On Wed, May 30, 2012, Jonathan Gough wrote:
>
> jonathan.jonathan-M-601A:~$ echo $LD_LIBRARY_PATH
> /usr/local/cuda/lib64:/usr/local/cuda/lib:
(Others can correct me, but I don't think LD_LIBRARY_PATH is relevant here.)
One thing that looks suspicious is the weird order of linking: (from the
log file):
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 \
-L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft -lcudart
./cuda/cuda.a -L/home/jonathan/amber12/lib -L/home/jonathan/amber12/lib
-lnetcdf
For machines that link based on order, it may be that the ./cuda/cuda.a
reference should come *before* the cuda libs, not after them. Try
editing the PMEMD_CU_LIBS variable in your config.h file to but the
"./cuda/cuda.a" part first rather than last.
No guarantees at all, but it's a simple thing to try, and might help.
....dac
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Received on Wed May 30 2012 - 11:30:03 PDT
