Vendor libconjugrad

README.md

@@ -41,9 +41,9 @@ For the padded version:
 We recommend compiling CCMpred on the machine that should run the computations so that it can be optimized for the appropriate CPU/GPU architecture.
 
 ### Downloading
-If you want to compile the most recent version, use the follwing to clone both CCMpred and its submodules:
+If you want to compile the most recent version, use the following to clone the latest version of CCMpred:
 
-	git clone --recursive https://github.com/soedinglab/CCMpred.git
+	git clone https://github.com/soedinglab/CCMpred.git
 
 ### Compilation
 With the sourcecode ready, simply run cmake with the default settings and libraries should be auto-detected:

lib/libconjugrad/.gitignore

@@ -0,0 +1,55 @@
+### C
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+#Binaries
+/bin
+
+# Libraries
+*.lib
+*.a
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+
+### vim
+
+[._]*.s[a-w][a-z]
+[._]s[a-w][a-z]
+*.un~
+Session.vim
+.netrwhist
+*~
+
+
+### CMake
+
+CMakeCache.txt
+CMakeFiles
+Makefile
+cmake_install.cmake
+install_manifest.txt
+_build
+
+
+### Python
+
+__pycache__/
+*.py[cod]
+

lib/libconjugrad/.ycm_extra_conf.py

@@ -0,0 +1,120 @@
+
+import os
+import ycm_core
+
+flags = [
+'-Wall',
+'-Wextra',
+'-Werror',
+'-Wc++98-compat',
+'-Wno-long-long',
+'-Wno-variadic-macros',
+'-fexceptions',
+'-DNDEBUG',
+
+'-std=c11',
+'-x',
+'c',
+'-I',
+'./include'
+]
+
+
+# Set this to the absolute path to the folder (NOT the file!) containing the
+# compile_commands.json file to use that instead of 'flags'. See here for
+# more details: http://clang.llvm.org/docs/JSONCompilationDatabase.html
+#
+# Most projects will NOT need to set this to anything; you can just change the
+# 'flags' list of compilation flags. Notice that YCM itself uses that approach.
+compilation_database_folder = ''
+
+if os.path.exists( compilation_database_folder ):
+  database = ycm_core.CompilationDatabase( compilation_database_folder )
+else:
+  database = None
+
+SOURCE_EXTENSIONS = [ '.cpp', '.cxx', '.cc', '.c', '.m', '.mm' ]
+
+def DirectoryOfThisScript():
+  return os.path.dirname( os.path.abspath( __file__ ) )
+
+
+def MakeRelativePathsInFlagsAbsolute( flags, working_directory ):
+  if not working_directory:
+    return list( flags )
+  new_flags = []
+  make_next_absolute = False
+  path_flags = [ '-isystem', '-I', '-iquote', '--sysroot=' ]
+  for flag in flags:
+    new_flag = flag
+
+    if make_next_absolute:
+      make_next_absolute = False
+      if not flag.startswith( '/' ):
+        new_flag = os.path.join( working_directory, flag )
+
+    for path_flag in path_flags:
+      if flag == path_flag:
+        make_next_absolute = True
+        break
+
+      if flag.startswith( path_flag ):
+        path = flag[ len( path_flag ): ]
+        new_flag = path_flag + os.path.join( working_directory, path )
+        break
+
+    if new_flag:
+      new_flags.append( new_flag )
+  return new_flags
+
+
+def IsHeaderFile( filename ):
+  extension = os.path.splitext( filename )[ 1 ]
+  return extension in [ '.h', '.hxx', '.hpp', '.hh' ]
+
+
+def GetCompilationInfoForFile( filename ):
+  # The compilation_commands.json file generated by CMake does not have entries
+  # for header files. So we do our best by asking the db for flags for a
+  # corresponding source file, if any. If one exists, the flags for that file
+  # should be good enough.
+  if IsHeaderFile( filename ):
+    basename = os.path.splitext( filename )[ 0 ]
+    for extension in SOURCE_EXTENSIONS:
+      replacement_file = basename + extension
+      if os.path.exists( replacement_file ):
+        compilation_info = database.GetCompilationInfoForFile(
+          replacement_file )
+        if compilation_info.compiler_flags_:
+          return compilation_info
+    return None
+  return database.GetCompilationInfoForFile( filename )
+
+
+def FlagsForFile( filename, **kwargs ):
+  if database:
+    # Bear in mind that compilation_info.compiler_flags_ does NOT return a
+    # python list, but a "list-like" StringVec object
+    compilation_info = GetCompilationInfoForFile( filename )
+    if not compilation_info:
+      return None
+
+    final_flags = MakeRelativePathsInFlagsAbsolute(
+      compilation_info.compiler_flags_,
+      compilation_info.compiler_working_dir_ )
+
+    # NOTE: This is just for YouCompleteMe; it's highly likely that your project
+    # does NOT need to remove the stdlib flag. DO NOT USE THIS IN YOUR
+    # ycm_extra_conf IF YOU'RE NOT 100% SURE YOU NEED IT.
+    try:
+      final_flags.remove( '-stdlib=libc++' )
+    except ValueError:
+      pass
+  else:
+    relative_to = DirectoryOfThisScript()
+    final_flags = MakeRelativePathsInFlagsAbsolute( flags, relative_to )
+
+  return {
+    'flags': final_flags,
+    'do_cache': True
+  }

lib/libconjugrad/CMakeLists.txt

@@ -0,0 +1,64 @@
+cmake_minimum_required(VERSION 3.8)
+include(CheckLanguage)
+
+project(libconjugrad)
+set(LIBCONJUGRAD_MAJOR_VERSION 0)
+set(LIBCONJUGRAD_MINOR_VERSION 0)
+set(LIBCONJUGRAD_PATCH_VERSION 4)
+set(LIBCONJUGRAD_VERSION ${LIBCONJUGRAD_MAJOR_VERSION}.${LIBCONJUGRAD_MINOR_VERSION}.${LIBCONJUGRAD_PATCH_VERSION})
+
+if(CMAKE_VERSION VERSION_GREATER 2.8.11)
+	cmake_policy(SET CMP0022 OLD)
+endif(CMAKE_VERSION VERSION_GREATER 2.8.11)
+
+set(CMAKE_C_FLAGS "-std=c99 -O3 -g -lm")
+set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
+
+include_directories("${PROJECT_SOURCE_DIR}/include")
+
+set(SOURCES src/conjugrad.c src/debug.c)
+
+if(NOT DEFINED WITH_SIMD)
+	set(WITH_SIMD ansi)
+endif(NOT DEFINED WITH_SIMD)
+
+if(NOT DEFINED WITH_CUDA)
+	set(WITH_CUDA ON)
+endif(NOT DEFINED WITH_CUDA)
+
+if(WITH_SIMD STREQUAL ansi)
+	add_definitions(-DCONJUGRAD_SIMD=0)
+	list(APPEND SOURCES src/arithmetic_ansi.c)
+elseif(WITH_SIMD STREQUAL sse)
+	add_definitions(-DCONJUGRAD_SIMD=1)
+	list(APPEND SOURCES src/arithmetic_simd.c)
+elseif(WITH_SIMD STREQUAL avx)
+	add_definitions(-DCONJUGRAD_SIMD=2)
+	list(APPEND SOURCES src/arithmetic_simd.c)
+endif(WITH_SIMD STREQUAL ansi)
+
+set(BUILD_SHARED_LIBS OFF)
+
+if(WITH_CUDA)
+	find_package(CUDA)
+	check_language(CUDA)
+	enable_language(CUDA)
+
+	#list(APPEND SOURCES src/conjugrad_cuda.c src/help_functions.cu src/conjugrad_kernels.cu)
+	list(APPEND SOURCES src/conjugrad_cuda.c src/conjugrad_kernels.cu)
+
+	include_directories(${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
+endif(WITH_CUDA)
+
+add_library(conjugrad ${SOURCES})
+
+install(TARGETS conjugrad DESTINATION lib)
+
+add_executable(rosenbrock EXCLUDE_FROM_ALL samples/rosenbrock.c)
+target_link_libraries(rosenbrock conjugrad)
+
+add_executable(polynomial EXCLUDE_FROM_ALL samples/polynomial.c)
+target_link_libraries(polynomial conjugrad)
+
+add_executable(sphere EXCLUDE_FROM_ALL samples/sphere.c)
+target_link_libraries(sphere conjugrad)

lib/libconjugrad/include/arithmetic.h

@@ -0,0 +1,34 @@
+#ifndef CONJUGRAD_ARITHMETIC_H
+#define CONJUGRAD_ARITHMETIC_H
+
+#include "conjugrad.h"
+
+
+// set all vector elements to 0
+void vec0(conjugrad_float_t *dst, int n);
+
+// copy src onto dst
+void veccpy(conjugrad_float_t *dst, conjugrad_float_t *src, int n);
+
+// dst += src
+//void veciaddv(conjugrad_float_t *dst, conjugrad_float_t *src, int n);
+
+// dst *= f
+void vecimulc(conjugrad_float_t *dst, conjugrad_float_t f, int n);
+
+// dst -= f * src
+void vecifma(conjugrad_float_t *dst, conjugrad_float_t *src, conjugrad_float_t f, int n);
+
+// dst = f * b - a
+void vecsfms(conjugrad_float_t *dst, conjugrad_float_t *a, conjugrad_float_t f, conjugrad_float_t *b, int n);
+
+// dst = sum_n v[n] * w[n]
+conjugrad_float_t vecdot(conjugrad_float_t *v, conjugrad_float_t *w, int n);
+
+// dst = sum_n v[n]^2
+conjugrad_float_t vecnorm(conjugrad_float_t *v, int n);
+
+
+conjugrad_float_t *vecalloc(int n);
+
+#endif