Merging major development on MRC models and optimized reading for BioEM 2.1

See merge request !7

temporary hack to get back good performance, this needs to be studied (and optimized) in more details

replace deprecated CUDA functions with the renamed (correct) ones to ensure compatibility with CUDA 10

[ci skip]

# Conflicts:
#	Manual/BioEM_Manual.pdf
#	Manual/BioEM_Manual.tex
#	Manual/Fig1_10Dec.eps
#	README.md
#	autotuner.cpp
#	bioem.cpp
#	bioem_algorithm.h
#	bioem_cuda.cu
#	doc/bib_manual.bib
#	include/autotuner.h
#	include/bioem.h
#	include/bioem_cuda_internal.h
#	include/defs.h
#	map.cpp
#	param.cpp

Although for pdflatex this issue generates just a warning, some other tools (e.g., pandoc) have bigger problems with it

profiling: improving NVTX profiling CPU+GPU execution

See merge request !5

nvtx+summary: improving nvtx by tracing initialization, which also fixes potential bogus first measurement of Projection for the summary

bugfix (from valgrind): even when CC is not used, it should be initialized to a…

See merge request !4