xref: /petsc/config/PETSc/Configure.py (revision 5faf1eaced1425ad67e7b8ff021671dbc16e45df)

import config.base

import os
import re

# 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'
    return

  def __str2__(self):
    desc = []
    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')
    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-ios=<bool>',              nargs.ArgBool(None, 0, 'Build an iPhone/iPad version of PETSc library'))
    return

  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.languages     = framework.require('PETSc.options.languages',   self.setCompilers)
    self.debugging     = framework.require('PETSc.options.debugging',   self.setCompilers)
    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 os.listdir(os.path.join('config','PETSc','options')):
      (utilityName, ext) = os.path.splitext(utility)
      if not utilityName.startswith('.') and not utilityName.startswith('#') and ext == '.py' and not utilityName == '__init__':
        utilityObj                    = self.framework.require('PETSc.options.'+utilityName, self)
        utilityObj.headerPrefix       = self.headerPrefix
        utilityObj.archProvider       = self.arch
        utilityObj.languageProvider   = self.languages
        utilityObj.installDirProvider = self.installdir
        utilityObj.externalPackagesDirProvider = self.externalpackagesdir
        setattr(self, utilityName.lower(), utilityObj)

    for utility in os.listdir(os.path.join('config','BuildSystem','config','utilities')):
      (utilityName, ext) = os.path.splitext(utility)
      if not utilityName.startswith('.') and not utilityName.startswith('#') and ext == '.py' and not utilityName == '__init__':
        utilityObj                    = self.framework.require('config.utilities.'+utilityName, self)
        utilityObj.headerPrefix       = self.headerPrefix
        utilityObj.archProvider       = self.arch
        utilityObj.languageProvider   = self.languages
        utilityObj.installDirProvider = self.installdir
        utilityObj.externalPackagesDirProvider = self.externalpackagesdir
        setattr(self, utilityName.lower(), utilityObj)

    for utility in os.listdir(os.path.join('config','BuildSystem','config','packages')):
      (utilityName, ext) = os.path.splitext(utility)
      if not utilityName.startswith('.') and not utilityName.startswith('#') and ext == '.py' and not utilityName == '__init__':
        utilityObj                    = self.framework.require('config.packages.'+utilityName, self)
        utilityObj.headerPrefix       = self.headerPrefix
        utilityObj.archProvider       = self.arch
        utilityObj.languageProvider   = self.languages
        utilityObj.installDirProvider = self.installdir
        utilityObj.externalPackagesDirProvider = self.externalpackagesdir
        setattr(self, utilityName.lower(), utilityObj)

    if os.path.isdir(os.path.join('config', 'BuildSystem', 'config', 'packages')):
      for package in os.listdir(os.path.join('config', 'BuildSystem', 'config', 'packages')):
        (packageName, ext) = os.path.splitext(package)
        if not packageName.startswith('.') and not packageName.startswith('#') and ext == '.py' and not packageName == '__init__' and not packageName == 'PETSc':
          packageObj                    = framework.require('config.packages.'+packageName, self)
          packageObj.archProvider       = self.arch
          packageObj.languageProvider   = self.languages
          packageObj.precisionProvider  = self.scalartypes
          packageObj.indexProvider      = self.indexTypes
          packageObj.installDirProvider = self.installdir
          packageObj.externalPackagesDirProvider = self.externalpackagesdir
          setattr(self, packageName.lower(), packageObj)
    # 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
    self.blaslapack.headerPrefix = self.headerPrefix
    self.mpi.headerPrefix        = self.headerPrefix
    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','mathimf'])
    functions = ['access', '_access', 'clock', 'drand48', 'getcwd', '_getcwd', 'getdomainname', 'gethostname',
                 'gettimeofday', 'getwd', 'memalign', 'memmove', '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']
    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')
    if self.framework.argDB['prefix']:
      installdir = self.framework.argDB['prefix']
      fd.write('prefix='+installdir+'\n')
      fd.write('exec_prefix=${prefix}\n')
      fd.write('includedir=${prefix}/include\n')
      fd.write('libdir='+os.path.join(installdir,'lib')+'\n')
    else:
      fd.write('prefix='+self.petscdir.dir+'\n')
      fd.write('exec_prefix=${prefix}\n')
      fd.write('includedir=${prefix}/include\n')
      fd.write('libdir='+os.path.join(self.petscdir.dir,self.arch.arch,'lib')+'\n')

    self.setCompilers.pushLanguage('C')
    fd.write('ccompiler='+self.setCompilers.getCompiler()+'\n')
    self.setCompilers.popLanguage()
    if hasattr(self.compilers, 'C++'):
      self.setCompilers.pushLanguage('C++')
      fd.write('cxxcompiler='+self.setCompilers.getCompiler()+'\n')
      self.setCompilers.popLanguage()
    if hasattr(self.compilers, 'FC'):
      self.setCompilers.pushLanguage('FC')
      fd.write('fcompiler='+self.setCompilers.getCompiler()+'\n')
      self.setCompilers.popLanguage()
    fd.write('blaslapacklibs='+self.libraries.toStringNoDupes(self.blaslapack.lib)+'\n')

    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: '+self.allincludes+'\n')

    plibs = self.libraries.toStringNoDupes(['-L'+os.path.join(self.petscdir.dir,self.arch.arch,'lib'),' -lpetsc'])
    if self.framework.argDB['prefix']:
      fd.write('Libs: '+plibs.replace(os.path.join(self.petscdir.dir,self.arch.arch),self.framework.argDB['prefix'])+'\n')
    else:
      fd.write('Libs: '+plibs+'\n')
    fd.write('Libs.private: '+' '.join(self.packagelibs+self.libraries.math+self.compilers.flibs+self.compilers.cxxlibs)+' '+self.compilers.LIBS)

    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','modules')):
      os.makedirs(os.path.join(self.petscdir.dir,self.arch.arch,'lib','modules'))
    if self.framework.argDB['prefix']:
      installdir  = self.framework.argDB['prefix']
      installarch = ''
      installpath = os.path.join(installdir,'bin')
      fd = open(os.path.join(self.petscdir.dir,self.arch.arch,'lib','modules',self.petscdir.version),'w')
    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','modules',self.petscdir.version+'-'+self.arch.arch),'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*'))

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

    # 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.addMakeMacro('CXX_FLAGS',self.setCompilers.getCompilerFlags())
      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'):
      self.setCompilers.pushLanguage('FC')
      # need FPPFLAGS in config/setCompilers
      self.addDefine('HAVE_FORTRAN','1')
      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.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.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()
    includes = [os.path.join(self.petscdir.dir,'include'),os.path.join(self.petscdir.dir,self.arch.arch,'include')]
    libs = []
    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]
      libs.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))
    self.packagelibs = libs
    if self.framework.argDB['with-single-library']:
      self.alllibs = self.libraries.toStringNoDupes(['-L'+os.path.join(self.petscdir.dir,self.arch.arch,'lib'),' -lpetsc']+libs+self.libraries.math+self.compilers.flibs+self.compilers.cxxlibs)+' '+self.compilers.LIBS
      self.addMakeMacro('PETSC_WITH_EXTERNAL_LIB',self.alllibs)
    else:
      self.alllibs = self.libraries.toStringNoDupes(['-L'+os.path.join(self.petscdir.dir,self.arch.arch,'lib'),'-lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys']+libs+self.libraries.math+self.compilers.flibs+self.compilers.cxxlibs)+' '+self.compilers.LIBS
    self.PETSC_EXTERNAL_LIB_BASIC = self.libraries.toStringNoDupes(libs+self.libraries.math+self.compilers.flibs+self.compilers.cxxlibs)+' '+self.compilers.LIBS
    if self.framework.argDB['prefix'] and self.setCompilers.CSharedLinkerFlag not in ['-L']:
      installdir = self.framework.argDB['prefix']
      lib_basic = self.PETSC_EXTERNAL_LIB_BASIC.replace(self.setCompilers.CSharedLinkerFlag+os.path.join(self.petscdir.dir,self.arch.arch,'lib'),self.setCompilers.CSharedLinkerFlag+os.path.join(installdir,'lib'))
    else:
      lib_basic = self.PETSC_EXTERNAL_LIB_BASIC
    self.addMakeMacro('PETSC_EXTERNAL_LIB_BASIC',lib_basic)
    self.allincludes = self.headers.toStringNoDupes(includes)
    self.addMakeMacro('PETSC_CC_INCLUDES',self.allincludes)
    self.PETSC_CC_INCLUDES = self.allincludes
    if hasattr(self.compilers, 'FC'):
      if self.compilers.fortranIsF90:
        self.addMakeMacro('PETSC_FC_INCLUDES',self.headers.toStringNoDupes(includes,includes))
      else:
        self.addMakeMacro('PETSC_FC_INCLUDES',self.headers.toStringNoDupes(includes))

    self.addMakeMacro('DESTDIR',self.installdir)
    self.addDefine('LIB_DIR','"'+os.path.join(self.installdir,'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.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 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 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')
    fd.write('\"Libraries compiled on %s on %s \\n\"\n' % (time.ctime(time.time()), platform.node()))
    fd.write('\"Machine characteristics: %s\\n\"\n' % (platform.platform()))
    fd.write('\"Using PETSc directory: %s\\n\"\n' % (escape(self.petscdir.dir)))
    fd.write('\"Using PETSc arch: %s\\n\"\n' % (escape(self.arch.arch)))
    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 ${COPTFLAGS} ${CFLAGS}\\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 ${FOPTFLAGS} ${FFLAGS} %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 %s %s\\n\"\n' % ('-I'+escape(os.path.join(self.petscdir.dir, self.arch.arch, 'include')), '-I'+escape(os.path.join(self.petscdir.dir, 'include')), escape(self.PETSC_CC_INCLUDES)))
    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()
    if self.framework.argDB['with-single-library']:
      petsclib = '-lpetsc'
    else:
      petsclib = '-lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys'
    fd.write('\"Using libraries: %s%s -L%s %s %s\\n\"\n' % (escape(self.setCompilers.CSharedLinkerFlag), escape(os.path.join(self.petscdir.dir, self.arch.arch, 'lib')), escape(os.path.join(self.petscdir.dir, self.arch.arch, 'lib')), escape(petsclib), escape(self.PETSC_EXTERNAL_LIB_BASIC)))
    fd.write('\"-----------------------------------------\\n\";\n')
    fd.close()
    return

  def dumpCMakeConfig(self):
    '''
    Writes configuration-specific values to ${PETSC_ARCH}/conf/PETScConfig.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:
        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,'conf','PETScConfig.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), 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'):
      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), e:
        self.framework.logPrint('Booting CMake in PETSC_ARCH failed:\n' + str(e))
      except (ImportError, KeyError), e:
        self.framework.logPrint('Importing cmakeboot failed:\n' + str(e))
      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() 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 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.  Falls back
    on __FUNCT__ which PETSc source defines, but most users do not, thus
    stack traces through user code are better when the compiler's
    variant is used.'''
    def getFunctionName(lang):
      name = '__FUNCT__'
      self.pushLanguage(lang)
      if self.checkLink('', "if (__func__[0] != 'm') return 1;"):
        name = '__func__'
      elif self.checkLink('', "if (__FUNCTION__[0] != 'm') return 1;"):
        name = '__FUNCTION__'
      self.popLanguage()
      return name
    langs = []

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

  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('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.petscdir.dir)
      self.addDefine('DIR','"'+petscdir.replace('\\','\\\\')+'"')
    else:
      self.addDefine('PATH_SEPARATOR','\':\'')
      self.addDefine('REPLACE_DIR_SEPARATOR','\'\\\\\'')
      self.addDefine('DIR_SEPARATOR','\'/\'')
      self.addDefine('DIR', '"'+self.petscdir.dir+'"')

    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():
      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('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(self.petscdir.dir,self.arch.arch,'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,'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, 0775)
    except OSError, 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 "========================================="'])
      self.installdir = self.framework.argDB['prefix']
    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} test"',\
                                              '-@echo "========================================="'])
      self.installdir = os.path.join(self.petscdir.dir,self.arch.arch)
      return

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

  def configureFortranFlush(self):
    if hasattr(self.compilers, 'FC'):
      for baseName in ['flush','flush_']:
        if self.libraries.check('', baseName, otherLibs = self.compilers.flibs, fortranMangle = 1):
          self.addDefine('HAVE_'+baseName.upper(), 1)
          return

  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()
      for i in postPackages: i.postProcess()
    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 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,'conf','petscvariables')
    self.framework.makeRuleHeader  = os.path.join(self.arch.arch,'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.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.configureFortranFlush)
    self.executeTest(self.configureAtoll)
    # dummy rules, always needed except for remote builds
    self.addMakeRule('remote','')
    self.addMakeRule('remoteclean','')

    self.Dump()
    self.dumpConfigInfo()
    self.dumpMachineInfo()
    self.postProcessPackages()
    self.dumpCMakeConfig()
    self.dumpCMakeLists()
    self.cmakeBoot()
    self.DumpPkgconfig()
    self.DumpModule()
    self.framework.log.write('================================================================================\n')
    self.logClear()
    return