hi,
Could you clarify if you have built the serial version of AMBER GPU and
whether all the sample code in the NVIDIA CUDA samples folder have been
compiled without issue?
br,
g
On 9 May 2013 02:53, Blake Mertz <mertzjb.gmail.com> wrote:
> Jason,
>
> Thanks for the clarification on setting CUDA_HOME (I did list it in my
> email, but it was a big sloppy mess, you I can see how you missed it).
> So here's my new environment settings:
>
> root.NEI-GPU:/usr/local/src/amber12# echo $CUDA_HOME
> /usr/local/cuda
>
> root.NEI-GPU:/usr/local/src/amber12# echo $LD_LIBRARY_PATH
>
> /usr/local/src/amber12/lib:/usr/local/src/amber12/lib64:/usr/local/cuda/lib:/usr/local/cuda/lib64
>
> My default gcc was v4.7, so I had to re-route the gcc softlink to
> v4.6, which I guess makes sense, since I had CUDA_HOME pointed towards
> nvidia-cuda-toolkit before. This time I can't compile PMEMD
> successfully, ironically with the same error as the 'make test' I
> reported on in my original email:
>
> Starting installation of Amber12 (cuda parallel) at Wed May 8
> 21:35:42 EDT 2013
> .
> cd pmemd && make cuda_parallel
> make[2]: Entering directory `/usr/local/src/amber12/src/pmemd'
> make -C src/ cuda_parallel
> make[3]: Entering directory `/usr/local/src/amber12/src/pmemd/src'
> make -C ./cuda
> make[4]: Entering directory `/usr/local/src/amber12/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory `/usr/local/src/amber12/src/pmemd/src/cuda'
> make -C ./cuda
> make[4]: Entering directory `/usr/local/src/amber12/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory `/usr/local/src/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 gbsa.o \
> ./cuda/cuda.a -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib
> -lcurand -lcufft -lcudart -L/usr/local/src/amber12/lib
> -L/usr/local/src/amber12/lib -lnetcdf
> ./cuda/cuda.a(kCalculateGBBornRadii.o): In function `cudaError
> cudaFuncSetShared
> MemConfig<void ()>(void (*)(), cudaSharedMemConfig)':
>
> tmpxft_00001f62_00000000-6_kCalculateGBBornRadii.compute_30.cudafe1.cpp:(.text._
>
>
> Z26cudaFuncSetSharedMemConfigIFvvEE9cudaErrorPT_19cudaSharedMemConfig[cudaError
>
> cudaFuncSetSharedMemConfig<void ()>(void (*)(),
> cudaSharedMemConfig)]+0x1c): undefined reference to
> `cudaFuncSetSharedMemConfig'
> collect2: ld returned 1 exit status
> make[3]: *** [pmemd.cuda.MPI] Error 1
> make[3]: Leaving directory `/usr/local/src/amber12/src/pmemd/src'
> make[2]: *** [cuda_parallel] Error 2
> make[2]: Leaving directory `/usr/local/src/amber12/src/pmemd'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/usr/local/src/amber12/src'
> make: *** [install] Error 2
>
> I would consider starting over from scratch (serial --> parallel -->
> parallel-cuda), but I don't see how that is the issue right now.
> Again, thanks for the initial quick reply, if you have more ideas,
> that's great.
>
> Blake
>
> On Wed, May 8, 2013 at 3:19 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Do you have CUDA_HOME set? You need to have this set to build Amber, so
> if
> > it's not set anymore, re-set it to the value it had when you compiled.
> >
> > Then try adding CUDA_HOME/lib and $CUDA_HOME/lib64 to your
> LD_LIBRARY_PATH:
> >
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib:$CUDA_HOME/lib64
> >
> > This should hopefully allow the shared library with the
> > cudaFuncSetSharedMemConfig
> > symbol to be located at runtime.
> >
> > Good luck,
> > Jason
> >
> >
> > On Wed, May 8, 2013 at 2:32 PM, Blake Mertz <mertzjb.gmail.com> wrote:
> >
> >> Hello,
> >>
> >> I've been following Jason Swails' blog post on compiling Amber12 and
> >> AmberTools12 (thanks, by the way), and can get serial, parallel, and
> >> parallel with cuda versions of PMEMD compiled on my workstation
> >> equipped with two GPUs, using both openmpi (v1.4) and mpich2. "make
> >> test" runs successfully for both the serial and parallel versions of
> >> PMEMD, but when I run make test for the cuda-based version of PMEMD, I
> >> get the following error message for each test:
> >>
> >> cd nmropt/pme/distance/ && ./Run.dist_pbc SPFP
> >> /usr/local/src/amber12/include/netcdf.mod
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> >> cudaFuncSetSharedMemConfig
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> >> cudaFuncSetSharedMemConfig
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> >> cudaFuncSetSharedMemConfig
> >> ./Run.dist_pbc: Program error
> >> make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
> >> cd nmropt/pme/nmropt_1_torsion/ && ./Run.nmropt_1_torsion SPFP
> >> /usr/local/src/amber12/include/netcdf.mod
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> >> cudaFuncSetSharedMemConfig
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: symbol lookup error:
> >> ../../../../../bin/pmemd.cuda_SPFP.MPI: undefined symbol:
> >> cudaFuncSetSharedMemConfig
> >> ./Run.nmropt_1_torsion: Program error
> >> make[3]: [test.pmemd.cuda.pme] Error 1 (ignored)
> >>
> >> I've searched for the symbol 'cudaFuncSetSharedMemConfig' without much
> >> luck -- no occurrences on the amber mailing list, and very few from a
> >> google search. The only reference I could find was for someone using
> >> openmpi v1.6, which I don't think applies to this particular
> >> situation, since I got the same error with openmpi and mpich-based
> >> PMEMD codes. Here is the relevant information with the steps and
> >> environment variables I used:
> >>
> >> - Debian v7
> >> - CUDA libraries and toolkit installed from Debian repositories,
> >> version 4.2.9-2, nvidia driver 304.88
> >> - openmpi v.1.4.5-1 and mpich2 v1.4.1-4.2
> >>
> >> root.NEI-GPU:/usr/local/src/amber12# echo $CUDA_HOME
> >> /usr/lib/nvidia-cuda-toolkit
> >>
> >> root.NEI-GPU:/usr/local/src/amber12# echo $LD_LIBRARY_PATH
> >>
> >>
> /usr/lib:/usr/lib/mpich2/lib:/usr/local/src/amber12/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64
> >>
> >> root.NEI-GPU:/usr/local/src/amber12# echo $AMBERHOME
> >> /usr/local/src/amber12
> >>
> >> root.NEI-GPU:/usr/local/src/amber12# mpif90 -show
> >> gfortran -Wl,-z,relro -I/usr/include/mpich2 -I/usr/include/mpich2
> >> -L/usr/lib -lmpichf90 -lmpichf90 -lmpich -lopa -lmpl -lrt -lcr
> >> -lpthread
> >>
> >> root.NEI-GPU:/usr/local/src/amber12# mpicc -show
> >> gcc -D_FORTIFY_SOURCE=2 -Wl,-z,relro -I/usr/include/mpich2 -L/usr/lib
> >> -lmpich -lopa -lmpl -lrt -lcr -lpthread
> >>
> >> To get the openmpi-based version of cuda PMEMD to compile, I had to
> >> add the -lmpi_cxx flag to PMEMD_CU_LIBS line in config.h, as per Tru
> >> Huynh's suggestion on the amber mailing list:
> >>
> >> http://archive.ambermd.org/201210/0097.html
> >>
> >> I've been banging on this for a few days now, and thought I had it
> >> licked after successfully compiling the cuda-based PMEMD, but I'm
> >> definitely stuck on getting these tests to pass. Any help would be
> >> awesome. Thanks!
> >>
> >> Blake
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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Received on Thu May 09 2013 - 01:00:02 PDT
