Still won't work...
Shake is in double-precision even in SPSP mode...
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Alan
Sent: Wednesday, May 05, 2010 07:03
To: AMBER Mailing List
Subject: Re: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA
Hi Jason,
Well, I tried pmemd.cuda on macbookpro. First I know nvida 9600GT is not
supposed to be supported and this GPU is hardware revision 1.0 (so no double
precision). Besides, nVidia does a hell for Mac by not providing all drivers
in 64 bits.
Knowing all that, even though, I followed your tips and definitely I have to
use configure.advanced. I created a config_data/mac_32_cuda_SPSP.gfortran,
did
./configure.advanced mac_32_cuda gfortran nopar
make -f Makefile.advanced install
and compilation failed only the last stage:
[snip]
a - cudpp_scan_c.o
gfortran -m32 -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/lib -L/usr/local/cuda/lib -lcufft -lcudart
./cuda/cuda.a -Wl
Undefined symbols:
"std::_Rb_tree_increment(std::_Rb_tree_node_base const*)", referenced
from:
std::_Rb_tree_const_iterator<std::pair<void* const, int>
>::operator++() in cuda.a(radixsort_c.o)
"std::ios_base::Init::Init()", referenced from:
__static_initialization_and_destruction_0(int, int) in cuda.a(gpu.o)
"std::ios_base::Init::~Init()", referenced from:
__ZNSt8ios_base4InitD1Ev$non_lazy_ptr in cuda.a(gpu.o)
(maybe you meant: __ZNSt8ios_base4InitD1Ev$non_lazy_ptr)
"operator delete[](void*)", referenced from:
[snip]
This is not a Cuda issue, it's something related to stdc++ (I guess) but I
don't know c/c++ much to solve this.
Cheers,
Alan
On Tue, May 4, 2010 at 17:12, Jason Swails <jason.swails.gmail.com> wrote:
> I have tried compiling pmemd.cuda on my macbook. It is difficult. You
> essentially have to use ./configure.advanced in the $AMBERHOME/src/pmemd in
> my experience. Also make sure you've built gnu 4.3 from macports, since I
> don't think cuda works with 4.4 and later...
>
> Then, to use the nvcc for mac (which only compiles in 32-bit), you have to
> add -m32 to all of the flags (cflags, cppflags, fflags, etc.).
>
> That's enough to get started, I suppose.
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed May 05 2010 - 09:30:03 PDT
