Well spotted Jack.
Indeed, I thought I had disabled cuda when I moved to iMac, but it was
still in my $PATH. However, it only worked after I had deleted
/usr/local/cuda.
Thanks,
Alan
On 4 March 2013 15:05, Jack Howarth <howa...@bromo.med.uc.edu> wrote:
> On Mon, Mar 04, 2013 at 07:59:03AM -0700, Alexander Hansen wrote:
> > On 3/4/13 7:39 AM, Alan wrote:
> > > Hi, I followed the issues with GMX 4.6 and waited. So today I gave a
> try
> > > and got this:
> > >
> > > [skip]
> > > make
> > > [ 0%] Building NVCC (Device) object
> > >
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o
> > > [ 0%] Building NVCC (Device) object
> > >
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
> > > Scanning dependencies of target gpu_utils
> > > [ 0%] Building CXX object
> > > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/dummy.cpp.o
> > > Linking CXX static library libgpu_utils.a
> > > /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols
> > > /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols
> > > [ 0%] Built target gpu_utils
> > > [ 0%] Building NVCC (Device) object
> > >
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> > > /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/
> pmalloc_cuda.cu
> > > <http://pmalloc_cuda.cu>(64): error: no instance of overloaded
> function
> > > "cudaMallocHost" matches the argument list
> > > argument types are: (void **, size_t, int)
> > >
> > > /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/
> pmalloc_cuda.cu
> > > <http://pmalloc_cuda.cu>(87): error: no instance of overloaded
> function
> > > "cudaMallocHost" matches the argument list
> > > argument types are: (void **, size_t, int)
> > >
> > > 2 errors detected in the compilation of
> > > "/tmp/tmpxft_000029fc_00000000-4_pmalloc_cuda.cpp1.ii".
> > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:264
> (message):
> > > Error generating file
> > >
> > >
> /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> > >
> > >
> > > make[2]: ***
> > >
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
> > > Error 1
> > > make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
> Error 2
> > > make: *** [all] Error 2
> > > ### execution of /tmp/fink._AHcW failed, exit code 2
> > > ### execution of /tmp/fink.9rNkw failed, exit code 2
> > > Removing runtime build-lock...
> > > Removing build-lock package...
> > > /sw/bin/dpkg-lockwait -r fink-buildlock-gromacs-4.6-2
> > > (Reading database ... 179750 files and directories currently
> installed.)
> > > Removing fink-buildlock-gromacs-4.6-2 ...
> > > Reading buildlock packages...
> > > /sw/bin/dpkg-lockwait -i
> /sw/fink/debs/gromacs_4.5.4-2_darwin-x86_64.deb
> > > Selecting previously deselected package gromacs.
> > > (Reading database ... 179749 files and directories currently
> installed.)
> > > Unpacking gromacs (from .../gromacs_4.5.4-2_darwin-x86_64.deb) ...
> > > Setting up gromacs (4.5.4-2) ...
> > >
> > > Updating the list of locally available binary packages.
> > > Failed: phase installing: gromacs-4.6-2 failed
> > >
> > > Package manager version: 0.34.5
> > > Distribution version: selfupdate-rsync Mon Mar 4 13:32:14 2013, 10.8,
> > > x86_64
> > > Trees: local/main stable/main local/injected
> > > Xcode.app: 4.6
> > > Xcode command-line tools: 4.5.0.0.1.1249367152
> > > Max. Fink build jobs: 4
> > >
> > >
> > >
> > > --
> > > Alan Wilter SOUSA da SILVA, DSc
> > > Bioinformatician, UniProt - PANDA, EMBL-EBI
> > > CB10 1SD, Hinxton, Cambridge, UK
> > > +44 1223 49 4588
> > >
> > >
> >
> >
> > I didn't see this when I built it here. You might start by updating
> > your Xcode command-line tools (e.g. via the Xcode Preferences).
>
> I believe that Alan must have some third-party CUDA devtools installed.
> There is no way fink can properly support that configuration so they
> needed to be disabled in .cshrc/.bashrc or moved aside/deinstalled first.
>
> >
> > --
> > Alexander Hansen, Ph.D.
> > Fink User Liaison
> > My package updates: http://finkakh.wordpress.com/
>
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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