On Fri, Nov 16, 2012 at 3:00 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
> Just to note a case of success for comparison, I was able to compile an
> amber12-with-patches version of pmemd.cuda on Monday. SPFP passed all tests
> on a C2070.
>
Yea, I also just built it and used it on Keeneland, and it worked as I
expected. I was just wondering if anyone had experienced libstdc++ being
omitted from the linking step, or knew why we should *not* see this error.
It appears to me that we shouldn't necessarily expect libstdc++ to be
searched by a gfortran linker, but this is all speculation. Basically --
could this be a problem? And if so, how do we address it?
Thanks,
Jason
>
> RHEL 6 Server
> GNU 4.4.6
> NVCC 4.2 V0.2.1221
> NVIDIA driver 295.41
>
> On Nov 16, 2012, at 1:42 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > Hi everyone,
> >
> > George and I were having some issues recently building an
> > amber12-with-patches version of pmemd.cuda. We were getting these types
> of
> > errors at the link stage:
> >
> > ./cuda/cuda.a(gpu.o):gpu.cpp:function gpu_startup_: error: undefined
> > reference to 'operator new(unsigned long)'
> > ./cuda/cuda.a(gpu.o):gpu.cpp:function gpu_startup_: error: undefined
> > reference to 'operator delete(void*)'
> > ... etc.
> >
> > new and delete are perfectly valid C++ operators, and it turns out that
> the
> > issue was that the linking is done by the Fortran compiler (in this case
> > gfortran), which was not actually loading the C++ standard library during
> > the link stage.
> >
> > Adding -lstdc++ to the PMEMD_LD variable in the config.h solved the
> > compilation issues. Has anyone else seen this before? This also happens
> > with the master branch, unsurprisingly.
> >
> > System specifications:
> > Ubuntu 11.10
> > GNU compilers version 4.6.1
> > NVCC version 4.2 V0.2.1221
> >
> > Same errors (and fix) seen with ifort Version 12.1.2
> >
> > Thoughts/comments?
> >
> > Thanks!
> > Jason
> >
> > P.S. Another note, the resulting pmemd.cuda_SPFP executable fails all
> > tests with the following error message:
> > Error: unknown error launching kernel kClearGBBuffers
> >
> > So maybe something isn't quite right with the system somehow? Driver
> > version 295.20. The available graphics cards are a GTS 420 and a GTX
> 470.
> > I'm not sure what's happening here...
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> >
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 16 2012 - 13:00:03 PST
