; charset=ISO-8859-1 >>>>> >>>>> On Tue, Jan 22, 2013 at 12:45 PM, James >>>>> Starlight<jmsstarlight@gmail.** >>>>> com <jmsstarli...@gmail.com>>wrote: >>>>> >>>>> Szilárd, >>>>>> >>>>>> Today I've tried to re-install cuda+gromacs and do apt-get >>>>>> distr-upgrade but the same error was obtained during gromacs >>>>>> >>>>>> I'm don't see how does the distribution upgrade relate to the issues >>>>> you >>>>> had (except if you have updated glibs to a newer version which is >>>>> *still* >>>>> incompatible with libcuda. You should probably try getting a more >>>>> recent >>>>> glibc and GCC version, one that libcuda is linked against. However, >>>>> I'm >>>>> not >>>>> sure what the source of your problem is, so I can't suggest a certain >>>>> solution. >>>>> >>>> I had a similar problem on Gentoo Linux >>>> (https://bugs.gentoo.org/show_**bug.cgi?id=452386<https://bugs.gentoo.org/show_bug.cgi?id=452386>), >>>> it helped to use a >>>> newer version of gcc (>=4.6). >>>> >>>> Cheers, >>>> >>>> Christoph >>>> >>> >>> >>> >>> I also had this problem, and found that (manually) updating GCC to >>> version >>> 4.6 or higher has fully solved some installation issues with GROMACS >>> 4.6. >>> Please note that, for older linux dists, updating via console 'apt-get >>> update' does not assure that you'd get newer versions of GCC, therefore, >>> in >>> this case, it should be downloaded and installed manually. >>> >>> Cheers >>> >>> >>> compilation. By the way where I could provide --add-needed option ? >>>>>> >>>>> CMAKE_EXE_LINKER_FLAGS=-wl,--**add-needed >>>>> >>>>> Cheers, >>>>> Szilárd >>>>> >>>>> >>>>> >>>>>> James >>>>>> >>>>>> >>>>>> 2013/1/21 Szilárd Páll<szilard.p...@cbr.su.se>: >>>>>> >>>>>>> Szilárd >>>>>>> >>>>>> -- >>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>>>>> posting! >>>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>>>> * Can't post? Read >>>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>>> >>>>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>> >>> Ricardo O S Soares >>> http://fisbio.fcfrp.usp.br/**joomla/ >>> <http://fisbio.fcfrp.usp.br/joomla/> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists