Hi Carlo, I think I know now what the problem is. The CUDA compiler, nvcc, uses a the host compiler to compile CPU code which is generated as C++ and therefore, a C++ compiler is needed. However, up until CUDA 5.0 nvcc did not recognize the Intel C++ compiler (icpc) and it would only accept icc as host compiler. As all host-compilers supported by nvcc happily compile C++ code with the compiler that is normally used for C (gcc, icc), I decided to pass the C compiler as host-compiler to nvcc. Although this has worked for a bunch of gcc versions as well as icc 12/13 on Linux, for some strange reason, in your case (and probably on Mac OS in general) this did not result in correct linking.
I still can't tell whether what Roland's fix does is needed or we could do it some other way. Thanks for the information, a fix will be implemented for an upcoming beta. Cheers, -- Szilárd On Tue, Dec 4, 2012 at 8:02 PM, Carlo Camilloni <carlo.camill...@gmail.com>wrote: > Dear Szilárd, > > My cmake version in the 2.8.9. The error is > > Linking C shared library libgmx.dylib > Undefined symbols for architecture x86_64: > "std::terminate()", referenced from: > do_memtest(unsigned int, int, int) in > libgpu_utils.a(gpu_utils_generated_gpu_utils.cu.o) > memtestState::allocate(unsigned int) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > "typeinfo for int", referenced from: > memtestState::allocate(unsigned int) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > "___cxa_allocate_exception", referenced from: > memtestState::allocate(unsigned int) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > "___cxa_begin_catch", referenced from: > memtestState::allocate(unsigned int) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > "___cxa_end_catch", referenced from: > memtestState::allocate(unsigned int) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > "___cxa_throw", referenced from: > memtestState::allocate(unsigned int) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > "___gxx_personality_v0", referenced from: > Dwarf Exception Unwind Info (__eh_frame) in > libgpu_utils.a(gpu_utils_generated_gpu_utils.cu.o) > Dwarf Exception Unwind Info (__eh_frame) in > libgpu_utils.a(gpu_utils_generated_memtestG80_core.cu.o) > ld: symbol(s) not found for architecture x86_64 > clang: error: linker command failed with exit code 1 (use -v to see > invocation) > make[2]: *** [src/gmxlib/libgmx.6.dylib] Error 1 > make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 > make: *** [all] Error 2 > > and is the same if I compile with clang/clang++ > or gcc-mp-4.7/g++-mp-4.7 (in order to get the openMP parallelisation that > is not > supported by clang) or gcc/g++ (compiling in the most simple fashion just > with cmake ../ -DGMX_CPU_ACCELERATION=SSE4.1) > > the code compiled with the all the above compilers and the standard gcc > for the nvcc part works and gives > reproducible results on simple systems. > > again in all the above cases it is enough to change the c compiler to a > c++ compiler > in src/gmxlib/CMakeFiles/gmx.dir/link.txt > > Best, > Carlo > > > > > > > Message: 1 > > Date: Mon, 3 Dec 2012 16:10:11 +0100 > > From: Szil?rd P?ll <szilard.p...@cbr.su.se> > > Subject: Re: [gmx-users] Build on OSX with 4.6beta1 > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: > > <cannyew5qx6mrvvnon0jj_-9ynnvx9b5vgh3g2g0_ugk-ig8...@mail.gmail.com> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi, > > > > I think this happens either because you have cmake 2.8.10 and the > > host-compiler gets double-set or because something gets messed up when > you > > use clang/clang++ with gcc as the CUDA host-compiler. Could you provide > the > > exact error output you are getting as well as cmake invocation? As I > don't > > have access to such a machine myself, I'll need some help with figuring > out > > what exactly is causing the trouble. > > > > Btw, the CUDA Mac OS X user guide states that you need to use "The gcc > > compiler and toolchain installed using Xcode" ( > > > http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-mac-os-x/index.html > > ). > > > > Note that on Intel CPUs, when running on a single node, you'll get much > > better performance (up to +30%!) if you use only OpenMP-based > > parallelization - which is the default with up to 16 threads (on Intel). > > > > Cheers, > > -- > > Szilárd > > > > > > On Fri, Nov 30, 2012 at 11:01 AM, Carlo Camilloni < > carlo.camill...@gmail.com > >> wrote: > > > >> Dear All, > >> > >> I have successfully compiled the beta1 of gromacs 4.6 on my macbook pro > >> with mountain lion. > >> I used the latest cuda and the clang/clang++ compilers in order to have > >> access to the AVX instructions. > >> mdrun works with great performances!! great job! > >> > >> two things: > >> > >> 1. the compilation was easy but not straightforward: > >> cmake ../ -DGMX_GPU=ON > >> -DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu > >> -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_C_COMPILER=/usr/bin/clang > >> -DCUDA_NVCC_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF > >> > >> and then I had to manually edit > >> src/gmxlib/CMakeFiles/gmx.dir/link.txt > >> > >> and change clang to clang++ > >> (I noted that in many other places it was correctly set, and without > this > >> change I got an error on some c++ related stuff) > >> > >> 2. is there any way to have openmp parallelisation on osx? > >> > >> Best, > >> Carlo > >> > >> > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
