Hi Vivek,
Not having GPUs on the head node is likely the problem. It looks like the
cuda libraries are not properly installed on the head node. Either have
the administrator make sure the head node is configured identically to the
compute nodes, with identical driver and compiler versions or request an
interactive login on one of the GPU enabled compute nodes and try
compiling there.
All the best
Ross
On 1/22/13 10:05 AM, "Vivek Shankar Bharadwaj" <vbharadw.mymail.mines.edu>
wrote:
>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 Wed Jan 23 2013 - 01:30:04 PST
