On Thu, May 9, 2013 at 9:15 AM, Blake Mertz <mertzjb.gmail.com> wrote:
> g,
>
> Thanks for pointing that out -- I should have thought to do that
> before tackling the more complex compilation. I get the same error
> when trying to compile cuda-based PMEMD in serial too:
>
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory `/usr/local/src/amber12/src/pmemd/src/cuda'
> gfortran -O3 -mtune=native -DCUDA -Duse_SPFP -o pmemd.cuda
> 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
> cudaFuncSetSharedMemConfig<void ()>(void (*)(), cudaSharedMemConfig)':
>
> tmpxft_000034d4_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
>
> My CUDA_HOME and LD_LIBRARY_PATH settings were the same as before:
>
> 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/cuda/lib:/usr/local/cuda/lib64:/usr/local/src/amber12/lib
>
> Do you know if any amber12 users have successfully compiled cuda-base
> PMEMD using the nvidia cuda libraries from a debian-based linux
> distributions' repositories (i.e. Debian, Ubuntu, Linux Mint, etc.)?
> Traditionally for me it's always been easier to maintain a functional
> OS by using nvidia drivers the 'Debian way' instead of the 'Nvidia
> way', which is why I haven't bothered to install the libraries and
> drivers from nvidia's website.
>
I have never tried this. Mostly, I don't trust this route. CUDA is a
relatively new technology that is rapidly evolving. Debian's philosophy
(which is common amongst linuxes) is to maintain a very stable system
(which means only maintenance-type updates for packages in its
repositories).
I will join the previous responder and suggest that you try compiling some
of the code in the CUDA SDK. Do those work?
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 09 2013 - 08:00:02 PDT
