Hi Alison,
What version of MPI are you using and what does mpif90 --show report?
The -lmpi_cxx library if needed by your mpi installation should
automatically be included by the mpif90 script. My suspicion is that your
MPI installation was configured for C and Fortran only and whoever installed
it skipped the C++ bindings. It is possible an autoconf would also skip this
if for example it did not find a c++ compiler at the time configure was run.
You also need to make sure you are using a MPI that support MPI v2.0. For
example MPICH2 will work but MPICH will not.
All the best
Ross
> -----Original Message-----
> From: Alison Lynton [mailto:a.lynton.curtin.edu.au]
> Sent: Sunday, June 26, 2011 8:34 PM
> To: AMBER Mailing List
> Subject: [AMBER] Problems Compiling Amber11 Parallel GPU
>
> 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::C
> reate(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)]+0
> x26): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Int
> racomm::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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 27 2011 - 08:30:04 PDT
