external libraries mtl4 and muparser added to lib directory

AMDiS/lib/mtl4/CMakeLists.txt

+project (mtl4) # GPU version 
+
+cmake_minimum_required(VERSION 2.8)
+option(ENABLE_GCOV "enable gnu coverage flags for gnu compiler" OFF)
+option(ENABLE_WARNINGS "Enable gnu specific warnings" ON)
+option(ENABLE_DEVELOPMENT "enable program parts under development" OFF)
+
+# adding the Path of our own Modules
+SET(CMAKE_MODULE_PATH $ENV{CMAKE_MODULE_PATH})
+SET(MTL4_ROOT_PATH ${CMAKE_CURRENT_SOURCE_DIR})
+#SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${MTL4_ROOT_PATH}/Cmake_Module)
+SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${MTL4_ROOT_PATH})
+
+#look for mtl4, use THIS directory as mtl dir
+find_package(MTL REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR})
+include_directories(${MTL_INCLUDE_DIRS})
+add_definitions(${MTL_CXX_DEFINITIONS})
+
+
+
+#REMAINING PART USES MTL4
+include(CheckCXXCompilerFlag)
+
+#let cmake look for the svn-version, only needed for packages?
+if (NOT MSVC)
+	find_package(Subversion)
+	if(Subversion_FOUND)
+		Subversion_WC_INFO(${CMAKE_CURRENT_SOURCE_DIR} mtlSubinfo)
+		set(CurrentRevision ${mtlSubinfo_WC_REVISION})
+#	message("current revision: ${mtlSubinfo_WC_REVISION}")
+	else(Subversion_FOUND)
+		set(CurrentRevision "0")
+	endif(Subversion_FOUND)
+endif (NOT MSVC)
+
+# if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+#   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lstdc++")
+# endif()
+
+configure_file(boost/numeric/mtl/version.hpp.in boost/numeric/mtl/version.hpp @ONLY)
+
+
+#look for compiler specific settings
+if (MSVC)
+	# to quiet DevStudio 2005 secure code warnings
+    add_definitions(/D_SCL_SECURE_NO_WARNINGS)
+    add_definitions(/D_CRT_SECURE_NO_WARNINGS)
+    add_definitions(/DMTL_ASSERT_FOR_THROW /D_CRT_SECURE_NO_DEPRECATE /DNOMINMAX /D_CONSOLE /D"_HAS_ITERATOR_DEBUGGING=0" /D"_SECURE_SCL=0" )
+	# specialty flags such as the C++ language exception model etc. come from the init flags determined by CMAKE
+	# you may override them, but I have not found it necessary
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG_INIT} /wd4018 /wd4099 /wd4522 /wd4996 /wd4355 /wd4244 /Z7")
+    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE_INIT} /wd4018 /wd4099 /wd4522 /wd4996 /wd4355 /wd4244 /Z7")
+endif (MSVC)
+
+if( "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND ENABLE_WARNINGS)
+  add_definitions("-Wall -Wextra -Wpointer-arith -Wcast-align -Wcast-qual -Wwrite-strings")
+  foreach(FLAG "-Wno-long-long") # "-Wno-unused-local-typedefs")
+    # message(STATUS "Check flag ${FLAG}")
+    mtl_check_cxx_compiler_flag(${FLAG} FLAG_OKAY)
+    if(FLAG_OKAY)
+      message(STATUS "Add ${FLAG}")
+      add_definitions("${FLAG}")
+    endif()
+  endforeach()
+endif()
+
+if (ENABLE_DEVELOPMENT)
+  add_definitions("-DMTL_WITH_DEVELOPMENT")
+endif()
+
+if (ENABLE_SHORT_ELE_PROD)
+  add_definitions("-DMTL_WITH_SHORT_ELE_PROD")
+endif()
+
+set(BUILDNAME "${TESTBUILDNAME}")
+enable_testing()
+include(CTest)
+
+set(MTL_IS_CONFIGURED True) # impede double double configuration in libs
+add_subdirectory(libs)	

AMDiS/lib/mtl4/CTestConfig.cmake

+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   ENABLE_TESTING()
+##   INCLUDE(CTest)
+set(CTEST_PROJECT_NAME "mtl4")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 CEST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "simunova.zih.tu-dresden.de")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=mtl4")
+set(CTEST_DROP_SITE_CDASH TRUE)
+# set(CTEST_CURL_OPTIONS "CURLOPT_SSL_VERIFYPEER_OFF")
+
+# build in parallel if not on Windows
+# if (NOT MSVC)
+#   message("now with make -j4")
+#   set(CTEST_BUILD_FLAGS -j4)
+# endif()
+
+while (${CTEST_ELAPSED_TIME} LESS 36)
+    set (START_TIME ${CTEST_ELAPSED_TIME})
+  ctest_start (Continuous)
+   ctest_sleep( ${START_TIME} 3 ${CTEST_ELAPSED_TIME})
+endwhile()

AMDiS/lib/mtl4/INSTALL

+-*- text -*-
+
+Software License for MTL
+
+Copyright (c) 2007-2008 The Trustees of Indiana University. 
+              2008 Dresden University of Technology and the Trustees of Indiana University.
+              2010 SimuNova UG, www.simunova.com. 
+All rights reserved.
+Authors: Peter Gottschling and Andrew Lumsdaine
+
+This file is part of the Matrix Template Library
+
+See also tools/license/license.mtl.txt in the distribution.
+---------------------------------------------------------------
+
+              The Matrix Template Library
+                     Version 4
+
+
+I. Installation
+===============
+
+see http://www.simunova.com/node/189

AMDiS/lib/mtl4/MTLConfig.cmake

+set(MTL_COMMON_CONFIG "${MTL_DIR}/tools/cmake/MTLCommon.cmake")
+if( EXISTS ${MTL_COMMON_CONFIG})
+	include(${MTL_COMMON_CONFIG})
+else()
+	message(ERROR "could not find the common mtl configuration. this is possibly a wrong installation of mtl.")
+endif()

AMDiS/lib/mtl4/README

+-*- text -*-
+
+Software License for MTL
+
+Copyright (c) 2007-2008 The Trustees of Indiana University. All rights reserved.
+Authors: Peter Gottschling and Andrew Lumsdaine
+
+This file is part of the Matrix Template Library
+
+See also license.mtl.txt in the distribution.
+---------------------------------------------------------------
+
+              The Matrix Template Library
+                      Version 4 
+
+I. Introduction
+===============
+
+The Matrix Template Library is a C++ class library for basic linear
+algebra. The MTL is designed for high-performance while at the same
+time taking advantage of the generic programming paradigm (ala the
+STL) to allow much greater flexibility and breadth of
+functionality. Many new and advanced programming techniques were used
+in the construction of this library.
+
+The MTL is a low level library in the sense that the user must be
+conscious of the matrix type being used, and that all computationally
+expensive operations are explicit. The MTL is not a C++ Matlab or
+Mathematica. Nevertheless, the interface is designed to be simple and easy
+to use.
+
+The matrix types provided include compressed sparse row/column,
+traditional row- and column-major dense, Morton-order, and block-recursive
+matrices. All matrix types share a common and easy to use interface.
+
+The algorithms consist of the traditional basic linear algebra
+routines (from the BLAS level-1 to 3) which includes matrix and vector
+arithmetic.
+
+
+II. Compilers
+=============
+
+The Matrix Template Library is written in compliance with the C++ standard
+and should be compilable with every compiler compliant with the standard.
+It has been tested (and passed) with the following compilers and architectures:
+
+Linux & MacOS
+-------------
+    clang++ 3.0 (32 bit)
+    g++ 4.1.3 (32 and 64 bit)
+    g++ 4.2.4 (64bit)
+    g++ 4.3.4 (32 and 64 bit)
+    g++ 4.4.3 (32 and 64 bit)
+    g++ 4.5.1 (64 bit)
+    g++ 4.6.0 (64 bit)
+    g++ 4.6.1 (64 bit)
+    icc 9.1 (32 and 64 bit)
+    icc 10.0 (32 and 64 bit)
+    icc 10.1 (32 and 64 bit)
+    icc 11.0 (32 and 64 bit)
+    icc 11.1 (32 and 64 bit)
+
+Windows
+-------
+    VC 8.0 from Visual Studio 2005 (32 bit)
+    VC 9.0 from Visual Studio 2008 (32 bit)
+    VC 10.0 from Visual Studio 2010 (32 bit)
+
+Compilers that are not standard-compliant (e.g. VC 6.0 from VS 2003) are not subject to support.
+
+
+III. Documentation
+==================
+
+The documentation can be generated with doxygen in the main directory and
+is found in the /libs/numeric/mtl/doc. You
+can also view the documentation at our web site:
+http://www.simunova.com/node/184
+At the moment, the documentation illustrates the basic operations and
+partially provides a reference manual of some classes and functions.
+A detailed description of more features, especially tuning opportunities,
+is in the works.
+
+There are also a large number of examples in the /libs/numeric/mtl/examples
+directory.
+
+
+IV. Installation Procedure
+==========================
+
+See the file INSTALL in this directory.
+
+
+
+V. Contact Information
+=======================
+
+The Matrix Template Library is available at the main distribution site:
+
+    http://www.mtl4.org
+
+This distribution includes:
+
+    - Source code for the MTL (all header files /boost/numeric/mtl)
+    - Some completing sources (header files /boost/numeric/meta_math)
+    - A test suite (/libs/numeric/mtl/test)
+    - Some example code (/libs/numeric/mtl/examples)
+
+Bug reports should be sent to mtl4@osl.iu.edu.
+
+Questions, comments, suggestions, and requests for additional
+information should also be directed to mtl4@osl.iu.edu.
+
+Subscribe at:
+
+     http://www.osl.iu.edu/mailman/listinfo.cgi/mtl4

AMDiS/lib/mtl4/SConstruct

+import getopt, sys, os, os.path, re, string
+
+######################
+# Helper functions
+######################
+
+# platform-dependent preprocessor definitions
+def macro_flag(env, flag):
+    if sys.platform == 'win32' and conf.env['CC'] == 'cl':
+        return '/D' + flag
+    else:
+        return '-D' + flag    
+
+# add debugging flags to environment
+def add_debug(env):
+    if sys.platform == 'win32' and conf.env['CC'] == 'cl':
+        env.Append(CCFLAGS = '/Z7')
+        env.Append(CCFLAGS = '/MDd')
+    else:
+        env.Append(CCFLAGS = '-g')
+    #print macro_flag(env, 'MTL_ASSERT_FOR_THROW')
+    env.Append(CCFLAGS = macro_flag(env, 'MTL_ASSERT_FOR_THROW'))
+   
+
+def check_g5():
+    print "platform ", sys.platform
+    if sys.platform == "darwin" :
+
+	system("/usr/bin/system_profiler SPHardwareDataType")
+	profile = os.popen("system_profiler SPHardwareDataType").read()
+	print profile
+	if profile.find("Mac G5") != -1:
+	    print "is G5"
+	    return 1
+    print "isn't G5"
+    return None
+
+
+def add_platform_flags(env):
+    if env['CC'] == 'cl':
+        # Turn off some warnings: 1. for problems with CRTP 2. with VC's own headers 
+        #                         3. alleged ambiguos assignment
+        # I hope we find a cleaner way to get rid of this warning
+        wd = ' /wd4355 /wd4996 /wd4522'
+        env.Append(CCFLAGS = '/EHa /D_CONSOLE /D_CRT_SECURE_NO_DEPRECATE /DNOMINMAX' +
+			     ' /D_SECURE_SCL=0' + wd)
+
+        # The following two if shouldn't be necessary
+        # Note that INCLUDE must be split and LIB must not :-P
+        if os.environ.has_key('INCLUDE') :
+            for p in os.environ['INCLUDE'].split(';'):
+                env.Append(CPPPATH = p)
+        if os.environ.has_key('LIB') :
+            env.Append(LIBPATH = os.environ['LIB'])
+
+
+# add optimization flags to environment
+# normal optimization for opt=1, for opt=2 high optimization
+# at the moment additional flags are added in this function
+# -> this needs to be cleaned up!
+def add_opt(env, opt):
+    if int(opt):
+        env.Append(CCFLAGS = macro_flag(env, 'NDEBUG'))
+    if sys.platform == 'win32' and conf.env['CC'] == 'cl':
+        if int(opt) == 1:
+            env.Append(CCFLAGS = '/O2 /Ot /Ob2')
+        elif int(opt) == 2:
+            env.Append(CCFLAGS = '/Ox')
+            env.Append(CCFLAGS = '/MD')
+    else:
+        if int(opt) == 2:
+    	    env.Append(CCFLAGS = '-O3')
+    	    if conf.env['CC'] == 'gcc':
+    	        env.Append(CCFLAGS = '-ffast-math')
+    	        #check_g5()
+            # env.Append(CCFLAGS = '-pg') # for profiling
+    	    # env.Append(LINKFLAGS = '-pg') # for profiling
+        elif int(opt) == 1:
+    	    env.Append(CCFLAGS = '-O2')
+            # env.Append(CCFLAGS = '-pg') # for profiling
+    	    # env.Append(LINKFLAGS = '-pg') # for profiling
+        
+    if env['CC'] != 'cl':
+        env.Append(CXXFLAGS = conf.env['CCFLAGS'])
+	
+
+def check_no_long_double(conf):
+    cc = conf.env['CC']
+    if cc == 'gcc':
+        # conf.env.Append(CXXFLAGS = '-Werror -Wreorder -pedantic -Wpointer-arith -Wcast-align -Wcast-qual -Wwrite-strings')
+	output = os.popen(cc + " --version").read()
+	st = output.split('\n')[0]
+	tmatch = re.search(".* \(GCC\) (\d\.\d)", st)
+	if tmatch and string.atof(tmatch.group(1)) == 4.0:
+	    conf.env.Append(CCFLAGS = '-Wno-long-double')
+	    # conf.env.Append(CXXFLAGS = '-Wno-long-double')
+
+
+def add_user_opt(env, add_optflag):
+     env.Append(CCFLAGS = add_optflag)
+     env.Append(CXXFLAGS = add_optflag)
+
+###############################
+# check for installed blas ...
+# search different libraries
+###############################
+def detected_blas(env): # blas library found
+   env.Append(CPPDEFINES = 'MTL_HAS_BLAS')
+
+def check_for_blas(env):
+ # symbolname
+ symname = 'dgemm_'
+ found_blas = 0
+
+ # get command line blas path
+ blas_path = ARGUMENTS.get('blas_path', '')
+ if blas_path:
+   print 'adding ' + blas_path + ' to LIBPATH.'
+   env.Append(LIBPATH = [ blas_path, blas_path + '/lib/' ])
+ 
+ # extra linker flags for blas
+ blas_ldflags = ARGUMENTS.get('blas_ldflags', '')
+ if blas_ldflags:
+   env.Append(_LIBFLAGS=blas_ldflags.split())
+
+ # get command line blas lib
+ blas_lib = ARGUMENTS.get('blas_lib', '')
+ if blas_lib:
+   myenv = env.Copy()
+   conf = Configure(myenv)
+   # check supplied lib
+   print "Checking for lib " + blas_lib + "..."
+   if conf.CheckLib(blas_lib, symname):
+     myenv = conf.Finish()
+     detected_blas(myenv)
+     myenv.Append(LIBS=[blas_lib])
+     return myenv
+ else:
+   print "Autodetecting BLAS support. See config.log for details!"
+     
+   ########################
+   # check for acml
+   myenv = env.Copy()
+   # new configure object
+   conf = Configure(myenv)
+   # additional libs needed for acml
+   myenv.Append(LIBS=['m', 'g2c'])
+   if conf.CheckLib('acml', symname):
+     detected_blas(myenv)
+     found_blas = 1
+   myenv = conf.Finish()
+   if(found_blas == 1):
+     return myenv
+  
+   ########################
+   # check for goto
+   myenv = env.Copy()
+   # new configure object
+   conf = Configure(myenv)
+   # additional libs needed for goto
+   myenv.Append(LIBS=['pthread'])
+   # extra linker flags for libgoto
+   # myenv.Append(_LIBFLAGS=['libs/numeric/mtl/build/xerbla.c'])
+   myenv.Append(_LIBFLAGS=['libs/numeric/mtl/build/xerbla.o']) # not portable !!! 
+   # myenv.Library('build/xerbla', 'build/xerbla.c')
+   # myenv.Append(LIBS=['xerbla'])
+   # myenv.Append(LIBPATH=['build'])
+
+   if conf.CheckLib('goto', symname) or conf.CheckLib('goto_opteron-64', symname) or \
+      conf.CheckLib('goto_coppermine-32', symname) or conf.CheckLib('goto_opteron-32', symname) or \
+      conf.CheckLib('goto_itanium2-64', symname) or conf.CheckLib('goto_katmai-32', symname) or \
+      conf.CheckLib('goto_northwood-32', symname) or conf.CheckLib('goto_prescott-32', symname) or \
+      conf.CheckLib('goto_prescott-64', symname):
+     detected_blas(myenv)
+     found_blas = 1
+   myenv = conf.Finish()
+   if(found_blas == 1):
+     return myenv
+  
+   ########################
+   # check for ATLAS
+   myenv = env.Copy()
+   # new configure object
+   conf = Configure(myenv)
+   # additional libs needed for goto
+   myenv.Append(LIBS=['f77blas', 'g2c'])
+   if conf.CheckLib('atlas', symname):
+     detected_blas(myenv)
+     found_blas = 1
+   myenv = conf.Finish()
+   if(found_blas == 1):
+     return myenv
+
+ return env
+ 
+
+ 
+###################################
+# Add UMFPACK (extremely simplistic)
+###################################
+
+def detected_umfpack(env): # umfpack library found
+   env.Append(CPPDEFINES = 'MTL_HAS_UMFPACK')
+
+def check_for_umfpack(env):
+ ufconfig_path = ARGUMENTS.get('ufconfig_path', '')
+ if ufconfig_path:
+   env.Prepend(CPPPATH = [ ufconfig_path ])
+ else:
+   print "UMFPACK only works with the UFconfig library."
+   print "Provide ufconfig_path."
+   print "Building continued without UMFPACK."
+   return env
+
+ amd_path = ARGUMENTS.get('amd_path', '')
+ if amd_path:
+   # print 'adding ' + amd_path + '/Lib to LIBPATH.'
+   env.Append(LIBPATH = [ amd_path + '/Lib' ])
+   #print 'adding ' + amd_path + '/Include to CPPPATH.'
+   env.Prepend(CPPPATH = [ amd_path + '/Include' ])
+   env.Prepend(LIBS=['amd'])
+   # print "nachher: ", env['CPPPATH']
+ else:
+   print "UMFPACK only works with the AMD library."
+   print "Provide amd_path."
+   print "Building continued without UMFPACK."
+   return env
+
+ # get command line umfpack path
+ umfpack_path = ARGUMENTS.get('umfpack_path', '')
+ if umfpack_path:
+   # print 'adding ' + umfpack_path + '/Lib to LIBPATH.'
+   env.Prepend(LIBPATH = [ umfpack_path + '/Lib' ])
+   env.Prepend(LIBS=['umfpack'])
+   # print 'adding ' + umfpack_path + '/Include to CPPPATH.'
+   env.Append(CPPPATH = [ umfpack_path + '/Include' ])
+   detected_umfpack(env)
+   return env
+ 
+
+
+
+######################
+# Start setting up env
+######################
+
+
+SourceSignatures('timestamp')
+
+env = Environment()
+# env.Decider('timestamp-newer')
+
+conf = Configure(env)
+check_no_long_double(conf)
+env = conf.Finish()
+
+# Search only for BLAS when explicitly asked for
+with_blas = ARGUMENTS.get('with_blas', 0)
+if int(with_blas):
+    env = check_for_blas(env)
+
+# Search only for UMFPACK when explicitly asked for
+with_umfpack = ARGUMENTS.get('with_umfpack', 0)
+if int(with_umfpack):
+    env = check_for_umfpack(env)
+
+
+
+
+######################
+# Include paths
+######################
+
+
+my_cpppath = []
+if os.environ.has_key('MTL_BOOST_ROOT') :
+    mtlp = os.environ['MTL_BOOST_ROOT']
+    my_cpppath.append(mtlp)
+if os.environ.has_key('BOOST_ROOT') :
+    my_cpppath.append(os.environ['BOOST_ROOT'])
+
+# In branches, the current directory is prepended
+pwd = os.getcwd()
+if not os.environ.has_key('MTL_BOOST_ROOT') \
+or not hasattr(os.path, 'samefile') or not os.path.samefile(pwd, mtlp):
+     my_cpppath = [pwd] + my_cpppath
+
+# Add directory of extern libraries if exist
+# Not needed currently
+#if os.path.exists('extern'):
+#    my_cpppath.append(os.path.abspath('extern'))
+
+env.Append(CPPPATH = my_cpppath)
+
+# Hack to select compiler explicitly
+# env['CXX'] = 'g++-4.1'
+
+
+######################
+# Opt. and debug flags
+######################
+
+
+opts = Options()
+opts.Add('opt', 'Set to 1 for normal optimization, 2 for high optimization', 0)
+opts.Add('debug', 'Set to 1 for debugging', 0)
+opts.Add('check', 'Set to 1 if test programs shall be ran', 0)
+opts.Add('with_concepts', 'Set to 1 if test programs shall be compiled with conceptg++ (must be in ~/bin)', 0)
+opts.Add('full_warnings', 'Set to 1 to turn on all possible warnings and transform into errors (currently only gcc)', 0)
+
+
+opts.Add('add_ccflag', 'Add extra CC compiler flags that aren\'t automatically set', '')
+opts.Add('add_cxxflag', 'Add extra CXX compiler flags that aren\'t automatically set', '')
+opts.Add('add_optflag', 'Add extra optimization flags that aren\'t automatically set', '')
+
+############
+# BLAS flags
+############
+
+opts.Add('with_blas', 'Link with BLAS (have to given each time :-( until we can save configurations)', 0)
+opts.Add('blas_path', 'Add path of blas library', '')
+opts.Add('blas_lib', 'Add name of blas library', '')
+opts.Add('blas_ldflags', 'Add LDFLAGS for blas library', '')
+
+############
+# UMFPACK flags
+############
+opts.Add('with_umfpack', 'Use UMFPACK. Needs umfpack_path and amd_path.', 0)
+opts.Add('umfpack_path', 'Add path of UMFPACK library', '')
+opts.Add('amd_path', 'Add path of AMD library', '')
+opts.Add('ufconfig_path', 'Add path of AMD library', '')
+