Do you have CUDA_HOME set? You need to have this set to build Amber, so if
it's not set anymore, re-set it to the value it had when you compiled.
Then try adding CUDA_HOME/lib and $CUDA_HOME/lib64 to your LD_LIBRARY_PATH:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib:$CUDA_HOME/lib64
This should hopefully allow the shared library with the
cudaFuncSetSharedMemConfig
symbol to be located at runtime.
Good luck,
Jason
On Wed, May 8, 2013 at 2:32 PM, Blake Mertz <mertzjb.gmail.com> wrote:
> Hello,
>
> I've been following Jason Swails' blog post on compiling Amber12 and
> AmberTools12 (thanks, by the way), and can get serial, parallel, and
> parallel with cuda versions of PMEMD compiled on my workstation
> equipped with two GPUs, using both openmpi (v1.4) and mpich2. "make
> test" runs successfully for both the serial and parallel versions of
> PMEMD, but when I run make test for the cuda-based version of PMEMD, I
> get the following error message for each test:
>
> cd nmropt/pme/distance/ && ./Run.dist_pbc SPFP
> /usr/local/src/amber12/include/netcdf.mod
> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> cudaFuncSetSharedMemConfig
> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> cudaFuncSetSharedMemConfig
> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> cudaFuncSetSharedMemConfig
> ./Run.dist_pbc: Program error
> make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
> cd nmropt/pme/nmropt_1_torsion/ && ./Run.nmropt_1_torsion SPFP
> /usr/local/src/amber12/include/netcdf.mod
> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> cudaFuncSetSharedMemConfig
> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> cudaFuncSetSharedMemConfig
> ./Run.nmropt_1_torsion: Program error
> make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
>
> I've searched for the symbol 'cudaFuncSetSharedMemConfig' without much
> luck -- no occurrences on the amber mailing list, and very few from a
> google search. The only reference I could find was for someone using
> openmpi v1.6, which I don't think applies to this particular
> situation, since I got the same error with openmpi and mpich-based
> PMEMD codes. Here is the relevant information with the steps and
> environment variables I used:
>
> - Debian v7
> - CUDA libraries and toolkit installed from Debian repositories,
> version 4.2.9-2, nvidia driver 304.88
> - openmpi v.1.4.5-1 and mpich2 v1.4.1-4.2
>
> root.NEI-GPU:/usr/local/src/amber12# echo $CUDA_HOME
> /usr/lib/nvidia-cuda-toolkit
>
> root.NEI-GPU:/usr/local/src/amber12# echo $LD_LIBRARY_PATH
>
> /usr/lib:/usr/lib/mpich2/lib:/usr/local/src/amber12/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64
>
> root.NEI-GPU:/usr/local/src/amber12# echo $AMBERHOME
> /usr/local/src/amber12
>
> root.NEI-GPU:/usr/local/src/amber12# mpif90 -show
> gfortran -Wl,-z,relro -I/usr/include/mpich2 -I/usr/include/mpich2
> -L/usr/lib -lmpichf90 -lmpichf90 -lmpich -lopa -lmpl -lrt -lcr
> -lpthread
>
> root.NEI-GPU:/usr/local/src/amber12# mpicc -show
> gcc -D_FORTIFY_SOURCE=2 -Wl,-z,relro -I/usr/include/mpich2 -L/usr/lib
> -lmpich -lopa -lmpl -lrt -lcr -lpthread
>
> To get the openmpi-based version of cuda PMEMD to compile, I had to
> add the -lmpi_cxx flag to PMEMD_CU_LIBS line in config.h, as per Tru
> Huynh's suggestion on the amber mailing list:
>
> http://archive.ambermd.org/201210/0097.html
>
> I've been banging on this for a few days now, and thought I had it
> licked after successfully compiling the cuda-based PMEMD, but I'm
> definitely stuck on getting these tests to pass. Any help would be
> awesome. Thanks!
>
> Blake
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 08 2013 - 12:30:03 PDT
