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-- Shahid. > > > 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 > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Dec 07 2010 - 13:30:03 PST