Hi Sasha,
This looks like some kind of namespace mangling between the C++ and C /
Fortran linking. Are you sure the compiler is the same for C++, C and
Fortran? Try:
mpicc -show
mpicxx -show
mpif90 -show
The other 'guess' is that the MPI library was built without C++ support.
All the best
Ross
> -----Original Message-----
> From: Sasha Buzko [mailto:obuzko.ucla.edu]
> Sent: Tuesday, December 14, 2010 3:02 PM
> To: AMBER Mailing List
> Subject: [AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand
>
> Dear Amber developers,
> I'm having some compilation problems while trying to compile CUDA source
> for Infiniband. The last 50 lines of the output are given below the
message.
>
> The OS is CentOS 5.5. Here's the full output of the uname -a command:
> Linux master 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010
> x86_64 x86_64 x86_64 GNU/Linux
>
> I'm using GNU compiler, version 4.1.2, and OpenMPI libraries compiled
> with the same. All environment variables are set correctly, and I run
> make clean before any compilation.
> Compilation of parallel pmemd.cuda.MPI for local execution went well and
> the code works as advertised (using mpich2). At the same time,
> compilation of conventional CPU code for pmemd.MPI over Infiniband went
> fine as well - using the same OpenMPI libraries. I tested its execution
> over multiple nodes with QDR IB, and everything looks normal.
>
> So the problem seems to be restricted to the parallel CUDA version. Are
> there any limitations in the source code that could appear in the IB
> version? Is there anything I could do to diagnose the problem?
> Thanks in advance for any suggestions.
>
> Best,
>
> Sasha
>
>
>
>
> ar: creating cuda.a
> a - cuda_info.o
> a - gpu.o
> a - gputypes.o
> a - kForcesUpdate.o
> a - kCalculateLocalForces.o
> a - kCalculateGBBornRadii.o
> a - kCalculatePMENonbondEnergy.o
> a - radixsort.o
> a - radixsort_c.o
> a - kCalculateGBNonbondEnergy1.o
> a - kCalculateGBNonbondEnergy2.o
> a - kShake.o
> a - kNeighborList.o
> a - kPMEInterpolation.o
> a - cudpp_scan.o
> a - cudpp_scan_c.o
> make[3]: Leaving directory `/usr/local/amber11/src/pmemd/src/cuda'
> make -C ./cuda
> make[3]: Entering directory `/usr/local/amber11/src/pmemd/src/cuda'
> make[3]: `cuda.a' is up to date.
> make[3]: Leaving directory `/usr/local/amber11/src/pmemd/src/cuda'
> make -C ./cuda
> make[3]: Entering directory `/usr/local/amber11/src/pmemd/src/cuda'
> make[3]: `cuda.a' is up to date.
> make[3]: Leaving directory `/usr/local/amber11/src/pmemd/src/cuda'
> make -C ./cuda
> make[3]: Entering directory `/usr/local/amber11/src/pmemd/src/cuda'
> make[3]: `cuda.a' is up to date.
> make[3]: Leaving directory `/usr/local/amber11/src/pmemd/src/cuda'
> mpif90 -O3 -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
> ./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::I
> nit(void
> (*)(void const*, void*, int, MPI::Datatype const&), bool)]+0x19):
> undefined reference to `ompi_mpi_cxx_op_intercept'
> ./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create(MPI::Group
> const&) const':
> gpu.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[MPI::Intraco
> mm::Create(MPI::Group
> const&) const]+0x2a): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o): In function `MPI::Graphcomm::Clone() const':
> gpu.cpp:(.text._ZNK3MPI9Graphcomm5CloneEv[MPI::Graphcomm::Clone()
> const]+0x25): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
> gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone()
> const]+0x25): 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::Intraco
> mm::Create_graph(int,
> int const*, int const*, bool) const]+0x2b): 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*)]+0x76): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiP
> KiPKbb[MPI::Intracomm::Create_cart(int,
> int const*, bool const*, bool) const]+0x8f): 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 Tue Dec 14 2010 - 16:00:03 PST
