xref: /petsc/config/PETSc/Configure.py (revision 5a21677cedc224e81ae6124df68302f07818b768)

import config.base

import os
import sys
import re
import cPickle
import string

# The sorted() builtin is not available with python-2.3
try: sorted
except NameError:
  def sorted(lst):
    lst.sort()
    return lst

class Configure(config.base.Configure):
  def __init__(self, framework):
    config.base.Configure.__init__(self, framework)
    self.headerPrefix = 'PETSC'
    self.substPrefix  = 'PETSC'
    self.installed = 0 # 1 indicates that Configure itself has already compiled and installed PETSc
    return

  def __str2__(self):
    desc = []
    if not self.installed:
      desc.append('xxx=========================================================================xxx')
      if self.make.getMakeMacro('MAKE_IS_GNUMAKE'):
        build_type = 'gnumake build'
      elif self.getMakeMacro('PETSC_BUILD_USING_CMAKE'):
        build_type = 'cmake build'
      else:
        build_type = 'legacy build'
      desc.append(' Configure stage complete. Now build PETSc libraries with (%s):' % build_type)
      desc.append('   make PETSC_DIR='+self.petscdir.dir+' PETSC_ARCH='+self.arch.arch+' all')
      desc.append('xxx=========================================================================xxx')
    else:
      desc.append('xxx=========================================================================xxx')
      desc.append(' Installation complete. You do not need to run make to compile or install the software')
      desc.append('xxx=========================================================================xxx')
    return '\n'.join(desc)+'\n'

  def setupHelp(self, help):
    import nargs
    help.addArgument('PETSc',  '-prefix=<dir>',                   nargs.Arg(None, '', 'Specifiy location to install PETSc (eg. /usr/local)'))
    help.addArgument('PETSc',  '-with-prefetch=<bool>',           nargs.ArgBool(None, 1,'Enable checking for prefetch instructions'))
    help.addArgument('Windows','-with-windows-graphics=<bool>',   nargs.ArgBool(None, 1,'Enable check for Windows Graphics'))
    help.addArgument('PETSc', '-with-default-arch=<bool>',        nargs.ArgBool(None, 1, 'Allow using the last configured arch without setting PETSC_ARCH'))
    help.addArgument('PETSc','-with-single-library=<bool>',       nargs.ArgBool(None, 1,'Put all PETSc code into the single -lpetsc library'))
    help.addArgument('PETSc','-with-fortran-bindings=<bool>',     nargs.ArgBool(None, 1,'Build PETSc fortran bindings in the library and corresponding module files'))
    help.addArgument('PETSc', '-with-ios=<bool>',              nargs.ArgBool(None, 0, 'Build an iPhone/iPad version of PETSc library'))
    help.addArgument('PETSc', '-with-xsdk-defaults', nargs.ArgBool(None, 0, 'Set the following as defaults for the xSDK standard: --enable-debug=1, --enable-shared=1, --with-precision=double, --with-index-size=32, locate blas/lapack automatically'))
    help.addArgument('PETSc', '-known-has-attribute-aligned=<bool>',nargs.ArgBool(None, None, 'Indicates __attribute((aligned(16)) directive works (the usual test will be skipped)'))
    help.addArgument('PETSc','-with-viewfromoptions=<bool>',      nargs.ArgBool(None, 1,'Support XXXSetFromOptions() calls, for calls with many small solvers turn this off'))
    help.addArgument('PETSc', '-with-display=<x11display>',       nargs.Arg(None, '', 'Specifiy DISPLAY env variable for use with matlab test)'))
    return

  def registerPythonFile(self,filename,directory):
    ''' Add a python file to the framework and registers its headerprefix, ... externalpackagedir
        directory is the directory where the file relative to the BuildSystem or config path in python notation with . '''
    (utilityName, ext) = os.path.splitext(filename)
    if not utilityName.startswith('.') and not utilityName.startswith('#') and ext == '.py' and not utilityName == '__init__':
      if directory: directory = directory+'.'
      utilityObj                             = self.framework.require(directory+utilityName, self)
      utilityObj.headerPrefix                = self.headerPrefix
      utilityObj.archProvider                = self.arch
      utilityObj.languageProvider            = self.languages
      utilityObj.installDirProvider          = self.installdir
      utilityObj.externalPackagesDirProvider = self.externalpackagesdir
      utilityObj.precisionProvider           = self.scalartypes
      utilityObj.indexProvider               = self.indexTypes
      setattr(self, utilityName.lower(), utilityObj)
      return utilityObj
    return None

  def setupDependencies(self, framework):
    config.base.Configure.setupDependencies(self, framework)
    self.programs      = framework.require('config.programs',           self)
    self.setCompilers  = framework.require('config.setCompilers',       self)
    self.compilers     = framework.require('config.compilers',          self)
    self.arch          = framework.require('PETSc.options.arch',        self.setCompilers)
    self.petscdir      = framework.require('PETSc.options.petscdir',    self.arch)
    self.installdir    = framework.require('PETSc.options.installDir',  self)
    self.scalartypes   = framework.require('PETSc.options.scalarTypes', self)
    self.indexTypes    = framework.require('PETSc.options.indexTypes',  self)
    self.languages     = framework.require('PETSc.options.languages',   self.setCompilers)
    self.debugging     = framework.require('PETSc.options.debugging',   self.compilers)
    self.indexTypes    = framework.require('PETSc.options.indexTypes',  self.compilers)
    self.compilers     = framework.require('config.compilers',          self)
    self.types         = framework.require('config.types',              self)
    self.headers       = framework.require('config.headers',            self)
    self.functions     = framework.require('config.functions',          self)
    self.libraries     = framework.require('config.libraries',          self)
    self.atomics       = framework.require('config.atomics',            self)
    self.make          = framework.require('config.packages.make',      self)
    self.blasLapack    = framework.require('config.packages.BlasLapack',self)
    self.cmake         = framework.require('config.packages.cmake',self)
    self.externalpackagesdir = framework.require('PETSc.options.externalpackagesdir',self)
    self.mpi           = framework.require('config.packages.MPI',self)

    for utility in sorted(os.listdir(os.path.join('config','PETSc','options'))):
      self.registerPythonFile(utility,'PETSc.options')

    for utility in sorted(os.listdir(os.path.join('config','BuildSystem','config','utilities'))):
      self.registerPythonFile(utility,'config.utilities')

    for package in sorted(os.listdir(os.path.join('config', 'BuildSystem', 'config', 'packages'))):
      obj = self.registerPythonFile(package,'config.packages')
      if obj:
        obj.archProvider                = self.framework.requireModule(obj.archProvider, obj)
        obj.languageProvider            = self.framework.requireModule(obj.languageProvider, obj)
        obj.installDirProvider          = self.framework.requireModule(obj.installDirProvider, obj)
        obj.externalPackagesDirProvider = self.framework.requireModule(obj.externalPackagesDirProvider, obj)
        obj.precisionProvider           = self.framework.requireModule(obj.precisionProvider, obj)
        obj.indexProvider               = self.framework.requireModule(obj.indexProvider, obj)

    # Force blaslapack and opencl to depend on scalarType so precision is set before BlasLapack is built
    framework.require('PETSc.options.scalarTypes', self.f2cblaslapack)
    framework.require('PETSc.options.scalarTypes', self.fblaslapack)
    framework.require('PETSc.options.scalarTypes', self.blaslapack)
    framework.require('PETSc.options.scalarTypes', self.opencl)
    framework.require('PETSc.Regression', self)

    self.programs.headerPrefix   = self.headerPrefix
    self.compilers.headerPrefix  = self.headerPrefix
    self.types.headerPrefix      = self.headerPrefix
    self.headers.headerPrefix    = self.headerPrefix
    self.functions.headerPrefix  = self.headerPrefix
    self.libraries.headerPrefix  = self.headerPrefix

    # Look for any user provided --download-xxx=directory packages
    for arg in sys.argv:
      if arg.startswith('--download-') and arg.find('=') > -1:
        pname = arg[11:arg.find('=')]
        if not hasattr(self,pname):
          dname = os.path.dirname(arg[arg.find('=')+1:])
          if os.path.isdir(dname) and not os.path.isfile(os.path.join(dname,pname+'.py')):
            self.framework.logPrint('User is registering a new package: '+arg)
            sys.path.append(dname)
            self.registerPythonFile(pname+'.py','')

    # test for a variety of basic headers and functions
    headersC = map(lambda name: name+'.h', ['setjmp','dos', 'endian', 'fcntl', 'float', 'io', 'limits', 'malloc', 'pwd', 'search', 'strings',
                                            'unistd', 'sys/sysinfo', 'machine/endian', 'sys/param', 'sys/procfs', 'sys/resource',
                                            'sys/systeminfo', 'sys/times', 'sys/utsname','string', 'stdlib',
                                            'sys/socket','sys/wait','netinet/in','netdb','Direct','time','Ws2tcpip','sys/types',
                                            'WindowsX', 'cxxabi','float','ieeefp','stdint','sched','pthread','inttypes','immintrin','zmmintrin'])
    functions = ['access', '_access', 'clock', 'drand48', 'getcwd', '_getcwd', 'getdomainname', 'gethostname',
                 'gettimeofday', 'getwd', 'memalign', 'mkstemp', 'popen', 'PXFGETARG', 'rand', 'getpagesize',
                 'readlink', 'realpath',  'sigaction', 'signal', 'sigset', 'usleep', 'sleep', '_sleep', 'socket',
                 'times', 'gethostbyname', 'uname','snprintf','_snprintf','lseek','_lseek','time','fork','stricmp',
                 'strcasecmp', 'bzero', 'dlopen', 'dlsym', 'dlclose', 'dlerror','get_nprocs','sysctlbyname',
                 '_set_output_format','_mkdir']
    libraries1 = [(['socket', 'nsl'], 'socket'), (['fpe'], 'handle_sigfpes')]
    self.headers.headers.extend(headersC)
    self.functions.functions.extend(functions)
    self.libraries.libraries.extend(libraries1)

    return

  def DumpPkgconfig(self):
    ''' Create a pkg-config file '''
    if not os.path.exists(os.path.join(self.petscdir.dir,self.arch.arch,'lib','pkgconfig')):
      os.makedirs(os.path.join(self.petscdir.dir,self.arch.arch,'lib','pkgconfig'))
    fd = open(os.path.join(self.petscdir.dir,self.arch.arch,'lib','pkgconfig','PETSc.pc'),'w')
    cflags_inc = ['-I${includedir}']
    if self.framework.argDB['prefix']:
      fd.write('prefix='+self.installdir.dir+'\n')
    else:
      fd.write('prefix='+self.petscdir.dir+'\n')
      cflags_inc.append('-I' + os.path.join('${prefix}', self.arch.arch, 'include'))
    fd.write('exec_prefix=${prefix}\n')
    fd.write('includedir=${prefix}/include\n')
    fd.write('libdir=${prefix}/lib\n')

    self.setCompilers.pushLanguage('C')
    fd.write('ccompiler='+self.setCompilers.getCompiler()+'\n')
    fd.write('cflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
    fd.write('cflags_dep='+self.compilers.dependenciesGenerationFlag.get('C','')+'\n')
    fd.write('ldflag_rpath='+self.setCompilers.CSharedLinkerFlag+'\n')
    self.setCompilers.popLanguage()
    if hasattr(self.compilers, 'C++'):
      self.setCompilers.pushLanguage('C++')
      fd.write('cxxcompiler='+self.setCompilers.getCompiler()+'\n')
      fd.write('cxxflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
      self.setCompilers.popLanguage()
    if hasattr(self.compilers, 'FC'):
      self.setCompilers.pushLanguage('FC')
      fd.write('fcompiler='+self.setCompilers.getCompiler()+'\n')
      fd.write('fflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
      self.setCompilers.popLanguage()

    fd.write('\n')
    fd.write('Name: PETSc\n')
    fd.write('Description: Library to solve ODEs and algebraic equations\n')
    fd.write('Version: %s\n' % self.petscdir.version)
    fd.write('Cflags: ' + ' '.join([self.setCompilers.CPPFLAGS] + cflags_inc) + '\n')
    fd.write('Libs: '+self.libraries.toStringNoDupes(['-L${libdir}', self.petsclib], with_rpath=False)+'\n')
    # Remove RPATH flags from library list.  User can add them using
    # pkg-config --variable=ldflag_rpath and pkg-config --libs-only-L
    fd.write('Libs.private: '+self.libraries.toStringNoDupes([f for f in self.packagelibs+self.complibs if not f.startswith(self.setCompilers.CSharedLinkerFlag)], with_rpath=False)+'\n')

    fd.close()
    return

  def DumpModule(self):
    ''' Create a module file '''
    if not os.path.exists(os.path.join(self.petscdir.dir,self.arch.arch,'lib','petsc','conf','modules')):
      os.makedirs(os.path.join(self.petscdir.dir,self.arch.arch,'lib','petsc','conf','modules'))
    if not os.path.exists(os.path.join(self.petscdir.dir,self.arch.arch,'lib','petsc','conf','modules','petsc')):
      os.makedirs(os.path.join(self.petscdir.dir,self.arch.arch,'lib','petsc','conf','modules','petsc'))
    if self.framework.argDB['prefix']:
      installdir  = self.installdir.dir
      installarch = ''
      installpath = os.path.join(installdir,'bin')
    else:
      installdir  = self.petscdir.dir
      installarch = self.arch.arch
      installpath = os.path.join(installdir,installarch,'bin')+':'+os.path.join(installdir,'bin')
    fd = open(os.path.join(self.petscdir.dir,self.arch.arch,'lib','petsc','conf','modules','petsc',self.petscdir.version),'w')
    fd.write('''\
#%%Module

proc ModulesHelp { } {
    puts stderr "This module sets the path and environment variables for petsc-%s"
    puts stderr "     see http://www.mcs.anl.gov/petsc/ for more information      "
    puts stderr ""
}
module-whatis "PETSc - Portable, Extensible Toolkit for Scientific Computation"

set petsc_dir   "%s"
set petsc_arch  "%s"

setenv PETSC_ARCH "$petsc_arch"
setenv PETSC_DIR "$petsc_dir"
prepend-path PATH "%s"
''' % (self.petscdir.version, installdir, installarch, installpath))
    fd.close()
    return

  def Dump(self):
    ''' Actually put the values into the configuration files '''
    # eventually everything between -- should be gone
    if self.mpi.usingMPIUni:
      #
      # Remove any MPI/MPICH include files that may have been put here by previous runs of ./configure
      self.executeShellCommand('rm -rf  '+os.path.join(self.petscdir.dir,self.arch.arch,'include','mpi*')+' '+os.path.join(self.petscdir.dir,self.arch.arch,'include','opa*'), log = self.log)

    self.setCompilers.pushLanguage('C')
    compiler = self.setCompilers.getCompiler()
    if compiler.endswith('mpicc') or compiler.endswith('mpiicc'):
      try:
        output   = self.executeShellCommand(compiler + ' -show', log = self.log)[0]
        compiler = output.split(' ')[0]
        self.addDefine('MPICC_SHOW','"'+output.strip().replace('\n','\\\\n')+'"')
      except:
        self.addDefine('MPICC_SHOW','"Unavailable"')
    else:
      self.addDefine('MPICC_SHOW','"Unavailable"')
    self.setCompilers.popLanguage()
#-----------------------------------------------------------------------------------------------------

    # Sometimes we need C compiler, even if built with C++
    self.setCompilers.pushLanguage('C')
    self.addMakeMacro('CC_FLAGS',self.setCompilers.getCompilerFlags())
    self.setCompilers.popLanguage()

    # And sometimes we need a C++ compiler even when PETSc is built with C
    if hasattr(self.compilers, 'CXX'):
      self.setCompilers.pushLanguage('Cxx')
      self.addDefine('HAVE_CXX','1')
      self.addMakeMacro('CXX_FLAGS',self.setCompilers.getCompilerFlags())
      cxx_linker = self.setCompilers.getLinker()
      self.addMakeMacro('CXX_LINKER',cxx_linker)
      self.addMakeMacro('CXX_LINKER_FLAGS',self.setCompilers.getLinkerFlags())
      self.setCompilers.popLanguage()

    # C preprocessor values
    self.addMakeMacro('CPP_FLAGS',self.setCompilers.CPPFLAGS)

    # compiler values
    self.setCompilers.pushLanguage(self.languages.clanguage)
    self.addMakeMacro('PCC',self.setCompilers.getCompiler())
    self.addMakeMacro('PCC_FLAGS',self.setCompilers.getCompilerFlags())
    self.setCompilers.popLanguage()
    # .o or .obj
    self.addMakeMacro('CC_SUFFIX','o')

    # executable linker values
    self.setCompilers.pushLanguage(self.languages.clanguage)
    pcc_linker = self.setCompilers.getLinker()
    self.addMakeMacro('PCC_LINKER',pcc_linker)
    self.addMakeMacro('PCC_LINKER_FLAGS',self.setCompilers.getLinkerFlags())
    self.setCompilers.popLanguage()
    # '' for Unix, .exe for Windows
    self.addMakeMacro('CC_LINKER_SUFFIX','')

    if hasattr(self.compilers, 'FC'):
      if self.framework.argDB['with-fortran-bindings']:
        self.addDefine('HAVE_FORTRAN','1')
      self.setCompilers.pushLanguage('FC')
      # need FPPFLAGS in config/setCompilers
      self.addMakeMacro('FPP_FLAGS',self.setCompilers.CPPFLAGS)

      # compiler values
      self.addMakeMacro('FC_FLAGS',self.setCompilers.getCompilerFlags())
      self.setCompilers.popLanguage()
      # .o or .obj
      self.addMakeMacro('FC_SUFFIX','o')

      # executable linker values
      self.setCompilers.pushLanguage('FC')
      # Cannot have NAG f90 as the linker - so use pcc_linker as fc_linker
      fc_linker = self.setCompilers.getLinker()
      if config.setCompilers.Configure.isNAG(fc_linker, self.log):
        self.addMakeMacro('FC_LINKER',pcc_linker)
      else:
        self.addMakeMacro('FC_LINKER',fc_linker)
      self.addMakeMacro('FC_LINKER_FLAGS',self.setCompilers.getLinkerFlags())
      # apple requires this shared library linker flag on SOME versions of the os
      if self.setCompilers.getLinkerFlags().find('-Wl,-commons,use_dylibs') > -1:
        self.addMakeMacro('DARWIN_COMMONS_USE_DYLIBS',' -Wl,-commons,use_dylibs ')
      self.setCompilers.popLanguage()

      # F90 Modules
      if self.setCompilers.fortranModuleIncludeFlag:
        self.addMakeMacro('FC_MODULE_FLAG', self.setCompilers.fortranModuleIncludeFlag)
      else: # for non-f90 compilers like g77
        self.addMakeMacro('FC_MODULE_FLAG', '-I')
      if self.setCompilers.fortranModuleIncludeFlag:
        self.addMakeMacro('FC_MODULE_OUTPUT_FLAG', self.setCompilers.fortranModuleOutputFlag)
    else:
      self.addMakeMacro('FC','')

    if hasattr(self.compilers, 'CUDAC'):
      self.setCompilers.pushLanguage('CUDA')
      self.addMakeMacro('CUDAC_FLAGS',self.setCompilers.getCompilerFlags())
      self.setCompilers.popLanguage()

    # shared library linker values
    self.setCompilers.pushLanguage(self.languages.clanguage)
    # need to fix BuildSystem to collect these separately
    self.addMakeMacro('SL_LINKER',self.setCompilers.getLinker())
    self.addMakeMacro('SL_LINKER_FLAGS','${PCC_LINKER_FLAGS}')
    self.setCompilers.popLanguage()
    # One of 'a', 'so', 'lib', 'dll', 'dylib' (perhaps others also?) depending on the library generator and architecture
    # Note: . is not included in this macro, consistent with AR_LIB_SUFFIX
    if self.setCompilers.sharedLibraryExt == self.setCompilers.AR_LIB_SUFFIX:
      self.addMakeMacro('SL_LINKER_SUFFIX', '')
      self.addDefine('SLSUFFIX','""')
    else:
      self.addMakeMacro('SL_LINKER_SUFFIX', self.setCompilers.sharedLibraryExt)
      self.addDefine('SLSUFFIX','"'+self.setCompilers.sharedLibraryExt+'"')

    self.addMakeMacro('SL_LINKER_LIBS','${PETSC_EXTERNAL_LIB_BASIC}')

#-----------------------------------------------------------------------------------------------------

    # CONLY or CPP. We should change the PETSc makefiles to do this better
    if self.languages.clanguage == 'C': lang = 'CONLY'
    else: lang = 'CXXONLY'
    self.addMakeMacro('PETSC_LANGUAGE',lang)

    # real or complex
    self.addMakeMacro('PETSC_SCALAR',self.scalartypes.scalartype)
    # double or float
    self.addMakeMacro('PETSC_PRECISION',self.scalartypes.precision)

    if self.framework.argDB['with-batch']:
      self.addMakeMacro('PETSC_WITH_BATCH','1')

    # Test for compiler-specific macros that need to be defined.
    if self.setCompilers.isCrayVector('CC', self.log):
      self.addDefine('HAVE_CRAY_VECTOR','1')

#-----------------------------------------------------------------------------------------------------
    if self.functions.haveFunction('gethostbyname') and self.functions.haveFunction('socket') and self.headers.haveHeader('netinet/in.h'):
      self.addDefine('USE_SOCKET_VIEWER','1')
      if self.checkCompile('#include <sys/socket.h>','setsockopt(0,SOL_SOCKET,SO_REUSEADDR,0,0)'):
        self.addDefine('HAVE_SO_REUSEADDR','1')

#-----------------------------------------------------------------------------------------------------
    # print include and lib for makefiles
    self.framework.packages.reverse()
    petscincludes = [os.path.join(self.petscdir.dir,'include'),os.path.join(self.petscdir.dir,self.arch.arch,'include')]
    petscincludes_install = [os.path.join(self.installdir.dir, 'include')] if self.framework.argDB['prefix'] else petscincludes
    includes = []
    self.packagelibs = []
    for i in self.framework.packages:
      if i.useddirectly:
        self.addDefine('HAVE_'+i.PACKAGE.replace('-','_'), 1)  # ONLY list package if it is used directly by PETSc (and not only by another package)
      if not isinstance(i.lib, list):
        i.lib = [i.lib]
      if i.linkedbypetsc: self.packagelibs.extend(i.lib)
      self.addMakeMacro(i.PACKAGE.replace('-','_')+'_LIB', self.libraries.toStringNoDupes(i.lib))
      if hasattr(i,'include'):
        if not isinstance(i.include,list):
          i.include = [i.include]
        includes.extend(i.include)
        self.addMakeMacro(i.PACKAGE.replace('-','_')+'_INCLUDE',self.headers.toStringNoDupes(i.include))
    if self.framework.argDB['with-single-library']:
      self.petsclib = '-lpetsc'
    else:
      self.petsclib = '-lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys'
    self.complibs = self.compilers.flibs+self.compilers.cxxlibs+self.compilers.LIBS.split()
    self.PETSC_WITH_EXTERNAL_LIB = self.libraries.toStringNoDupes(['-L${PETSC_DIR}/${PETSC_ARCH}/lib', self.petsclib]+self.packagelibs+self.complibs)
    self.PETSC_EXTERNAL_LIB_BASIC = self.libraries.toStringNoDupes(self.packagelibs+self.complibs)
    if self.framework.argDB['prefix'] and self.setCompilers.CSharedLinkerFlag not in ['-L']:
      string.replace(self.PETSC_EXTERNAL_LIB_BASIC,self.setCompilers.CSharedLinkerFlag+os.path.join(self.petscdir.dir,self.arch.arch,'lib'),self.setCompilers.CSharedLinkerFlag+os.path.join(self.installdir.dir,'lib'))

    self.addMakeMacro('PETSC_EXTERNAL_LIB_BASIC',self.PETSC_EXTERNAL_LIB_BASIC)
    allincludes = petscincludes + includes
    allincludes_install = petscincludes_install + includes
    self.PETSC_CC_INCLUDES = self.headers.toStringNoDupes(allincludes)
    self.PETSC_CC_INCLUDES_INSTALL = self.headers.toStringNoDupes(allincludes_install)
    self.addMakeMacro('PETSC_CC_INCLUDES',self.PETSC_CC_INCLUDES)
    self.addMakeMacro('PETSC_CC_INCLUDES_INSTALL', self.PETSC_CC_INCLUDES_INSTALL)
    if hasattr(self.compilers, 'FC'):
      def modinc(includes):
        return includes if self.compilers.fortranIsF90 else []
      self.addMakeMacro('PETSC_FC_INCLUDES',self.headers.toStringNoDupes(allincludes,modinc(allincludes)))
      self.addMakeMacro('PETSC_FC_INCLUDES_INSTALL',self.headers.toStringNoDupes(allincludes_install,modinc(allincludes_install)))

    self.addDefine('LIB_DIR','"'+os.path.join(self.installdir.dir,'lib')+'"')

    if self.framework.argDB['with-single-library']:
      # overrides the values set in conf/variables
      self.addMakeMacro('LIBNAME','${INSTALL_LIB_DIR}/libpetsc.${AR_LIB_SUFFIX}')
      self.addMakeMacro('SHLIBS','libpetsc')
      self.addMakeMacro('PETSC_LIB_BASIC','-lpetsc')
      self.addMakeMacro('PETSC_KSP_LIB_BASIC','-lpetsc')
      self.addMakeMacro('PETSC_TS_LIB_BASIC','-lpetsc')
      self.addMakeMacro('PETSC_TAO_LIB_BASIC','-lpetsc')
      self.addMakeMacro('PETSC_WITH_EXTERNAL_LIB',self.PETSC_WITH_EXTERNAL_LIB)
      self.addDefine('USE_SINGLE_LIBRARY', '1')
      if self.sharedlibraries.useShared:
        self.addMakeMacro('PETSC_SYS_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_VEC_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_MAT_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_DM_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_KSP_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_SNES_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_TS_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_TAO_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_CHARACTERISTIC_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_LIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_CONTRIB','${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}')
      else:
        self.addMakeMacro('PETSC_SYS_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_VEC_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_MAT_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_DM_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_KSP_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_SNES_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_TS_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_TAO_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_CHARACTERISTIC_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_LIB','${PETSC_WITH_EXTERNAL_LIB}')
        self.addMakeMacro('PETSC_CONTRIB','${PETSC_WITH_EXTERNAL_LIB}')

    if not os.path.exists(os.path.join(self.petscdir.dir,self.arch.arch,'lib')):
      os.makedirs(os.path.join(self.petscdir.dir,self.arch.arch,'lib'))

# add a makefile endtry for display
    if self.framework.argDB['with-display']:
      self.addMakeMacro('DISPLAY',self.framework.argDB['with-display'])

    # add a makefile entry for configure options
    self.addMakeMacro('CONFIGURE_OPTIONS', self.framework.getOptionsString(['configModules', 'optionsModule']).replace('\"','\\"'))
    return

  def dumpConfigInfo(self):
    import time
    fd = file(os.path.join(self.arch.arch,'include','petscconfiginfo.h'),'w')
    fd.write('static const char *petscconfigureoptions = "'+self.framework.getOptionsString(['configModules', 'optionsModule']).replace('\"','\\"')+'";\n')
    fd.close()
    return

  def dumpMachineInfo(self):
    import platform
    import datetime
    import time
    import script
    def escape(s):
      return s.replace('"',r'\"').replace(r'\ ',r'\\ ')
    fd = file(os.path.join(self.arch.arch,'include','petscmachineinfo.h'),'w')
    fd.write('static const char *petscmachineinfo = \"\\n\"\n')
    fd.write('\"-----------------------------------------\\n\"\n')
    buildhost = platform.node()
    if os.environ.get('SOURCE_DATE_EPOCH'):
      buildhost = "reproducible"
    buildtime = datetime.datetime.utcfromtimestamp(int(os.environ.get('SOURCE_DATE_EPOCH', time.time())))
    fd.write('\"Libraries compiled on %s on %s \\n\"\n' % (buildtime, buildhost))
    fd.write('\"Machine characteristics: %s\\n\"\n' % (platform.platform()))
    fd.write('\"Using PETSc directory: %s\\n\"\n' % (escape(self.installdir.petscDir)))
    fd.write('\"Using PETSc arch: %s\\n\"\n' % (escape(self.installdir.petscArch)))
    fd.write('\"-----------------------------------------\\n\";\n')
    fd.write('static const char *petsccompilerinfo = \"\\n\"\n')
    self.setCompilers.pushLanguage(self.languages.clanguage)
    fd.write('\"Using C compiler: %s %s \\n\"\n' % (escape(self.setCompilers.getCompiler()), escape(self.setCompilers.getCompilerFlags())))
    self.setCompilers.popLanguage()
    if hasattr(self.compilers, 'FC'):
      self.setCompilers.pushLanguage('FC')
      fd.write('\"Using Fortran compiler: %s %s  %s\\n\"\n' % (escape(self.setCompilers.getCompiler()), escape(self.setCompilers.getCompilerFlags()), escape(self.setCompilers.CPPFLAGS)))
      self.setCompilers.popLanguage()
    fd.write('\"-----------------------------------------\\n\";\n')
    fd.write('static const char *petsccompilerflagsinfo = \"\\n\"\n')
    fd.write('\"Using include paths: %s\\n\"\n' % (escape(self.PETSC_CC_INCLUDES_INSTALL.replace('${PETSC_DIR}', self.installdir.petscDir))))
    fd.write('\"-----------------------------------------\\n\";\n')
    fd.write('static const char *petsclinkerinfo = \"\\n\"\n')
    self.setCompilers.pushLanguage(self.languages.clanguage)
    fd.write('\"Using C linker: %s\\n\"\n' % (escape(self.setCompilers.getLinker())))
    self.setCompilers.popLanguage()
    if hasattr(self.compilers, 'FC'):
      self.setCompilers.pushLanguage('FC')
      fd.write('\"Using Fortran linker: %s\\n\"\n' % (escape(self.setCompilers.getLinker())))
      self.setCompilers.popLanguage()
    fd.write('\"Using libraries: %s%s -L%s %s %s\\n\"\n' % (escape(self.setCompilers.CSharedLinkerFlag), escape(os.path.join(self.installdir.petscDir, self.installdir.petscArch, 'lib')), escape(os.path.join(self.installdir.petscDir, self.installdir.petscArch, 'lib')), escape(self.petsclib), escape(self.PETSC_EXTERNAL_LIB_BASIC)))
    fd.write('\"-----------------------------------------\\n\";\n')
    fd.close()
    return

  def dumpCMakeConfig(self):
    '''
    Writes configuration-specific values to ${PETSC_ARCH}/lib/petsc/conf/PETScBuildInternal.cmake.
    This file is private to PETSc and should not be included by third parties
    (a suitable file can be produced later by CMake, but this is not it).
    '''
    def cmakeset(fd,key,val=True):
      if val == True: val = 'YES'
      if val == False: val = 'NO'
      fd.write('set (' + key + ' ' + val + ')\n')
    def ensurelist(a):
      if isinstance(a,list):
        return a
      else:
        return [a]
    def libpath(lib):
      'Returns a search path if that is what this item provides, else "" which will be cleaned out later'
      if not isinstance(lib,str): return ''
      if lib.startswith('-L'): return lib[2:]
      if lib.startswith('-R'): return lib[2:]
      if lib.startswith('-Wl,-rpath,'):
        # This case occurs when an external package needs a specific system library that is normally provided by the compiler.
        # In other words, the -L path is builtin to the wrapper or compiler, here we provide it so that CMake can locate the
        # corresponding library.
        return lib[len('-Wl,-rpath,'):]
      if lib.startswith('-'): return ''
      return os.path.dirname(lib)
    def cleanlib(lib):
      'Returns a library name if that is what this item provides, else "" which will be cleaned out later'
      if not isinstance(lib,str): return ''
      if lib.startswith('-l'):  return lib[2:]
      if lib.startswith('-Wl') or lib.startswith('-L'): return ''
      lib = os.path.splitext(os.path.basename(lib))[0]
      if lib.startswith('lib'): return lib[3:]
      return lib
    def nub(lst):
      'Return a list containing the first occurrence of each unique element'
      unique = []
      for elem in lst:
        if elem not in unique and elem != '':
          unique.append(elem)
      return unique
    try: reversed # reversed was added in Python-2.4
    except NameError:
      def reversed(lst): return lst[::-1]
    def nublast(lst):
      'Return a list containing the last occurrence of each unique entry in a list'
      return reversed(nub(reversed(lst)))
    def cmakeexpand(varname):
      return r'"${' + varname + r'}"'
    def uniqextend(lst,new):
      for x in ensurelist(new):
        if x not in lst:
          lst.append(x)
    def notstandardinclude(path):
      return path not in '/usr/include'.split() # /usr/local/include is not automatically included on FreeBSD
    def writeMacroDefinitions(fd):
      if self.mpi.usingMPIUni:
        cmakeset(fd,'PETSC_HAVE_MPIUNI')
      for pkg in self.framework.packages:
        if pkg.useddirectly:
          cmakeset(fd,'PETSC_HAVE_' + pkg.PACKAGE.replace('-','_'))
        for pair in pkg.defines.items():
          if pair[0].startswith('HAVE_') and pair[1]:
            cmakeset(fd, self.framework.getFullDefineName(pkg, pair[0]), pair[1])
      for name,val in self.functions.defines.items():
        cmakeset(fd,'PETSC_'+name,val)
      for dct in [self.defines, self.libraryoptions.defines]:
        for k,v in dct.items():
          if k.startswith('USE_'):
            cmakeset(fd,'PETSC_' + k, v)
      cmakeset(fd,'PETSC_USE_COMPLEX', self.scalartypes.scalartype == 'complex')
      cmakeset(fd,'PETSC_USE_REAL_' + self.scalartypes.precision.upper())
      cmakeset(fd,'PETSC_CLANGUAGE_'+self.languages.clanguage)
      if hasattr(self.compilers, 'FC'):
        cmakeset(fd,'PETSC_HAVE_FORTRAN')
        if self.compilers.fortranIsF90:
          cmakeset(fd,'PETSC_USING_F90')
        if self.compilers.fortranIsF2003:
          cmakeset(fd,'PETSC_USING_F2003')
      if hasattr(self.compilers, 'CXX'):
        cmakeset(fd,'PETSC_HAVE_CXX')
      if self.sharedlibraries.useShared:
        cmakeset(fd,'BUILD_SHARED_LIBS')
    def writeBuildFlags(fd):
      def extendby(lib):
        libs = ensurelist(lib)
        lib_paths.extend(map(libpath,libs))
        lib_libs.extend(map(cleanlib,libs))
      lib_paths = []
      lib_libs  = []
      includes  = []
      libvars   = []
      for pkg in self.framework.packages:
        if pkg.linkedbypetsc:
          extendby(pkg.lib)
          uniqextend(includes,pkg.include)
      extendby(self.libraries.math)
      extendby(self.libraries.rt)
      extendby(self.compilers.flibs)
      extendby(self.compilers.cxxlibs)
      extendby(self.compilers.LIBS.split())
      for libname in nublast(lib_libs):
        libvar = 'PETSC_' + libname.upper() + '_LIB'
        addpath = ''
        for lpath in nublast(lib_paths):
          addpath += '"' + str(lpath) + '" '
        fd.write('find_library (' + libvar + ' ' + libname + ' HINTS ' + addpath + ')\n')
        libvars.append(libvar)
      fd.write('mark_as_advanced (' + ' '.join(libvars) + ')\n')
      fd.write('set (PETSC_PACKAGE_LIBS ' + ' '.join(map(cmakeexpand,libvars)) + ')\n')
      includes = filter(notstandardinclude,includes)
      fd.write('set (PETSC_PACKAGE_INCLUDES ' + ' '.join(map(lambda i: '"'+i+'"',includes)) + ')\n')
    fd = open(os.path.join(self.arch.arch,'lib','petsc','conf','PETScBuildInternal.cmake'), 'w')
    writeMacroDefinitions(fd)
    writeBuildFlags(fd)
    fd.close()
    return

  def dumpCMakeLists(self):
    import sys
    if sys.version_info >= (2,4):
      import cmakegen
      try:
        cmakegen.main(self.petscdir.dir, log=self.framework.log)
      except (OSError) as e:
        self.framework.logPrint('Generating CMakeLists.txt failed:\n' + str(e))
    else:
      self.framework.logPrint('Skipping cmakegen due to old python version: ' +str(sys.version_info) )

  def cmakeBoot(self):
    import sys
    self.cmakeboot_success = False
    if sys.version_info >= (2,4) and hasattr(self.cmake,'cmake'):
      oldRead = self.argDB.readonly
      self.argDB.readonly = True
      try:
        import cmakeboot
        self.cmakeboot_success = cmakeboot.main(petscdir=self.petscdir.dir,petscarch=self.arch.arch,argDB=self.argDB,framework=self.framework,log=self.framework.log)
      except (OSError) as e:
        self.framework.logPrint('Booting CMake in PETSC_ARCH failed:\n' + str(e))
      except (ImportError, KeyError) as e:
        self.framework.logPrint('Importing cmakeboot failed:\n' + str(e))
      self.argDB.readonly = oldRead
      if self.cmakeboot_success:
        if hasattr(self.compilers, 'FC') and self.compilers.fortranIsF90 and not self.setCompilers.fortranModuleOutputFlag:
          self.framework.logPrint('CMake configured successfully, but could not be used by default because of missing fortranModuleOutputFlag\n')
        else:
          self.framework.logPrint('CMake configured successfully, using as default build\n')
          self.addMakeMacro('PETSC_BUILD_USING_CMAKE',1)
      else:
        self.framework.logPrint('CMake configuration was unsuccessful\n')
    else:
      self.framework.logPrint('Skipping cmakeboot due to old python version: ' +str(sys.version_info) )
    return

  def configurePrefetch(self):
    '''Sees if there are any prefetch functions supported'''
    if config.setCompilers.Configure.isSolaris(self.log) or self.framework.argDB['with-ios'] or not self.framework.argDB['with-prefetch']:
      self.addDefine('Prefetch(a,b,c)', ' ')
      return
    self.pushLanguage(self.languages.clanguage)
    if self.checkLink('#include <xmmintrin.h>', 'void *v = 0;_mm_prefetch((const char*)v,_MM_HINT_NTA);\n'):
      # The Intel Intrinsics manual [1] specifies the prototype
      #
      #   void _mm_prefetch(char const *a, int sel);
      #
      # but other vendors seem to insist on using subtly different
      # prototypes, including void* for the pointer, and an enum for
      # sel.  These are both reasonable changes, but negatively impact
      # portability.
      #
      # [1] http://software.intel.com/file/6373
      self.addDefine('HAVE_XMMINTRIN_H', 1)
      self.addDefine('Prefetch(a,b,c)', '_mm_prefetch((const char*)(a),(c))')
      self.addDefine('PREFETCH_HINT_NTA', '_MM_HINT_NTA')
      self.addDefine('PREFETCH_HINT_T0',  '_MM_HINT_T0')
      self.addDefine('PREFETCH_HINT_T1',  '_MM_HINT_T1')
      self.addDefine('PREFETCH_HINT_T2',  '_MM_HINT_T2')
    elif self.checkLink('#include <xmmintrin.h>', 'void *v = 0;_mm_prefetch(v,_MM_HINT_NTA);\n'):
      self.addDefine('HAVE_XMMINTRIN_H', 1)
      self.addDefine('Prefetch(a,b,c)', '_mm_prefetch((const void*)(a),(c))')
      self.addDefine('PREFETCH_HINT_NTA', '_MM_HINT_NTA')
      self.addDefine('PREFETCH_HINT_T0',  '_MM_HINT_T0')
      self.addDefine('PREFETCH_HINT_T1',  '_MM_HINT_T1')
      self.addDefine('PREFETCH_HINT_T2',  '_MM_HINT_T2')
    elif self.checkLink('', 'void *v = 0;__builtin_prefetch(v,0,0);\n'):
      # From GCC docs: void __builtin_prefetch(const void *addr,int rw,int locality)
      #
      #   The value of rw is a compile-time constant one or zero; one
      #   means that the prefetch is preparing for a write to the memory
      #   address and zero, the default, means that the prefetch is
      #   preparing for a read. The value locality must be a compile-time
      #   constant integer between zero and three. A value of zero means
      #   that the data has no temporal locality, so it need not be left
      #   in the cache after the access. A value of three means that the
      #   data has a high degree of temporal locality and should be left
      #   in all levels of cache possible. Values of one and two mean,
      #   respectively, a low or moderate degree of temporal locality.
      #
      # Here we adopt Intel's x86/x86-64 naming scheme for the locality
      # hints.  Using macros for these values in necessary since some
      # compilers require an enum.
      self.addDefine('Prefetch(a,b,c)', '__builtin_prefetch((a),(b),(c))')
      self.addDefine('PREFETCH_HINT_NTA', '0')
      self.addDefine('PREFETCH_HINT_T0',  '3')
      self.addDefine('PREFETCH_HINT_T1',  '2')
      self.addDefine('PREFETCH_HINT_T2',  '1')
    else:
      self.addDefine('Prefetch(a,b,c)', ' ')
    self.popLanguage()

  def configureAtoll(self):
    '''Checks if atoll exists'''
    if self.checkLink('#define _POSIX_C_SOURCE 200112L\n#include <stdlib.h>','long v = atoll("25")') or self.checkLink ('#include <stdlib.h>','long v = atoll("25")'):
       self.addDefine('HAVE_ATOLL', '1')

  def configureUnused(self):
    '''Sees if __attribute((unused)) is supported'''
    if self.framework.argDB['with-ios']:
      self.addDefine('UNUSED', ' ')
      return
    self.pushLanguage(self.languages.clanguage)
    if self.checkLink('__attribute((unused)) static int myfunc(__attribute((unused)) void *name){ return 1;}', 'int i = 0;\nint j = myfunc(&i);\ntypedef void* atype;\n__attribute((unused))  atype a;\n'):
      self.addDefine('UNUSED', '__attribute((unused))')
    else:
      self.addDefine('UNUSED', ' ')
    self.popLanguage()

  def configureIsatty(self):
    '''Check if the Unix C function isatty() works correctly
       Actually just assumes it does not work correctly on batch systems'''
    if not self.framework.argDB['with-batch']:
      self.addDefine('USE_ISATTY',1)

  def configureDeprecated(self):
    '''Check if __attribute((deprecated)) is supported'''
    self.pushLanguage(self.languages.clanguage)
    ## Recent versions of gcc and clang support __attribute((deprecated("string argument"))), which is very useful, but
    ## Intel has conspired to make a supremely environment-sensitive compiler.  The Intel compiler looks at the gcc
    ## executable in the environment to determine the language compatibility that it should attempt to emulate.  Some
    ## important Cray installations have built PETSc using the Intel compiler, but with a newer gcc module loaded (e.g.,
    ## 4.7).  Thus at PETSc configure time, the Intel compiler decides to support the string argument, but the gcc
    ## found in the default user environment is older and does not support the argument.  If GCC and Intel were cool
    ## like Clang and supported __has_attribute, we could avoid configure tests entirely, but they don't.  And that is
    ## why we can't have nice things.
    #
    # if self.checkCompile("""__attribute((deprecated("Why you shouldn't use myfunc"))) static int myfunc(void) { return 1;}""", ''):
    #   self.addDefine('DEPRECATED(why)', '__attribute((deprecated(why)))')
    if self.checkCompile("""__attribute((deprecated)) static int myfunc(void) { return 1;}""", ''):
      self.addDefine('DEPRECATED(why)', '__attribute((deprecated))')
    else:
      self.addDefine('DEPRECATED(why)', ' ')
    self.popLanguage()

  def configureAlign(self):
    '''Check if __attribute(align) is supported'''
    filename = 'conftestalign'
    includes = '''
#include <sys/types.h>
#if STDC_HEADERS
#include <stdlib.h>
#include <stdio.h>
#include <stddef.h>
#endif\n'''
    body     = '''
struct mystruct {int myint;} __attribute((aligned(16)));
FILE *f = fopen("'''+filename+'''", "w");
if (!f) exit(1);
fprintf(f, "%lu\\n", (unsigned long)sizeof(struct mystruct));
'''
    if 'known-has-attribute-aligned' in self.argDB:
      if self.argDB['known-has-attribute-aligned']:
        size = 16
      else:
        size = -3
    elif not self.argDB['with-batch']:
      self.pushLanguage(self.languages.clanguage)
      try:
        if self.checkRun(includes, body) and os.path.exists(filename):
          f    = file(filename)
          size = int(f.read())
          f.close()
          os.remove(filename)
        else:
          size = -4
      except:
        size = -1
        self.framework.logPrint('Error checking attribute(aligned)')
      self.popLanguage()
    else:
      self.framework.addBatchInclude(['#include <stdlib.h>', '#include <stdio.h>', '#include <sys/types.h>','struct mystruct {int myint;} __attribute((aligned(16)));'])
      self.framework.addBatchBody('fprintf(output, "  \'--known-has-attribute-aligned=%d\',\\n", sizeof(struct mystruct)==16);')
      size = -2
    if size == 16:
      self.addDefine('ATTRIBUTEALIGNED(size)', '__attribute((aligned (size)))')
      self.addDefine('HAVE_ATTRIBUTEALIGNED', 1)
    else:
      self.framework.logPrint('incorrect alignment. Found alignment:'+ str(size))
      self.addDefine('ATTRIBUTEALIGNED(size)', ' ')
    return

  def configureExpect(self):
    '''Sees if the __builtin_expect directive is supported'''
    self.pushLanguage(self.languages.clanguage)
    if self.checkLink('', 'if (__builtin_expect(0,1)) return 1;'):
      self.addDefine('HAVE_BUILTIN_EXPECT', 1)
    self.popLanguage()

  def configureFunctionName(self):
    '''Sees if the compiler supports __func__ or a variant.'''
    def getFunctionName(lang):
      name = '"unknown"'
      self.pushLanguage(lang)
      for fname in ['__func__','__FUNCTION__']:
        code = "if ("+fname+"[0] != 'm') return 1;"
        if self.checkCompile('',code) and self.checkLink('',code):
          name = fname
          break
      self.popLanguage()
      return name
    langs = []

    self.addDefine('FUNCTION_NAME_C', getFunctionName('C'))
    if hasattr(self.compilers, 'CXX'):
      self.addDefine('FUNCTION_NAME_CXX', getFunctionName('Cxx'))

  def configureIntptrt(self):
    '''Determine what to use for uintptr_t'''
    def staticAssertSizeMatchesVoidStar(inc,typename):
      # The declaration is an error if either array size is negative.
      # It should be okay to use an int that is too large, but it would be very unlikely for this to be the case
      return self.checkCompile(inc, ('#define STATIC_ASSERT(cond) char negative_length_if_false[2*(!!(cond))-1]\n'
                                     + 'STATIC_ASSERT(sizeof(void*) == sizeof(%s));'%typename))
    self.pushLanguage(self.languages.clanguage)
    if self.checkCompile('#include <stdint.h>', 'int x; uintptr_t i = (uintptr_t)&x;'):
      self.addDefine('UINTPTR_T', 'uintptr_t')
    elif staticAssertSizeMatchesVoidStar('','unsigned long long'):
      self.addDefine('UINTPTR_T', 'unsigned long long')
    elif staticAssertSizeMatchesVoidStar('#include <stdlib.h>','size_t') or staticAssertSizeMatchesVoidStar('#include <string.h>', 'size_t'):
      self.addDefine('UINTPTR_T', 'size_t')
    elif staticAssertSizeMatchesVoidStar('','unsigned long'):
      self.addDefine('UINTPTR_T', 'unsigned long')
    elif staticAssertSizeMatchesVoidStar('','unsigned'):
      self.addDefine('UINTPTR_T', 'unsigned')
    else:
      raise RuntimeError('Could not find any unsigned integer type matching void*')
    self.popLanguage()

  def configureRTLDDefault(self):
    if self.checkCompile('#include <dlfcn.h>\n void *ptr =  RTLD_DEFAULT;'):
      self.addDefine('RTLD_DEFAULT','1')
    return

  def configureSolaris(self):
    '''Solaris specific stuff'''
    if os.path.isdir(os.path.join('/usr','ucblib')):
      try:
        flag = getattr(self.setCompilers, self.language[-1]+'SharedLinkerFlag')
      except AttributeError:
        flag = None
      if flag is None:
        self.compilers.LIBS += ' -L/usr/ucblib'
      else:
        self.compilers.LIBS += ' '+flag+'/usr/ucblib'
    return

  def configureLinux(self):
    '''Linux specific stuff'''
    # TODO: Test for this by mallocing an odd number of floats and checking the address
    self.addDefine('HAVE_DOUBLE_ALIGN_MALLOC', 1)
    return

  def configureWin32(self):
    '''Win32 non-cygwin specific stuff'''
    kernel32=0
    if self.libraries.add('Kernel32.lib','GetComputerName',prototype='#include <Windows.h>', call='GetComputerName(NULL,NULL);'):
      self.addDefine('HAVE_WINDOWS_H',1)
      self.addDefine('HAVE_GETCOMPUTERNAME',1)
      kernel32=1
    elif self.libraries.add('kernel32','GetComputerName',prototype='#include <Windows.h>', call='GetComputerName(NULL,NULL);'):
      self.addDefine('HAVE_WINDOWS_H',1)
      self.addDefine('HAVE_GETCOMPUTERNAME',1)
      kernel32=1
    if kernel32:
      if self.framework.argDB['with-windows-graphics']:
        self.addDefine('USE_WINDOWS_GRAPHICS',1)
      if self.checkLink('#include <Windows.h>','LoadLibrary(0)'):
        self.addDefine('HAVE_LOADLIBRARY',1)
      if self.checkLink('#include <Windows.h>','GetProcAddress(0,0)'):
        self.addDefine('HAVE_GETPROCADDRESS',1)
      if self.checkLink('#include <Windows.h>','FreeLibrary(0)'):
        self.addDefine('HAVE_FREELIBRARY',1)
      if self.checkLink('#include <Windows.h>','GetLastError()'):
        self.addDefine('HAVE_GETLASTERROR',1)
      if self.checkLink('#include <Windows.h>','SetLastError(0)'):
        self.addDefine('HAVE_SETLASTERROR',1)
      if self.checkLink('#include <Windows.h>\n','QueryPerformanceCounter(0);\n'):
        self.addDefine('USE_MICROSOFT_TIME',1)
    if self.libraries.add('Advapi32.lib','GetUserName',prototype='#include <Windows.h>', call='GetUserName(NULL,NULL);'):
      self.addDefine('HAVE_GET_USER_NAME',1)
    elif self.libraries.add('advapi32','GetUserName',prototype='#include <Windows.h>', call='GetUserName(NULL,NULL);'):
      self.addDefine('HAVE_GET_USER_NAME',1)

    if not self.libraries.add('User32.lib','GetDC',prototype='#include <Windows.h>',call='GetDC(0);'):
      self.libraries.add('user32','GetDC',prototype='#include <Windows.h>',call='GetDC(0);')
    if not self.libraries.add('Gdi32.lib','CreateCompatibleDC',prototype='#include <Windows.h>',call='CreateCompatibleDC(0);'):
      self.libraries.add('gdi32','CreateCompatibleDC',prototype='#include <Windows.h>',call='CreateCompatibleDC(0);')

    self.types.check('int32_t', 'int')
    if not self.checkCompile('#include <sys/types.h>\n','uid_t u;\n'):
      self.addTypedef('int', 'uid_t')
      self.addTypedef('int', 'gid_t')
    if not self.checkLink('#if defined(PETSC_HAVE_UNISTD_H)\n#include <unistd.h>\n#endif\n','int a=R_OK;\n'):
      self.framework.addDefine('R_OK', '04')
      self.framework.addDefine('W_OK', '02')
      self.framework.addDefine('X_OK', '01')
    if not self.checkLink('#include <sys/stat.h>\n','int a=0;\nif (S_ISDIR(a)){}\n'):
      self.framework.addDefine('S_ISREG(a)', '(((a)&_S_IFMT) == _S_IFREG)')
      self.framework.addDefine('S_ISDIR(a)', '(((a)&_S_IFMT) == _S_IFDIR)')
    if self.checkCompile('#include <Windows.h>\n','LARGE_INTEGER a;\nDWORD b=a.u.HighPart;\n'):
      self.addDefine('HAVE_LARGE_INTEGER_U',1)

    # Windows requires a Binary file creation flag when creating/opening binary files.  Is a better test in order?
    if self.checkCompile('#include <Windows.h>\n#include <fcntl.h>\n', 'int flags = O_BINARY;'):
      self.addDefine('HAVE_O_BINARY',1)

    if self.compilers.CC.find('win32fe') >= 0:
      self.addDefine('HAVE_WINDOWS_COMPILERS',1)
      self.addDefine('PATH_SEPARATOR','\';\'')
      self.addDefine('DIR_SEPARATOR','\'\\\\\'')
      self.addDefine('REPLACE_DIR_SEPARATOR','\'/\'')
      self.addDefine('CANNOT_START_DEBUGGER',1)
      (petscdir,error,status) = self.executeShellCommand('cygpath -w '+self.installdir.petscDir, log = self.log)
      self.addDefine('DIR','"'+petscdir.replace('\\','\\\\')+'"')
      (petscdir,error,status) = self.executeShellCommand('cygpath -m '+self.installdir.petscDir, log = self.log)
      self.addMakeMacro('wPETSC_DIR',petscdir)
    else:
      self.addDefine('PATH_SEPARATOR','\':\'')
      self.addDefine('REPLACE_DIR_SEPARATOR','\'\\\\\'')
      self.addDefine('DIR_SEPARATOR','\'/\'')
      self.addDefine('DIR','"'+self.installdir.petscDir+'"')
      self.addMakeMacro('wPETSC_DIR',self.installdir.petscDir)
    self.addDefine('ARCH','"'+self.installdir.petscArch+'"')
    return

#-----------------------------------------------------------------------------------------------------
  def configureCygwinBrokenPipe(self):
    '''Cygwin version <= 1.7.18 had issues with pipes and long commands invoked from gnu-make
    http://cygwin.com/ml/cygwin/2013-05/msg00340.html '''
    if config.setCompilers.Configure.isCygwin(self.log):
      import platform
      import re
      r=re.compile("([0-9]+).([0-9]+).([0-9]+)")
      m=r.match(platform.release())
      major=int(m.group(1))
      minor=int(m.group(2))
      subminor=int(m.group(3))
      if ((major < 1) or (major == 1 and minor < 7) or (major == 1 and minor == 7 and subminor <= 18)):
        self.addMakeMacro('PETSC_CYGWIN_BROKEN_PIPE','1')
    return

#-----------------------------------------------------------------------------------------------------
  def configureDefaultArch(self):
    conffile = os.path.join('lib','petsc','conf', 'petscvariables')
    if self.framework.argDB['with-default-arch']:
      fd = file(conffile, 'w')
      fd.write('PETSC_ARCH='+self.arch.arch+'\n')
      fd.write('PETSC_DIR='+self.petscdir.dir+'\n')
      fd.write('include '+os.path.join('$(PETSC_DIR)','$(PETSC_ARCH)','lib','petsc','conf','petscvariables')+'\n')
      fd.close()
      self.framework.actions.addArgument('PETSc', 'Build', 'Set default architecture to '+self.arch.arch+' in '+conffile)
    elif os.path.isfile(conffile):
      try:
        os.unlink(conffile)
      except:
        raise RuntimeError('Unable to remove file '+conffile+'. Did a different user create it?')
    return

#-----------------------------------------------------------------------------------------------------
  def configureScript(self):
    '''Output a script in the conf directory which will reproduce the configuration'''
    import nargs
    import sys
    scriptName = os.path.join(self.arch.arch,'lib','petsc','conf', 'reconfigure-'+self.arch.arch+'.py')
    args = dict([(nargs.Arg.parseArgument(arg)[0], arg) for arg in self.framework.clArgs])
    if 'with-clean' in args:
      del args['with-clean']
    if 'configModules' in args:
      if nargs.Arg.parseArgument(args['configModules'])[1] == 'PETSc.Configure':
        del args['configModules']
    if 'optionsModule' in args:
      if nargs.Arg.parseArgument(args['optionsModule'])[1] == 'config.compilerOptions':
        del args['optionsModule']
    if not 'PETSC_ARCH' in args:
      args['PETSC_ARCH'] = 'PETSC_ARCH='+str(self.arch.arch)
    f = file(scriptName, 'w')
    f.write('#!'+sys.executable+'\n')
    f.write('if __name__ == \'__main__\':\n')
    f.write('  import sys\n')
    f.write('  import os\n')
    f.write('  sys.path.insert(0, os.path.abspath(\'config\'))\n')
    f.write('  import configure\n')
    # pretty print repr(args.values())
    f.write('  configure_options = [\n')
    for itm in sorted(args.values()):
      f.write('    \''+str(itm)+'\',\n')
    f.write('  ]\n')
    f.write('  configure.petsc_configure(configure_options)\n')
    f.close()
    try:
      os.chmod(scriptName, 0o775)
    except OSError as e:
      self.framework.logPrint('Unable to make reconfigure script executable:\n'+str(e))
    self.framework.actions.addArgument('PETSc', 'File creation', 'Created '+scriptName+' for automatic reconfiguration')
    return

  def configureInstall(self):
    '''Setup the directories for installation'''
    if self.framework.argDB['prefix']:
      self.addMakeRule('shared_install','',['-@echo "Now to install the libraries do:"',\
                                              '-@echo "'+self.installdir.installSudo+'make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} install"',\
                                              '-@echo "========================================="'])
    else:
      self.addMakeRule('shared_install','',['-@echo "Now to check if the libraries are working do:"',\
                                              '-@echo "make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} check"',\
                                              '-@echo "========================================="'])
      return

  def configureGCOV(self):
    if self.framework.argDB['with-gcov']:
      self.addDefine('USE_GCOV','1')
    return

  def configureViewFromOptions(self):
    if not self.framework.argDB['with-viewfromoptions']:
      self.addDefine('SKIP_VIEWFROMOPTIONS',1)

  def postProcessPackages(self):
    postPackages=[]
    for i in self.framework.packages:
      if hasattr(i,'postProcess'): postPackages.append(i)
    if postPackages:
      # ctetgen needs petsc conf files. so attempt to create them early
      self.framework.dumpConfFiles()
      # tacky fix for dependency of Aluimia on Pflotran; requested via petsc-dev Matt provide a correct fix
      for i in postPackages:
        if i.name.upper() in ['PFLOTRAN']:
          i.postProcess()
          postPackages.remove(i)
      for i in postPackages: i.postProcess()
      for i in postPackages:
        if i.installedpetsc:
          self.installed = 1
          break
    return

  def configure(self):
    if not os.path.samefile(self.petscdir.dir, os.getcwd()):
      raise RuntimeError('Wrong PETSC_DIR option specified: '+str(self.petscdir.dir) + '\n  Configure invoked in: '+os.path.realpath(os.getcwd()))
    if self.framework.argDB['prefix'] and os.path.isdir(self.framework.argDB['prefix']) and os.path.samefile(self.framework.argDB['prefix'],self.petscdir.dir):
      raise RuntimeError('Incorrect option --prefix='+self.framework.argDB['prefix']+' specified. It cannot be same as PETSC_DIR!')
    if self.framework.argDB['prefix'] and self.framework.argDB['prefix'].find(' ') > -1:
      raise RuntimeError('Your --prefix '+self.framework.argDB['prefix']+' has spaces in it; this is not allowed.\n Use a --prefix that does not have spaces in it')
    if self.framework.argDB['prefix'] and os.path.isdir(self.framework.argDB['prefix']) and os.path.samefile(self.framework.argDB['prefix'],os.path.join(self.petscdir.dir,self.arch.arch)):
      raise RuntimeError('Incorrect option --prefix='+self.framework.argDB['prefix']+' specified. It cannot be same as PETSC_DIR/PETSC_ARCH!')
    self.framework.header          = os.path.join(self.arch.arch,'include','petscconf.h')
    self.framework.cHeader         = os.path.join(self.arch.arch,'include','petscfix.h')
    self.framework.makeMacroHeader = os.path.join(self.arch.arch,'lib','petsc','conf','petscvariables')
    self.framework.makeRuleHeader  = os.path.join(self.arch.arch,'lib','petsc','conf','petscrules')
    if self.libraries.math is None:
      raise RuntimeError('PETSc requires a functional math library. Please send configure.log to petsc-maint@mcs.anl.gov.')
    if self.languages.clanguage == 'Cxx' and not hasattr(self.compilers, 'CXX'):
      raise RuntimeError('Cannot set C language to C++ without a functional C++ compiler.')
    self.executeTest(self.configureRTLDDefault)
    self.executeTest(self.configurePrefetch)
    self.executeTest(self.configureUnused)
    self.executeTest(self.configureDeprecated)
    self.executeTest(self.configureIsatty)
    self.executeTest(self.configureExpect);
    self.executeTest(self.configureAlign);
    self.executeTest(self.configureFunctionName);
    self.executeTest(self.configureIntptrt);
    self.executeTest(self.configureSolaris)
    self.executeTest(self.configureLinux)
    self.executeTest(self.configureWin32)
    self.executeTest(self.configureCygwinBrokenPipe)
    self.executeTest(self.configureDefaultArch)
    self.executeTest(self.configureScript)
    self.executeTest(self.configureInstall)
    self.executeTest(self.configureGCOV)
    self.executeTest(self.configureAtoll)
    self.executeTest(self.configureViewFromOptions)

    self.Dump()
    self.dumpConfigInfo()
    self.dumpMachineInfo()
    self.dumpCMakeConfig()
    self.dumpCMakeLists()
    # need to save the current state of BuildSystem so that postProcess() packages can read it in and perhaps run make install
    self.framework.storeSubstitutions(self.framework.argDB)
    self.framework.argDB['configureCache'] = cPickle.dumps(self.framework)
    self.framework.argDB.save(force = True)
    self.cmakeBoot()
    self.DumpPkgconfig()
    self.DumpModule()
    self.postProcessPackages()
    self.framework.log.write('================================================================================\n')
    self.logClear()
    return