On Sun, Oct 07, 2012 at 09:35:48PM +0000, Su, Shiquan wrote:
> Dear Amber Team:
> Thanks Jason Swails, Tru Huynh, and David A Case. All your suggestions and guidances help me through the installation.
> Now I can install Amber 12 using intel compiler.
> I still have the problem using gnu compiler, I attached the module list result at the end:
>
> gpu.cpp:(.text._ZN3MPI9Intercomm5MergeEb[MPI::Intercomm::Merge(bool)]+0x26): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone() const':
> gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int, int) const]+0x24): more undefined references to `MPI::Comm::Comm()' follow
> ./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI3WinE[vtable for MPI::Win]+0x48): undefined reference to `MPI::Win::Free()'
> ./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
> collect2: ld returned 1 exit status
> make[3]: *** [pmemd.cuda.MPI] Error 1
> make[3]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10072012/amber12/src/pmemd/src'
> make[2]: *** [cuda_parallel] Error 2
> make[2]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10072012/amber12/src/pmemd'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10072012/amber12/src'
> make: *** [install] Error 2
imho, you just need to fix your config.h
PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart
changed to:
PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart -lmpi_cxx
and run make once more.
>
> [shiquan1.kidlogin2 amber12]$ module list
> Currently Loaded Modulefiles:
> 1) modules 5) PE-gnu 9) swtools
> 2) torque/2.5.11 6) openmpi/1.5.1-gnu 10) numpy/1.4.1
> 3) moab/6.1.5 7) cuda/4.2 11) netcdf/4.1.1
> 4) gold 8) python/2.7 12) gcc/4.4.0
are you sure that your openmpi/1.5.1-gnu is using gcc/4.4.0 ?
otoh, you could try to make an mpich/cuda version as the developpers are hinting.
Best regards,
Tru
--
Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru.pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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Received on Mon Oct 08 2012 - 06:30:03 PDT
