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(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::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::Create_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::Create_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::Cartcomm::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(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::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::Create_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::Create_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::Cartcomm::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
>
>
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Received on Tue Nov 20 2012 - 13:00:02 PST
