it worked. a VERY BIG THANK YOU!
On Sat, Mar 15, 2014 at 3:43 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> After entering part of your error message into google, this was the first
> result:
>
> http://archive.ambermd.org/201304/0492.html
>
> Try following the advice there and add '-lstdc++' to the cuda linker flags
> (PMEMD_CU_LIBS in config.h).
>
> Hope this helps,
>
> -Dan
>
>
>
> On Sat, Mar 15, 2014 at 12:30 AM, Ayesha Fatima
> <ayeshafatima.69.gmail.com>wrote:
>
> > Dear Amberists,
> > I have installed Ubuntu 13.10 on a system with NVIDIA GTX680 and CUDA
> 5.5.
> > During installation, after some errors we finally managed. We also
> > installed Amber 12 and updated the AmberTools 12 to version 13. When we
> > want configure cuda on it, we get the following error
> > -----------------------------
> > 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-5.5/lib64 -L/usr/local/cuda-5.5/lib
> > -lcurand -lcufft -lcudart -L/home/william/amber12/lib
> > /home/william/amber12/lib/libnetcdf.a
> > /usr/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol '_Znam.
> > .GLIBCXX_3.4'
> > /usr/lib/x86_64-linux-gnu/libstdc++.so.6: error adding symbols: DSO
> missing
> > from command line
> > collect2: error: ld returned 1 exit status
> > make[3]: *** [pmemd.cuda] Error 1
> > make[3]: Leaving directory `/home/william/amber12/src/pmemd/src'
> > make[2]: *** [cuda] Error 2
> > make[2]: Leaving directory `/home/william/amber12/src/pmemd'
> > make[1]: *** [cuda] Error 2
> > make[1]: Leaving directory `/home/william/amber12/src'
> > make: *** [install] Error 2
> > ---------------------------------------------
> > We have searched the AMBER mailing list and found that someone had asked
> to
> > add lstdc++ linker flag.
> > I would appreciate if someone on the list would let me know how to add
> it.
> > On the internet there were options of '-Wl,' and '-lm'. but none seem to
> > work.
> > i shall appreciate the help
> > Thank you
> > Ayesha Fatima
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Mar 15 2014 - 01:30:03 PDT
