GitLab

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

Changed CMake scripts to work correctly if the FFTW threading support was built into the main library instead of a separate library

Removed AVX code, since it had very little effect on performance and would have required a more complicated build process.  Also worked around a compilation error with clang.

Eliminated having CMake run programs to check for CUDA and OpenCL compatible GPUs.  They mostly just caused problems.

Removed ALREADY_MODIFIED_PATH variable in gpu sniffer link stanza, which I am pretty sure would not have worked as desired.

Modified link path in platforms/cuda/CMakeLists.txt to increase likelihood that CUDA_HAVE_GPU flag will be set.

Changed link line for gpu sniffing program so it works on Windows with new single FindCuda location.

FindCUDA.cmake.

based on the FindCUDA.cmake that was in the platforms/cuda/cuda-make directory.
Setting of CUDA_NVCC_FLAGS is now in top-level CMakeLists.txt, in case I ever figure out how
to get this working with the cmake 2.8 installed system version of FindCUDA.cmake.
Before this change, there were three separate FindCUDA.cmake areas.  Now there is just one.

Downgraded recent cmake changes to ghastly compliance with cmake 2.4, for the benefit of the simtk dart server.

Modified Cuda FreeEnergy plugin to use a different windows export macro than main openmm library and cuda library.
Modified CUDA_NVCC_FLAGS to be consistent with Peter's latest version in all three locations they are defined.
Added "-Xcompiler '/MD'" to CUDA_NVCC_FLAGS on Windows to avoid link error in Cuda FreeEnergy plugin.