I had the same error after applying bugfix 17, and (re)patching it again is what solved the problem. See my post and Ross's solution from the archive:
http://archive.ambermd.org/201108/0525.html
If you look at AmberTools bugfix 13, it mentioned that this is needed for Amber11 bugfix 17.
--Farid
________________________________________
From: Carlos P Sosa [cpsosa.msi.umn.edu]
Sent: Thursday, August 25, 2011 1:04 PM
To: amber.ambermd.org
Subject: [AMBER] Potential problem with CUDA version in release 18?
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 - 13:30:02 PDT
