Not sure what's wrong with the Intel compilers, but it is _well known_ that CUDA only supports GCC 4.5 for CUDA 4.1 (and supposedly CUDA 4.2 supports GCC 4.6, but I didn't check to confirm). CUDA 5 is supposed to support GCC 4.6, but GCC 4.7 is not supported AFAIK. I hope that helps somehow.
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Thomas Evangelidis [tevang3.gmail.com]
Sent: Thursday, December 06, 2012 9:37 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file
I've done that already and I also get an error with serial cuda
compilation. Serial compilation and MPI work well, but when I add the -cuda
flag I get errors like the following. Do you have any idea what may be
wrong?
export AMBERHOME=/home/thomas/Programs/amber12
export PATH=$AMBERHOME/exe:$PATH
export LD_LIBRARY_PATH=$AMBERHOME/lib:$LD_LIBRARY_PATH
source /home/thomas/Programs/Intel_Compilers/bin/compilervars.sh intel64
export MPI_HOME=/usr/local/mpich-1.4.1p1_icc
export MKL_HOME=/home/thomas/Programs/Intel_Compilers/mkl
export CUDA_HOME=/usr/local/cuda
export SSE_TYPES=SSE4.1,SSE4.2
./configure -cuda intel
make install
...
...
/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
kForcesUpdate.cu
./kForcesUpdate.cu(87): Advisory: Loop was not unrolled, cannot deduce loop
trip count
./kForcesUpdate.cu(127): Advisory: Loop was not unrolled, cannot deduce
loop trip count
/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
kCalculateLocalForces.cu
/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
kCalculateGBBornRadii.cu
/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
kCalculatePMENonbondEnergy.cu
/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
kCalculateGBNonbondEnergy1.cu
/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]
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 = 20; K = unsigned int; V = unsigned int; cudaError_t =
cudaError]’:
kNLRadixSort.cu:53:48: 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 = 24; K = unsigned int; V = unsigned int; cudaError_t =
cudaError]’:
kNLRadixSort.cu:60:48: 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 = 28; K = unsigned int; V = unsigned int; cudaError_t =
cudaError]’:
kNLRadixSort.cu:67:48: 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 = 32; K = unsigned int; V = unsigned int; cudaError_t =
cudaError]’:
kNLRadixSort.cu:74:48: 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
On 6 December 2012 02:30, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Dec 5, 2012, at 6:18 PM, Thomas Evangelidis <tevang3.gmail.com> wrote:
>
> > 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.
>
> My guess is there is a reason that NVIDIA disabled nvcc with newer GCC
> versions, and the errors you are seeing are a result of that
> incompatibility.
>
> If you do not have an older GCC version to use, I suggest that you go back
> to the intel compilers. The biggest thing to worry about with those
> compilers is to make sure that you set up your environment correctly with
> them. Intel provides sourceable scripts for both bash and csh to do this
> for you.
>
> Good luck.
>
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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/
_______________________________________________
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
Received on Thu Dec 06 2012 - 10:30:01 PST
