Farid,
I agree, my bugfixes from about a month ago does have all the patches
needed. I checked both files.
Thanks
On Thu, Aug 25, 2011 at 3:09 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> 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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>
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>
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>
>
>
>
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>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Carlos P Sosa, Ph.D.
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 - 13:30:03 PDT
