Hi,
I'd appreciate a 'push' in the right direction for troubleshooting a pmemd.cuda
compilation.
I have ---updated to AmberTools 1.5, applied the AT15_Amber11.py, applied the
most recent bugfix.all.tar.bz2, successfully built the Ambertools 1.5 version,
the AMBER-serial versions, but am having an issue at the final stage of
compilation of the pmemd -cuda version.
The prerequeisites established on Ross's ambermd page are all satisfied ---and
the earlier (prep-patched version worked fine on my Quad-Tesla system).
The pmemd.cuda compilation is choking with an underfined reference to a netcdf
routine---and I am not sure about what to look into.
This looks like a missing routine (was their a netcdf update that I am
missing?).
An ASIDE:
________________________________________________________________________________
I noted one pecularity even in compiling the pmemd serial version in that it was
not finding the *.mod files:
$(NETCDF):
$(MAKE) -C ../netcdf/src install
# cp ../netcdf/include/*.mod ./src
# DLH-this path doesn't exist guys.
# I think we want the include under AmberTools
cp ../../AmberTools/include/*.mod ./src
when I made this small pathchange to me pmemd Makefile the serial version
compiled fine.
_______________________________________________________________________________
This is the issue I am running into with attempts to compile (gnu compilers) the
CUDA enabled version--thanks for pointing me in some possible directions for
trouble shooting this. Danni
ERROR UPON ATTEMPT TO COMPILE THE GPU/CUDA VERSION.
make[3]: Leaving directory `/usr/local/lib/amber11/src/pmemd/src/cuda'
gfortran -O3 -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 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 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 -L/usr/local/cuda/lib64
-L/usr/local/cuda/lib -lcufft -lcudart ./cuda/cuda.a
bintraj.o: In function `__bintraj_mod__checkerror':
bintraj.f90:(.text+0xae): undefined reference to `__netcdf__nf90_strerror'
bintraj.o: In function `__bintraj_mod__open_binary_files':
bintraj.f90:(.text+0x1db): undefined reference to `__netcdf__nf90_create'
bintraj.f90:(.text+0x234): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x279): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x2ae): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x2e3): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x31b): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x359): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x397): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x3d5): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x413): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.o:bintraj.f90:(.text+0x451): more undefined references to
`__netcdf__nf90_put_att_text' follow
bintraj.o: In function `__bintraj_mod__open_binary_files':
bintraj.f90:(.text+0x4f0): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x587): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x5bf): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x686): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x6c4): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x717): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x75a): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x7f9): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x8a5): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x94f): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x98d): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0xa37): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0xa75): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0xacd): undefined reference to `__netcdf__nf90_set_fill'
bintraj.f90:(.text+0xb01): undefined reference to `__netcdf__nf90_enddef'
bintraj.f90:(.text+0xc9f): undefined reference to
`__netcdf__nf90_put_var_1d_text'
bintraj.f90:(.text+0xe43): undefined reference to
`__netcdf__nf90_put_var_1d_text'
bintraj.f90:(.text+0x103c): undefined reference to
`__netcdf__nf90_put_var_1d_text'
bintraj.f90:(.text+0x108f): undefined reference to `__netcdf__nf90_create'
bintraj.f90:(.text+0x10e6): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x1133): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x1170): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x11a5): undefined reference to `__netcdf__nf90_def_dim'
bintraj.f90:(.text+0x11dd): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x121b): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x1259): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x1297): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x12d5): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.o:bintraj.f90:(.text+0x1313): more undefined references to
`__netcdf__nf90_put_att_text' follow
bintraj.o: In function `__bintraj_mod__open_binary_files':
bintraj.f90:(.text+0x13a5): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x1434): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x146c): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x1533): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x1571): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x15a9): undefined reference to
`__netcdf__nf90_put_att_one_fourbytereal'
bintraj.f90:(.text+0x15d9): undefined reference to `__netcdf__nf90_set_fill'
bintraj.f90:(.text+0x1605): undefined reference to `__netcdf__nf90_enddef'
bintraj.f90:(.text+0x17a8): undefined reference to
`__netcdf__nf90_put_var_1d_text'
bintraj.f90:(.text+0x1992): undefined reference to
`__netcdf__nf90_def_var_manydims'
bintraj.f90:(.text+0x19d0): undefined reference to `__netcdf__nf90_put_att_text'
bintraj.f90:(.text+0x1a08): undefined reference to
`__netcdf__nf90_put_att_one_fourbytereal'
bintraj.o: In function `__bintraj_mod__close_binary_files':
bintraj.f90:(.text+0x1a44): undefined reference to `__netcdf__nf90_close'
bintraj.f90:(.text+0x1a6a): undefined reference to `__netcdf__nf90_close'
bintraj.o: In function `__bintraj_mod__write_binary_crds_axis_flipped':
bintraj.f90:(.text+0x1cf1): undefined reference to
`__netcdf__nf90_put_var_2d_fourbytereal'
bintraj.o: In function `__bintraj_mod__write_binary_crds':
bintraj.f90:(.text+0x1f0f): undefined reference to
`__netcdf__nf90_put_var_2d_eightbytereal'
bintraj.o: In function `__bintraj_mod__write_binary_vels_axis_flipped':
bintraj.f90:(.text+0x2192): undefined reference to
`__netcdf__nf90_put_var_2d_fourbytereal'
bintraj.o: In function `__bintraj_mod__write_binary_vels':
bintraj.f90:(.text+0x2391): undefined reference to
`__netcdf__nf90_put_var_2d_eightbytereal'
bintraj.o: In function `__bintraj_mod__write_binary_cell_dat':
bintraj.f90:(.text+0x25b4): undefined reference to
`__netcdf__nf90_put_var_1d_eightbytereal'
bintraj.f90:(.text+0x2735): undefined reference to
`__netcdf__nf90_put_var_1d_eightbytereal'
bintraj.o: In function `__bintraj_mod__end_binary_frame':
bintraj.f90:(.text+0x295b): undefined reference to
`__netcdf__nf90_put_var_1d_eightbytereal'
bintraj.f90:(.text+0x297e): undefined reference to `__netcdf__nf90_sync'
bintraj.f90:(.text+0x2b01): undefined reference to
`__netcdf__nf90_put_var_1d_eightbytereal'
bintraj.f90:(.text+0x2b24): undefined reference to `__netcdf__nf90_sync'
./cuda/cuda.a(gpu.o): In function `gpu_amrset_':
gpu.cpp:(.text+0x2438): undefined reference to `curandCreateGenerator'
gpu.cpp:(.text+0x244e): undefined reference to
`curandSetPseudoRandomGeneratorSeed'
./cuda/cuda.a(kForcesUpdate.o): In function `kRandom':
tmpxft_00006c7e_00000000-4_kForcesUpdate.compute_20.cudafe1.cpp:(.text+0x3b56):
undefined reference to `curandGenerateNormalDouble'
collect2: ld returned 1 exit status
make[2]: *** [pmemd.cuda] Error 1
make[2]: Leaving directory `/usr/local/lib/amber11/src/pmemd/src'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/usr/local/lib/amber11/src/pmemd'
make: *** [cuda] Error 2
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Received on Wed Dec 28 2011 - 14:30:02 PST
