Dear Developers:
The first quick question is: how to set the flag "-DMPI" and "-DMPICH_IGNORE_CXX_SEEK" in the Makefile. I kept seeing the compiler using these flags during the compilation, but I just can not find where they are set. And I also don't know how to check their values.
The second question is much longer. I followed the instruction of "AmberTools 12 Reference Manual" inside the package to install a mpi enabled cuda version of Amber12.
I first do:
./configure gnu
make install
And I get everything fine, so I assume I got the serial version installed correctly. The I do:
./configure -mpi -cuda gnu
make install
The mpi package I am using is openmpi/1.6.0 , I tried several version and also the mvapich2/1.8, basically I got all the same error like the following:
Any idea what happens here? Thank you. Waiting for your reply anxiously.
make[5]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
mpif90 -O3 -mtune=native -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/sw/keeneland/cuda/4.2/linux_binary/lib64 -L/sw/keeneland/cuda/4.2/linux_binary/lib -lcurand -lcufft -lcudart -L/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/lib -L/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/lib -lnetcdf
./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::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]+0x9e): 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::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::Cartcomm::Sub(bool const*) const':
gpu.cpp:(.text._ZNK3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*) const]+0x79): 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]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intercomm::Merge(bool) const':
gpu.cpp:(.text._ZNK3MPI9Intercomm5MergeEb[MPI::Intercomm::Merge(bool) const]+0x26): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int, int) const]+0x24): 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 `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src'
make[3]: *** [cuda_parallel] Error 2
make[3]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src'
make[1]: [cuda_parallel] Error 2 (ignored)
make[1]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/AmberTools/src'
make[1]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src'
Starting installation of Amber12 (cuda parallel) at Tue Oct 2 16:22:23 EDT 2012.
cd pmemd && make cuda_parallel
make[2]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd'
make -C src/ cuda_parallel
make[3]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src/cuda'
mpif90 -O3 -mtune=native -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/sw/keeneland/cuda/4.2/linux_binary/lib64 -L/sw/keeneland/cuda/4.2/linux_binary/lib -lcurand -lcufft -lcudart -L/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/lib -L/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/lib -lnetcdf
./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::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]+0x9e): 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::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::Cartcomm::Sub(bool const*) const':
gpu.cpp:(.text._ZNK3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*) const]+0x79): 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]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intercomm::Merge(bool) const':
gpu.cpp:(.text._ZNK3MPI9Intercomm5MergeEb[MPI::Intercomm::Merge(bool) const]+0x26): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int, int) const]+0x24): 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 `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd/src'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src/pmemd'
make[1]: *** [cuda_parallel] Error 2
make[1]: Leaving directory `/nics/e/sw/keeneland/amber/12/centos5.5_gnu4.4.0_10022012/amber12/src'
make: *** [install] Error 2
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Received on Wed Oct 03 2012 - 13:00:05 PDT
