- adding script to fix whitespace in C++ code,

Minor improvements to documentation of data-preparation, to clarify about mono wav files and utterance/speaker order agreement.

Change src/configure to also exclude gcc version 4.8.1 and to refuse to continue if 'bad' versionf of gcc are in use.
Also add warning about OS X El Capitan, about matrix-library bug.

$ ./configure --mkl-root=/opt/intel/mkl --static-math=yes
...
Configuring MKL library directory: Found: /opt/intel/mkl/lib/intel64
MKL configured with threading: sequential, libs:  -Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64/libmkl_core.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a -Wl,--end-group
MKL include directory configured as: /opt/intel/mkl/include
Configuring MKL threading as sequential
MKL threading libraries configured as   -lpthread -lm
Using Intel MKL as the linear algebra library.
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): In function `mkl_serv_set_memory_limit':
mkl_memory.c:(.text+0x49c): undefined reference to `dlsym'
mkl_memory.c:(.text+0x4b2): undefined reference to `dlsym'
mkl_memory.c:(.text+0x4c8): undefined reference to `dlsym'
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): In function `mkl_serv_allocate':
mkl_memory.c:(.text+0x1251): undefined reference to `dlsym'
mkl_memory.c:(.text+0x1267): undefined reference to `dlsym'
...

New:
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<float>, for dim = 1024, speed was 10.1076 gigaflops.
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<float> [transposed], for dim = 1024, speed was 11.8711 gigaflops.
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<double>, for dim = 1024, speed was 7.10019 gigaflops.
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<double> [transposed], for dim = 1024, speed was 7.81977 gigaflops.

Old:
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<float>, for dim = 1024, speed was 4.57783 gigaflops.
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<float> [transposed], for dim = 1024, speed was 7.96795 gigaflops.
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<double>, for dim = 1024, speed was 3.61182 gigaflops.
LOG (TestCuMatrixTraceMatMat():cu-matrix-speed-test.cc:458) For CuMatrix::TraceMatMat<double> [transposed], for dim = 1024, speed was 6.39571 gigaflops.

LOG (TestCuMatrixTransposeCross():cu-matrix-speed-test.cc:91) For CuMatrix::TransposeCross<float>, for dim = 1024, speed was 14.0498 gigaflops.
LOG (TestCuMatrixTransposeS():cu-matrix-speed-test.cc:72) For CuMatrix::TransposeS<float>, for dim = 1024, speed was 16.845 gigaflops.
LOG (TestCuMatrixTransposeNS():cu-matrix-speed-test.cc:56) For CuMatrix::TransposeNS<float>, for dim = 1024, speed was 14.2464 gigaflops.
LOG (TestCuMatrixTransposeCross():cu-matrix-speed-test.cc:91) For CuMatrix::TransposeCross<double>, for dim = 1024, speed was 10.4523 gigaflops.
LOG (TestCuMatrixTransposeS():cu-matrix-speed-test.cc:72) For CuMatrix::TransposeS<double>, for dim = 1024, speed was 9.65529 gigaflops.
LOG (TestCuMatrixTransposeNS():cu-matrix-speed-test.cc:56) For CuMatrix::TransposeNS<double>, for dim = 1024, speed was 8.52148 gigaflops.

Add barrier for correct timing.

Original performance:
LOG (TestCuMatrixTransposeCross():cu-matrix-speed-test.cc:91) For CuMatrix::TransposeCross<float>, for dim = 1024, speed was 4.26727 gigaflops.
LOG (TestCuMatrixTransposeS():cu-matrix-speed-test.cc:72) For CuMatrix::TransposeS<float>, for dim = 1024, speed was 5.97203 gigaflops.
LOG (TestCuMatrixTransposeNS():cu-matrix-speed-test.cc:56) For CuMatrix::TransposeNS<float>, for dim = 1024, speed was 3.0816 gigaflops.
LOG (TestCuMatrixTransposeCross():cu-matrix-speed-test.cc:91) For CuMatrix::TransposeCross<double>, for dim = 1024, speed was 3.95059 gigaflops.
LOG (TestCuMatrixTransposeS():cu-matrix-speed-test.cc:72) For CuMatrix::TransposeS<double>, for dim = 1024, speed was 4.36189 gigaflops.
LOG (TestCuMatrixTransposeNS():cu-matrix-speed-test.cc:56) For CuMatrix::TransposeNS<double>, for dim = 1024, speed was 2.39275 gigaflops.

Old:
LOG (TestCuFindRowMaxId():cu-matrix-speed-test.cc:264) For CuMatrix::FindRowMaxId<float>, for dim = 1024, speed was 3.99218 gigaflops.
LOG (TestCuFindRowMaxId():cu-matrix-speed-test.cc:264) For CuMatrix::FindRowMaxId<double>, for dim = 1024, speed was 3.46283 gigaflops.

New:
LOG (TestCuFindRowMaxId():cu-matrix-speed-test.cc:264) For CuMatrix::FindRowMaxId<float>, for dim = 1024, speed was 66.2965 gigaflops.
LOG (TestCuFindRowMaxId():cu-matrix-speed-test.cc:264) For CuMatrix::FindRowMaxId<double>, for dim = 1024, speed was 58.442 gigaflops.

Now GetParams requires vector allocated already. Changes in nnet\nnet-various.h at Apr 21, 2016

minor fix to am-diag-gmm.cc to prevent a crash when clustering to a UBM when there are too few Gaussians and some zero counts.

fix small bug regarding online-ivector-features (for online-nnet2/nnet3 setup) regarding how silence-weighting is applied in iVector estimation. (thanks: xiang li)

- some TODO's are to be decided:
  - Can we remove the: 'IsKaldiError()'? (It's very 'dirty' function. And it's used only in the table-I/O to suppress printing 'what' messages from KALDI_ERR. IMHO, it may not be a good idea to suppress this.)
  - With Kirill's log-handler, the log is sent and then there's no abort() for errors/asserts (seems like a bad idea, but it is the way it worked previously).

some cosmetic changes: add comments to RNNLM rescoring utilities to refer to each other; improve messages printed out by 'configure'

some cosmetic changes: add comments to RNNLM rescoring utilities to refer to each other; improve messages printed out by 'configure'

in nnet2 and nnet3 decoders to allow more flexible feature pipelines.

- e.what() contains stackttrace or is empty string
- we should also consider changing:
  'std::cerr << e.what();' -> 'fprintf(stderr, e.what().c_str());'
- fprintf is thread-safe and it is better not to mix 'std::cerr' and
  'stderr', and 'stderr' is already used for logging...

Also add an additional unit test for the topological sorting function

another fix to ComposeCompactLatticeDeterministic(), and a fix (plus cleanup) to word-align-lattice.cc, that affects the --test=true option of lattice-align-words for some topologies including chain models.

Update to ComposeCompactLatticeDeterministic to fix a bug regarding the olabel (which shouldn't matter in our normal use-cases), and make final-probs application more efficient.

- reordering cudamatrix/cu-array-inl.h, so the methods appear in the same
  order as in cudamatrix/cu-array.h
- adding asserts for 0-dim of CuArray