Hi everyone,
I am trying to install the cuda version of Amber12 on a Ubuntu 10.04
server. I have installed cuda ver 4.2 and the latest Nvidia driver
(NVIDIA-Linux-x86_64-310.32.run)
I am getting the following error. It seems like a library issue. But I have
added all the required paths into the LD_LIBRARY PATH variable. The
installation is on the head node and there are no GPUs on the headnode.
Could this be a problem? I did not have any issues while installing the
driver though.
make[5]: Leaving directory `/home/local/amber12/src/pmemd/src/cuda'
gfortran -O3 -mtune=native -DCUDA -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 \
./cuda/cuda.a -L/usr/local/cuda//lib64 -L/usr/local/cuda//lib
-lcurand -lcufft -lcudart -L/home/local/amber12/lib
-L/home/local/amber12/lib -lnetcdf
/usr/local/cuda//lib64/libcudart.so: undefined reference to
`std::_List_node_base::_M_unhook().GLIBCXX_3.4.14'
/usr/local/cuda//lib64/libcudart.so: undefined reference to
`std::_List_node_base::_M_hook(std::_List_node_base*).GLIBCXX_3.4.14'
collect2: ld returned 1 exit status
make[4]: *** [pmemd.cuda] Error 1
make[4]: Leaving directory `/home/local/amber12/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/home/local/amber12/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/local/amber12/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory `/home/local/amber12/AmberTools/src'
make[1]: Entering directory `/home/local/amber12/src'
Any help will be appreciated.
Thank you.
--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Tue Jan 22 2013 - 10:30:02 PST
