Hi All
This might not be the right place for this question...
I had some trouble compiling the Parallel GPU version of Amber11. In the end, to get it working I had to add -lmpi_cxx to the PMEMD_CU_LIBS line of config.h
I've had a read through the help for configure and I can't see any flags that would have helped me, but I thought I would ask if anyone knows what I have done wrong in the configure process please? I also figured it was worth posting this to the list as I believe other people have had this trouble in the past - for example, this post: http://archive.ambermd.org/201012/0307.html
I've included the errors I was experiencing below.
Thanks
Ali
Alison Lynton
Senior Systems Engineer
Curtin University of Technology | Curtin IT Services | Building 204 | Room 521
Telephone 08 9266 2986 | Facsimile 08 9266 1072
Email a.lynton.curtin.edu.au | Website www.curtin.edu.au
“CRICOS provider code 00301J”
mpif90 -O3 -mtune=generic -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -o pmemd.cuda.MPI gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcufft -lcudart ./cuda/cuda.a /usr/local/amber11/lib/libnetcdf.a
./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone() const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Split(int, int) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int, int) const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)':
gpu.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)]+0x1f): undefined reference to `ompi_mpi_cxx_op_intercept'
./cuda/cuda.a(gpu.o): In function `MPI::Graphcomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Graphcomm5CloneEv[MPI::Graphcomm::Clone() const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const]+0x124): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Sub(bool const*)':
gpu.cpp:(.text._ZN3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*)]+0x7b): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create(MPI::Group const&) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[MPI::Intracomm::Create(MPI::Group const&) const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intercomm::Merge(bool)':
gpu.cpp:(.text._ZN3MPI9Intercomm5MergeEb[MPI::Intercomm::Merge(bool)]+0x26): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): 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[2]: *** [pmemd.cuda.MPI] Error 1
make[2]: Leaving directory `/usr/local/amber11/src/pmemd/src'
make[1]: *** [cuda_parallel] Error 2
make[1]: Leaving directory `/usr/local/amber11/src/pmemd'
make: *** [cuda_parallel] Error 2
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Received on Sun Jun 26 2011 - 21:00:04 PDT
