Hi Jason,
Sorry for getting back to you late. I have been out of my office for some time.
I am back in town again.
Here is the installation lines that trace back to the origin of the installation error.
make[5]: Entering directory `/truba/sw/centos6.4-intel/app/amber/amber12-gcc-mpi/amber12/src/pmemd/src/cuda'
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -I/include -IB40C -IB40C/KernelCommon -I/usr/mpi/gcc/openmpi-1.6.5/include -c cuda_info.F90
mpicc -O3 -mtune=native -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -I/include -IB40C -IB40C/KernelCommon -I/usr/mpi/gcc/openmpi-1.6.5/include -c gpu.cpp
In file included from gpu.cpp:29:
gputypes.h:21:18: error: cuda.h: No such file or directory
gputypes.h:22:19: error: cufft.h: No such file or directory
gputypes.h:23:20: error: curand.h: No such file or directory
gputypes.h:24:30: error: vector_functions.h: No such file or directory
gputypes.h:25:30: error: cuda_runtime_api.h: No such file or directory
gputypes.h:26:27: error: builtin_types.h: No such file or directory
In file included from gpu.cpp:29:
gputypes.h:111: error: expected initializer before ‘PMEDouble2’
gputypes.h:112: error: expected initializer before ‘PMEDouble4’
gputypes.h:114: error: expected initializer before ‘PMEFloat2’
gputypes.h:115: error: expected initializer before ‘PMEFloat4’
gputypes.h:116: error: ‘cufftComplex’ does not name a type
gputypes.h:360: error: expected initializer before ‘const’
gputypes.h:361: error: expected initializer before ‘const’
gputypes.h:365: error: expected initializer before ‘const’
gputypes.h:366: error: expected initializer before ‘const’
gputypes.h:498: error: expected initializer before ‘const’
gputypes.h:499: error: expected initializer before ‘const’
...
...
...
Let me know if you need some more lines ..
Regards,
Jenk Andac
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: amber.ambermd.org
Sent: Thursday, April 3, 2014 10:03 PM
Subject: Re: [AMBER] pmemd.cuda.mpi installation
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 Sun Apr 06 2014 - 11:00:02 PDT
