On Thu, 2014-04-03 at 11:47 -0700, Cenk (Jenk) Andac wrote:
> Hi Jason,
>
> Thank you for replying. I have tried installing pmemd.cuda.MPI with the new parameter you suggested.
>
> Unfortunately installation failed again..
>
>
> Here is the error message ..
>
> gputypes.h:1870: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h:1871: error: ‘cudaMemset’ was not declared in this scope
> gputypes.h:1868: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1872: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h: In member function ‘void GpuBuffer<T>::Allocate() [with T = NTPData]’:
> gputypes.h:1828: instantiated from ‘GpuBuffer<T>::GpuBuffer(int, bool, bool) [with T = NTPData]’
> gpu.cpp:5261: instantiated from here
> gputypes.h:1851: error: ‘cudaHostAlloc’ was not declared in this scope
> gputypes.h:1851: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1852: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h:1855: error: ‘cudaHostGetDevicePointer’ was not declared in this scope
> gputypes.h:1851: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1856: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h:1868: error: ‘cudaMalloc’ was not declared in this scope
> gputypes.h:1868: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1870: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h:1871: error: ‘cudaMemset’ was not declared in this scope
> gputypes.h:1868: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1872: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h: In member function ‘void GpuBuffer<T>::Deallocate() [with T = NTPData]’:
> gputypes.h:1834: instantiated from ‘GpuBuffer<T>::~GpuBuffer() [with T = NTPData]’
> gpu.cpp:8983: instantiated from here
> gputypes.h:1885: error: ‘cudaFreeHost’ was not declared in this scope
> gputypes.h:1896: error: ‘cudaFree’ was not declared in this scope
> gputypes.h:1899: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1899: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h: In member function ‘void GpuBuffer<T>::Deallocate() [with T = NLEntry]’:
> gputypes.h:1834: instantiated from ‘GpuBuffer<T>::~GpuBuffer() [with T = NLEntry]’
> gpu.cpp:8983: instantiated from here
> gputypes.h:1885: error: ‘cudaFreeHost’ was not declared in this scope
> gputypes.h:1896: error: ‘cudaFree’ was not declared in this scope
> gputypes.h:1899: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1899: error: ‘cudaThreadExit’ was not declared in this scope
> gputypes.h: In member function ‘void GpuBuffer<T>::Deallocate() [with T = NLRecord]’:
> gputypes.h:1834: instantiated from ‘GpuBuffer<T>::~GpuBuffer() [with T = NLRecord]’
> gpu.cpp:8983: instantiated from here
> gputypes.h:1885: error: ‘cudaFreeHost’ was not declared in this scope
> gputypes.h:1896: error: ‘cudaFree’ was not declared in this scope
> gputypes.h:1899: error: ‘cudaGetErrorString’ was not declared in this scope
> gputypes.h:1899: error: ‘cudaThreadExit’ was not declared in this scope
> make[4]: *** [gpu.o] Error 1
> make[4]: Leaving directory `/truba/sw/centos6.4-intel/app/amber/amber12-gcc-mpi/amber12/src/pmemd/src/cuda'
> make[3]: *** [cuda/cuda.a] Error 2
> make[3]: Leaving directory `/truba/sw/centos6.4-intel/app/amber/amber12-gcc-mpi/amber12/src/pmemd/src'
> make[2]: *** [cuda_parallel] Error 2
> make[2]: Leaving directory `/truba/sw/centos6.4-intel/app/amber/amber12-gcc-mpi/amber12/src/pmemd'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/truba/sw/centos6.4-intel/app/amber/amber12-gcc-mpi/amber12/src'
> make: *** [install] Error 2
>
>
> Would you think that some other problems may be involved?
These are all the CUDA symbols defined by the standard CUDA API.
Unfortunately you cut off too much of the text from the terminal to
identify what went wrong. (I suspect libcuda is not being linked in,
but since you didn't include the link line I can't say for certain).
Try this:
./configure -cuda -mpi gnu
**edit config.h ONLY adding -lmpi_cxx to the PMEMD_FLIBSF variable**
make install
Also make sure you don't have automatic text wrapping set on your text
editor; the PMEMD_FLIBSF flag has to be defined entirely on a single
line in config.h
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 03 2014 - 12:30:03 PDT
