Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 5 Dec 2012 17:54:30 -0500

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
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Received on Wed Dec 05 2012 - 15:00:02 PST
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