[gmx-users] Re: gmx-users Digest, Vol 104, Issue 7

[Carlo Camilloni]

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.pall at cbr.su.se>
> Subject: Re: [gmx-users] Build on OSX with 4.6beta1
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<CANnYEw5qX6mrVvnON0jj_-9YnnVX9b5VGh3g2G0_UgK-ig8gCQ at 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.camilloni at 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
>> 
>> 
>> --
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>