On Tue, Dec 7, 2010 at 7:33 AM, M. Shahid <mohammad.shahid.gmail.com> wrote:
> Hi Jason,
>
> Thanks for the info that pmemd.cuda and snow leopard are incompatible.
> And it seems my impression too now after retrying with:
>
> booting snow leopard in 32 bit mode,
> passing -m32 flags to the nvcc compiler,
> changing gnu compilers by gcc_select etc.
>
> and knowing that version 4.2.1 (of gcc/g++/gfortran, Apple Inc. build 5664)
> of the compilers are working with
>
Are you sure that your gfortran is of version 4.2.1, the same as gcc/g++?
> amber11 and GPU computing SDK (driver/toolkit versions 3.2.17) in 64 bit
> mode of snow leopard.
>
> However two things I noticed that the configure script is looking
> for /usr/local/cuda/lib64
>
This directory is unnecessary. You can just remove it (I wouldn't make a
link, since you don't want other applications thinking 64-bit libraries are
actually there)
while it was there with /usr/local/cuda/lib. so I made a link.
> another, you mentioned libgfortran.dylib but i don't see it in
> my /usr/local/cuda/lib folder.
>
It's not there. It's in the gcc library folder, and is the library that
allows you to link C-objects and Fortran-objects. I was just using it as an
example for architecture incompatibilities.
All the best,
Jason
> Best regards,
>
> --
> Shahid.
>
>
> On Mon, Dec 6, 2010 at 10:08 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, Dec 6, 2010 at 10:44 AM, M. Shahid <mohammad.shahid.gmail.com
> > >wrote:
> >
> > > Hi,
> > >
> > > I have a related problem of compiling pmemd.cuda in snow leopard
> x84_64:
> > >
> >
> > I think the best course of action here is to consider pmemd.cuda and Snow
> > Leopard incompatible. In any case, it appears as though current
> generation
> > Apple desktops aren't even shipping with NVidia cards (only the Macbook
> > [Pro] line has NVidia GPUs), and Apple hardware is tightly controlled, so
> > the consumer is completely at the mercy of Apple as to the small
> selection
> > of hardware that will be present in any of their machines. Furthermore,
> > the
> > Mac OS X 10.6 CUDA toolkit is 32-bit, which often clashes with the
> > mixed-architecture "disaster" that is Snow Leopard. You can force 32-bit
> > builds with -m32 for the MacPorts GNU compilers, or you can force 64-bit
> > builds with -m64 for nvcc, but they'll invariably have problems when
> trying
> > to link with their own libraries (i.e. libgfortran.dylib or
> > libcufft.dylib).
> >
> >
> > > serial and parallel installations are successful using
> configure_openmpi
> > > (openmpi-1.4.3).
> > >
> > > when configured using ./configure -cuda gnu
> > > and then make cuda
> > > the compilation stops here:
> > >
> > > gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> > -DBINTRAJ
> > > -DCUDA -I/usr/local/cuda/include -c gpu.cpp
> > > In file included from gpu.cpp:23:
> > > gputypes.h:835: error: ISO C++ forbids declaration of ‘uint’ with no
> type
> > >
> >
> > You can get rid of this error by defining uint as an unsigned integer in
> > gputypes.h (typedef unsigned int uint;). However, you're just going to
> get
> > more errors after you take care of this one.
> >
> > Good luck,
> > Jason
> >
> >
> > > gputypes.h:835: error: expected ‘;’ before ‘*’ token
> > > gputypes.h:1137: error: ‘uint’ was not declared in this scope
> > > gputypes.h:1137: error: template argument 1 is invalid
> > > gpu.cpp: In function ‘void gpu_setup_system_(int*, double*, int*, int*,
> > > int*, int*)’:
> > > gpu.cpp:517: error: ‘uint’ was not declared in this scope
> > > gpu.cpp:517: error: template argument 1 is invalid
> > > gpu.cpp:578: error: ‘struct cudaSimulation’ has no member named
> > > ‘pRandomCarry’
> > > gpu.cpp:578: error: request for member ‘_pDevData’ in ‘*
> > > gpu->_gpuContext::pbRandomCarry’, which is of non-class type ‘int’
> > > gpu.cpp: In function ‘void gpu_amrset_(int*)’:
> > > gpu.cpp:5889: error: request for member ‘_pSysData’ in ‘*
> > > gpu->_gpuContext::pbRandomCarry’, which is of non-class type ‘int’
> > > gpu.cpp:5893: error: request for member ‘Upload’ in ‘*
> > > gpu->_gpuContext::pbRandomCarry’, which is of non-class type ‘int’
> > >
> > >
> > > The cuda sdk examples were compiled with gcc4.2.1 and the deviceQuery
> > > output
> > > is as expected.
> > >
> > > Any suggestions how to go from here?
> > >
> > > Best regards,
> > >
> > > --
> > > Shahid.
> > >
> > > On Mon, Dec 6, 2010 at 4:17 PM, George Tzotzos <gtzotzos.me.com>
> wrote:
> > >
> > > > Many thanks to both you and Tim.
> > > >
> > > > I'll retry shortly.
> > > >
> > > > All the best
> > > >
> > > > George
> > > >
> > > > On Dec 6, 2010, at 4:06 PM, case wrote:
> > > >
> > > > > On Mon, Dec 06, 2010, Timothy J Giese wrote:
> > > > >> On 12/06/2010 08:28 AM, George Tzotzos wrote:
> > > > >>>
> > > > >>> 1. Installed gcc44 from MacPorts
> > > > >>>
> > > > >>> 2. Downloaded and installed mpich2 from
> > > > http://www.mcs.anl.gov/research/projects/mpich2/
> > > > >
> > > > > Just to add to Tim's comments, we recommend using the
> > > "configure_openmpi"
> > > > > script (in $AMBERHOME/AmberTools/src) if you are having trouble
> with
> > > MPI
> > > > > installation. This is a tested script; doesn't mean it won't fail,
> > but
> > > > at
> > > > > least then we will know exactly what you did, and it takes care of
> > all
> > > > the
> > > > > environment variables and so on. Just saying that you "installed
> > > mpich2"
> > > > > leaves a lot of unknowns.
> > > > >
> > > > > ....dac
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 07 2010 - 08:00:03 PST
