Hi Ross,
This is the output:
$ mpif90 -show
gfortran -I/gpfs/apps/mpi/openmpi/1.4.5/gcc/include -pthread
-I/gpfs/apps/mpi/openmpi/1.4.5/gcc/lib -L/usr/lib64 -L/usr/local/lib
-Wl,--rpath -Wl,/usr/local/lib -L/usr/lib64
-L/gpfs/apps/mpi/openmpi/1.4.5/gcc/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte
-lopen-pal -lrdmacm -libverbs -lpsm_infinipath -ltorque -lnuma -ldl
-Wl,--export-dynamic -lnsl -lutil -lm -ldl
thanks,
Thomas
On 20 November 2012 23:09, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Thomas,
>
> Is your mpi configured for gfortran?
>
> Try mpif90 -show
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
>
> On 11/20/12 12:47 PM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
>
> >Thanks Ross! The serial pmemd.CUDA compiles but pmemd.CUDA.MPI fails with
> >the following output. Do you have any idea what went wrong?
> >
> >
> >mpif90 -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -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 nbips.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 binrestart.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 findmask.o remd.o
> >multipmemd.o remd_exchg.o amd.o \
> > ./cuda/cuda.a -L/gpfs/home/lspro220u1/Opt/cuda-4.2/cuda/lib64
> >-L/gpfs/home/lspro220u1/Opt/cuda-4.2/cuda/lib -lcurand -lcufft -lcudart
> >-L/gpfs/home/lspro220u1/Opt/amber12/lib
> >-L/gpfs/home/lspro220u1/Opt/amber12/lib -lnetcdf
> >./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(vo
> >id
> >(*)(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::Clone() const':
> >gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone()
> >const]+0x2a): 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): 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::Intracomm::Create_cart(int, int
> >const*, bool const*, bool) const':
> >gpu.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Cr
> >eate_cart(int,
> >int const*, bool const*, bool) const]+0x8f): 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::C
> >reate_graph(int,
> >int const*, int const*, bool) const]+0x2b): undefined reference to
> >`MPI::Comm::Comm()'
> >./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcom
> >m::Clone()
> >const]+0x25): 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[4]: *** [pmemd.cuda.MPI] Error 1
> >make[4]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src'
> >make[3]: *** [cuda_parallel] Error 2
> >make[3]: Leaving directory `/gpfs/home/lspro220u1/Opt/amber12/src/pmemd'
> >make[2]: *** [cuda_parallel] Error 2
> >make[2]: Leaving directory `/gpfs/home/lspro220u1/Opt/amber12/src'
> >make[1]: [cuda_parallel] Error 2 (ignored)
> >make[1]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/AmberTools/src'
> >make[1]: Entering directory `/gpfs/home/lspro220u1/Opt/amber12/src'
> >Starting installation of Amber12 (cuda parallel) at Tue Nov 20 22:45:23
> >EET
> >2012.
> >cd pmemd && make cuda_parallel
> >make[2]: Entering directory `/gpfs/home/lspro220u1/Opt/amber12/src/pmemd'
> >make -C src/ cuda_parallel
> >make[3]: Entering directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src'
> >make -C ./cuda
> >make[4]: Entering directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make[4]: `cuda.a' is up to date.
> >make[4]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make -C ./cuda
> >make[4]: Entering directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make[4]: `cuda.a' is up to date.
> >make[4]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make -C ./cuda
> >make[4]: Entering directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make[4]: `cuda.a' is up to date.
> >make[4]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make -C ./cuda
> >make[4]: Entering directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make[4]: `cuda.a' is up to date.
> >make[4]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make -C ./cuda
> >make[4]: Entering directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >make[4]: `cuda.a' is up to date.
> >make[4]: Leaving directory
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src/cuda'
> >mpif90 -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -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 nbips.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 binrestart.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 findmask.o remd.o
> >multipmemd.o remd_exchg.o amd.o \
> > ./cuda/cuda.a -L/gpfs/home/lspro220u1/Opt/cuda-4.2/cuda/lib64
> >-L/gpfs/home/lspro220u1/Opt/cuda-4.2/cuda/lib -lcurand -lcufft -lcudart
> >-L/gpfs/home/lspro220u1/Opt/amber12/lib
> >-L/gpfs/home/lspro220u1/Opt/amber12/lib -lnetcdf
> >./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(vo
> >id
> >(*)(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::Clone() const':
> >gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone()
> >const]+0x2a): 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): 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::Intracomm::Create_cart(int, int
> >const*, bool const*, bool) const':
> >gpu.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Cr
> >eate_cart(int,
> >int const*, bool const*, bool) const]+0x8f): 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::C
> >reate_graph(int,
> >int const*, int const*, bool) const]+0x2b): undefined reference to
> >`MPI::Comm::Comm()'
> >./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcom
> >m::Clone()
> >const]+0x25): 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
> >`/gpfs/home/lspro220u1/Opt/amber12/src/pmemd/src'
> >make[2]: *** [cuda_parallel] Error 2
> >make[2]: Leaving directory `/gpfs/home/lspro220u1/Opt/amber12/src/pmemd'
> >make[1]: *** [cuda_parallel] Error 2
> >make[1]: Leaving directory `/gpfs/home/lspro220u1/Opt/amber12/src'
> >make: *** [install] Error 2
> >
> >
> >
> >
> >
> >On 20 November 2012 18:28, Ross Walker <ross.rosswalker.co.uk> wrote:
> >
> >> Hi Thomas,
> >>
> >> Can you quickly try GCC instead and see if that works?
> >>
> >> >From a completely clean tree - best to untar and start from scratch.
> >>
> >> ./configure -cuda gnu (say yes to applying the patches)
> >> ./configure -cuda gnu (say yes again)
> >> ..Repeat until configure doesn't ask you to patch anymore - this is an
> >> unfortunate bug in the patching system that we can't retroactively fix..
> >>
> >> ./configure -cuda gnu
> >> make install
> >>
> >> There is no difference in performance for GPU runs between the GNU or
> >> Intel compilers and the GNU ones (amazingly!) seem to be more stable
> >>these
> >> days.
> >>
> >> All the best
> >> Ross
> >>
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Nov 20 2012 - 13:30:03 PST
