.gitignore.main

@@ -28,6 +28,9 @@ src/misc/version.inc
 # noise simulations
 save/nsv/*.dat
 
+# fftw wisdoms
+save/fftw/*.fftw
+
 # ctags
 tags
 GTAGS

.travis.yml

 language: c
 
+env:
+
 addons:
   apt:
     packages: &default_packages
@@ -8,52 +10,44 @@ addons:
       - libpng-dev
 
 matrix:
+  allow_failures:
+    - env: MAYFAIL=1
   include:
-    - env: PARALLEL=1
+    - name: "Makefile PARALLEL"
+      env: PARALLEL=1
       os: linux
-      compiler: gcc
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapacke-dev
+            - gcc-5
+            - liblapacke-dev
 
-    - env:
+    - name: "Makefile + test + utest"
+      env:
       os: linux
-      compiler: gcc
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
+            - gcc-5
+            - liblapacke-dev
       script:
         - make test
         - make utest
 
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapacke-dev
-
-    - env: SLINK=1
-      os: linux
-      compiler: gcc
-      sudo: required
-      dist: trusty
-      addons:
-        apt:
-          packages:
-            - *default_packages
-            - gfortran
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapacke-dev liblapack-dev
-
-    - env: OMP=0
+    - name: "Makefile Clang"
+      env: OMP=0
       os: linux
       compiler: clang
       sudo: required
@@ -62,149 +56,109 @@ matrix:
         apt:
           packages:
             - *default_packages
+            - liblapacke-dev
+            - libblocksruntime-dev
       script:
         - make test
         - make utest
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapacke-dev
 
-    - env: OMP=1
+    - name: "Makefile OpenMP"
+      env: OMP=1
       os: linux
-      compiler: gcc
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
+            - gcc-5
+            - liblapacke-dev
       script:
         - make test
         - make utest
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapacke-dev
 
-    - env: NOLAPACKE=1
+    - name: "Makefile NOLAPACKE"
+      env: NOLAPACKE=1
       os: linux
-      compiler: gcc
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
+            - gcc-5
             - gfortran
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapack-dev
+            - liblapack-dev
 
-    - env: CUDA=1 CUDA_BASE=/usr/local/cuda-7.5/
+    - name: "CMake GCC-5"
+      env: MAYFAIL=1
       os: linux
-      compiler: clang-3.5
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
-      before_install:
-        - wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1404/x86_64/cuda-repo-ubuntu1404_7.5-18_amd64.deb
-        - sudo dpkg -i cuda-repo-ubuntu1404_7.5-18_amd64.deb
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq clang-3.5
-        - sudo apt-get install -qq --no-install-recommends cuda-drivers cuda-core-7.5 cuda-cudart-dev-7.5 cuda-cufft-dev-7.5 cuda-cublas-dev-7.5
-        - sudo apt-get install -qq liblapacke-dev
+            - gcc-5
+            - libatlas-base-dev
+            - liblapacke-dev
+      before_script:
+        - mkdir build && cd build
+        # NB: CC is automatically set to `compiler` by Travis
+        - cmake .. -DLINALG_VENDOR=ATLAS -DBART_ENABLE_MEM_CFL=OFF -DBUILD_TESTING=OFF -DBART_LOG_BACKEND=OFF -DUSE_OPENMP=ON -DBART_GENERATE_DOC=OFF
 
-    - env: BUILD_NAME="CMake"
+    - name: "CMake GCC-5 NOLAPACKE"
+      env: MAYFAIL=1
       os: linux
-      compiler: gcc
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
+            - gcc-5
             - gfortran
-      before_install:
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapack-dev liblapacke-dev
-      script:
-        - wget http://www.netlib.org/blas/blast-forum/cblas.tgz
-        - tar zxvf cblas.tgz && rm cblas.tgz
-        - pushd CBLAS
-        - |
-          cat << EOF > Makefile.in
-          SHELL = /bin/sh
-          PLAT = LINUX
-          CBLIB = ../lib/libcblas.so
-          CFLAGS = -O3 -DADD_ -fPIC
-          FFLAGS = -O3 -fPIC
-          CC = gcc
-          FC = gfortran
-          LOADER = $(FC)
-          ARCH = cc
-          ARCHFLAGS = -shared -o
-          RANLIB = echo
-          EOF
-        - cd src && make all && sudo cp -v ../lib/libcblas.so /usr/lib/
-        - popd
+            - libatlas-base-dev
+            - liblapack-dev
+      before_script:
         - mkdir build && cd build
-        - export FC=$(which gfortran)
-        - CC=gcc CXX=g++ cmake -DLINALG_VENDOR=LAPACKE -DLAPACKE_DIR=/usr/lib -DUSE_MATLAB=OFF ..
-        - make
+        # NB: CC is automatically set to `compiler` by Travis
+        - cmake .. -DBART_ENABLE_MEM_CFL=OFF -DBUILD_TESTING=OFF -DBART_LOG_BACKEND=OFF -DUSE_OPENMP=ON -DBART_GENERATE_DOC=OFF -DBART_NO_LAPACKE=ON
 
-    - env: BUILD_NAME="CMake + CUDA" CUDA_BASE=/usr/local/cuda-7.5/
+    - name: "CMake GCC-5/G++-5 (with mem-CFL support) + utest"
+      env: MAYFAIL=1
       os: linux
-      compiler: clang-3.5
+      compiler: gcc-5
       sudo: required
       dist: trusty
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - *default_packages
-            - gfortran
-      before_install:
-        - wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1404/x86_64/cuda-repo-ubuntu1404_7.5-18_amd64.deb
-        - sudo dpkg -i cuda-repo-ubuntu1404_7.5-18_amd64.deb
-        - sudo apt-get update -qq
-        - sudo apt-get install -qq clang-3.5
-        - sudo apt-get install -qq --no-install-recommends cuda-drivers cuda-core-7.5 cuda-cudart-dev-7.5 cuda-cufft-dev-7.5 cuda-cublas-dev-7.5
-        - sudo apt-get install -qq liblapack-dev liblapacke-dev
-      script:
-        - wget http://www.netlib.org/blas/blast-forum/cblas.tgz
-        - tar zxvf cblas.tgz && rm cblas.tgz
-        - pushd CBLAS
-        - |
-          cat << EOF > Makefile.in
-          SHELL = /bin/sh
-          PLAT = LINUX
-          CBLIB = ../lib/libcblas.so
-          CFLAGS = -O3 -DADD_ -fPIC
-          FFLAGS = -O3 -fPIC
-          CC = gcc
-          FC = gfortran
-          LOADER = $(FC)
-          ARCH = cc
-          ARCHFLAGS = -shared -o
-          RANLIB = echo
-          EOF
-        - cd src && make all && sudo cp -v ../lib/libcblas.so /usr/lib/
-        - popd
+            - gcc-5
+            - g++-5
+            - libatlas-base-dev
+            - liblapacke-dev
+      before_script:
         - mkdir build && cd build
-        - export FC=$(which gfortran)
-        - CC=gcc CXX=g++ cmake -DLINALG_VENDOR=LAPACKE -DLAPACKE_DIR=/usr/lib -DUSE_MATLAB=OFF -DUSE_CUDA=ON -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_BASE} ..
-        - make
-
-    - env: MACPORTS=0
-      os: osx
-      compiler: gcc-4.8
-      script:
+        # NB: CC is automatically set to `compiler` by Travis
+        - CXX=g++-5 cmake .. -DLINALG_VENDOR=ATLAS -DBART_ENABLE_MEM_CFL=ON -DBUILD_TESTING=ON -DBART_LOG_BACKEND=OFF -DUSE_OPENMP=ON -DBART_GENERATE_DOC=OFF
+      after_script:
         - make test
-        # make utest
-      before_install:
-        - brew update
-        - brew install fftw gcc48 homebrew/science/openblas
 
 script:
   - make bart

ACKNOWLEDGEMENTS

 
-Contributors:
+We want to acknowledge the following persons for supporting
+BART by contributing source code, testing, feedback, data,
+bug reports, etc.
+
+
+(alphabetrical)
 
 Marcus T. Alley
+Michael Anderson
+Jakob Asslaender
 Dara Bahri
+Soumick Chatterjee
 Joseph Y. Cheng
+Sofia Dimoudi
 Siddharth Iyer
-Miki Lustig
-Mark Murphy
+Hans Johnson
+Christian Holme
+Gregory R. Lee
+Evan G. Levine
+Tim Loderhose
+Michael Lustig
+Lyu Mengye
+Damien Nguyen
 Frank Ong
-Jonathan Tamir
+Sebastian Rosenzweig
+Nick Scholand
+David Smith
+Jonathan I. Tamir
+Michelle Tamir (logo)
+Johannes Toger
 Martin Uecker
 Shreyas S. Vasanawala
 Sana Vaziri
-Pat Virtue
+Patrick Virtue
+Simon Yeung
 Tao Zhang
 
-Logo designed by: Michelle Tamir
-
-
-Different parts of this software have been written for
-projects funded by:
-
-American Heart Association Grant 12BGIA9660006
-NIH Grant P41RR09784 and Grant R01EB009690
-UC Discovery Grant 193037
-Sloan Research Fellowship
-GE Healthcare
-
-A personal donation by David Donoho
-
-
-

LICENSE

-Copyright (c) 2013-2017. The Regents of the University of California.
-Copyright (c) 2013-2017. BART Developer Team and Contributors.
-Copyright (c) 2012. Intel Coorperation. (src/lapacke/)
+Copyright (c) 2013-2018. The Regents of the University of California.
+Copyright (c) 2013-2018. BART Developer Team and Contributors.
+Copyright (c) 2012. Intel Corporation. (src/lapacke/)
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

Makefile

 # Copyright 2013-2015. The Regents of the University of California.
-# Copyright 2015-2016. Martin Uecker <martin.uecker@med.uni-goettingen.de>
+# Copyright 2015-2018. Martin Uecker <martin.uecker@med.uni-goettingen.de>
 # All rights reserved. Use of this source code is governed by
 # a BSD-style license which can be found in the LICENSE file.
 
@@ -15,6 +15,7 @@ MAKEFLAGS += -R
 # use for parallel make
 AR=./ar_lock.sh
 
+MKL?=0
 CUDA?=0
 ACML?=0
 OMP?=1
@@ -23,6 +24,14 @@ DEBUG?=0
 FFTWTHREADS?=1
 ISMRMRD?=0
 
+LOG_BACKEND?=0
+LOG_SIEMENS_BACKEND?=0
+LOG_ORCHESTRA_BACKEND?=0
+LOG_GADGETRON_BACKEND?=0
+ENABLE_MEM_CFL?=0
+MEMONLY_CFL?=0
+
+
 DESTDIR ?= /
 PREFIX ?= usr/
 
@@ -91,14 +100,13 @@ CFLAGS ?= $(OPT) -Wmissing-prototypes
 CXXFLAGS ?= $(OPT)
 
 ifeq ($(BUILDTYPE), MacOSX)
-	CC ?= gcc-mp-4.7
+	CC ?= gcc-mp-6
 else
 	CC ?= gcc
 	# for symbols in backtraces
 	LDFLAGS += -rdynamic
 endif
 
-CXX ?= g++
 
 
 
@@ -123,6 +131,9 @@ CUDA_BASE ?= /usr/local/
 
 ACML_BASE ?= /usr/local/acml/acml4.4.0/gfortran64_mp/
 
+# mkl
+MKL_BASE ?= /opt/intel/mkl/lib/intel64/ 
+
 # fftw
 
 ifneq ($(BUILDTYPE), MacOSX)
@@ -177,6 +188,7 @@ MODULES_lrmatrix = -llowrank -liter -llinops
 MODULES_estdims = -lnoncart -llinops
 MODULES_ismrmrd = -lismrm
 MODULES_wavelet = -llinops -lwavelet
+MODULES_wshfl = -llinops -lwavelet -liter -llowrank -llinops
 
 
 MAKEFILES = $(root)/Makefiles/Makefile.*
@@ -186,6 +198,19 @@ MAKEFILES = $(root)/Makefiles/Makefile.*
 -include $(MAKEFILES)
 
 
+# clang
+
+ifeq ($(findstring clang,$(CC)),clang)
+	CFLAGS += -fblocks
+	LDFLAGS += -lBlocksRuntime
+endif
+
+
+CXX ?= g++
+LINKER ?= $(CC)
+
+
+
 ifeq ($(ISMRMRD),1)
 TMRI += ismrmrd
 MODULES_bart += -lismrm
@@ -221,9 +246,9 @@ default all clean allclean distclean doc/commands.txt doxygen test utest gputest
 else
 
 
-CPPFLAGS += $(DEPFLAG) -I$(srcdir)/
-CFLAGS += -std=gnu11 -I$(srcdir)/
-CXXFLAGS += -I$(srcdir)/
+CPPFLAGS += $(DEPFLAG) -iquote $(srcdir)/
+CFLAGS += -std=gnu11
+CXXFLAGS += -std=c++11
 
 
 
@@ -297,6 +322,12 @@ endif
 endif
 endif
 
+ifeq ($(MKL),1)
+BLAS_H := -I$(MKL_BASE)/include
+BLAS_L := -L$(MKL_BASE)/lib/intel64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core
+CPPFLAGS += -DUSE_MKL -DMKL_Complex8="complex float" -DMKL_Complex16="complex double"
+CFLAGS += -DUSE_MKL -DMKL_Complex8="complex float" -DMKL_Complex16="complex double"
+endif
 
 
 
@@ -311,6 +342,10 @@ ifeq ($(SLINK),1)
 	PNG_L += -lz
 endif
 
+ifeq ($(LINKER),icc)
+	PNG_L += -lz
+endif
+
 
 
 # fftw
@@ -338,11 +373,41 @@ ISMRM_H :=
 ISMRM_L :=
 endif
 
+# Enable in-memory CFL files
+
+ifeq ($(ENABLE_MEM_CFL),1)
+CPPFLAGS += -DUSE_MEM_CFL
+miscextracxxsrcs += $(srcdir)/misc/mmiocc.cc
+LDFLAGS += -lstdc++
+endif
+
+# Only allow in-memory CFL files (ie. disable support for all other files)
+
+ifeq ($(MEMONLY_CFL),1)
+CPPFLAGS += -DMEMONLY_CFL
+miscextracxxsrcs += $(srcdir)/misc/mmiocc.cc
+LDFLAGS += -lstdc++
+endif
+
+# Logging backends
+
+ifeq ($(LOG_BACKEND),1)
+CPPFLAGS += -DUSE_LOG_BACKEND
+ifeq ($(LOG_SIEMENS_BACKEND),1)
+miscextracxxsrcs += $(srcdir)/misc/UTrace.cc
+endif
+ifeq ($(LOG_ORCHESTRA_BACKEND),1)
+miscextracxxsrcs += $(srcdir)/misc/Orchestra.cc
+endif
+endif
+
+
 # change for static linking
 
 ifeq ($(SLINK),1)
 # work around fortran problems with static linking
 LDFLAGS += -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,--allow-multiple-definition
+LIBS += -lmvec
 BLAS_L += -llapack -lblas -lgfortran -lquadmath
 endif
 
@@ -426,14 +491,14 @@ endif
 
 .SECONDEXPANSION:
 $(TARGETS): % : src/main.c $(srcdir)/%.o $$(MODULES_%) $(MODULES)
-	$(CC) $(LDFLAGS) $(CFLAGS) -Dmain_real=main_$@ -o $@ $+ $(FFTW_L) $(CUDA_L) $(BLAS_L) $(PNG_L) $(ISMRM_L) -lm
+	$(LINKER) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -Dmain_real=main_$@ -o $@ $+ $(FFTW_L) $(CUDA_L) $(BLAS_L) $(PNG_L) $(ISMRM_L) $(LIBS) -lm
 #	rm $(srcdir)/$@.o
 
 UTESTS=$(shell $(root)/utests/utests-collect.sh ./utests/$@.c)
 
 .SECONDEXPANSION:
 $(UTARGETS): % : utests/utest.c utests/%.o $$(MODULES_%) $(MODULES)
-	$(CC) $(LDFLAGS) $(CFLAGS) -DUTESTS="$(UTESTS)" -o $@ $+ $(FFTW_L) $(CUDA_L) $(BLAS_L) -lm
+	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DUTESTS="$(UTESTS)" -o $@ $+ $(FFTW_L) $(CUDA_L) $(BLAS_L) $(LIBS) -lm
 
 
 # linker script version - does not work on MacOS X
@@ -495,7 +560,6 @@ install: bart $(root)/doc/commands.txt
 	install bart $(DESTDIR)/$(PREFIX)/bin/
 	install -d $(DESTDIR)/$(PREFIX)/share/doc/bart/
 	install $(root)/doc/*.txt $(root)/README $(DESTDIR)/$(PREFIX)/share/doc/bart/
-	install -d $(DESTDIR)/$(PREFIX)/lib/bart/commands/
 
 
 # generate release tar balls (identical to github)

README

@@ -49,6 +49,10 @@ Updates and further information can be found here:
 GCC compiler, the FFTW library, and optionally CUDA.
 (see recon/Makefile to turn options on or off)
 
+The minimum GCC supported is 5.0. It should also be possible
+to use the clang compiler, but older version before version
+4.0 are known to cause problems.
+
 The software can be used in combination with Matlab or octave.
 
 
@@ -81,11 +85,11 @@ To install the required libraries on Debian and Ubuntu run:
 ### 2.1.2. Mac OS X
 
 Xcode is required and it is recommended to install a newer version 
-of gcc (4.7 seems to work) from MacPorts (http://www.macports.org/).
+of gcc from MacPorts (http://www.macports.org/).
 
 
     $ sudo port install fftw-3-single
-    $ sudo port install gcc47
+    $ sudo port install gcc6
     $ sudo port install libpng
     $ sudo port install openblas
 
@@ -99,8 +103,14 @@ of gcc (4.7 seems to work) from MacPorts (http://www.macports.org/).
 
 ### 2.1.3. Windows
 
+Note that Windows is currently not supported. Nevertheless, many people
+use BART on Windows. If you have trouble to get it to work, you may
+want to try an older version (e.g. version 4.00).
+
+
 The recommended way to use BART on Windows is with the Windows Subsystem for
-Linux (WSL) which is available for Windows 10.
+Linux (WSL) which is available for Windows 10. If you use WSL, you need to
+use the clang compiler.
 
 
 BART should also work with Cygwin:

build_targets.mk

 # Main build targets
 #
-TBASE=show slice crop resize join transpose squeeze flatten zeros ones flip circshift extract repmat bitmask reshape version delta copy casorati vec
-TFLP=scale invert conj fmac saxpy sdot spow cpyphs creal carg normalize cdf97 pattern nrmse mip avg cabs zexpj
+TBASE=show slice crop resize join transpose squeeze flatten zeros ones flip circshift extract repmat bitmask reshape version delta copy casorati vec poly index
+TFLP=scale invert conj fmac saxpy sdot spow cpyphs creal carg normalize cdf97 pattern nrmse mip avg cabs zexp
 TNUM=fft fftmod fftshift noise bench threshold conv rss filter mandelbrot wavelet window var std
-TRECO=pics pocsense sqpics itsense nlinv nufft rof sake wave lrmatrix estdims estshift estdelay wavepsf
+TRECO=pics pocsense sqpics itsense nlinv nufft rof sake wave lrmatrix estdims estshift estdelay wavepsf wshfl
 TCALIB=ecalib ecaltwo caldir walsh cc ccapply calmat svd estvar whiten
 TMRI=homodyne poisson twixread fakeksp
 TSIM=phantom traj

cmake/BARTConfig.cmake.in

+# Copyright 2018. Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+# All rights reserved. Use of this source code is governed by
+# a BSD-style license which can be found in the LICENSE file.
+# \author Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+
+@PACKAGE_INIT@
+
+set(BART_ENABLE_MEM_CFL @BART_ENABLE_MEM_CFL@)
+set(BART_FPIC @BART_FPIC@)
+set(BART_FFTWTHREADS @BART_FFTWTHREADS@)
+set(BART_DISABLE_PNG @BART_DISABLE_PNG@)
+set(BART_ISMRMRD @BART_ISMRMRD@)
+set(BART_LOCAL_FFTW @BART_LOCAL_FFTW@)
+set(BART_LOG_BACKEND @BART_LOG_BACKEND@)
+set(BART_LOG_SIEMENS_BACKEND @BART_LOG_SIEMENS_BACKEND@)
+set(BART_LOG_ORCHESTRA_BACKEND @BART_LOG_ORCHESTRA_BACKEND@)
+set(BART_LOG_GADGETRON_BACKEND @BART_LOG_GADGETRON_BACKEND@)
+set(BART_NO_LAPACKE @BART_NO_LAPACKE@)
+set(BART_MATLAB @BART_MATLAB@)
+set(BART_MEMONLY_CFL @BART_MEMONLY_CFL@)
+set(BART_USE_CUDA @USE_CUDA@)
+set(BART_USE_NATIVE_CUDA @BART_USE_NATIVE_CUDA@)
+set(BART_USE_OPENMP @USE_OPENMP@)
+set(BART_REDEFINE_PRINTF_FOR_TRACE @BART_REDEFINE_PRINTF_FOR_TRACE@)
+
+set(BART_LINALG_VENDOR "@LINALG_VENDOR@")
+set(LINALG_VENDOR "@LINALG_VENDOR@")
+
+# ------------------------------------------------------------------------------
+
+get_filename_component(BART_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+
+list(INSERT CMAKE_MODULE_PATH 0 ${BART_CMAKE_DIR})
+
+include(CMakeFindDependencyMacro)
+
+include(${BART_CMAKE_DIR}/BARTFindBLASlib.cmake)
+
+if(BART_ISMRMRD)
+  find_dependency(ISMRMRD)
+endif()
+
+if(NOT BART_LOCAL_FFTW)
+  if(CMAKE_VERSION VERSION_LESS 3.9)
+    find_package(FFTW 3 REQUIRED COMPONENTS FFTWF FFTWF_MT)
+  else()
+    find_dependency(FFTW 3 COMPONENTS FFTWF FFTWF_MT)
+  endif()
+else()
+  find_dependency(Threads)
+endif()
+
+if(NOT BART_DISABLE_PNG)
+  find_dependency(PNG)
+  if(CMAKE_VERSION VERSION_LESS 3.5)
+    add_library(PNG::PNG SHARED IMPORTED GLOBAL)
+    set_target_properties(PNG::PNG
+      PROPERTIES
+      IMPORTED_LOCATION "${PNG_LIBRARY}"
+      INTERFACE_DEFINITIONS "${PNG_DEFINITIONS}"
+      INTERFACE_INCLUDE_DIRECTORIES "${PNG_INCLUDE_DIRS}"
+      INTERFACE_LINK_LIBRARIES "${PNG_LIBRARIES}"
+      )
+  endif()
+endif()
+
+if(BART_USE_OPENMP)
+  if(CMAKE_VERSION VERSION_LESS 3.11)
+    # Actually CMake 3.9 should be enough for OpenMP::OpenMP support,
+    # however, until CMake 3.11 we might get problems with the
+    # INTERFACE_COMPILE_OPTIONS property if we are compiling with
+    # CMake's native CUDA compilation
+    find_package(BOpenMP REQUIRED) # BOpenMP is FindOpenMP.cmake from 3.12
+  else()
+    find_package(OpenMP REQUIRED)
+  endif()
+endif()
+
+if(BART_USE_NATIVE_CUDA)
+  find_dependency(CUDAlibs COMPONENTS CUBLAS CUFFT)
+endif()
+
+list(REMOVE_AT CMAKE_MODULE_PATH 0)
+
+# ==============================================================================
+
+set_and_check(BARTTargetForEmbedding "${BART_CMAKE_DIR}/BARTTargetsForEmbedding.cmake")
+include(${BARTTargetForEmbedding})
+
+set(BARTTargetGeneral "${BART_CMAKE_DIR}/BARTTargets.cmake")
+if(NOT TARGET BART::BART AND EXISTS ${BARTTargetGeneral})
+  include(${BARTTargetGeneral})
+endif()
+
+# ==============================================================================
+

cmake/BARTFindBLASlib.cmake

+# Copyright 2018. Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+# All rights reserved. Use of this source code is governed by
+# a BSD-style license which can be found in the LICENSE file.
+# \author Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+
+macro(setup_linalg_vendor_on_success vendor target)
+  if(${target}_FOUND)
+    set(LINALG_VENDOR_LIB ${ARGN})
+    set(LINALG_VENDOR_FOUND TRUE)
+    set(LINALG_VENDOR ${vendor} CACHE STRING "Vendor type for linear algebra library" FORCE)
+    set(LINALG_VENDOR_TGT ${target})
+  endif()
+endmacro()
+
+##==============================================================
+
+if(NOT "${LINALG_VENDOR}" STREQUAL "")
+  # If the user specifies LINALG_VENDOR, make sure we find what he wants
+  set(FIND_PACKAGE_ARG "REQUIRED")
+else()
+  set(FIND_PACKAGE_ARG)
+endif()
+
+## Switch based on the linear algebra optimized library to 
+## use.  Note that the first library successfully found
+## will be used 
+##
+## -*-*- Try with only a BLAS library first if BART_NO_LAPACKE is set
+if(BART_NO_LAPACKE AND (NOT LINALG_VENDOR OR LINALG_VENDOR STREQUAL "BLAS"))
+  find_package(LAPACKE ${FIND_PACKAGE_ARG} COMPONENTS lapack cblas blas)
+  setup_linalg_vendor_on_success("BLAS" LAPACKE LAPACKE::LAPACK LAPACKE::CBLAS LAPACKE::BLAS)
+endif()
+
+## -*-*- Try AMD BLIS/libFlame next
+if(NOT LINALG_VENDOR OR LINALG_VENDOR MATCHES "AMD_FLAME")
+  find_package(libFlame ${FIND_PACKAGE_ARG})
+  setup_linalg_vendor_on_success("AMD_FLAME" libFlame libFlame::libFlame)
+
+  if(libFlame_FOUND)
+    if(NOT BART_NO_LAPACKE)
+      find_package(LAPACKE REQUIRED COMPONENTS LAPACKE)
+      get_target_property(
+	libFlame_INTERFACE_LINK_LIBRARIES
+	${LINALG_VENDOR_LIB}
+	INTERFACE_LINK_LIBRARIES)
+      set_target_properties(${LINALG_VENDOR_LIB} PROPERTIES
+	INTERFACE_LINK_LIBRARIES "${libFlame_INTERFACE_LINK_LIBRARIES};LAPACKE::LAPACKE")
+    endif()
+  endif()
+endif()
+
+## -*-*- Try OpenBLAS next
+if(NOT LINALG_VENDOR OR LINALG_VENDOR MATCHES "OpenBLAS")
+  find_package(OpenBLAS ${FIND_PACKAGE_ARG})
+  setup_linalg_vendor_on_success("OpenBLAS" OpenBLAS OpenBLAS::OpenBLAS)
+endif()
+
+##
+## -*-*- Try ATLAS version next
+if(NOT LINALG_VENDOR OR LINALG_VENDOR MATCHES "ATLAS")
+  find_package(ATLAS ${FIND_PACKAGE_ARG})
+  setup_linalg_vendor_on_success("ATLAS" ATLAS ATLAS::ATLAS)
+endif()
+
+##
+## -*-*- Try Generic LAPACKE version Last
+if(NOT LINALG_VENDOR OR LINALG_VENDOR MATCHES "LAPACKE")
+  #NOTE: By specifying Fortran here, linking to lapack becomes easier
+  # See https://blog.kitware.com/fortran-for-cc-developers-made-easier-with-cmake/
+  if(NOT WIN32)
+    enable_language(Fortran)
+  endif()
+  ## Only very new versions of LAPACK (> 3.5.0) have built in support
+  ## for cblas and lapacke.  This method is not very robust to older
+  ## versions of lapack that might be able to be supported.
+  ## It is know to work local builds
+  find_package(LAPACKE ${FIND_PACKAGE_ARG})
+  setup_linalg_vendor_on_success("LAPACKE" LAPACKE LAPACKE::LAPACKE LAPACKE::LAPACKE LAPACKE::CBLAS LAPACKE::BLAS)
+endif()
+
+# Fix weird error when compiling on Mac...
+if(APPLE)
+  include_directories(${${LINALG_VENDOR_TGT}_INCLUDE_DIRS})
+endif()
+
+##
+## -*-*- Finally, set include_directories -*-*-*
+if(NOT LINALG_VENDOR_FOUND)
+   message(FATAL_ERROR "No valid linear algebra libraries found!")
+endif()

cmake/FindATLAS.cmake

@@ -2,23 +2,17 @@
 # FindATLAS
 # -------------
 #
-# Find the ATLAS library
+# Find ATLAS include dirs and libraries
 #
-# Using ATLAS:
+# Use this module by invoking find_package with the form::
 #
-# ::
+#   find_package(ATLAS
+#     [REQUIRED]             # Fail with error if ATLAS is not found
+#     )
 #
 #   [OPTIONAL]  set(ATLAS_REQUIRE_THREADED [TRUE|FALSE]) to find threaded versions of the libraries
-#   find_package(ATLAS REQUIRED)
-#   include_directories(${ATLAS_INCLUDE_DIRS})
-#   add_executable(foo foo.cc)
-#   target_link_libraries(foo ${ATLAS_LIBRARIES})
-#   -- OR --
-#   target_link_libraries(foo ${ATLAS_PARALLEL_LIBRARIES})
 #
-# This module sets the following variables:
-#
-# ::
+# This module defines::
 #
 #   ATLAS_FOUND            - set to true if the library is found
 #   ATLAS_INCLUDE_DIRS     - list of required include directories
@@ -27,30 +21,72 @@
 #   ATLAS_VERSION_MINOR    - minor version number
 #   ATLAS_VERSION_PATCH    - patch version number
 #   ATLAS_VERSION_STRING   - version number as a string (ex: "0.2.18")
+#
+#
+# This module reads hints about search locations from variables
+# (either CMake variables or environment variables)::
+#
+#   ATLAS_ROOT             - Preferred installation prefix for ATLAS
+#   ATLAS_DIR              - Preferred installation prefix for ATLAS
+#
+#
+#   ATLAS::ATLAS           - Imported target for the ATLAS library
+#
 
-#=============================================================================
+# ==============================================================================
 # Copyright 2016 Hans J. Johnson <hans-johnson@uiowa.edu>
+# Copyright 2018 Damien Nguyen <damien.nguyen@alumni.epfl.ch>
 #
 # Distributed under the OSI-approved BSD License (the "License")
 #
 # This software is distributed WITHOUT ANY WARRANTY; without even the
 # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-#=============================================================================
-#
+# ==============================================================================
 
 set(ATLAS_SEARCH_PATHS
+  ${ATLAS_ROOT}
+  $ENV{ATLAS_ROOT}
   ${ATLAS_DIR}
   $ENV{ATLAS_DIR}
-  $ENV{CMAKE_PREFIX_PATH}
   ${CMAKE_PREFIX_PATH}
+  $ENV{CMAKE_PREFIX_PATH}
   /usr
-  /usr/local
-  /usr/local/opt/openblas  ## Mac Homebrew install path
+  /usr/local/
+  /usr/local/opt # homebrew on mac
+  /opt
+  /opt/local
   /opt/ATLAS
   )
 
-set(CMAKE_PREFIX_PATH ${ATLAS_SEARCH_PATHS})
-list(REMOVE_DUPLICATES CMAKE_PREFIX_PATH)
+set(PATH_SUFFIXES_LIST
+  lib64/atlas-sse3 #openSUSE 13.2 (Harlequin)
+  lib64/atlas-sse2 #openSUSE 13.2 (Harlequin)
+  lib64/atlas-sse  #openSUSE 13.2 (Harlequin)
+  lib64/atlas      #openSUSE 13.2 (Harlequin)
+  lib64
+  lib/atlas-sse3 #openSUSE 13.2 (Harlequin)
+  lib/atlas-sse2 #openSUSE 13.2 (Harlequin)
+  lib/atlas-sse  #openSUSE 13.2 (Harlequin)
+  lib/atlas      #openSUSE 13.2 (Harlequin)
+  lib
+)
+
+if(APPLE)
+  list(APPEND PATH_SUFFIXES_LIST openblas/lib)
+endif()
+
+# ==============================================================================
+# Prepare some helper variables
+
+set(ATLAS_INCLUDE_DIRS)
+set(ATLAS_LIBRARIES)
+
+set(ATLAS_THREAD_PREFIX "")
+if(ATLAS_REQUIRE_THREADED)
+  set(ATLAS_THREAD_PREFIX "pt")
+endif()
+
+# ==============================================================================
 
 ## First try to find ATLAS with NO_MODULE,
 ## As of 20160706 version 0.2.18 there is limited cmake support for ATLAS
@@ -61,62 +97,55 @@ if(ATLAS_VERSION)
   set(ATLAS_VERSION_STRING ${ATLAS_VERSION})
   unset(ATLAS_VERSION) # Use cmake conventional naming
 endif()
-##################################################################################################
+
+# ==============================================================================
 ### First search for headers
+
 find_path(ATLAS_CBLAS_INCLUDE_DIR 
   NAMES cblas.h 
   PATHS ${ATLAS_SEARCH_PATHS} 
   PATH_SUFFIXES include include/openblas)
-find_path(ATLAS_LAPACKE_INCLUDE_DIR 
-             NAMES lapacke.h 
-             PATHS ${ATLAS_SEARCH_PATHS} 
-             PATH_SUFFIXES include)
-
-##################################################################################################
-set(PATH_SUFFIXES_LIST
-  lib64/atlas-sse3 #openSUSE 13.2 (Harlequin)
-  lib64/atlas-sse2 #openSUSE 13.2 (Harlequin)
-  lib64/atlas-sse  #openSUSE 13.2 (Harlequin)
-  lib64/atlas      #openSUSE 13.2 (Harlequin)
-  lib64
-  lib/atlas-sse3 #openSUSE 13.2 (Harlequin)
-  lib/atlas-sse2 #openSUSE 13.2 (Harlequin)
-  lib/atlas-sse  #openSUSE 13.2 (Harlequin)
-  lib/atlas      #openSUSE 13.2 (Harlequin)
-  lib
-)
 	   
+# ==============================================================================
 ### Second, search for libraries
+
 find_library(ATLAS_LIB
   NAMES atlas
   PATHS ${ATLAS_SEARCH_PATHS}
   PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
 
-set(ATLAS_THREAD_PREFIX "")
-if(ATLAS_REQUIRE_THREADED)
-  set(ATLAS_THREAD_PREFIX "pt")
-endif()
 find_library(CBLAS_LIB 
   NAMES ${ATLAS_THREAD_PREFIX}cblas
   PATHS ${LAPACKE_SEARCH_PATHS}
   PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
+
 find_library(LAPACK_LIB 
   NAMES ${ATLAS_THREAD_PREFIX}lapack
   PATHS ${LAPACKE_SEARCH_PATHS}
   PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
-find_library(LAPACKE_LIB 
-                 NAMES ${ATLAS_THREAD_PREFIX}lapacke
-                 PATHS ${LAPACKE_SEARCH_PATHS}
-                 PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
+
+if(NOT DEFINED ATLAS_NO_LAPACKE OR NOT ATLAS_NO_LAPACKE)
+  if(ATLAS_LIB)
+    include(CheckLibraryExists)
+    check_library_exists(${ATLAS_LIB} LAPACKE_cheev  "" HAVE_LAPACKE_CHEEV)
+    check_library_exists(${ATLAS_LIB} LAPACKE_zgesdd "" HAVE_LAPACKE_ZGESDD)
+    
+    if(NOT HAVE_LAPACKE_CHEEV OR NOT HAVE_LAPACKE_ZGESDD)
+      message(WARNING "ATLAS has no LAPACKE symbols. Attempting to look for a LAPACKE library")
+      find_package(LAPACKE QUIET REQUIRED COMPONENTS lapacke)
+      list(APPEND ATLAS_LIBRARIES ${LAPACKE_LIBRARIES})
+    endif()
+  endif()
+  set(LAPACKE_LIB_VAR "LAPACKE_LIBRARIES")
+else()
+  set(LAPACKE_LIB_VAR "")
+endif()
+
 find_library(F77BLAS_LIB 
   NAMES ${ATLAS_THREAD_PREFIX}f77blas
   PATHS ${LAPACKE_SEARCH_PATHS}
   PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
 
-# ------------------------------------------------------------------------
-#  Extract version information
-# ------------------------------------------------------------------------
-
 # WARNING: We may not be able to determine the version of some ATLAS
 set(ATLAS_VERSION_MAJOR 0)
 set(ATLAS_VERSION_MINOR 0)
@@ -125,36 +154,81 @@ if(ATLAS_VERSION_STRING)
   string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\1" ATLAS_VERSION_MAJOR "${ATLAS_VERSION_STRING}")
   string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\2" ATLAS_VERSION_MINOR "${ATLAS_VERSION_STRING}")
   string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\3" ATLAS_VERSION_PATCH "${ATLAS_VERSION_STRING}")
-else()
+elseif(ATLAS_LIB)
   set(ATLAS_VERSION_STRING "ATLAS.UNKOWN.VERSION")
+else()
+  set(ATLAS_VERSION_STRING)
 endif()
 
-#======================
+# ==============================================================================
 # Checks 'REQUIRED', 'QUIET' and versions.
+
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(ATLAS FOUND_VAR ATLAS_FOUND
   REQUIRED_VARS
   ATLAS_CBLAS_INCLUDE_DIR
-                ATLAS_LAPACKE_INCLUDE_DIR
-                LAPACKE_LIB
+  ${LAPACKE_INCLUDE_VAR}
+  ${LAPACKE_LIB_VAR}
   LAPACK_LIB
   F77BLAS_LIB
   CBLAS_LIB
   ATLAS_LIB
   VERSION_VAR ATLAS_VERSION_STRING
   )
+
+# ------------------------------------------------------------------------------
+
 if (ATLAS_FOUND)
-  set(ATLAS_INCLUDE_DIRS ${ATLAS_CBLAS_INCLUDE_DIR} ${ATLAS_CBLAS_INCLUDE_DIR})
+  list(APPEND ATLAS_INCLUDE_DIRS
+    ${ATLAS_CBLAS_INCLUDE_DIR}
+    ${ATLAS_CBLAS_INCLUDE_DIR})
   list(REMOVE_DUPLICATES ATLAS_INCLUDE_DIRS)
+  
   if("${CMAKE_C_COMPILER_ID}" MATCHES ".*Clang.*" OR
      "${CMAKE_C_COMPILER_ID}" MATCHES ".*GNU.*" OR
      "${CMAKE_C_COMPILER_ID}" MATCHES ".*Intel.*"
       ) #NOT MSVC
     set(MATH_LIB m)
   endif()
-  list(APPEND ATLAS_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB} ${F77BLAS_LIB} ${CBLAS_LIB} ${ATLAS_LIB} ${MATH_LIB})
+  
+  list(APPEND ATLAS_LIBRARIES ${LAPACKE_LIBRARIES} ${LAPACK_LIB} ${F77BLAS_LIB} ${CBLAS_LIB} ${ATLAS_LIB} ${MATH_LIB})
+  
+  if(NOT TARGET ATLAS::ATLAS)
+    get_filename_component(LIB_EXT "${ATLAS_LIB}" EXT)
+    if(LIB_EXT STREQUAL ".a" OR LIB_EXT STREQUAL ".lib")
+      set(LIB_TYPE STATIC)
+    else()
+      set(LIB_TYPE SHARED)
+    endif()
+    add_library(ATLAS::ATLAS ${LIB_TYPE} IMPORTED GLOBAL)
+    set(_tmp_dep_libs "${LAPACKE_LIBRARIES};${LAPACK_LIB};${F77BLAS_LIB};${CBLAS_LIB};${MATH_LIB}")
+    list(REMOVE_DUPLICATES _tmp_dep_libs)
+    set_target_properties(ATLAS::ATLAS
+      PROPERTIES
+      IMPORTED_LOCATION "${ATLAS_LIB}"
+      INTERFACE_INCLUDE_DIRECTORIES "${ATLAS_INCLUDE_DIRS}"
+      INTERFACE_LINK_LIBRARIES "${_tmp_dep_libs}")
+  endif()
+  
+  if(NOT ATLAS_FIND_QUIETLY)
+    get_target_property(_dep_libs ATLAS::ATLAS INTERFACE_LINK_LIBRARIES)
+
+    set(_version "${ATLAS_VERSION_STRING}")
+    if(_version STREQUAL "ATLAS.UNKOWN.VERSION")
+      set(_version)
+    else()
+      set(_version " (${_version})")
+    endif()
+    
+    message(STATUS "Found ATLAS${_version} and defined the ATLAS::ATLAS imported target:")
+    message(STATUS "  - include:      ${ATLAS_INCLUDE_DIRS}")
+    message(STATUS "  - library:      ${ATLAS_LIB}")
+    message(STATUS "  - dependencies: ${_dep_libs}")
+  endif()
 endif()
 
+# ==============================================================================
+
 mark_as_advanced(
   ATLAS_FOUND
   ATLAS_INCLUDE_DIRS
@@ -165,11 +239,5 @@ mark_as_advanced(
   ATLAS_VERSION_STRING
   )
 
-## For debugging
-message(STATUS "ATLAS_FOUND                  :${ATLAS_FOUND}:  - set to true if the library is found")
-message(STATUS "ATLAS_INCLUDE_DIRS           :${ATLAS_INCLUDE_DIRS}: - list of required include directories")
-message(STATUS "ATLAS_LIBRARIES              :${ATLAS_LIBRARIES}: - list of libraries to be linked")
-message(STATUS "ATLAS_VERSION_MAJOR          :${ATLAS_VERSION_MAJOR}: - major version number")
-message(STATUS "ATLAS_VERSION_MINOR          :${ATLAS_VERSION_MINOR}: - minor version number")
-message(STATUS "ATLAS_VERSION_PATCH          :${ATLAS_VERSION_PATCH}: - patch version number")
-message(STATUS "ATLAS_VERSION_STRING         :${ATLAS_VERSION_STRING}: - version number as a string")
+# ==============================================================================
+

cmake/FindBPython.cmake

+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file Copyright.txt or https://cmake.org/licensing for details.
+
+#[=======================================================================[.rst:
+# FindBPython
+# ----------
+
+# Find Python interpreter, compiler and development environment (include
+# directories and libraries).
+
+# Three components are supported:
+
+# * ``Interpreter``: search for Python interpreter.
+# * ``Compiler``: search for Python compiler. Only offered by IronPython.
+# * ``Development``: search for development artifacts (include directories and
+#   libraries).
+
+# If no ``COMPONENTS`` is specified, ``Interpreter`` is assumed.
+
+# To ensure consistent versions between components ``Interpreter``, ``Compiler``
+# and ``Development``, specify all components at the same time::
+
+#   find_package (BPython COMPONENTS Interpreter Development)
+
+# This module looks preferably for version 3 of Python. If not found, version 2
+# is searched.
+# To manage concurrent versions 3 and 2 of Python, use :module:`FindBPython3` and
+# :module:`FindBPython2` modules rather than this one.
+
+# Imported Targets
+# ^^^^^^^^^^^^^^^^
+
+# This module defines the following :ref:`Imported Targets <Imported Targets>`:
+
+# ``Python::Interpreter``
+#   Python interpreter. Target defined if component ``Interpreter`` is found.
+# ``Python::Compiler``
+#   Python compiler. Target defined if component ``Compiler`` is found.
+# ``Python::Python``
+#   Python library. Target defined if component ``Development`` is found.
+
+# Result Variables
+# ^^^^^^^^^^^^^^^^
+
+# This module will set the following variables in your project
+# (see :ref:`Standard Variable Names <CMake Developer Standard Variable Names>`):
+
+# ``Python_FOUND``
+#   System has the Python requested components.
+# ``Python_Interpreter_FOUND``
+#   System has the Python interpreter.
+# ``Python_EXECUTABLE``
+#   Path to the Python interpreter.
+# ``Python_INTERPRETER_ID``
+#   A short string unique to the interpreter. Possible values include:
+#     * Python
+#     * ActivePython
+#     * Anaconda
+#     * Canopy
+#     * IronPython
+# ``Python_STDLIB``
+#   Standard platform independent installation directory.
+
+#   Information returned by
+#   ``distutils.sysconfig.get_python_lib(plat_specific=False,standard_lib=True)``.
+# ``Python_STDARCH``
+#   Standard platform dependent installation directory.
+
+#   Information returned by
+#   ``distutils.sysconfig.get_python_lib(plat_specific=True,standard_lib=True)``.
+# ``Python_SITELIB``
+#   Third-party platform independent installation directory.
+
+#   Information returned by
+#   ``distutils.sysconfig.get_python_lib(plat_specific=False,standard_lib=False)``.
+# ``Python_SITEARCH``
+#   Third-party platform dependent installation directory.
+
+#   Information returned by
+#   ``distutils.sysconfig.get_python_lib(plat_specific=True,standard_lib=False)``.
+# ``Python_Compiler_FOUND``
+#   System has the Python compiler.
+# ``Python_COMPILER``
+#   Path to the Python compiler. Only offered by IronPython.
+# ``Python_COMPILER_ID``
+#   A short string unique to the compiler. Possible values include:
+#     * IronPython
+# ``Python_Development_FOUND``
+#   System has the Python development artifacts.
+# ``Python_INCLUDE_DIRS``
+#   The Python include directories.
+# ``Python_LIBRARIES``
+#   The Python libraries.
+# ``Python_LIBRARY_DIRS``
+#   The Python library directories.
+# ``Python_RUNTIME_LIBRARY_DIRS``
+#   The Python runtime library directories.
+# ``Python_VERSION``
+#   Python version.
+# ``Python_VERSION_MAJOR``
+#   Python major version.
+# ``Python_VERSION_MINOR``
+#   Python minor version.
+# ``Python_VERSION_PATCH``
+#   Python patch version.
+
+# Hints
+# ^^^^^
+
+# ``Python_ROOT_DIR``
+#   Define the root directory of a Python installation.
+
+# ``Python_USE_STATIC_LIBS``
+#   * If not defined, search for shared libraries and static libraries in that
+#     order.
+#   * If set to TRUE, search **only** for static libraries.
+#   * If set to FALSE, search **only** for shared libraries.
+
+# Commands
+# ^^^^^^^^
+
+# This module defines the command ``Python_add_library`` which have the same
+# semantic as :command:`add_library` but take care of Python module naming rules
+# (only applied if library is of type ``MODULE``) and add dependency to target
+# ``Python::Python``::
+
+#   Python_add_library (my_module MODULE src1.cpp)
+
+# If library type is not specified, ``MODULE`` is assumed.
+#]=======================================================================]
+
+set(_PYTHON_PREFIX Python)
+set(Python_FIND_REQUIRED ${BPython_FIND_REQUIRED})
+set(Python_FIND_QUIETLY ${BPython_FIND_QUIETLY})
+set(Python_FIND_VERSION ${BPython_FIND_VERSION})
+set(Python_FIND_VERSION_MAJOR ${BPython_FIND_VERSION_MAJOR})
+set(Python_FIND_VERSION_MINOR ${BPython_FIND_VERSION_MINOR})
+set(Python_FIND_VERSION_PATCH ${BPython_FIND_VERSION_PATCH})
+set(Python_FIND_VERSION_TWEAK ${BPython_FIND_VERSION_TWEAK})
+set(Python_FIND_VERSION_COUNT ${BPython_FIND_VERSION_COUNT})
+set(Python_FIND_VERSION_EXACT ${BPython_FIND_VERSION_EXACT})
+set(Python_FIND_COMPONENTS ${BPython_FIND_COMPONENTS})
+foreach(_comp ${BPython_FIND_COMPONENTS})
+  set(Python_FIND_REQUIRED_${_comp} ${BPython_FIND_REQUIRED_${_comp}})
+endforeach()
+
+if (DEFINED Python_FIND_VERSION)
+  set (_Python_REQUIRED_VERSION_MAJOR ${Python_FIND_VERSION_MAJOR})
+
+  include (${CMAKE_CURRENT_LIST_DIR}/FindPythonSupport.cmake)
+else()
+  # iterate over versions in quiet and NOT required modes to avoid multiple
+  # "Found" messages and prematurally failure.
+  set (_Python_QUIETLY ${BPython_FIND_QUIETLY})
+  set (_Python_REQUIRED ${BPython_FIND_REQUIRED})
+  set (Python_FIND_QUIETLY TRUE)
+  set (Python_FIND_REQUIRED FALSE)
+
+  set (_Python_REQUIRED_VERSIONS 3 2)
+  set (_Python_REQUIRED_VERSION_LAST 2)
+
+  foreach (_Python_REQUIRED_VERSION_MAJOR IN LISTS _Python_REQUIRED_VERSIONS)
+    set (Python_FIND_VERSION ${_Python_REQUIRED_VERSION_MAJOR})
+    include (${CMAKE_CURRENT_LIST_DIR}/FindPythonSupport.cmake)
+    if (Python_FOUND OR
+        _Python_REQUIRED_VERSION_MAJOR EQUAL _Python_REQUIRED_VERSION_LAST)
+      break()
+    endif()
+    # clean-up some CACHE variables to ensure look-up restart from scratch
+    foreach (_Python_ITEM IN LISTS _Python_CACHED_VARS)
+      unset (${_Python_ITEM} CACHE)
+    endforeach()
+  endforeach()
+
+  unset (Python_FIND_VERSION)
+
+  set (BPython_FIND_QUIETLY ${_Python_QUIETLY})
+  set (BPython_FIND_REQUIRED ${_Python_REQUIRED})
+  if (Python_FIND_REQUIRED OR NOT Python_FIND_QUIETLY)
+    # call again validation command to get "Found" or error message
+    find_package_handle_standard_args (Python HANDLE_COMPONENTS
+                                              REQUIRED_VARS ${_Python_REQUIRED_VARS}
+                                              VERSION_VAR Python_VERSION)
+  endif()
+endif()
+
+if (COMMAND __Python_add_library)
+  macro (Python_add_library)
+    __Python_add_library (Python ${ARGV})
+  endmacro()
+endif()
+
+unset (_PYTHON_PREFIX)

cmake/FindCUDAlibs.cmake

+#.rst:
+# FindCUDAlibs
+# -------------
+#
+# Find CUDA include dirs and libraries
+#
+# Use this module by invoking find_package with the form::
+#
+#   find_package(CUDAlibs
+#     [REQUIRED]             # Fail with error if LAPACKE is not found
+#     [COMPONENTS <comp>...] # List of components to look for
+#     )                      # Not specifying any components is equivalent to
+#                              looking for the BASIC libraries
+#
+# Valid names for COMPONENTS libraries are::
+#
+#   ALL         - Find all libraries
+#   BASIC       - Equivalent to CUDART;CUBLAS;CUFFT
+#
+#   CUDART      - CUDA RT library
+#   CUBLAS      - CUDA BLAS library
+#   CUFFT       - CUDA FFT library
+#   CUFFTW      - CUDA FFTW library
+#   CUPTI       - CUDA Profiling Tools Interface library.
+#   CURAND      - CUDA Random Number Generation library.
+#   CUSOLVER    - CUDA Direct Solver library.
+#   CUSPARSE    - CUDA Sparse Matrix library.
+#   NPP         - NVIDIA Performance Primitives lib.
+#   NPPC        - NVIDIA Performance Primitives lib (core).
+#   NPPI        - NVIDIA Performance Primitives lib (image processing).
+#   NPPIAL      - NVIDIA Performance Primitives lib (image processing).
+#   NPPICC      - NVIDIA Performance Primitives lib (image processing).
+#   NPPICOM     - NVIDIA Performance Primitives lib (image processing).
+#   NPPIDEI     - NVIDIA Performance Primitives lib (image processing).
+#   NPPIF       - NVIDIA Performance Primitives lib (image processing).
+#   NPPIG       - NVIDIA Performance Primitives lib (image processing).
+#   NPPIM       - NVIDIA Performance Primitives lib (image processing).
+#   NPPIST      - NVIDIA Performance Primitives lib (image processing).
+#   NPPISU      - NVIDIA Performance Primitives lib (image processing).
+#   NPPITC      - NVIDIA Performance Primitives lib (image processing).
+#   NPPS        - NVIDIA Performance Primitives lib (signal processing).
+#   NVBLAS      - NVIDIA BLAS library
+#
+#  Not specifying COMPONENTS is identical to choosing ALL
+#
+# This module reads hints about search locations from variables
+# (either CMake variables or environment variables)::
+#
+#   CUDA_TOOLKIT_ROOT_DIR
+#   CUDA_ROOT
+#
+# The following :prop_tgt:`IMPORTED` targets are defined if required::
+#
+#   CUDAlibs::CUDART         - Imported target for the CUDA RT library
+#   CUDAlibs::CUBLAS         - Imported target for the CUDA cublas library
+#   CUDAlibs::CUFFT          - Imported target for the CUDA cufft library
+#   CUDAlibs::CUFFTW         - Imported target for the CUDA cufftw library
+#   CUDAlibs::CUPTI          - Imported target for the CUDA cupti library
+#   CUDAlibs::CURAND         - Imported target for the CUDA curand library
+#   CUDAlibs::CUSOLVER       - Imported target for the CUDA cusolver library
+#   CUDAlibs::CUSPARSE       - Imported target for the CUDA cusparse library
+#   CUDAlibs::NPP            - Imported target for the CUDA npp library
+#   CUDAlibs::NPPC           - Imported target for the CUDA nppc library
+#   CUDAlibs::NPPI           - Imported target for the CUDA nppi library
+#   CUDAlibs::NPPIAL         - Imported target for the CUDA nppial library
+#   CUDAlibs::NPPICC         - Imported target for the CUDA nppicc library
+#   CUDAlibs::NPPICOM        - Imported target for the CUDA nppicom library
+#   CUDAlibs::NPPIDEI        - Imported target for the CUDA nppidei library
+#   CUDAlibs::NPPIF          - Imported target for the CUDA nppif library
+#   CUDAlibs::NPPIG          - Imported target for the CUDA nppig library
+#   CUDAlibs::NPPIM          - Imported target for the CUDA nppim library
+#   CUDAlibs::NPPIST         - Imported target for the CUDA nppist library
+#   CUDAlibs::NPPISU         - Imported target for the CUDA nppisu library
+#   CUDAlibs::NPPITC         - Imported target for the CUDA nppitc library
+#   CUDAlibs::NPPS           - Imported target for the CUDA npps library
+#   CUDAlibs::NVBLAS         - Imported target for the CUDA nvblas library
+#
+
+# ==============================================================================
+# Copyright 2018 Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+#
+# Distributed under the OSI-approved BSD License (the "License")
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# ==============================================================================
+
+if(CMAKE_VERSION VERSION_LESS 3.8)
+  message(FATAL_ERROR "Cannot use find_package(CUDAlibs ...) with CMake < 3.8! Use find_package(CUDA) instead.")
+endif()
+
+# ------------------------------------------------------------------------------
+
+set(_cuda_root_dir_hint)
+foreach(_dir ${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES})
+  get_filename_component(_dirname "${_dir}" DIRECTORY)
+  list(APPEND _cuda_root_dir_hint ${_dirname})
+endforeach()
+
+set(CUDAlibs_SEARCH_PATHS
+  ${_cuda_root_dir_hint}
+  ${CUDA_ROOT}
+  $ENV{CUDA_ROOT}
+  ${CUDA_TOOLKIT_ROOT_DIR}
+  $ENV{CUDA_TOOLKIT_ROOT_DIR}
+  ${CMAKE_PREFIX_PATH}
+  $ENV{CMAKE_PREFIX_PATH}
+  /usr
+  /usr/local
+  /usr/local/cuda
+  /opt
+  /opt/local
+  )
+
+set(PATH_SUFFIXES_LIST lib/x64 lib64 libx64 lib lib/Win32 lib libWin32)
+
+if(WIN32)
+  set(_root_dir "C:/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA")
+  file(GLOB _children RELATIVE ${_root_dir} ${_root_dir}/*)
+  list(SORT _children)
+  list(REVERSE _children)
+  foreach(_child ${_children})
+    if(IS_DIRECTORY ${_root_dir}/${_child} AND ${_child} MATCH "v[0-9]+.[0-9]")
+      list(APPEND CUDAlibs_SEARCH_PATHS ${_root_dir}/${child})
+    endif()
+  endforeach()
+endif()
+
+# ==============================================================================
+# Prepare some helper variables
+
+set(CUDAlibs_REQUIRED_VARS)
+
+# ==============================================================================
+
+macro(cuda_find_library component)
+  string(TOLOWER ${COMPONENT} libnames)
+
+  find_library(CUDAlibs_${component}_LIB
+    NAMES ${libnames}
+    PATHS ${CUDAlibs_SEARCH_PATHS}
+    PATH_SUFFIXES ${PATH_SUFFIXES_LIST}
+    NO_DEFAULT_PATH)
+
+  if(CUDAlibs_${component}_LIB)
+    set(CUDAlibs_${component}_LIB_FOUND 1)
+  endif()
+  list(APPEND CUDAlibs_REQUIRED_VARS "CUDAlibs_${component}_LIB")
+  
+  if(CUDAlibs_${component}_LIB_FOUND)
+    set(CUDAlibs_${component}_FOUND 1)
+  else()
+    set(CUDAlibs_${component}_FOUND 0)
+  endif()
+endmacro()
+
+# ------------------------------------------------------------------------------
+
+set(CUDAlibs_ALL_LIBS "CUDART;CUBLAS;CUFFT;CUFFTW;CUPTI;CURAND;CUSOLVER;CUSPARSE;NPP;NPPC;NPPI;NPPIAL;NPPICC;NPPICOM;NPPIDEI;NPPIF;NPPIG;NPPIM;NPPIST;NPPISU;NPPITC;NPPS;NVBLAS")
+
+# List dependent libraries for relevant targets
+set(CUDAlibs_DEP_CUFFTW "CUFFT")
+set(CUDAlibs_DEP_NPPIAL "NPPC")
+set(CUDAlibs_DEP_NPPICC "NPPC")
+set(CUDAlibs_DEP_NPPICOM "NPPC")
+set(CUDAlibs_DEP_NPPIDEI "NPPC")
+set(CUDAlibs_DEP_NPPIF "NPPC")
+set(CUDAlibs_DEP_NPPIG "NPPC")
+set(CUDAlibs_DEP_NPPIM "NPPC")
+set(CUDAlibs_DEP_NPPIST "NPPC")
+set(CUDAlibs_DEP_NPPISU "NPPC")
+set(CUDAlibs_DEP_NPPITC "NPPC")
+set(CUDAlibs_DEP_NPPS "NPPC")
+set(CUDAlibs_DEP_NVBLAS "CUBLAS")
+
+# ------------------------------------------------------------------------------
+
+if(NOT CUDAlibs_FIND_COMPONENTS OR CUDAlibs_FIND_COMPONENTS STREQUAL "BASIC")
+  set(CUDAlibs_FIND_COMPONENTS "CUDART;CUBLAS;CUFFT")
+elseif(CUDAlibs_FIND_COMPONENTS STREQUAL "ALL")
+  set(CUDAlibs_FIND_COMPONENTS ${CUDAlibs_ALL_LIBS})
+endif()
+
+foreach(COMPONENT ${CUDAlibs_FIND_COMPONENTS})
+  string(TOUPPER ${COMPONENT} UPPERCOMPONENT)
+
+  if (${UPPERCOMPONENT} IN_LIST CUDAlibs_ALL_LIBS)
+    cuda_find_library(${UPPERCOMPONENT})
+    foreach(_dep "${CUDAlibs_DEP_${UPPERCOMPONENT}}")
+      if(NOT "${_dep}" STREQUAL "")
+	cuda_find_library(${_dep})
+      endif()
+    endforeach()
+  else()
+    message(FATAL_ERROR "Unknown component: ${COMPONENT}")
+  endif()
+
+  mark_as_advanced(
+    CUDAlibs_${UPPERCOMPONENT}_LIB
+    CUDAlibs_${UPPERCOMPONENT}_INCLUDE_DIR)
+endforeach()
+
+# ==============================================================================
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(CUDAlibs
+  FOUND_VAR CUDAlibs_FOUND
+  REQUIRED_VARS ${CUDAlibs_REQUIRED_VARS}
+  HANDLE_COMPONENTS)
+
+# ==============================================================================
+
+if(CUDAlibs_FOUND)
+  # Inspired by FindBoost.cmake
+  foreach(COMPONENT ${CUDAlibs_FIND_COMPONENTS})
+    string(TOUPPER ${COMPONENT} UPPERCOMPONENT)
+
+    if(NOT TARGET CUDAlibs::${UPPERCOMPONENT} AND CUDAlibs_${UPPERCOMPONENT}_FOUND)
+      get_filename_component(LIB_EXT "${CUDAlibs_${UPPERCOMPONENT}_LIB}" EXT)
+      if(LIB_EXT STREQUAL ".a" OR LIB_EXT STREQUAL ".lib")
+        set(LIB_TYPE STATIC)
+      else()
+        set(LIB_TYPE SHARED)
+      endif()
+
+      add_library(CUDAlibs::${UPPERCOMPONENT} ${LIB_TYPE} IMPORTED GLOBAL)
+      set_target_properties(CUDAlibs::${UPPERCOMPONENT} PROPERTIES
+	IMPORTED_LOCATION "${CUDAlibs_${UPPERCOMPONENT}_LIB}"
+        INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES}")
+
+      # ------------------------------------------------------------------------
+      
+      set(_dependent_libraries)
+      foreach(_dep "${CUDAlibs_DEP_${UPPERCOMPONENT}}")
+	list(APPEND _dependent_libraries ${_dep})
+      endforeach()
+
+      if(NOT "${_dependent_libraries}" STREQUAL "")
+	message(STATUS "Adding dependencies: ${_dependent_libraries}")
+	set_target_properties(CUDAlibs::${UPPERCOMPONENT} PROPERTIES
+          INTERFACE_LINK_LIBRARIES "${_dependent_libraries}")
+      endif()
+    endif()
+  endforeach()
+
+  # ----------------------------------------------------------------------------
+
+  if(NOT CUDAlibs_FIND_QUIETLY)
+    message(STATUS "Found CUDAlibs and defined the following imported targets:")
+    foreach(_comp ${CUDAlibs_FIND_COMPONENTS})
+      message(STATUS "  - CUDAlibs::${_comp}")
+    endforeach()
+  endif()
+endif()
+
+# ==============================================================================
+
+mark_as_advanced(
+  CUDAlibs_FOUND
+  )
+

cmake/FindFFTW.cmake

+#.rst:
+# FindFFTW
+# -------------
+#
+# Find FFTW3 include dirs and libraries
+#
+# Use this module by invoking find_package with the form::
+#
+#   find_package(Boost
+#     [REQUIRED]             # Fail with error if FFTW is not found
+#     [VERSION [2,3]]        # Version of FFTW to look for (only considers major version)
+#     [COMPONENTS <libs>...] # List of libraries to look for
+#     )
+#
+# Valid names for COMPONENTS libraries are::
+#
+#   ALL                      - Find all libraries
+#   FFTW                     - Find a FFTW (double) library
+#   FFTW_MT                  - Find a FFTW multi-threaded (double) library
+#   FFTWF                    - Find a FFTW (single) library
+#   FFTWF_MT                 - Find a FFTW multi-threaded (single) library
+#
+#  Not specifying COMPONENTS is identical to choosing ALL
+#
+# This module defines::
+#
+#   FFTW_FOUND            - True if headers and requested libraries were found
+#   FFTW_VERSION          - Version of the FFTW libraries
+#   FFTW_INCLUDE_DIRS     - FFTW include directories
+#   FFTW_LIBRARIES        - FFTW component libraries to be linked
+#
+#
+# This module reads hints about search locations from variables
+# (either CMake variables or environment variables)::
+#
+#   FFTW_ROOT             - Preferred installation prefix for FFTW
+#   FFTW_DIR              - Preferred installation prefix for FFTW
+#
+#
+# The following :prop_tgt:`IMPORTED` targets are also defined::
+#
+#   FFTW::FFTW            - Imported target for the FFTW (double) library
+#   FFTW::FFTW_MT         - Imported target for the FFTW multi-thread (double) library
+#   FFTW::FFTWF           - Imported target for the FFTW (single) library
+#   FFTW::FFTWF_MT        - Imported target for the FFTW multi-thread (single) library
+#
+
+# ==============================================================================
+# Copyright 2018 Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+#
+# Distributed under the OSI-approved BSD License (the "License")
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# ==============================================================================
+
+set(FFTW_SEARCH_PATHS
+  ${FFTW_ROOT}
+  $ENV{FFTW_ROOT}
+  ${FFTW_DIR}
+  $ENV{FFTW_DIR}
+  ${CMAKE_PREFIX_PATH}
+  $ENV{CMAKE_PREFIX_PATH}
+  /sw
+  /usr
+  /usr/local/
+  /usr/local/opt # homebrew on mac
+  /opt
+  /opt/local
+  /opt/FFTW
+  )
+
+set(INC_PATH_SUFFIXES_LIST
+  include
+  include/fftw
+  include/fftw3
+)
+
+set(LIB_PATH_SUFFIXES_LIST
+  lib64
+  lib
+  lib/fftw
+  lib/x86_64-linux-gnu
+  lib32
+)
+
+# ==============================================================================
+# Prepare some helper variables
+
+set(FFTW_REQUIRED_VARS)
+set(FFTW_INCLUDE_DIRS)
+set(FFTW_LIBRARIES)
+
+# ==============================================================================
+
+macro(_find_library_with_header component libnames incnames)
+  find_library(FFTW_${component}_LIB
+    NAMES ${libnames}
+    PATHS ${FFTW_SEARCH_PATHS}
+    PATH_SUFFIXES ${LIB_PATH_SUFFIXES_LIST})
+  if(FFTW_${component}_LIB)    
+    set(FFTW_${component}_LIB_FOUND 1)
+  endif()
+  list(APPEND FFTW_REQUIRED_VARS "FFTW_${component}_LIB")
+
+  # If necessary, look for the header file as well
+  if(NOT "${incnames}" STREQUAL "")
+    find_path(FFTW_${component}_INCLUDE_DIR
+      NAMES ${incnames}
+      PATHS ${FFTW_SEARCH_PATHS}
+      PATH_SUFFIXES ${INC_PATH_SUFFIXES_LIST})
+    list(APPEND FFTW_REQUIRED_VARS "FFTW_${component}_INCLUDE_DIR")
+    if(FFTW_${component}_LIB)
+      set(FFTW_${component}_INC_FOUND 1)
+    endif()
+  else()
+    set(FFTW_${component}_INC_FOUND 1)
+  endif()
+  
+  if(FFTW_${component}_LIB_FOUND AND FFTW_${component}_INC_FOUND)
+    set(FFTW_${component}_FOUND 1)
+  else()
+    set(FFTW_${component}_FOUND 0)
+  endif()
+endmacro()
+
+macro(_mangle_names)
+endmacro()
+
+# ------------------------------------------------------------------------------
+
+# Make sure that all components are in capitals
+set(_tmp_component_list)
+foreach(_comp ${FFTW_FIND_COMPONENTS})
+  string(TOUPPER ${_comp} _comp)
+  list(APPEND _tmp_component_list ${_comp})
+endforeach()
+set(FFTW_FIND_COMPONENTS ${_tmp_component_list})
+set(_tmp_component_list)
+
+# ------------------------------------------------------------------------------
+
 ## FFTW can be compiled and subsequently linked against
 ## various data types.
 ## There is a single set of include files, and then muttiple libraries,
 ## One for each type.  I.e. libfftw.a-->double, libfftwf.a-->float
 
-set(FFTW_INC_SEARCHPATH
-  /sw/include
-  /usr/include
-  /usr/local/include
-  /usr/include/fftw
-  /usr/include/fftw3
-  /usr/local/include/fftw
-  /usr/local/include/fftw3
-)
 
-find_path(FFTW_INCLUDE_PATH fftw3.h ${FFTW_INC_SEARCHPATH})
+if(NOT FFTW_FIND_COMPONENTS OR FFTW_FIND_COMPONENTS STREQUAL "ALL")
+  set(FFTW_FIND_ALL_COMPONENTS 1)
+  set(FFTW_FIND_COMPONENTS "FFTW;FFTW_MT;FFTWF;FFTWF_MT")
+endif()
 
-if(FFTW_INCLUDE_PATH)
-  file(TO_CMAKE_PATH "${FFTW_INCLUDE_PATH}" FFTW_INCLUDE_PATH)
-  set(FFTW_INCLUDE ${FFTW_INCLUDE_PATH})
+if(NOT DEFINED FFTW_FIND_VERSION_MAJOR)
+  set(FFTW_FIND_VERSION_MAJOR 3)
 endif()
 
-if(FFTW_INCLUDE)
-  include_directories(${FFTW_INCLUDE})
+if(FFTW_FIND_VERSION_MAJOR EQUAL 2)
+  set(_fftw_suffix "")
+elseif(FFTW_FIND_VERSION_MAJOR EQUAL 3)
+  set(_fftw_suffix "3")
+else()
+  message(FATAL_ERROR "Unsupported version number for FFTW")
 endif()
 
-get_filename_component(FFTW_INSTALL_BASE_PATH ${FFTW_INCLUDE_PATH} PATH)
+# ------------------------------------------------------------------------------
 
-set(FFTW_LIB_SEARCHPATH
-  ${FFTW_INSTALL_BASE_PATH}/lib
-  ${FFTW_INSTALL_BASE_PATH}/lib64
-  /usr/lib/fftw
-  /usr/local/lib/fftw
-)
+foreach(_comp ${FFTW_FIND_COMPONENTS})
+  if(_comp STREQUAL "FFTW")
+    _find_library_with_header(${_comp} fftw${_fftw_suffix} fftw${_fftw_suffix}.h)
+  elseif(_comp STREQUAL "FFTW_MT")
+    _find_library_with_header(${_comp} fftw${_fftw_suffix}_threads fftw${_fftw_suffix}.h)
+  elseif(_comp STREQUAL "FFTWF" AND FFTW_FIND_VERSION_MAJOR GREATER 2)
+    _find_library_with_header(${_comp} fftw${_fftw_suffix}f fftw${_fftw_suffix}.h)
+  elseif(_comp STREQUAL "FFTWF_MT" AND FFTW_FIND_VERSION_MAJOR GREATER 2)
+    _find_library_with_header(${_comp} fftw${_fftw_suffix}f_threads fftw${_fftw_suffix}.h)
+  else()
+    message(FATAL_ERROR "Unknown component (looked for FFTW ${FFTW_FIND_VERSION_MAJOR}): ${_comp}")
+  endif()
+  mark_as_advanced(
+    FFTW_${_comp}_LIB
+    FFTW_${_comp}_INCLUDE_DIR)
+endforeach()
+
+# ==============================================================================
 
-if(USE_FFTWD)
-  mark_as_advanced(FFTWD_LIB)
-  find_library(FFTWD_LIB fftw3 ${FFTW_LIB_SEARCHPATH}) #Double Precision Lib
-  find_library(FFTWD_THREADS_LIB fftw3_threads ${FFTW_LIB_SEARCHPATH}) #Double Precision Lib only if compiled with threads support
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(FFTW
+  FOUND_VAR FFTW_FOUND
+  REQUIRED_VARS ${FFTW_REQUIRED_VARS}
+  HANDLE_COMPONENTS)
 
-  if(FFTWD_LIB)
-    set(FFTWD_FOUND 1)
-    get_filename_component(FFTW_LIBDIR ${FFTWD_LIB} PATH)
-    if(FFTWD_THREADS_LIB)
-      set(FFTWD_LIB ${FFTWD_LIB} ${FFTWD_THREADS_LIB} )
+# ==============================================================================
+
+if(FFTW_FOUND)  
+  # Inspired by FindBoost.cmake
+  foreach(_comp ${FFTW_FIND_COMPONENTS})
+    if(NOT TARGET FFTW::${_comp} AND FFTW_${_comp}_FOUND)
+      get_filename_component(LIB_EXT "${FFTW_${_comp}_LIB}" EXT)
+      if(LIB_EXT STREQUAL ".a" OR LIB_EXT STREQUAL ".lib")
+        set(LIB_TYPE STATIC)
+      else()
+        set(LIB_TYPE SHARED)
       endif()
+      add_library(FFTW::${_comp} ${LIB_TYPE} IMPORTED GLOBAL)
+      set_target_properties(FFTW::${_comp}
+	PROPERTIES
+	IMPORTED_LOCATION "${FFTW_${_comp}_LIB}"
+        INTERFACE_INCLUDE_DIRECTORIES "${FFTW_${_comp}_INCLUDE_DIR}")
     endif()
+
+    if(FFTW_${_comp}_FOUND)
+      set(APPEND FFTW_INCLUDE_DIRS "${FFTW_${_comp}_INCLUDE_DIR}")
+      set(APPEND FFTW_LIBRARIES "${FFTW_${_comp}_LIB}")
     endif()
+  endforeach()
 
-if(USE_FFTWF)
-  mark_as_advanced(FFTWF_LIB)
-  find_library(FFTWF_LIB fftw3f ${FFTW_LIB_SEARCHPATH}) #Single Precision Lib
-  find_library(FFTWF_THREADS_LIB fftw3f_threads ${FFTW_LIB_SEARCHPATH}) #Single Precision Lib only if compiled with threads support
+  # ----------------------------------------------------------------------------
 
-  if(FFTWF_LIB)
-    set(FFTWF_FOUND 1)
-    get_filename_component(FFTW_LIBDIR ${FFTWF_LIB} PATH)
-    if(FFTWF_THREADS_LIB)
-      set(FFTWF_LIB ${FFTWF_LIB} ${FFTWF_THREADS_LIB} )
-    endif()
+  if(NOT FFTW_FIND_QUIETLY)
+    message(STATUS "Found FFTW and defined the following imported targets:")
+    foreach(_comp ${FFTW_FIND_COMPONENTS})
+      message(STATUS "  - FFTW::${_comp}:")
+      message(STATUS "      + include: ${FFTW_${_comp}_INCLUDE_DIR}")
+      message(STATUS "      + library: ${FFTW_${_comp}_LIB}")
+    endforeach()
   endif()
 endif()
 
-set(FFTWD_LIBRARIES ${FFTWD_LIB})
-set(FFTWF_LIBRARIES ${FFTWF_LIB})
+# ==============================================================================
+
+mark_as_advanced(
+  FFTW_FOUND
+  FFTW_INCLUDE_DIRS
+  FFTW_LIBRARIES
+  )
+

cmake/FindLAPACKE.cmake

@@ -2,189 +2,248 @@
 # FindLAPACKE
 # -------------
 #
-# Find the LAPACKE library
+# Find LAPACKE include dirs and libraries
 #
-# Using LAPACKE:
+# Use this module by invoking find_package with the form::
 #
-# ::
+#   find_package(LAPACKE
+#     [REQUIRED]             # Fail with error if LAPACKE is not found
+#     [COMPONENTS <libs>...] # List of libraries to look for
+#     )
 #
-#   find_package(LAPACKE REQUIRED)
-#   include_directories(${LAPACKE_INCLUDE_DIRS})
-#   add_executable(foo foo.cc)
-#   target_link_libraries(foo ${LAPACKE_LIBRARIES})
+# Valid names for COMPONENTS libraries are::
 #
-# This module sets the following variables:
+#   ALL                      - Find all libraries
+#   LAPACKE_H                - Find the lapacke.h header file
+#   LAPACKE                  - Find a LAPACKE library
+#   LAPACK                   - Find a LAPACK library
+#   CBLAS                    - Find a CBLAS library
+#   BLAS                     - Find a BLAS library
 #
-# ::
+#  Not specifying COMPONENTS is identical to choosing ALL
+#
+# This module defines::
+#
+#   LAPACKE_FOUND            - True if headers and requested libraries were found
+#   LAPACKE_INCLUDE_DIRS     - LAPACKE include directories
+#   LAPACKE_LIBRARIES        - LAPACKE component libraries to be linked
+#
+#
+# This module reads hints about search locations from variables
+# (either CMake variables or environment variables)::
+#
+#   LAPACKE_ROOT             - Preferred installation prefix for LAPACKE
+#   LAPACKE_DIR              - Preferred installation prefix for LAPACKE
+#
+#
+# The following :prop_tgt:`IMPORTED` targets are also defined::
+#
+#   LAPACKE::LAPACKE         - Imported target for the LAPACKE library
+#   LAPACKE::LAPACK          - Imported target for the LAPACK library
+#   LAPACKE::CBLAS           - Imported target for the CBLAS library
+#   LAPACKE::BLAS            - Imported target for the BLAS library
 #
-#   LAPACKE_FOUND - set to true if the library is found
-#   LAPACKE_INCLUDE_DIRS - list of required include directories
-#   LAPACKE_LIBRARIES - list of libraries to be linked
-#   LAPACKE_VERSION_MAJOR - major version number
-#   LAPACKE_VERSION_MINOR - minor version number
-#   LAPACKE_VERSION_PATCH - patch version number
-#   LAPACKE_VERSION_STRING - version number as a string (ex: "0.2.18")
 
-#=============================================================================
-# Copyright 2016 Hans J. Johnson <hans-johnson@uiowa.edu>
+# ==============================================================================
+# Copyright 2018 Damien Nguyen <damien.nguyen@alumni.epfl.ch>
 #
 # Distributed under the OSI-approved BSD License (the "License")
 #
 # This software is distributed WITHOUT ANY WARRANTY; without even the
 # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-#=============================================================================
-#
+# ==============================================================================
+
 set(LAPACKE_SEARCH_PATHS
+  ${LAPACKE_ROOT}
+  $ENV{LAPACKE_ROOT}
   ${LAPACKE_DIR}
   $ENV{LAPACKE_DIR}
-  $ENV{CMAKE_PREFIX_PATH}
   ${CMAKE_PREFIX_PATH}
+  $ENV{CMAKE_PREFIX_PATH}
   /usr
-  /usr/local
-  /usr/local/opt/lapack  ## Mac Homebrew install path
+  /usr/local/
+  /usr/local/opt # homebrew on mac
+  /opt
+  /opt/local
   /opt/LAPACKE
   )
-message(STATUS "LAPACKE_SEARCH_PATHS: ${LAPACKE_SEARCH_PATHS}")
 
-set(CMAKE_PREFIX_PATH ${LAPACKE_SEARCH_PATHS})
-list(REMOVE_DUPLICATES CMAKE_PREFIX_PATH)
+set(LIB_PATH_SUFFIXES
+  lib64
+  lib
+  lib/x86_64-linux-gnu
+  lib32
+  )
+
+set(INC_PATH_SUFFIXES
+  include
+  include/lapack
+  include/lapacke/
+  lapack/include
+  lapacke/include
+  )
 
-## First try to find LAPACKE with NO_MODULE,
-## As of 20160706 version 0.2.18 there is limited cmake support for LAPACKE
-## that is not as complete as this version, if found, use it
-## to identify the LAPACKE_VERSION_STRING and improve searching.
-find_package(LAPACKE NO_MODULE QUIET)
-if(LAPACKE_FOUND)
-  if(EXISTS ${LAPACKE_DIR}/lapacke-config-version.cmake)
-    include(${LAPACKE_DIR}/lapacke-config-version.cmake)
-    set(LAPACKE_VERSION_STRING ${PACKAGE_VERSION})
-    unset(PACKAGE_VERSION) # Use cmake conventional naming
-  endif()
-  find_package(LAPACK NO_MODULE QUIET) #Require matching versions here!
-  find_package(BLAS NO_MODULE QUIET)   #Require matching versions here!
+if(APPLE)
+  list(APPEND LIB_PATH_SUFFIXES lapack/lib openblas/lib)
+elseif(WIN32)
+  list(APPEND LAPACKE_SEARCH_PATHS "C:/Program Files (x86)/LAPACK")
+  list(APPEND LAPACKE_SEARCH_PATHS "C:/Program Files/LAPACK")
 endif()
 
-##################################################################################################
-### First search for headers
-find_path(LAPACKE_CBLAS_INCLUDE_DIR 
-             NAMES cblas.h 
-             PATHS ${LAPACKE_SEARCH_PATHS} 
-             PATH_SUFFIXES include include/lapack)
-find_path(LAPACKE_LAPACKE_INCLUDE_DIR 
-             NAMES lapacke.h 
-             PATHS ${LAPACKE_SEARCH_PATHS} 
-             PATH_SUFFIXES include)
+# ==============================================================================
+# Prepare some helper variables
 
-##################################################################################################
-### Second, search for libraries
-set(PATH_SUFFIXES_LIST
-  lib64
-  lib
-)
-find_library(LAPACKE_LIB 
-                 NAMES lapacke
-                 PATHS ${LAPACKE_SEARCH_PATHS}
-                 PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
-find_library(CBLAS_LIB 
-                 NAMES cblas
+set(LAPACKE_INCLUDE_DIRS)
+set(LAPACKE_LIBRARIES)
+set(LAPACKE_REQUIRED_VARS)
+set(LAPACKE_FIND_ALL_COMPONENTS 0)
+
+# ==============================================================================
+
+macro(_find_library_with_header component incname)
+  find_library(LAPACKE_${component}_LIB
+    NAMES ${ARGN}
+    NAMES_PER_DIR
     PATHS ${LAPACKE_SEARCH_PATHS}
-                 PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
-find_library(LAPACK_LIB 
-                 NAMES lapack
+    PATH_SUFFIXES ${LIB_PATH_SUFFIXES})
+  if(LAPACKE_${component}_LIB)    
+    set(LAPACKE_${component}_LIB_FOUND 1)
+  endif()
+  list(APPEND LAPACKE_REQUIRED_VARS "LAPACKE_${component}_LIB")
+
+  # If necessary, look for the header file as well
+  if(NOT "${incname}" STREQUAL "")
+    find_path(LAPACKE_${component}_INCLUDE_DIR
+      NAMES ${incname}
       PATHS ${LAPACKE_SEARCH_PATHS}
-                 PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
-find_library(BLAS_LIB 
-                 NAMES blas
+      PATH_SUFFIXES ${INC_PATH_SUFFIXES})
+    list(APPEND LAPACKE_REQUIRED_VARS "LAPACKE_${component}_INCLUDE_DIR")
+    if(LAPACKE_${component}_LIB)
+      set(LAPACKE_${component}_INC_FOUND 1)
+    endif()
+  else()
+    set(LAPACKE_${component}_INC_FOUND 1)
+  endif()
+  
+  if(LAPACKE_${component}_LIB_FOUND AND LAPACKE_${component}_INC_FOUND)
+    set(LAPACKE_${component}_FOUND 1)
+  else()
+    set(LAPACKE_${component}_FOUND 0)
+  endif()
+endmacro()
+
+# ------------------------------------------------------------------------------
+
+if(NOT LAPACKE_FIND_COMPONENTS OR LAPACKE_FIND_COMPONENTS STREQUAL "ALL")
+  set(LAPACKE_FIND_ALL_COMPONENTS 1)
+  set(LAPACKE_FIND_COMPONENTS "LAPACKE;LAPACK;CBLAS;BLAS")
+endif(NOT LAPACKE_FIND_COMPONENTS OR LAPACKE_FIND_COMPONENTS STREQUAL "ALL")
+
+# Make sure that all components are in capitals
+set(_tmp_component_list)
+foreach(_comp ${LAPACKE_FIND_COMPONENTS})
+  string(TOUPPER ${_comp} _comp)
+  list(APPEND _tmp_component_list ${_comp})
+endforeach()
+set(LAPACKE_FIND_COMPONENTS ${_tmp_component_list})
+set(_tmp_component_list)
+
+foreach(_comp ${LAPACKE_FIND_COMPONENTS})
+  if(_comp STREQUAL "LAPACKE")
+    _find_library_with_header(${_comp} lapacke.h lapacke liblapacke)
+  elseif(_comp STREQUAL "LAPACKE_H")
+    find_path(LAPACKE_${_comp}_INCLUDE_DIR
+      NAMES lapacke.h
       PATHS ${LAPACKE_SEARCH_PATHS}
-                 PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
-
-## TODO: Get version components
-# ------------------------------------------------------------------------
-#  Extract version information
-# ------------------------------------------------------------------------
-
-# WARNING: We may not be able to determine the version of some LAPACKE
-set(LAPACKE_VERSION_MAJOR 0)
-set(LAPACKE_VERSION_MINOR 0)
-set(LAPACKE_VERSION_PATCH 0)
-if(LAPACKE_VERSION_STRING)
-  string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\1" LAPACKE_VERSION_MAJOR "${LAPACKE_VERSION_STRING}")
-  string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\2" LAPACKE_VERSION_MINOR "${LAPACKE_VERSION_STRING}")
-  string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\3" LAPACKE_VERSION_PATCH "${LAPACKE_VERSION_STRING}")
+      PATH_SUFFIXES include lapack/include)
+    list(APPEND LAPACKE_REQUIRED_VARS "LAPACKE_${_comp}_INCLUDE_DIR")
+    if(LAPACKE_${_comp}_LIB)
+      set(LAPACKE_${_comp}_INC_FOUND 1)
     endif()
+  elseif(_comp STREQUAL "LAPACK")
+    _find_library_with_header(${_comp} "" lapack liblapack)
+  elseif(_comp STREQUAL "CBLAS")
+    _find_library_with_header(${_comp} cblas.h cblas libcblas)
+  elseif(_comp STREQUAL "BLAS")
+    _find_library_with_header(${_comp} "" blas blas)
+  else()
+    message(FATAL_ERROR "Unknown component: ${_comp}")
+  endif()
+  mark_as_advanced(
+    LAPACKE_${_comp}_LIB
+    LAPACKE_${_comp}_INCLUDE_DIR)
+endforeach()
+
+# ==============================================================================
 
-#======================
-# Checks 'REQUIRED', 'QUIET' and versions.
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(LAPACKE FOUND_VAR LAPACKE_FOUND
-  REQUIRED_VARS LAPACKE_CBLAS_INCLUDE_DIR
-                LAPACKE_LAPACKE_INCLUDE_DIR
-                LAPACKE_LIB
-                LAPACK_LIB
-                CBLAS_LIB
-                BLAS_LIB
-  VERSION_VAR LAPACKE_VERSION_STRING
-)
+find_package_handle_standard_args(LAPACKE
+  FOUND_VAR LAPACKE_FOUND
+  REQUIRED_VARS ${LAPACKE_REQUIRED_VARS}
+  HANDLE_COMPONENTS)
+
+# ==============================================================================
 
 if(LAPACKE_FOUND)
-  set(LAPACKE_INCLUDE_DIRS ${LAPACKE_CBLAS_INCLUDE_DIR} ${LAPACKE_CBLAS_INCLUDE_DIR})
-  list(REMOVE_DUPLICATES LAPACKE_INCLUDE_DIRS)
+  foreach(_comp ${LAPACKE_FIND_COMPONENTS})
+    list(APPEND LAPACKE_INCLUDE_DIRS ${LAPACKE_${_comp}_INCLUDE_DIR})
+    list(APPEND LAPACKE_LIBRARIES ${LAPACKE_${_comp}_LIB})
+  endforeach()
+  
   if("${CMAKE_C_COMPILER_ID}" MATCHES ".*Clang.*" OR
       "${CMAKE_C_COMPILER_ID}" MATCHES ".*GNU.*" OR
       "${CMAKE_C_COMPILER_ID}" MATCHES ".*Intel.*"
       ) #NOT MSVC
-    set(MATH_LIB m)
+    set(MATH_LIB "m")
+    list(APPEND LAPACKE_LIBRARIES m)
   endif()
-  list(APPEND LAPACKE_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB} ${BLAS_LIB} ${CBLAS_LIB})
-  # Check for a common combination, and find required gfortran support libraries
   
-  if(1)
-    if("${CMAKE_C_COMPILER_ID}" MATCHES ".*Clang.*" AND "${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
-          message(STATUS "\n\n WARNING: ${CMAKE_C_COMPILER} identified as ${CMAKE_C_COMPILER_ID}\n"
-                                   "AND: ${CMAKE_Fortran_COMPILER} identified as ${CMAKE_Fortran_COMPILER_ID}\n"
-                               "\n"
-                               "may be require special configurations.  The most common is the need to"
-                               "explicitly link C programs against the gfortran support library.")
-                              
-    endif()
-  else()
-    ## This code automated code is hard to determine if it is robust in many different environments.
-    # Check for a common combination, and find required gfortran support libraries
-    if("${CMAKE_C_COMPILER_ID}" MATCHES ".*Clang.*" AND "${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
-       include(FortranCInterface)
-       FortranCInterface_VERIFY() 
-       if(NOT FortranCInterface_VERIFIED_C)
-          message(FATAL_ERROR "C and fortran compilers are not compatible:\n${CMAKE_Fortran_COMPILER}:${CMAKE_C_COMPILER}")
+  if(NOT "${LAPACKE_INCLUDE_DIRS}" STREQUAL "")
+    list(REMOVE_DUPLICATES LAPACKE_INCLUDE_DIRS)
   endif()
 
-       execute_process(COMMAND ${CMAKE_Fortran_COMPILER} -print-file-name=libgfortran.a OUTPUT_VARIABLE FORTRANSUPPORTLIB ERROR_QUIET)
-       string(STRIP ${FORTRANSUPPORTLIB} FORTRANSUPPORTLIB)
-       if(EXISTS "${FORTRANSUPPORTLIB}")
-         list(APPEND LAPACKE_LIBRARIES ${FORTRANSUPPORTLIB})
-         message(STATUS "Appending fortran support lib: ${FORTRANSUPPORTLIB}")
+  # ----------------------------------------------------------------------------
+
+  # Inspired by FindBoost.cmake
+  foreach(_comp ${LAPACKE_FIND_COMPONENTS})
+    if(NOT TARGET LAPACKE::${_comp} AND LAPACKE_${_comp}_FOUND)
+      get_filename_component(LIB_EXT "${LAPACKE_${_comp}_LIB}" EXT)
+      if(LIB_EXT STREQUAL ".a" OR LIB_EXT STREQUAL ".lib")
+        set(LIB_TYPE STATIC)
       else()
-         message(FATAL_ERROR "COULD NOT FIND libgfortran.a support library:${FORTRANSUPPORTLIB}:")
+        set(LIB_TYPE SHARED)
       endif()
+      add_library(LAPACKE::${_comp} ${LIB_TYPE} IMPORTED GLOBAL)
+      if(LAPACKE_INCLUDE_DIRS)
+        set_target_properties(LAPACKE::${_comp} PROPERTIES
+          INTERFACE_INCLUDE_DIRECTORIES "${LAPACKE_INCLUDE_DIRS}")
       endif()
+      if(EXISTS "${LAPACKE_${_comp}_LIB}")
+        set_target_properties(LAPACKE::${_comp} PROPERTIES
+          IMPORTED_LOCATION "${LAPACKE_${_comp}_LIB}")
       endif()
-  list(APPEND LAPACKE_LIBRARIES ${MATH_LIB})
+      set_target_properties(LAPACKE::${_comp} PROPERTIES
+        INTERFACE_LINK_LIBRARIES "${MATH_LIB}")
     endif()
+  endforeach()
+
+  # ----------------------------------------------------------------------------
+
+  if(NOT LAPACKE_FIND_QUIETLY)
+    message(STATUS "Found LAPACKE and defined the following imported targets:")
+    foreach(_comp ${LAPACKE_FIND_COMPONENTS})
+      message(STATUS "  - LAPACKE::${_comp}:")
+      message(STATUS "      + include:      ${LAPACKE_INCLUDE_DIRS}")
+      message(STATUS "      + library:      ${LAPACKE_${_comp}_LIB}")
+      message(STATUS "      + dependencies: ${MATH_LIB}")
+    endforeach()
+  endif()
+endif()
+
+# ==============================================================================
 
 mark_as_advanced(
   LAPACKE_FOUND
   LAPACKE_INCLUDE_DIRS
   LAPACKE_LIBRARIES
-  LAPACKE_VERSION_MAJOR
-  LAPACKE_VERSION_MINOR
-  LAPACKE_VERSION_PATCH
-  LAPACKE_VERSION_STRING
   )
-
-## For debugging
-message(STATUS "LAPACKE_FOUND                  :${LAPACKE_FOUND}:  - set to true if the library is found")
-message(STATUS "LAPACKE_INCLUDE_DIRS           :${LAPACKE_INCLUDE_DIRS}: - list of required include directories")
-message(STATUS "LAPACKE_LIBRARIES              :${LAPACKE_LIBRARIES}: - list of libraries to be linked")
-message(STATUS "LAPACKE_VERSION_MAJOR          :${LAPACKE_VERSION_MAJOR}: - major version number")
-message(STATUS "LAPACKE_VERSION_MINOR          :${LAPACKE_VERSION_MINOR}: - minor version number")
-message(STATUS "LAPACKE_VERSION_PATCH          :${LAPACKE_VERSION_PATCH}: - patch version number")
-message(STATUS "LAPACKE_VERSION_STRING         :${LAPACKE_VERSION_STRING}: - version number as a string")

cmake/FindOpenBLAS.cmake

@@ -2,22 +2,16 @@
 # FindOpenBLAS
 # -------------
 #
-# Find the OpenBLAS library
+# Find OpenBLAS include dirs and libraries
 #
-# Using OpenBLAS:
+# Use this module by invoking find_package with the form::
 #
-# ::
+#   find_package(OpenBLAS
+#     [REQUIRED]             # Fail with error if OpenBLAS is not found
+#     )
 #
-#   find_package(OpenBLAS REQUIRED)
-#   include_directories(${OpenBLAS_INCLUDE_DIRS})
-#   add_executable(foo foo.cc)
-#   target_link_libraries(foo ${OpenBLAS_LIBRARIES})
-#   -- OR --
-#   target_link_libraries(foo ${OpenBLAS_PARALLEL_LIBRARIES})
 #
-# This module sets the following variables:
-#
-# ::
+# This module defines::
 #
 #   OpenBLAS_FOUND            - set to true if the library is found
 #   OpenBLAS_INCLUDE_DIRS     - list of required include directories
@@ -28,31 +22,62 @@
 #   OpenBLAS_VERSION_MINOR    - minor version number
 #   OpenBLAS_VERSION_PATCH    - patch version number
 #   OpenBLAS_VERSION_STRING   - version number as a string (ex: "0.2.18")
+#
+#
+# This module reads hints about search locations from variables
+# (either CMake variables or environment variables)::
+#
+#   OpenBLAS_ROOT             - Preferred installation prefix for OpenBLAS
+#   OpenBLAS_DIR              - (for compatibility purposes)
+#
+#
+#   OpenBLAS::OpenBLAS        - Imported target for the OpenBLAS library
+#
 
-#=============================================================================
+# ==============================================================================
 # Copyright 2016 Hans J. Johnson <hans-johnson@uiowa.edu>
+# Copyright 2018 Damien Nguyen <damien.nguyen@alumni.epfl.ch>
 #
 # Distributed under the OSI-approved BSD License (the "License")
 #
 # This software is distributed WITHOUT ANY WARRANTY; without even the
 # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-#=============================================================================
-#
-set(OpenBLAS_HAS_PARALLEL_LIBRARIES FALSE)
+# ==============================================================================
 
 set(OpenBLAS_SEARCH_PATHS
+  ${OpenBLAS_ROOT}
+  $ENV{OpenBLAS_ROOT}
   ${OpenBLAS_DIR}
   $ENV{OpenBLAS_DIR}
-  $ENV{CMAKE_PREFIX_PATH}
   ${CMAKE_PREFIX_PATH}
+  $ENV{CMAKE_PREFIX_PATH}
   /usr
-  /usr/local
-  /usr/local/opt/openblas  ## Mac Homebrew install path
+  /usr/local/
+  /usr/local/opt # homebrew on mac
+  /opt
+  /opt/local
   /opt/OpenBLAS
   )
 
-set(CMAKE_PREFIX_PATH ${OpenBLAS_SEARCH_PATHS})
-list(REMOVE_DUPLICATES CMAKE_PREFIX_PATH)
+set(PATH_SUFFIXES_LIST
+  lib64
+  lib
+  lib/x86_64-linux-gnu
+  lib32
+)
+
+if(APPLE)
+  list(APPEND PATH_SUFFIXES_LIST openblas/lib)
+endif()
+
+# ==============================================================================
+# Prepare some helper variables
+
+set(OpenBLAS_INCLUDE_DIRS)
+set(OpenBLAS_LIBRARIES)
+set(OpenBLAS_HAS_PARALLEL_LIBRARIES FALSE)
+
+# ==============================================================================
 
 ## First try to find OpenBLAS with NO_MODULE,
 ## As of 20160706 version 0.2.18 there is limited cmake support for OpenBLAS
@@ -63,33 +88,47 @@ if(OpenBLAS_VERSION)
   set(OpenBLAS_VERSION_STRING ${OpenBLAS_VERSION})
   unset(OpenBLAS_VERSION) # Use cmake conventional naming
 endif()
-##################################################################################################
+
+# ==============================================================================
 ### First search for headers
+
 find_path(OpenBLAS_CBLAS_INCLUDE_DIR 
   NAMES cblas.h 
   PATHS ${OpenBLAS_SEARCH_PATHS} 
   PATH_SUFFIXES include include/openblas)
-find_path(OpenBLAS_LAPACKE_INCLUDE_DIR 
-             NAMES lapacke.h 
-             PATHS ${OpenBLAS_SEARCH_PATHS} 
-             PATH_SUFFIXES include)
 
-##################################################################################################
+# ==============================================================================
 ### Second, search for libraries
-set(PATH_SUFFIXES_LIST
-  lib64
-  lib
-)
+
 find_library(OpenBLAS_LIB 
   NAMES openblas
   PATHS ${OpenBLAS_SEARCH_PATHS}
   PATH_SUFFIXES ${PATH_SUFFIXES_LIST})
 
-if(EXISTS ${OpenBLAS_LIB})
+if(OpenBLAS_LIB)
   get_filename_component(OpenBLAS_LIB_DIR i${OpenBLAS_LIB} DIRECTORY)
+
+  include(CheckLibraryExists)
+  check_library_exists(${OpenBLAS_LIB} LAPACKE_cheev  "" HAVE_LAPACKE_CHEEV)
+  check_library_exists(${OpenBLAS_LIB} LAPACKE_zgesdd "" HAVE_LAPACKE_ZGESDD)
+
+  if(NOT HAVE_LAPACKE_CHEEV OR NOT HAVE_LAPACKE_ZGESDD)
+    message(WARNING "OpenBLAS has no LAPACKE symbols. Attempting to look for a LAPACKE library")
+    find_package(LAPACKE QUIET COMPONENTS LAPACKE)
+    if(LAPACKE_FOUND)
+      message(STATUS "Found LAPACKE: ${LAPACKE_LIBRARIES}")
+      list(APPEND OpenBLAS_LIBRARIES ${LAPACKE_LIBRARIES})
+    else()
+      message(WARNING "Unable to find a LAPACKE library. Consider configuring CMake with BART_NO_LAPACKE=ON")
+    endif()
+  else()
+    # Make sure we find lapacke.h
+    find_package(LAPACKE QUIET COMPONENTS LAPACKE_H)
   endif()
+endif()
+
 ## Find the named parallel version of openblas
-set(OpenBLAS_SEARCH_VERSIONS ${OpenBLAS_VERSION_STRING} 0.2.19 0.2.18 0.2.17 0.2.16)
+set(OpenBLAS_SEARCH_VERSIONS ${OpenBLAS_VERSION_STRING} 0.3.2 0.3.1 0.3.0 0.2.19 0.2.18 0.2.17 0.2.16)
 list(REMOVE_DUPLICATES OpenBLAS_SEARCH_VERSIONS)
 foreach(checkVersion ${OpenBLAS_SEARCH_VERSIONS})
   find_library(OpenBLAS_PARALLEL_LIB 
@@ -106,10 +145,6 @@ foreach(checkVersion ${OpenBLAS_SEARCH_VERSIONS})
   endif()
 endforeach()
 
-# ------------------------------------------------------------------------
-#  Extract version information
-# ------------------------------------------------------------------------
-
 # WARNING: We may not be able to determine the version of some OpenBLAS
 set(OpenBLAS_VERSION_MAJOR 0)
 set(OpenBLAS_VERSION_MINOR 0)
@@ -120,20 +155,26 @@ if(OpenBLAS_VERSION_STRING)
   string(REGEX REPLACE "([0-9]+).([0-9]+).([0-9]+)" "\\3" OpenBLAS_VERSION_PATCH "${OpenBLAS_VERSION_STRING}")
 endif()
 
-#======================
+# ==============================================================================
 # Checks 'REQUIRED', 'QUIET' and versions.
+
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(OpenBLAS FOUND_VAR OpenBLAS_FOUND
   REQUIRED_VARS 
   OpenBLAS_CBLAS_INCLUDE_DIR
-                OpenBLAS_LAPACKE_INCLUDE_DIR
   OpenBLAS_LIB
+  LAPACKE_INCLUDE_DIRS
   VERSION_VAR OpenBLAS_VERSION_STRING
 )
 
+# ------------------------------------------------------------------------------
+
 if (OpenBLAS_FOUND)
-  set(OpenBLAS_INCLUDE_DIRS ${OpenBLAS_CBLAS_INCLUDE_DIR} ${OpenBLAS_CBLAS_INCLUDE_DIR})
+  list(APPEND OpenBLAS_INCLUDE_DIRS
+    ${OpenBLAS_CBLAS_INCLUDE_DIR}
+    ${LAPACKE_INCLUDE_DIRS})
   list(REMOVE_DUPLICATES OpenBLAS_INCLUDE_DIRS)
+  
   if("${CMAKE_C_COMPILER_ID}" MATCHES ".*Clang.*" OR
      "${CMAKE_C_COMPILER_ID}" MATCHES ".*GNU.*" OR
      "${CMAKE_C_COMPILER_ID}" MATCHES ".*Intel.*"
@@ -141,11 +182,53 @@ if (OpenBLAS_FOUND)
     set(MATH_LIB m)
   endif()
   list(APPEND OpenBLAS_LIBRARIES ${OpenBLAS_LIB} ${MATH_LIB})
+
   if(OpenBLAS_HAS_PARALLEL_LIBRARIES)
     list(APPEND OpenBLAS_PARALLEL_LIBRARIES ${OpenBLAS_PARALLEL_LIB})
   endif()
+
+  # ----------------------------------------------------------------------------
+
+  if(NOT TARGET OpenBLAS::OpenBLAS)
+    get_filename_component(LIB_EXT "${LAPACKE_${UPPERCOMPONENT}_LIB}" EXT)
+    if(LIB_EXT STREQUAL ".a" OR LIB_EXT STREQUAL ".lib")
+      set(LIB_TYPE STATIC)
+    else()
+      set(LIB_TYPE SHARED)
+    endif()
+    add_library(OpenBLAS::OpenBLAS ${LIB_TYPE} IMPORTED GLOBAL)
+    set(_tmp_dep_libs "${MATH_LIB};${LAPACKE_LIBRARIES}")
+    list(REMOVE_DUPLICATES _tmp_dep_libs)
+    set_target_properties(OpenBLAS::OpenBLAS
+      PROPERTIES
+      INTERFACE_INCLUDE_DIRECTORIES "${OpenBLAS_INCLUDE_DIRS}"
+      INTERFACE_LINK_LIBRARIES "${_tmp_dep_libs}")
+    
+    if(OpenBLAS_HAS_PARALLEL_LIBRARIES)
+      set_target_properties(OpenBLAS::OpenBLAS
+	PROPERTIES
+	IMPORTED_LOCATION "${OpenBLAS_PARALLEL_LIB}")
+    else()
+      set_target_properties(OpenBLAS::OpenBLAS
+	PROPERTIES
+	IMPORTED_LOCATION "${OpenBLAS_LIB}")
+    endif()
+  endif()
+
+  # ----------------------------------------------------------------------------
+
+  if(NOT OpenBLAS_FIND_QUIETLY)
+    get_target_property(_lib OpenBLAS::OpenBLAS IMPORTED_LOCATION)
+    get_target_property(_dep_libs OpenBLAS::OpenBLAS INTERFACE_LINK_LIBRARIES)
+    message(STATUS "Found OpenBLAS and defined the OpenBLAS::OpenBLAS imported target:")
+    message(STATUS "  - include:      ${OpenBLAS_INCLUDE_DIRS}")
+    message(STATUS "  - library:      ${_lib}")
+    message(STATUS "  - dependencies: ${_dep_libs}")
+  endif()
 endif()
 
+# ==============================================================================
+
 mark_as_advanced(
   OpenBLAS_FOUND
   OpenBLAS_INCLUDE_DIRS
@@ -158,13 +241,3 @@ mark_as_advanced(
   OpenBLAS_VERSION_STRING
   )
 
-## For debugging
-message(STATUS "OpenBLAS_FOUND                  :${OpenBLAS_FOUND}:  - set to true if the library is found")
-message(STATUS "OpenBLAS_INCLUDE_DIRS           :${OpenBLAS_INCLUDE_DIRS}: - list of required include directories")
-message(STATUS "OpenBLAS_LIBRARIES              :${OpenBLAS_LIBRARIES}: - list of libraries to be linked")
-message(STATUS "OpenBLAS_HAS_PARALLEL_LIBRARIES :${OpenBLAS_HAS_PARALLEL_LIBRARIES}: - determine if there are parallel libraries compiled")
-message(STATUS "OpenBLAS_PARALLEL_LIBRARIES     :${OpenBLAS_PARALLEL_LIBRARIES}: - list of libraries for parallel implementations")
-message(STATUS "OpenBLAS_VERSION_MAJOR          :${OpenBLAS_VERSION_MAJOR}: - major version number")
-message(STATUS "OpenBLAS_VERSION_MINOR          :${OpenBLAS_VERSION_MINOR}: - minor version number")
-message(STATUS "OpenBLAS_VERSION_PATCH          :${OpenBLAS_VERSION_PATCH}: - patch version number")
-message(STATUS "OpenBLAS_VERSION_STRING         :${OpenBLAS_VERSION_STRING}: - version number as a string")

cmake/FindlibFlame.cmake

+#.rst:
+# FindlibFlame
+# -------------
+#
+# Find libFlame include dirs and libraries
+#
+# Use this module by invoking find_package with the form::
+#
+#   find_package(libFlame
+#     [REQUIRED]             # Fail with error if libFlame is not found
+#     )
+#
+# This module defines::
+#
+#   libFlame_FOUND            - True if headers and requested libraries were found
+#   libFlame_INCLUDE_DIRS     - libFlame include directories
+#   libFlame_LIBRARIES        - libFlame component libraries to be linked
+#
+#
+# This module reads hints about search locations from variables
+# (either CMake variables or environment variables)::
+#
+#   libFlame_ROOT             - Preferred installation prefix
+#   libFlame_DIR              - Preferred installation prefix
+#
+#
+# The following :prop_tgt:`IMPORTED` targets are also defined::
+#
+#   libFlame::libFlame        - Target for specific component dependency
+#                               (shared or static library)
+#
+
+# ==============================================================================
+# Copyright 2018 Damien Nguyen <damien.nguyen@alumni.epfl.ch>
+#
+# Distributed under the OSI-approved BSD License (the "License")
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# ==============================================================================
+
+set(libFlame_SEARCH_PATHS
+  ${libFlame_ROOT}
+  $ENV{libFlame_ROOT}
+  ${libFlame_DIR}
+  $ENV{libFlame_DIR}
+  $ENV{CMAKE_PREFIX_PATH}
+  ${CMAKE_PREFIX_PATH}
+  /usr
+  /usr/local/
+  /usr/local/amd
+  /opt
+  /opt/amd
+  /opt/local
+  )
+
+find_library(libFlame_LIBRARY
+  NAMES flame
+  PATHS ${libFlame_SEARCH_PATHS}
+  PATH_SUFFIXES lib lib32 lib64 libflame/lib
+  )
+
+if(libFLame_LIBRARY)
+  get_filename_component(libFlame_ROOT_HINT ${libFlame_LIBRARY} PATH) # for CMake > 2.8.11 we should really use DIRECTORY
+  get_filename_component(libFlame_ROOT_HINT ${libFlame_ROOT_HINT} PATH)  
+endif()
+
+find_path(libFlame_INCLUDE_DIR
+  NAMES FLAME.h flame.h
+  HINTS ${libFlame_ROOT_HINT}
+  PATHS ${libFlame_SEARCH_PATHS}
+  PATH_SUFFIXES include libflame/include
+  )
+
+set(libFlame_LAPACKE_COMPONENTS cblas)
+
+# ==============================================================================
+
+if(libFLame_LIBRARY)
+  include(CheckLibraryExists)
+  check_library_exists(${libFlame_LIBRARY} zgesdd_ "" HAVE_ZGESDD)
+  check_library_exists(${libFlame_LIBRARY} zgelss_ "" HAVE_ZGELSS)
+  
+  if(HAVE_ZGESDD AND HAVE_ZGELSS)
+    set(HAVE_LAPACK_INTERFACE 1)
+  else()
+    set(HAVE_LAPACK_INTERFACE 0)
+  endif()
+  
+  set(LAPACK_LIB_VAR "")
+  if(NOT HAVE_LAPACK_INTERFACE)
+    message(STATUS "libFlame has no LAPACK interface, looking for a LAPACK library")
+    list(APPEND libFlame_LAPACKE_COMPONENTS lapack)
+  endif()
+
+  # ----------------------------------------------------------------------------
+
+  find_package(LAPACKE QUIET REQUIRED COMPONENTS ${libFlame_LAPACKE_COMPONENTS})
+endif()
+
+# ==============================================================================
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(libFlame
+  FOUND_VAR libFlame_FOUND
+  REQUIRED_VARS
+  libFlame_INCLUDE_DIR
+  libFlame_LIBRARY
+  LAPACKE_FOUND
+  LAPACKE_LIBRARIES
+  LAPACKE_INCLUDE_DIRS
+  )
+
+# ==============================================================================
+
+if(libFlame_FOUND)
+  set(libFlame_INCLUDE_DIRS)
+  list(APPEND libFlame_INCLUDE_DIRS
+    ${libFlame_INCLUDE_DIR}
+    ${LAPACKE_INCLUDE_DIRS})
+  list(REMOVE_DUPLICATES libFlame_INCLUDE_DIRS)
+
+  set(libFlame_LIBRARIES)
+  list(APPEND libFlame_LIBRARIES
+    ${libFlame_LIBRARY}
+    ${LAPACKE_LIBRARIES})
+  
+  # ----------------------------------------------------------------------------
+
+  if(NOT TARGET libFlame::libFlame)
+    get_filename_component(LIB_EXT "${libFlame_LIBRARY}" EXT)
+    if(LIB_EXT STREQUAL ".a" OR LIB_EXT STREQUAL ".lib")
+      set(LIB_TYPE STATIC)
+    else()
+      set(LIB_TYPE SHARED)
+    endif()
+    add_library(libFlame::libFlame ${LIB_TYPE} IMPORTED GLOBAL)
+    set_target_properties(libFlame::libFlame PROPERTIES
+      IMPORTED_LOCATION "${libFlame_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${libFlame_INCLUDE_DIRS}"
+      INTERFACE_LINK_LIBRARIES "${LAPACKE_LIBRARIES}"
+      )
+  endif()
+  
+  # ----------------------------------------------------------------------------
+  ## For debugging
+  if(NOT libFlame_FIND_QUIETLY)
+    get_target_property(_dep_libs libFlame::libFlame INTERFACE_LINK_LIBRARIES)
+    message(STATUS "Found libFlame and defined the libFlame::libFlame imported target:")
+    message(STATUS "  - include:      ${libFlame_INCLUDE_DIR}")
+    message(STATUS "  - library:      ${libFlame_LIBRARY}")
+    message(STATUS "  - dependencies: ${_dep_libs}")
+  endif()
+endif()
+
+
+# ==============================================================================
+
+mark_as_advanced(
+  libFlame_LIBRARY
+  libFlame_INCLUDE_DIR
+  libFlame_CBLAS_INCLUDE_DIR
+  )
+
+# ==============================================================================
+

cmake/bart_configure_add_header.cmake

+set(_required_vars INFILE OUTFILE PREFIX)
+foreach(_var ${_required_vars})
+  if(NOT DEFINED "${_var}")
+    message(FATAL_ERROR "Variable ${_var} is undefined!")
+  endif()
+endforeach()
+
+if(NOT EXISTS "${INFILE}")
+  message(FATAL_ERROR "\n\nMissing input file '${INFILE}' for generating '${OUTFILE}'\n\n")
+endif()
+
+# ==============================================================================
+
+file(READ "${INFILE}" _file_content)
+
+set(_prefix_string)
+foreach(_line ${PREFIX})
+  set(_prefix_string "${_prefix_string}\n${_line}")
+endforeach()
+
+file(WRITE "${OUTFILE}" "${_prefix_string}\n\n\n${_file_content}")