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)
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Received on Sat Mar 15 2014 - 01:00:02 PDT
