I am using CUDA 4.2 but changed the /usr/local/cuda/include/host_config.h
to not complain with my gcc compiler version. I have posted an older
message about intel compilers failing to install pmemd.cuda, and Ross
recommended the GNU compilers as they are more stable with CUDA.
Thomas
On 6 December 2012 00:54, Jason Swails <jason.swails.gmail.com> wrote:
> What is your CUDA version? My understanding was that nvcc version 4.2
> didn't work with GCC later than 4.6. And AMBER doesn't yet work with CUDA
> 5.0. So my guess is that you will need to revert to an older GCC or the
> intel compilers if you want to have pmemd.cuda.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Dec 5, 2012, at 10:42 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
>
> > On 5 December 2012 15:41, case <case.biomaps.rutgers.edu> wrote:
> >
> >> On Wed, Dec 05, 2012, Thomas Evangelidis wrote:
> >>>
> >>> Do you know what this error means and how can be solved? I use Fedora
> 17
> >>> 64bit with gcc and gfortran 4.7.2.
> >>>
> >>> ./configure -cuda gnu
> >>> make install
> >>> ...
> >>> ...
> >>> gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> >>> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
> >>> -I/home/thomas/Programs/amber12/include -c binrestart.F90
> >>> binrestart.F90:48.7:
> >>>
> >>> use netcdf
> >>> 1
> >>> Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module
> >> file
> >>
> >> Have you been using other compilers before? I suspect that you just
> need
> >> to
> >> go to $AMBERHOME/include and remove any netcdf.* files you find there.
> >>
> >> I'm not sure why the configure script is not doing this, but see if it
> >> helps.
> >>
> >>
> > Yes, I had remnants of the old 3.4 version. I did a clean install with
> just
> > gcc and gfortran 4.7.2. The serial programs were installed successfully,
> > but when I compile serial cuda I get a long error message:
> >
> >
> > /usr/local/cuda/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13
> > -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30
> > -DCUDA -Duse_SPFP -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon
> -c
> > kNLRadixSort.cu
> > B40C/radixsort_single_grid.cu: In instantiation of ‘cudaError_t
> > b40c::SingleGridRadixSortingEnactor<K,
> > V>::EnactSort(b40c::MultiCtaRadixSortStorage<K, V>&) [with int
> > LOWER_KEY_BITS = 12; K = unsigned int; V = unsigned int; cudaError_t =
> > cudaError]’:
> > kNLRadixSort.cu:39:48: required from here
> > B40C/radixsort_single_grid.cu:282:1: error: ‘GetWorkDecomposition’ was
> not
> > declared in this scope, and no declarations were found by
> > argument-dependent lookup at the point of instantiation [-fpermissive]
> > B40C/radixsort_single_grid.cu:282:1: note: declarations in dependent
> base
> > ‘b40c::MultiCtaRadixSortingEnactor<unsigned int, unsigned int,
> > b40c::MultiCtaRadixSortStorage<unsigned int, unsigned int> >’ are not
> found
> > by unqualified lookup
> > B40C/radixsort_single_grid.cu:282:1: note: use
> ‘this->GetWorkDecomposition’
> > instead
> > B40C/radixsort_single_grid.cu:291:1: error: ‘PreSort’ was not declared
> in
> > this scope, and no declarations were found by argument-dependent lookup
> at
> > the point of instantiation [-fpermissive]
> > B40C/radixsort_single_grid.cu:291:1: note: declarations in dependent
> base
> > ‘b40c::MultiCtaRadixSortingEnactor<unsigned int, unsigned int,
> > b40c::MultiCtaRadixSortStorage<unsigned int, unsigned int> >’ are not
> found
> > by unqualified lookup
> > B40C/radixsort_single_grid.cu:291:1: note: use ‘this->PreSort’ instead
> > B40C/radixsort_single_grid.cu: In instantiation of ‘cudaError_t
> > b40c::SingleGridRadixSortingEnactor<K,
> > V>::EnactSort(b40c::MultiCtaRadixSortStorage<K, V>&) [with int
> > LOWER_KEY_BITS = 16; K = unsigned int; V = unsigned int; cudaError_t =
> > cudaError]’:
> > kNLRadixSort.cu:46:48: required from here
> > B40C/radixsort_single_grid.cu:282:1: error: ‘GetWorkDecomposition’ was
> not
> > declared in this scope, and no declarations were found by
> > argument-dependent lookup at the point of instantiation [-fpermissive]
> > B40C/radixsort_single_grid.cu:282:1: note: declarations in dependent
> base
> > ‘b40c::MultiCtaRadixSortingEnactor<unsigned int, unsigned int,
> > b40c::MultiCtaRadixSortStorage<unsigned int, unsigned int> >’ are not
> found
> > by unqualified lookup
> > B40C/radixsort_single_grid.cu:282:1: note: use
> ‘this->GetWorkDecomposition’
> > instead
> > B40C/radixsort_single_grid.cu:291:1: error: ‘PreSort’ was not declared
> in
> > this scope, and no declarations were found by argument-dependent lookup
> at
> > the point of instantiation [-fpermissive]
> >
> > (and the stack trace continues...)
> >
> >
> > thanks,
> > Thomas
> > _______________________________________________
> > 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
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Dec 05 2012 - 15:30:02 PST
