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
