[AMBER] Potential problem with CUDA version in release 18?

From: Carlos P Sosa <cpsosa.msi.umn.edu>
Date: Thu, 25 Aug 2011 13:04:19 -0500 (CDT)

Farid,

I patched AmberTools 1.5 when I installed AMBER 11 about a month ago. I
did not see a new patch set for AmberTools. The code was working before I
applied patch 17.

On Thu, Aug 25, 2011 at 12:39 PM, Ismail, Mohd F. <farid.ou.edu> wrote:

    Did you patch AmberTools 1.5?

    I think the instruction mentions that AmberTools need to be patched too.


    --Farid
    ________________________________________
    From: Carlos P Sosa [cpsosa.msi.umn.edu]
    Sent: Thursday, August 25, 2011 12:26 PM
    To: amber.ambermd.org
    Subject: [AMBER] Potential problem with CUDA version in release 18?

    Hello,

    I just applied patches 17 to bring my version up to Release 18 and found
    this problem. gpu_armset is not in pmemd directory. Did I miss
something
    when patching?

    Thanks,

    make[3]: Leaving directory
    `/home/applications/AMBER/11/amber11/src/pmemd/src/cuda'
    gfortran -O3 -DCUDA -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
    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 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 -L/usr/local/cuda-3.2/lib64 -L/usr/local/cuda-3.2/lib
    -lcufft -lcudart ./cuda/cuda.a
    /home/applications/AMBER/11/amber11/lib/libnetcdf.a
    ./cuda/cuda.a(gpu.o): In function `gpu_amrset_':
    gpu.cpp:(.text+0x2438): undefined reference to `curandCreateGenerator'
    gpu.cpp:(.text+0x244e): undefined reference to
    `curandSetPseudoRandomGeneratorSeed'
    ./cuda/cuda.a(kForcesUpdate.o): In function `kRandom':
    tmpxft_00005864_00000000-4_kForcesUpdate.compute_20.cudafe1.cpp:(.text+0x3b56):
    undefined reference to `curandGenerateNormalDouble'
    collect2: ld returned 1 exit status
    make[2]: *** [pmemd.cuda] Error 1
    make[2]: Leaving directory
    `/home/applications/AMBER/11/amber11/src/pmemd/src'
    make[1]: *** [cuda] Error 2
    make[1]: Leaving directory
`/home/applications/AMBER/11/amber11/src/pmemd'
    make: *** [cuda] Error 2

    Carlos P Sosa
    Biomedical Informatics and Computational Biology (BICB) Consultant
    Minnesota Supercomputing Institute
    for Advanced Computational Research
    University of Minnesota
    Walter Library 509
    117 Pleasant Street
    Minneapolis, MN 55455



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Received on Thu Aug 25 2011 - 11:30:02 PDT
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