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Merge pull request #33 from FastNFT/release-0.2
Release 0.2
2 parents 0fc4df7 + b5b8b61 commit becba5d

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Lines changed: 33922 additions & 3750 deletions

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‎.gitignore‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,8 +21,12 @@
2121
# Ignore MacOS hidden files in subdirectories
2222
/**/*.DS_Store
2323

24-
# Ignore mex files in matlab subdirectory
25-
/matlab/*.mexmaci64
24+
# Ignore mex and dSYM files in matlab subdirectory and deeper
25+
/matlab/**/*.mexmaci64
26+
/matlab/**/*.mexa64
27+
/matlab/**/*.mexw32
28+
/matlab/**/*.mexw64
29+
/matlab/**/*.dSYM
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2731
# Unignore file types (including in subdirectories)
2832
!/**/*.c

‎.travis.yml‎

Lines changed: 19 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,23 @@ matrix:
1010
packages:
1111
- gcc-5
1212
- gfortran-5
13-
env: GCC_VER="5" CC=/usr/bin/gcc-5 FC=/usr/bin/gfortran-5"
13+
- os: linux
14+
addons:
15+
apt:
16+
sources:
17+
- ubuntu-toolchain-r-test
18+
packages:
19+
- gcc-5
20+
- gfortran-5
21+
- libfftw3-dev
1422

15-
script: cmake . && make && make test
23+
before_script:
24+
- sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 100
25+
- sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-5 100
26+
- mkdir build
27+
- cd build
28+
29+
script:
30+
- if dpkg -s libfftw3-dev; then cmake .. -DENABLE_FFTW=ON; else cmake ..; fi
31+
- make
32+
- make test CTEST_OUTPUT_ON_FAILURE=1

‎CHANGELOG.md‎

Lines changed: 28 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,33 @@
11
# Changelog
22

3+
## [0.2.0] -- 2018-09
34

5+
### Added
6+
7+
- New public function fnft_nsev_inverse implementing a fast inverse NFT for the vanishing nonlinear Schroedinger equation (the inversion of the continuous spectrum is fast, bound states are added using a standard Darboux transform)
8+
- New public function fnft_version returning current version of FNFT
9+
- The version of FNFT can now be supplemented with a suffix
10+
- The FFTW library can be used to compute internal FFTs instead of the standard Kiss FFT
11+
- Building of the tests can now be turned off
12+
- The number of samples D in fnft_nsev and fnft_kdvv no longer has to be a power of two
13+
- The subsampling factor in the SUBSAMPLE_AND_REFINE method for locating the discrete spectrum in fnft_nsev can now be controlled by the user
14+
- System-wide installation using "make install" is now possible
15+
- New private function fnft__nse_finvscatter implementing fast inverse scattering
16+
- New private function fnft__poly_specfact implementing Kolmogorov's method for spectral factorization
17+
- New private function fnft__poly_eval implementing Horner's method
18+
- New private functions fnft__akns_fscatter and fnft__akns_scatter_matrix implementing forward scattering for general AKNS systems
19+
- New private functions fnft__akns_lambda_to_z and fnft__akns_z_to_lambda that centralize the continuous-time/discrete-time coordinate transforms
20+
21+
### Changed
22+
23+
- Forward scattering functions fnft__nse_fscatter, fnft__nse_scatter_matrix, fnft__kdv_fscatter and fnft__kdv_scatter_matrix now make use of their more general AKNS counter parts
24+
25+
### Fixed
26+
27+
- M could not be much larger than D in fnft_nsev
28+
- dists[1] was not set correctly under some circumstances in nsev_compare_nfs
29+
- Some public headers were including private ones
30+
- Compiler warning about __Thread_local
431

532
## [0.1.1] -- 2018-05-14
633

@@ -14,4 +41,4 @@
1441
- Fixed: Some return codes in fnft_nsep had not been checked
1542
- Fixed: misc_merge did not work correctly for empty input vectors
1643
- Fixed: The continuous spectrum in mex_fnft_nsev_example.m was plotted over t, not xi
17-
- Fixed: A superfluous parameter kappa was given in the documentation of mex_fnft_kdvv
44+
- Fixed: A superfluous parameter kappa was given in the documentation of mex_fnft_kdvv

‎CMakeLists.txt‎

Lines changed: 138 additions & 79 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,29 @@
1+
# This file is part of FNFT.
2+
#
3+
# FNFT is free software; you can redistribute it and/or
4+
# modify it under the terms of the version 2 of the GNU General
5+
# Public License as published by the Free Software Foundation.
6+
#
7+
# FNFT is distributed in the hope that it will be useful,
8+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
9+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10+
# GNU General Public License for more details.
11+
#
12+
# You should have received a copy of the GNU General Public License
13+
# along with this program. If not, see <http://www.gnu.org/licenses/>.
14+
#
15+
# Contributors:
16+
# Sander Wahls (TU Delft) 2017-2018.
17+
# Marius Brehler (TU Dortmund) 2018.
18+
119
cmake_minimum_required(VERSION 3.5)
220
project(fnft C)
321

422
set(FNFT_VERSION_MAJOR 0)
5-
set(FNFT_VERSION_MINOR 1)
6-
set(FNFT_VERSION_PATCH 1)
23+
set(FNFT_VERSION_MINOR 2)
24+
set(FNFT_VERSION_PATCH 0)
25+
set(FNFT_VERSION_SUFFIX "") # should not be longer than FNFT_SUFFIX_MAXLEN
26+
set(FNFT_VERSION ${FNFT_VERSION_MAJOR}.${FNFT_VERSION_MINOR}.${FNFT_VERSION_PATCH}${FNFT_VERSION_SUFFIX})
727

828
include(CheckIncludeFiles)
929
include(CheckFunctionExists)
@@ -13,40 +33,59 @@ include(CheckLanguage)
1333
# options
1434
option(DEBUG "Compile with debugging symbols" OFF)
1535
option(WITH_MATLAB "Build the Matlab interface" ON)
16-
option(MACHINE_SPECIFIC_OPTIMIZATION "Activate optimizations specific for this machine" OFF)
36+
option(MACHINE_SPECIFIC_OPTIMIZATION "Activate optimizations specific for this machine" ON)
1737
option(ADDRESS_SANITIZER "Enable address sanitzer for known compilers" OFF)
18-
if (MACHINE_SPECIFIC_OPTIMIZATION)
19-
message("Optimizing for this specific machine.")
20-
endif()
38+
option(ENABLE_FFTW "Use FFTW if it is available" OFF)
39+
option(BUILD_TESTS "Build tests" ON)
2140

2241
# check for complex.h
2342
check_include_files(complex.h HAVE_COMPLEX_H)
2443
if (NOT HAVE_COMPLEX_H)
25-
message(ERROR "Compiler does not provide complex.h")
44+
message(FATAL_ERROR "Compiler does not provide complex.h")
2645
endif()
2746

2847
# check if math code requires us to link libm
2948
check_function_exists(log2 HAVE_LOG2)
3049
if (NOT HAVE_LOG2)
31-
message("Adding libm to the required libraries, repeating test.")
32-
list(APPEND CMAKE_REQUIRED_LIBRARIES m)
33-
check_function_exists(log2 HAVE_LOG2_2)
34-
if (NOT HAVE_LOG2_2)
35-
message(ERROR "no log2")
36-
else()
37-
set(LIBM m)
38-
endif()
50+
message("++ Adding libm to the required libraries, repeating test.")
51+
list(APPEND CMAKE_REQUIRED_LIBRARIES m)
52+
check_function_exists(log2 HAVE_LOG2_2)
53+
if (NOT HAVE_LOG2_2)
54+
message(FATAL_ERROR "no log2")
55+
else()
56+
set(LIBM m)
57+
endif()
3958
else()
40-
set(LIBM )
59+
set(LIBM )
4160
endif()
4261

4362
# check if thread local storage is available
44-
check_c_source_compiles("_Thread_local int g; int main() { g = 1; return g; }" HAVE__THREAD_LOCAL)
45-
if (NOT HAVE__THREAD_LOCAL)
46-
check_c_source_compiles("__thread int g; int main() { g = 1; return g; }" HAVE___THREAD)
47-
if (NOT HAVE___THREAD)
48-
message(WARNING "Thread local storage is not available. fnft_errwarn_setprintf will not be thread-safe.")
49-
endif()
63+
check_c_source_compiles("__thread int g; int main() { g = 1; return g; }" HAVE___THREAD)
64+
if (NOT HAVE___THREAD)
65+
check_c_source_compiles("_Thread_local int g; int main() { g = 1; return g; }" HAVE__THREAD_LOCAL)
66+
if (NOT HAVE__THREAD_LOCAL)
67+
message(WARNING "Thread local storage is not available. fnft_errwarn_setprintf will not be thread-safe.")
68+
endif()
69+
endif()
70+
71+
# check if FFTW3 is available
72+
find_library(FFTW3_LIB fftw3)
73+
find_path(FFTW3_INCLUDE fftw3.h)
74+
if (FFTW3_LIB AND FFTW3_INCLUDE)
75+
if (ENABLE_FFTW)
76+
message("++ FFTW3 found and enabled. Run cmake with \"-DENABLE_FFTW=OFF\" to disable.")
77+
set(HAVE_FFTW3 1) # for updating fnft_config.h
78+
else()
79+
message("++ FFTW3 found but NOT enabled. Run cmake with \"-DENABLE_FFTW=ON\" to enable.")
80+
endif()
81+
else()
82+
if (ENABLE_FFTW)
83+
message(FATAL_ERROR "FFTW3 NOT found but set to enabled the by user. Run cmake WITHOUT \"-DENABLE_FFTW=ON\" to disable.")
84+
else()
85+
set(FFTW3_LIB "")
86+
set(FFTW3_INCLUDE "")
87+
message("++ FFTW3 NOT found. Using Kiss FFT instead.")
88+
endif()
5089
endif()
5190

5291
# header files
@@ -56,52 +95,68 @@ include(CheckCCompilerFlag)
5695

5796
# configure C compiler
5897
if (CMAKE_COMPILER_IS_GNUCC) # gcc
59-
if (DEBUG)
60-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g")
61-
endif()
98+
if (DEBUG)
99+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g")
100+
message("++ Enabling debugging symbols in the C compiler")
101+
endif()
62102
if (ADDRESS_SANITIZER)
63-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fno-omit-frame-pointer")
103+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fno-omit-frame-pointer")
104+
message("++ Enabling address sanitizer")
64105
endif()
65106
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
66-
if (MACHINE_SPECIFIC_OPTIMIZATION)
67-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native")
68-
endif()
69-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall -Wextra -pedantic -Werror=implicit-function-declaration")
107+
if (MACHINE_SPECIFIC_OPTIMIZATION)
108+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native")
109+
message("++ Enabling machine specific optimization in the C compiler")
110+
endif()
111+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall -Wextra -pedantic -Werror=implicit-function-declaration")
70112
else()
71-
message(WARNING "Compiler is not gcc. Will try to use -O3 (or if debug) flag.")
72-
if (DEBUG)
73-
check_c_compiler_flag("-g" HAS_C_G_FLAG)
74-
if (HAS_C_G_FLAG)
75-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS}$ -g")
76-
endif()
77-
else()
78-
check_c_compiler_flag("-O3" HAS_C_O3_FLAG)
79-
if (HAS_C_O3_FLAG)
80-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
81-
endif()
82-
if (MACHINE_SPECIFIC_OPTIMIZATION)
83-
message(WARNING "Compiler is not gcc. Will try to use -march=native flag.")
84-
check_c_compiler_flag("-march=native" HAS_C_MARCH_NATIVE_FLAG)
85-
if (HAS_C_MARCH_NATIVE_FLAG)
86-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native")
87-
endif()
88-
endif()
89-
endif()
113+
message(WARNING "++ Compiler is not gcc. Will try to set flags anyway.")
114+
if (DEBUG)
115+
check_c_compiler_flag("-g" HAS_C_G_FLAG)
116+
if (HAS_C_G_FLAG)
117+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g")
118+
message("++ Enabled -g flag in the C compiler")
119+
endif()
120+
else()
121+
check_c_compiler_flag("-O3" HAS_C_O3_FLAG)
122+
if (HAS_C_O3_FLAG)
123+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
124+
message("++ Enabled -O3 flag in the C compiler")
125+
endif()
126+
if (MACHINE_SPECIFIC_OPTIMIZATION)
127+
check_c_compiler_flag("-march=native" HAS_C_MARCH_NATIVE_FLAG)
128+
if (HAS_C_MARCH_NATIVE_FLAG)
129+
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native")
130+
message("++ Enabled -march=native flag in the C compiler")
131+
endif()
132+
endif()
133+
endif()
90134
endif()
91135

92136
# generate config header file
93137
configure_file(include/fnft_config.h.in ${CMAKE_CURRENT_SOURCE_DIR}/include/fnft_config.h)
94138
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
95139
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include/private)
96140
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include/3rd_party/kiss_fft)
141+
include_directories(${FFTW3_INCLUDE})
97142

98143
# configure Fortran support
99144
enable_language(Fortran)
100145
if (CMAKE_Fortran_COMPILER_ID MATCHES GNU) # gfortran
101-
set (CMAKE_Fortran_FLAGS " -O3 -cpp -ffree-line-length-none")
146+
set (CMAKE_Fortran_FLAGS " -O3 -cpp -ffree-line-length-none")
147+
if (DEBUG)
148+
set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g")
149+
message("++ Enabling debugging symbols in the Fortran compiler")
150+
endif()
151+
if (MACHINE_SPECIFIC_OPTIMIZATION)
152+
set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -march=native")
153+
message("++ Enabling machine specific optimization in the Fortran compiler")
154+
endif()
102155
endif ()
103156

104-
enable_testing()
157+
if (BUILD_TESTS)
158+
enable_testing()
159+
endif()
105160

106161
# sources
107162
file(GLOB SOURCES "src/*.c")
@@ -113,47 +168,51 @@ file(GLOB_RECURSE TEST_SOURCES "test/*_test*.c")
113168

114169
# generate shared library
115170
add_library(fnft SHARED ${SOURCES} ${PRIVATE_SOURCES} ${KISS_FFT_SOURCES} ${EISCOR_SOURCES})
116-
set_target_properties(fnft PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/lib")
171+
target_link_libraries(fnft ${FFTW3_LIB})
172+
file(GLOB PUBLIC_HEADERS "include/*.h")
173+
set_target_properties(fnft PROPERTIES VERSION ${FNFT_VERSION} SOVERSION ${FNFT_VERSION_MAJOR} LIBRARY_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/lib" PUBLIC_HEADER "${PUBLIC_HEADERS}")
117174

118175
# installation under Linux
119-
install(TARGETS fnft DESTINATION lib)
176+
install(TARGETS fnft LIBRARY DESTINATION lib PUBLIC_HEADER DESTINATION include)
120177

121178
# generate examples
122179
foreach (srcfile ${EXAMPLE_SOURCES})
123-
get_filename_component(example ${srcfile} NAME_WE)
124-
add_executable(${example} ${srcfile})
125-
target_link_libraries(${example} fnft ${LIBM})
126-
set_target_properties(${example} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/examples")
180+
get_filename_component(example ${srcfile} NAME_WE)
181+
add_executable(${example} ${srcfile})
182+
target_link_libraries(${example} fnft ${LIBM} ${FFTW3_LIB})
183+
set_target_properties(${example} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/examples")
127184
endforeach()
128185

129186
# generate tests
130-
foreach (srcfile ${TEST_SOURCES})
131-
get_filename_component(dir ${srcfile} DIRECTORY)
132-
get_filename_component(test ${srcfile} NAME_WE)
133-
add_executable(${test} ${srcfile})
134-
target_link_libraries(${test} fnft ${LIBM})
135-
add_test(NAME ${test} COMMAND ${test})
136-
set_target_properties(${test} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${dir}")
137-
endforeach()
187+
if (BUILD_TESTS)
188+
foreach (srcfile ${TEST_SOURCES})
189+
get_filename_component(dir ${srcfile} DIRECTORY)
190+
get_filename_component(test ${srcfile} NAME_WE)
191+
add_executable(${test} ${srcfile})
192+
target_link_libraries(${test} fnft ${LIBM} ${FFTW3_LIB})
193+
add_test(NAME ${test} COMMAND ${test})
194+
set_target_properties(${test} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${dir}")
195+
endforeach()
196+
endif()
138197

139198
# Try to build the Matlab interface if requested
140199
if (WITH_MATLAB)
141200
check_language(CXX)
142201
if (CMAKE_CXX_COMPILER)
143-
enable_language(CXX) # sometimes required by FindMatlab below
202+
enable_language(CXX) # sometimes required by FindMatlab below
144203
else()
145-
message("Could not find a C++ compiler, which is sometimes required to localize Matlab.")
146-
message("If the build process fails, deactivate the localization with the -DWITH_MATLAB=OFF switch.")
204+
message("++ Could not find a C++ compiler, which is sometimes required to localize Matlab.")
205+
message("++ If the build process fails, deactivate the localization with the -DWITH_MATLAB=OFF switch.")
147206
endif()
148-
find_package(Matlab COMPONENTS MX_LIBRARY)
149-
if (Matlab_FOUND)
150-
file(GLOB MEX_SOURCES "matlab/mex_*.c")
151-
foreach (srcfile ${MEX_SOURCES})
152-
get_filename_component(mexfile ${srcfile} NAME_WE)
153-
matlab_add_mex(NAME ${mexfile} SRC ${srcfile} LINK_TO fnft ${LIBM})
154-
set_target_properties(${mexfile} PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/matlab")
155-
target_compile_options(${mexfile} PRIVATE -DMEX_DOUBLE_HANDLE)
156-
# -DMEX_DOUBLE_HANDLE avoids the new complex interleaved API
157-
endforeach()
158-
endif()
207+
find_package(Matlab COMPONENTS MX_LIBRARY)
208+
if (Matlab_FOUND)
209+
file(GLOB MEX_SOURCES "matlab/mex_*.c")
210+
foreach (srcfile ${MEX_SOURCES})
211+
get_filename_component(mexfile ${srcfile} NAME_WE)
212+
matlab_add_mex(NAME ${mexfile} SRC ${srcfile} LINK_TO fnft ${LIBM} ${FFTW3_LIB})
213+
set_target_properties(${mexfile} PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/matlab")
214+
target_compile_options(${mexfile} PRIVATE -DMEX_DOUBLE_HANDLE)
215+
# -DMEX_DOUBLE_HANDLE avoids the new complex interleaved API
216+
endforeach()
217+
endif()
159218
endif()

‎Doxyfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -444,7 +444,7 @@ EXTRACT_PACKAGE = NO
444444
# included in the documentation.
445445
# The default value is: NO.
446446

447-
EXTRACT_STATIC = NO
447+
EXTRACT_STATIC = YES
448448

449449
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
450450
# locally in source files will be included in the documentation. If set to NO,

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