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
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Received on Tue Apr 30 2013 - 09:30:02 PDT
