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
