Dear Jason M. Swails:
I am the software manager of amer12 on Keeneland. I once did succeed to install the MPI version. by "./configure -mpi -cuda gnu", and "make install". I need to do the installation again, but I just can not succeed this time.
After all, I just want to finish a standard installation of Amber12 including the MPI version (configured by "./configure -mpi -cuda gnu") . If you can do this successfully, would you please have a try on Keeneland, and send me your instruction? If you could not, would you please confirm the error with me? Thank you.
On Oct 3, 2012, at 9:33 PM, Jason Swails wrote:
> On Wed, Oct 3, 2012 at 3:57 PM, Su, Shiquan <ssu2.utk.edu> wrote:
>
>> Dear Developers:
>>
>
>
>> 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':
>>
>>
>
> I have never had problems compiling pmemd.cuda.MPI on Keeneland. What do
> the following commands return:
>
> mpif90 -show
> module list
> ?
>
> Also, why not just use Keeneland's Amber 12 build? You can just do
>
> module load amber/12
>
> and you will have access to pmemd.cuda and pmemd.cuda.MPI in your PATH.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Thu Oct 04 2012 - 10:30:03 PDT
