Try adding "-lstdc++" to the linker flags...
This is probably GCC 4.6 or later...
On Tue, Apr 30, 2013 at 9:17 AM, Kanin Wichapong
<kanin.wichapong.gmail.com>wrote:
> Dear Sirs,
>
> I got this error during the AMBER cuda installation:
>
> 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-5.0/lib64 -L/usr/local/cuda-5.0/lib
> -lcurand -lcufft -lcudart -L/home/kanin/PROGs/AMBER-12/amber12/lib
> -L/home/kanin/PROGs/AMBER-12/amber12/lib -lnetcdf
> /usr/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol '_Znam.
> .GLIBCXX_3.4'
> /usr/bin/ld: note: '_Znam..GLIBCXX_3.4' is defined in DSO
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6 so try adding it to the linker
> command line
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6: could not read symbols: Invalid
> operation
> collect2: error: ld returned 1 exit status
> make[3]: *** [pmemd.cuda] Error 1
> make[3]: Leaving directory
> `/home/kanin/PROGs/AMBER-12/amber12/src/pmemd/src'
> make[2]: *** [cuda] Error 2
> make[2]: Leaving directory `/home/kanin/PROGs/AMBER-12/amber12/src/pmemd'
> make[1]: *** [cuda] Error 2
> make[1]: Leaving directory `/home/kanin/PROGs/AMBER-12/amber12/src'
> make: *** [install] Error 2
>
>
> I tried to google for the solutions but unfortunately I couldn't find the
> right solutions and I can't fix the problems.
>
> I already installed * *installed Nvidia driver (version 304.05) and CUDA
> Toolbox (version 5.0.35) and already set the LIBRARY for the cuda. My
> computer is Ubuntu13.04.
>
> Any body has some ideas to solve this problems.
>
> Thank you so much in advance for your help or any suggestions.
>
> Best Regards,
> Kanin Wichapong
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 30 2013 - 11:30:02 PDT
