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.
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
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> AMBER-Developers.ambermd.org
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>
>
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Received on Fri Nov 16 2012 - 12:30:02 PST
