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
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Received on Sat Mar 15 2014 - 00:00:03 PDT
