If it's any help, I've written a rough guide that goes through the
installation steps that I went through. It's not very pretty and could be
better, but it worked for me. I'll attach it to this email. hopefully it
might help.
br,
g
On 9 May 2013 15:28, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>
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Received on Fri May 10 2013 - 10:00:02 PDT
