from __future__ import generators
import config.base

import os
import re
import itertools
from hashlib import md5 as new_md5

def sliding_window(seq, n=2):
  """
  Returns a sliding window (of width n) over data from the iterable
  s -> (s0,s1,...s[n-1]), (s1,s2,...,sn), ...
  """
  it     = iter(seq)
  result = tuple(itertools.islice(it, n))
  if len(result) == n:
    yield result
  for elem in it:
    result = result[1:] + (elem,)
    yield result

class FakePETScDir:
  def __init__(self):
    self.dir = 'UNKNOWN'

class Package(config.base.Configure):
  def __init__(self, framework):
    config.base.Configure.__init__(self, framework)
    self.headerPrefix        = 'PETSC'
    self.substPrefix         = 'PETSC'
    self.arch                = None # The architecture identifier
    self.externalPackagesDir = os.path.abspath('externalpackages')

    # These are determined by the configure tests
    self.found            = 0
    self.setNames()
    self.include          = []
    self.dinclude         = []   # all includes in this package and all those it depends on
    self.lib              = []
    self.dlib             = []   # all libraries in this package and all those it depends on
    self.directory        = None # path of the package installation point; for example /usr/local or /home/bsmith/mpich-2.0.1

    self.version          = ''   # the version of the package that PETSc will build with the --download-package option
    self.versionname      = ''   # string name that appears in package include file, for example HYPRE_RELEASE_VERSION
    self.versioninclude   = ''   # include file that contains package version information; if not provided uses includes[0]
    self.minversion       = ''   # minimum version of the package that is supported
    self.maxversion       = ''   # maximum version of the package that is supported
    self.foundversion     = ''   # version of the package actually found
    self.version_tuple    = ''   # version of the package actually found (tuple)
    self.requiresversion  = 0    # error if the version information is not found
    self.requirekandr     = 0    # package requires KandR compiler flags to build

    # These are specified for the package
    self.required               = 0    # 1 means the package is required
    self.devicePackage          = 0    # 1 if PETSC_HAVE_DEVICE should be defined by
                                       # inclusion of this package
    self.lookforbydefault       = 0    # 1 means the package is not required, but always look for and use if found
                                       # cannot tell the difference between user requiring it with --with-PACKAGE=1 and
                                       # this flag being one so hope user never requires it. Needs to be fixed in an overhaul of
                                       # args database so it keeps track of what the user set vs what the program set
    self.useddirectly           = 1    # 1 indicates used by PETSc directly, 0 indicates used by a package used by PETSc
    self.linkedbypetsc          = 1    # 1 indicates PETSc shared libraries (and PETSc executables) need to link against this library
    self.gitcommit              = None # Git commit to use for downloads
    self.gitcommitmain          = None # Git commit to use for petsc/main or similar non-release branches
    self.gcommfile              = None # File within the git clone - that has the gitcommit for the current build - saved
    self.gitsubmodules          = []   # List of git submodues that should be cloned along with the repo
    self.download               = []   # list of URLs where repository or tarballs may be found (git is tested before tarballs)
    self.deps                   = []   # other packages whose dlib or include we depend on, usually we also use self.framework.require()
    self.odeps                  = []   # dependent packages that are optional
    self.defaultLanguage        = 'C'  # The language in which to run tests
    self.liblist                = [[]] # list of libraries we wish to check for (packages can override with their own generateLibList() method)
    self.extraLib               = []   # additional libraries needed to link
    self.includes               = []   # headers to check for
    self.macros                 = []   # optional macros we wish to check for in the headers
    self.functions              = []   # functions we wish to check for in the libraries
    self.functionsDefine        = []   # optional functions we wish to check for in the libraries that should generate a PETSC_HAVE_ define
    self.functionsFortran       = 0    # 1 means the symbols in self.functions are Fortran symbols, so name-mangling is done
    self.functionsCxx           = [0, '', ''] # 1 means the symbols in self.functions symbol are C++ symbol, so name-mangling with prototype/call is done
    self.buildLanguages         = ['C']  # Languages the package is written in, hence also the compilers needed to build it. Normally only contains one
                                         # language, but can have multiple, such as ['FC', 'Cxx']. In PETSc's terminology, languages are C, Cxx, FC, CUDA, HIP, SYCL.
                                         # We use the first language in the list to check include headers, library functions and versions.
    self.noMPIUni               = 0    # 1 means requires a real MPI
    self.libDirs                = ['lib', 'lib64']   # search locations of libraries in the package directory tree; self.libDir is self.installDir + self.libDirs[0]
    self.includedir             = 'include' # location of includes in the package directory tree
    self.license                = None # optional license text
    self.excludedDirs           = []   # list of directory names that could be false positives, SuperLU_DIST when looking for SuperLU
    self.downloadonWindows      = 0  # 1 means the --download-package works on Microsoft Windows
    self.minCxxVersion          = framework.compilers.setCompilers.cxxDialectRange['Cxx'][0] # minimum c++ standard version required by the package, e.g. 'c++11'
    self.maxCxxVersion          = framework.compilers.setCompilers.cxxDialectRange['Cxx'][1] # maximum c++ standard version allowed by the package, e.g. 'c++14', must be greater than self.minCxxVersion
    self.publicInstall          = 1  # Installs the package in the --prefix directory if it was given. Packages that are only used
                                     # during the configuration/installation process such as sowing, make etc should be marked as 0
    self.parallelMake           = 1  # 1 indicates the package supports make -j np option

    self.precisions             = ['__fp16','single','double','__float128']; # Floating point precision package works with
    self.complex                = 1  # 0 means cannot use complex
    self.requires32bitint       = 0  # 1 means that the package will not work with 64-bit integers
    self.requires32bitintblas   = 1  # 1 means that the package will not work with 64-bit integer BLAS/LAPACK
    self.skippackagewithoptions = 0  # packages like fblaslapack and MPICH do not support --with-package* options so do not print them in help
    self.skippackagelibincludedirs = 0 # packages like make do not support --with-package-lib and --with-package-include so do not print them in help
    self.alternativedownload    = [] # Used by, for example mpi.py to print useful error messages, which does not support --download-mpi but one can use --download-mpich
    self.usesopenmp             = 'no'  # yes, no, unknown package is built to use OpenMP
    self.usespthreads           = 'no'  # yes, no, unknown package is built to use Pthreads
    self.cmakelistsdir          = '' # Location of CMakeLists.txt - if not located at the top level of the package dir

    # Outside coupling
    self.defaultInstallDir      = ''
    self.PrefixWriteCheck       = 1 # check if specified prefix location is writable for 'make install'

    self.isMPI                  = 0 # Is an MPI implementation, needed to check for compiler wrappers
    self.hastests               = 0 # indicates that PETSc make alltests has tests for this package
    self.hastestsdatafiles      = 0 # indicates that PETSc make alltests has tests for this package that require DATAFILESPATH to be set
    self.makerulename           = '' # some packages do too many things with the make stage; this allows a package to limit to, for example, just building the libraries
    self.installedpetsc         = 0  # configure actually compiled and installed PETSc
    self.installwithbatch       = 1  # install the package even though configure in the batch mode; f2blaslapack and fblaslapack for example
    self.builtafterpetsc        = 0  # package is compiled/installed after PETSc is compiled

    self.downloaded             = 0  # 1 indicates that this package is being downloaded during this run (internal use only)
    self.testoptions            = '' # Any PETSc options that should be used when this package is installed and the test harness is run
    self.executablename         = '' # full path of executable, for example cmake, bfort etc
    return

  def __str__(self):
    '''Prints the location of the packages includes and libraries'''
    output = ''
    if self.found:
      output = self.name+':\n'
      if self.foundversion:
        if hasattr(self,'versiontitle'):
          output += '  '+self.versiontitle+':  '+self.foundversion+'\n'
        else:
          output += '  Version:    '+self.foundversion+'\n'
      else:
        if self.version:      output += '  Version:    '+self.version+'\n'
      if self.include:        output += '  Includes:   '+self.headers.toStringNoDupes(self.include)+'\n'
      if self.lib:            output += '  Libraries:  '+self.libraries.toStringNoDupes(self.lib)+'\n'
      if self.executablename: output += '  Executable: '+getattr(self,self.executablename)+'\n'
      if self.usesopenmp == 'yes': output += '  uses OpenMP; use export OMP_NUM_THREADS=<p> or -omp_num_threads <p> to control the number of threads\n'
      if self.usesopenmp == 'unknown': output += '  Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> yourprogram -log_view) \n'
      if self.usespthreads == 'yes': output += '  uses PTHREADS; please consult the documentation on how to control the number of threads\n'
    return output

  def setupDependencies(self, framework):
    config.base.Configure.setupDependencies(self, framework)
    self.setCompilers    = framework.require('config.setCompilers', self)
    self.compilers       = framework.require('config.compilers', self)
    self.fortran         = framework.require('config.compilersFortran', self)
    self.compilerFlags   = framework.require('config.compilerFlags', self)
    self.types           = framework.require('config.types', self)
    self.headers         = framework.require('config.headers', self)
    self.libraries       = framework.require('config.libraries', self)
    self.programs        = framework.require('config.programs', self)
    self.sourceControl   = framework.require('config.sourceControl',self)
    try:
      import PETSc.options
      self.sharedLibraries = framework.require('PETSc.options.sharedLibraries', self)
      self.petscdir        = framework.require('PETSc.options.petscdir', self.setCompilers)
      self.petscclone      = framework.require('PETSc.options.petscclone',self.setCompilers)
      self.havePETSc       = True
    except ImportError:
      self.havePETSc       = False
      self.petscdir        = FakePETScDir()
    # All packages depend on make
    self.make          = framework.require('config.packages.make',self)
    if not self.isMPI and not self.package in ['make','cuda','hip','sycl','thrust','hwloc','x','bison','python']:
      # force MPI to be the first package (except for those listed above) configured since all other packages
      # may depend on its compilers defined here
      self.mpi         = framework.require('config.packages.MPI',self)
    return

  def setupHelp(self,help):
    '''Prints help messages for the package'''
    import nargs
    if not self.skippackagewithoptions:
      help.addArgument(self.PACKAGE,'-with-'+self.package+'=<bool>',nargs.ArgBool(None,self.required+self.lookforbydefault,'Indicate if you wish to test for '+self.name))
      help.addArgument(self.PACKAGE,'-with-'+self.package+'-dir=<dir>',nargs.ArgDir(None,None,'Indicate the root directory of the '+self.name+' installation',mustExist = 1))
      help.addArgument(self.PACKAGE,'-with-'+self.package+'-pkg-config=<dir>', nargs.ArgDir(None, None, 'Look for '+self.name+' using pkg-config utility optional directory to look in',mustExist = 1))
      if not self.skippackagelibincludedirs:
        help.addArgument(self.PACKAGE,'-with-'+self.package+'-include=<dirs>',nargs.ArgDirList(None,None,'Indicate the directory of the '+self.name+' include files'))
        help.addArgument(self.PACKAGE,'-with-'+self.package+'-lib=<libraries: e.g. [/Users/..../lib'+self.package+'.a,...]>',nargs.ArgLibrary(None,None,'Indicate the '+self.name+' libraries'))
    if self.download:
      help.addArgument(self.PACKAGE, '-download-'+self.package+'=<no,yes,filename,url>', nargs.ArgDownload(None, 0, 'Download and install '+self.name))
      if hasattr(self, 'download_git'):
        help.addArgument(self.PACKAGE, '-download-'+self.package+'-commit=commitid', nargs.ArgString(None, 0, 'Switch from installing release tarballs to git repo - using the specified commit of '+self.name))
      else:
        help.addArgument(self.PACKAGE, '-download-'+self.package+'-commit=commitid', nargs.ArgString(None, 0, 'The commit id from a git repository to use for the build of '+self.name))
      help.addDownload(self.package,self.download)
    return

  def setNames(self):
    '''Setup various package names
    name:         The module name (usually the filename)
    package:      The lowercase name
    PACKAGE:      The uppercase name
    pkgname:      The name of pkg-config (.pc) file
    downloadname:     Name for download option (usually name)
    downloaddirnames: names for downloaded directory (first part of string) (usually downloadname)
    '''
    import sys
    if hasattr(sys.modules.get(self.__module__), '__file__'):
      self.name       = os.path.splitext(os.path.basename(sys.modules.get(self.__module__).__file__))[0]
    else:
      self.name           = 'DEBUGGING'
    self.PACKAGE          = self.name.upper()
    self.package          = self.name.lower()
    self.pkgname          = self.package
    self.downloadname     = self.name
    self.downloaddirnames = [self.downloadname]
    return

  def getDefaultPrecision(self):
    '''The precision of the library'''
    if hasattr(self, 'precisionProvider'):
      if hasattr(self.precisionProvider, 'precision'):
        return self.precisionProvider.precision
    if hasattr(self, '_defaultPrecision'):
      return self._defaultPrecision
    return 'double'
  def setDefaultPrecision(self, defaultPrecision):
    '''The precision of the library'''
    self._defaultPrecision = defaultPrecision
    return
  defaultPrecision = property(getDefaultPrecision, setDefaultPrecision, doc = 'The precision of the library')

  def getDefaultScalarType(self):
    '''The scalar type for the library'''
    if hasattr(self, 'precisionProvider'):
      if hasattr(self.precisionProvider, 'scalartype'):
        return self.precisionProvider.scalartype
    return self._defaultScalarType
  def setDefaultScalarType(self, defaultScalarType):
    '''The scalar type for the library'''
    self._defaultScalarType = defaultScalarType
    return
  defaultScalarType = property(getDefaultScalarType, setDefaultScalarType, doc = 'The scalar type for of the library')

  def getDefaultIndexSize(self):
    '''The index size for the library'''
    if hasattr(self, 'indexProvider'):
      if hasattr(self.indexProvider, 'integerSize'):
        return self.indexProvider.integerSize
    return self._defaultIndexSize
  def setDefaultIndexSize(self, defaultIndexSize):
    '''The index size for the library'''
    self._defaultIndexSize = defaultIndexSize
    return
  defaultIndexSize = property(getDefaultIndexSize, setDefaultIndexSize, doc = 'The index size for of the library')

  def checkNoOptFlag(self):
    flags = ''
    flag = '-O0 '
    if self.setCompilers.checkCompilerFlag(flag): flags = flags+flag
    flag = '-mfp16-format=ieee'
    if self.setCompilers.checkCompilerFlag(flag): flags = flags+flag
    return flags

  def getSharedFlag(self,cflags):
    for flag in ['-PIC', '-fPIC', '-KPIC', '-qpic', '-fpic']:
      if cflags.find(flag) >=0: return flag
    return ''

  def getPointerSizeFlag(self,cflags):
    for flag in ['-m32', '-m64', '-xarch=v9','-q64','-mmic']:
      if cflags.find(flag) >=0: return flag
    return ''

  def getDebugFlags(self,cflags):
    outflags = []
    for flag in cflags.split():
      if flag in ['-g','-g3','-Z7']:
        outflags.append(flag)
    return ' '.join(outflags)

  def getWindowsNonOptFlags(self,cflags):
    outflags = []
    for flag in cflags.split():
      if flag in ['-MT','-MTd','-MD','-MDd','-threads']:
        outflags.append(flag)
    return ' '.join(outflags)

  def rmArgs(self,args,rejects):
    self.logPrint('Removing configure arguments '+str(rejects))
    return [arg for arg in args if not arg in rejects]

  def rmArgsPair(self,args,rejects,remove_ahead=True):
    '''Remove an argument and the next argument from a list of arguments'''
    '''For example: --ccbin compiler'''
    '''If remove_ahead is true, arguments rejects specifies the first entry in the pair and the following argument is removed, otherwise rejects specifies the second entry in the pair and the previous argument is removed as well.'''
    self.logPrint('Removing paired configure arguments '+str(rejects))
    rejects = set(rejects)
    nargs   = []
    skip    = -1
    for flag, next_flag in sliding_window(args):
      if skip == 1:
        skip = 0
        continue
      skip = 0

      flag_to_check = flag if remove_ahead else next_flag
      if flag_to_check in rejects:
        skip = 1
      else:
        nargs.append(flag)
    if remove_ahead is False and skip == 0: # append last flag
      nargs.append(next_flag)
    return nargs

  def rmArgsStartsWith(self,args,rejectstarts):
    rejects = []
    if not isinstance(rejectstarts, list): rejectstarts = [rejectstarts]
    for i in rejectstarts:
      rejects.extend([arg for arg in args if arg.startswith(i)])
    return self.rmArgs(args,rejects)

  def addArgStartsWith(self,args,sw,value):
    keep = []
    found = 0
    for i in args:
      if i.startswith(sw+'="'):
        i = i[:-1] + ' ' + value + '"'
        found = 1
      keep.append(i)
    if not found:
      keep.append(sw+'="' + value + '"')
    return keep

  def removeWarningFlags(self,flags):
    flags = self.rmArgs(
      flags,
      {
        '-Werror', '-Wall', '-Wwrite-strings', '-Wno-strict-aliasing', '-Wno-unknown-pragmas',
        '-Wno-unused-variable', '-Wno-unused-dummy-argument', '-std=c89', '-pedantic','--coverage',
        '-Mfree', '-fdefault-integer-8', '-fsanitize=address', '-fstack-protector'
      }
    )
    return ['-g' if f == '-g3' else f for f in flags]

  def __remove_flag_pair(self, flags, flag_to_remove, pair_prefix):
    """
    Remove FLAG_TO_REMOVE from FLAGS

    Parameters
    ----------
    - flags          - iterable (or string) of flags to remove from
    - flag_to_remove - the flag to remove
    - pair_prefix    - (Optional) if not None, indicates that FLAG_TO_REMOVE is in a pair, and
                       is prefixed by str(pair_prefix). For example, pair_prefix='-Xcompiler' indicates
                       that the flag is specified as <COMPILER_NAME> -Xcompiler FLAG_TO_REMOVE

    Return
    ------
    flags - list of post-processed flags
    """
    if isinstance(flags, str):
      flags = flags.split()

    if pair_prefix is None:
      return self.rmArgs(flags, {flag_to_remove})
    assert isinstance(pair_prefix, str)
    # deals with bare PAIR_PREFIX FLAG_TO_REMOVE
    flag_str = ' '.join(self.rmArgsPair(flags, {flag_to_remove}, remove_ahead=False))
    # handle PAIR_PREFIX -fsome_other_flag,FLAG_TO_REMOVE
    flag_str = re.sub(r',{}\s'.format(flag_to_remove), ' ', flag_str)
    # handle PAIR_PREFIX -fsome_other_flag,FLAG_TO_REMOVE,-fyet_another_flag
    flag_str = re.sub(r',{},'.format(flag_to_remove), ',', flag_str)
    # handle PAIR_PREFIX FLAG_TO_REMOVE,-fsome_another_flag
    flag_str = re.sub(r'\s{},'.format(flag_to_remove), ' ', flag_str)
    return flag_str.split()

  def removeVisibilityFlag(self, flags, pair_prefix=None):
    """Remove -fvisibility=hidden from flags."""
    return self.__remove_flag_pair(flags, '-fvisibility=hidden', pair_prefix)

  def removeCoverageFlag(self, flags, pair_prefix=None):
    """Remove --coverage from flags."""
    return self.__remove_flag_pair(flags, '--coverage', pair_prefix)

  def removeStdCxxFlag(self,flags):
    '''Remove the -std=[CXX_VERSION] flag from the list of flags, but only for CMake packages'''
    if issubclass(type(self),config.package.CMakePackage):
      # only cmake packages get their std flags removed since they use
      # -DCMAKE_CXX_STANDARD to set the std flag
      cmakeLists = os.path.join(self.packageDir,self.cmakelistsdir,'CMakeLists.txt')
      with open(cmakeLists,'r') as fd:
        refcxxstd = re.compile(r'^\s*(?!#)(set\()(CMAKE_CXX_STANDARD\s[A-z0-9\s]*)')
        for line in fd:
          match = refcxxstd.search(line)
          if match:
            # from set(CMAKE_CXX_STANDARD <val> [CACHE <type> <docstring> [FORCE]]) extract
            # <val> CACHE <type> <docstring> [FORCE]
            cmakeSetCmd = match.groups()[1].split()[1:]
            if (len(cmakeSetCmd) == 1) or 'CACHE' not in cmakeSetList:
              # The worst behaved, we have a pure "set". we shouldn't rely on
              # CMAKE_CXX_STANDARD, since the package overrides it unconditionally. Thus
              # we leave the std flag in the compiler flags.
              self.logPrint('removeStdCxxFlag: CMake Package {pkg} had an overriding \'set\' command in their CMakeLists.txt:\n\t{cmd}\nLeaving std flags in'.format(pkg=self.name,cmd=line.strip()),indent=1)
              return flags
            self.logPrint('removeStdCxxFlag: CMake Package {pkg} did NOT have an overriding \'set\' command in their CMakeLists.txt:\n\t{cmd}\nRemoving std flags'.format(pkg=self.name,cmd=line.strip()),indent=1)
            # CACHE was found in the set command, meaning we can override it from the
            # command line. So we continue on to remove the std flags.
            break
      stdFlags = ('-std=c++','-std=gnu++')
      return [f for f in flags if not f.startswith(stdFlags)]
    return flags


  def updatePackageCFlags(self,flags):
    '''To turn off various warnings or errors the compilers may produce with external packages, remove or add appropriate compiler flags'''
    outflags = self.removeVisibilityFlag(flags.split())
    outflags = self.removeWarningFlags(outflags)
    outflags = self.removeCoverageFlag(outflags)
    if self.requirekandr:
      outflags += self.setCompilers.KandRFlags
    return ' '.join(outflags)

  def updatePackageFFlags(self,flags):
    outflags = self.removeVisibilityFlag(flags.split())
    outflags = self.removeWarningFlags(outflags)
    outflags = self.removeCoverageFlag(outflags)
    with self.Language('FC'):
      if config.setCompilers.Configure.isNAG(self.getLinker(), self.log):
         outflags.extend(['-mismatch','-dusty','-dcfuns'])
      if config.setCompilers.Configure.isGfortran100plus(self.getCompiler(), self.log):
        outflags.append('-fallow-argument-mismatch')
    return ' '.join(outflags)

  def updatePackageCxxFlags(self,flags):
    outflags = self.removeVisibilityFlag(flags.split())
    outflags = self.removeWarningFlags(outflags)
    outflags = self.removeCoverageFlag(outflags)
    outflags = self.removeStdCxxFlag(outflags)
    return ' '.join(outflags)

  def updatePackageCUDAFlags(self, flags):
    outflags = self.removeVisibilityFlag(flags, pair_prefix='-Xcompiler')
    outflags = self.removeCoverageFlag(outflags, pair_prefix='-Xcompiler')
    return ' '.join(outflags)

  def getDefaultLanguage(self):
    '''The language in which to run tests'''
    if hasattr(self, 'forceLanguage'):
      return self.forceLanguage
    if hasattr(self, 'languageProvider'):
      if hasattr(self.languageProvider, 'defaultLanguage'):
        return self.languageProvider.defaultLanguage
      elif hasattr(self.languageProvider, 'clanguage'):
        return self.languageProvider.clanguage
    return self._defaultLanguage
  def setDefaultLanguage(self, defaultLanguage):
    '''The language in which to run tests'''
    if hasattr(self, 'languageProvider'):
      del self.languageProvider
    self._defaultLanguage = defaultLanguage
    return
  defaultLanguage = property(getDefaultLanguage, setDefaultLanguage, doc = 'The language in which to run tests')

  def getArch(self):
    '''The architecture identifier'''
    if hasattr(self, 'archProvider'):
      if hasattr(self.archProvider, 'arch'):
        return self.archProvider.arch
    return self._arch
  def setArch(self, arch):
    '''The architecture identifier'''
    self._arch = arch
    return
  arch = property(getArch, setArch, doc = 'The architecture identifier')

  # This construct should be removed and just have getInstallDir() handle the process
  def getDefaultInstallDir(self):
    '''The installation directory of the library'''
    if hasattr(self, 'installDirProvider'):
      if hasattr(self.installDirProvider, 'dir'):
        return self.installDirProvider.dir
    return self._defaultInstallDir
  def setDefaultInstallDir(self, defaultInstallDir):
    '''The installation directory of the library'''
    self._defaultInstallDir = defaultInstallDir
    return
  defaultInstallDir = property(getDefaultInstallDir, setDefaultInstallDir, doc = 'The installation directory of the library')

  def getExternalPackagesDir(self):
    '''The directory for downloaded packages'''
    if hasattr(self, 'externalPackagesDirProvider'):
      if hasattr(self.externalPackagesDirProvider, 'dir'):
        return self.externalPackagesDirProvider.dir
    elif not self.framework.externalPackagesDir is None:
      return os.path.abspath('externalpackages')
    return self._externalPackagesDir
  def setExternalPackagesDir(self, externalPackagesDir):
    '''The directory for downloaded packages'''
    self._externalPackagesDir = externalPackagesDir
    return
  externalPackagesDir = property(getExternalPackagesDir, setExternalPackagesDir, doc = 'The directory for downloaded packages')

  def getSearchDirectories(self):
    '''By default, do not search any particular directories, but try compiler default paths'''
    return ['']

  def getInstallDir(self):
    '''Calls self.Install() to install the package'''
    '''Returns --prefix (or the value computed from --package-prefix-hash) if provided otherwise $PETSC_DIR/$PETSC_ARCH'''
    '''Special case for packages such as sowing that are have self.publicInstall == 0 it always locates them in $PETSC_DIR/$PETSC_ARCH'''
    '''Special case if --package-prefix-hash then even self.publicInstall == 0 are installed in the prefix location'''
    self.confDir    = self.installDirProvider.confDir  # private install location; $PETSC_DIR/$PETSC_ARCH for PETSc
    self.packageDir = self.getDir()
    self.setupDownload()
    if not self.packageDir: self.packageDir = self.downLoad()
    self.updateGitDir()
    self.updatehgDir()
    if (self.publicInstall or 'package-prefix-hash' in self.argDB) and not ('package-prefix-hash' in self.argDB and (hasattr(self,'postProcess') or self.builtafterpetsc)):
      self.installDir = self.defaultInstallDir
    else:
      self.installDir = self.confDir
    if self.PrefixWriteCheck and self.publicInstall and not 'package-prefix-hash' in self.argDB and self.installDirProvider.installSudo:
      if self.installDirProvider.dir in ['/usr','/usr/local']: prefixdir = os.path.join(self.installDirProvider.dir,'petsc')
      else: prefixdir = self.installDirProvider.dir
      msg='''\
Specified prefix-dir: %s is read-only! "%s" cannot install at this location! Suggest:
      sudo mkdir %s
      sudo chown $USER %s
Now rerun configure''' % (self.installDirProvider.dir, '--download-'+self.package, prefixdir, prefixdir)
      raise RuntimeError(msg)
    self.includeDir = os.path.join(self.installDir, 'include')
    self.libDir = os.path.join(self.installDir, self.libDirs[0])
    installDir = self.Install()
    if not installDir:
      raise RuntimeError(self.package+' forgot to return the install directory from the method Install()\n')
    return os.path.abspath(installDir)

  def getChecksum(self,source, chunkSize = 1024*1024):
    '''Return the md5 checksum for a given file, which may also be specified by its filename
       - The chunkSize argument specifies the size of blocks read from the file'''
    if hasattr(source, 'close'):
      f = source
    else:
      f = open(source, 'rb')
    m = new_md5()
    size = chunkSize
    buf  = f.read(size)
    while buf:
      m.update(buf)
      buf = f.read(size)
    f.close()
    return m.hexdigest()

  def generateLibList(self, directory, liblist = None):
    '''Generates full path list of libraries from self.liblist'''
    if liblist == None: liblist = self.liblist
    if [] in liblist: liblist.remove([]) # process null list later
    if liblist == []: # most packages don't have a liblist - so return an empty list
      return [[]]
    alllibs = []
    if not directory:  # compiler default path - so also check compiler default libs.
      alllibs.insert(0,[])
    elif directory in self.libraries.sysDirs:
      self.logPrint('generateLibList: systemDir detected! skipping: '+str(directory))
      directory = ''
    for libSet in liblist:
      libs = []
      use_L = 0
      for library in libSet:
        # if the library name starts with 'lib' or uses '-lfoo' then add in -Lpath. Otherwise - add the fullpath
        if library.startswith('-l') or library.startswith('lib'):
          libs.append(library)
          use_L = 1
        else:
          libs.append(os.path.join(directory, library))
      if use_L and directory:
        libs.insert(0,'-L'+directory)
      libs.extend(self.extraLib)
      alllibs.append(libs)
    return alllibs

  def getIncludeDirs(self, prefix, includeDirs):
    if not isinstance(includeDirs, list):
      includeDirs = [includeDirs]
    iDirs = [inc for inc in includeDirs if os.path.isabs(inc)] + [os.path.join(prefix, inc) for inc in includeDirs if not os.path.isabs(inc)]
    return [inc for inc in iDirs if os.path.exists(inc)]

  def addToArgs(self,args,key,value):
    found = 0
    for i in range(0,len(args)):
      if args[i].startswith(key+'='):
        args[i] = args[i][0:-1] + ' '+ value +'"'
        found = 1
    if not found: args.append(key+'="'+value+'"')

  def generateGuesses(self):
    d = self.checkDownload()
    if d:
      if not self.liblist or not self.liblist[0] or self.builtafterpetsc :
        yield('Download '+self.PACKAGE, d, [], self.getIncludeDirs(d, self.includedir))
      for libdir in self.libDirs:
        libdirpath = os.path.join(d, libdir)
        if not os.path.isdir(libdirpath):
          self.logPrint(self.PACKAGE+': Downloaded DirPath not found.. skipping: '+libdirpath)
          continue
        for l in self.generateLibList(libdirpath):
          yield('Download '+self.PACKAGE, d, l, self.getIncludeDirs(d, self.includedir))
      raise RuntimeError('Downloaded '+self.package+' could not be used. Please check install in '+d+'\n')

    if 'with-'+self.package+'-pkg-config' in self.argDB:
      if self.argDB['with-'+self.package+'-pkg-config']:
        #  user provided path to look for pkg info
        if 'PKG_CONFIG_PATH' in os.environ: path = os.environ['PKG_CONFIG_PATH']
        else: path = None
        os.environ['PKG_CONFIG_PATH'] = self.argDB['with-'+self.package+'-pkg-config']

      l,err,ret  = config.base.Configure.executeShellCommand('pkg-config '+self.pkgname+' --libs', timeout=60, log = self.log)
      l = l.strip()
      i,err,ret  = config.base.Configure.executeShellCommand('pkg-config '+self.pkgname+' --cflags', timeout=60, log = self.log)
      i = i.strip()
      if self.argDB['with-'+self.package+'-pkg-config']:
        if path: os.environ['PKG_CONFIG_PATH'] = path
        else: os.environ['PKG_CONFIG_PATH'] = ''
      yield('pkg-config located libraries and includes '+self.PACKAGE, None, l.split(), i)
      raise RuntimeError('pkg-config could not locate correct includes and libraries for '+self.package)


    if 'with-'+self.package+'-dir' in self.argDB:
      d = self.argDB['with-'+self.package+'-dir']
      # error if package-dir is in externalpackages
      if os.path.realpath(d).find(os.path.realpath(self.externalPackagesDir)) >=0:
        fakeExternalPackagesDir = d.replace(os.path.realpath(d).replace(os.path.realpath(self.externalPackagesDir),''),'')
        raise RuntimeError('Bad option: '+'--with-'+self.package+'-dir='+self.argDB['with-'+self.package+'-dir']+'\n'+
                           fakeExternalPackagesDir+' is reserved for --download-package scratch space. \n'+
                           'Do not install software in this location nor use software in this directory.')

      if not self.liblist or not self.liblist[0]:
          yield('User specified root directory '+self.PACKAGE, d, [], self.getIncludeDirs(d, self.includedir))

      for libdir in self.libDirs:
        libdirpath = os.path.join(d, libdir)
        if not os.path.isdir(libdirpath):
          self.logPrint(self.PACKAGE+': UserSpecified DirPath not found.. skipping: '+libdirpath)
          continue
        for l in self.generateLibList(libdirpath):
          yield('User specified root directory '+self.PACKAGE, d, l, self.getIncludeDirs(d, self.includedir))

      if 'with-'+self.package+'-include' in self.argDB:
        raise RuntimeError('Do not set --with-'+self.package+'-include if you set --with-'+self.package+'-dir')
      if 'with-'+self.package+'-lib' in self.argDB:
        raise RuntimeError('Do not set --with-'+self.package+'-lib if you set --with-'+self.package+'-dir')
      raise RuntimeError('--with-'+self.package+'-dir='+self.argDB['with-'+self.package+'-dir']+' did not work')

    if 'with-'+self.package+'-include' in self.argDB and not 'with-'+self.package+'-lib' in self.argDB:
      if self.liblist and self.liblist[0]:
        raise RuntimeError('If you provide --with-'+self.package+'-include you must also supply with-'+self.package+'-lib\n')
    if 'with-'+self.package+'-lib' in self.argDB and not 'with-'+self.package+'-include' in self.argDB:
      if self.includes:
        raise RuntimeError('If you provide --with-'+self.package+'-lib you must also supply with-'+self.package+'-include\n')
    if 'with-'+self.package+'-include-dir' in self.argDB:
        raise RuntimeError('Use --with-'+self.package+'-include; not --with-'+self.package+'-include-dir')

    if 'with-'+self.package+'-include' in self.argDB or 'with-'+self.package+'-lib' in self.argDB:
      if self.liblist and self.liblist[0]:
        libs  = self.argDB['with-'+self.package+'-lib']
        slibs = str(self.argDB['with-'+self.package+'-lib'])
      else:
        libs  = []
        slibs = 'NoneNeeded'
      inc  = []
      d  = None
      if self.includes:
        inc = self.argDB['with-'+self.package+'-include']
        # hope that package root is one level above first include directory specified
        if inc:
          d   = os.path.dirname(inc[0])

      if not isinstance(inc, list): inc = inc.split(' ')
      if not isinstance(libs, list): libs = libs.split(' ')
      inc = [os.path.abspath(i) for i in inc]
      yield('User specified '+self.PACKAGE+' libraries', d, libs, inc)
      msg = '--with-'+self.package+'-lib='+slibs
      if self.includes:
        msg += ' and \n'+'--with-'+self.package+'-include='+str(self.argDB['with-'+self.package+'-include'])
      msg += ' did not work'
      raise RuntimeError(msg)

    for d in self.getSearchDirectories():
      if d:
        if not os.path.isdir(d):
          self.logPrint(self.PACKAGE+': SearchDir DirPath not found.. skipping: '+d)
          continue
        includedir = self.getIncludeDirs(d, self.includedir)
        for libdir in self.libDirs:
          libdirpath = os.path.join(d, libdir)
          if not os.path.isdir(libdirpath):
            self.logPrint(self.PACKAGE+': DirPath not found.. skipping: '+libdirpath)
            continue
          for l in self.generateLibList(libdirpath):
            yield('Package specific search directory '+self.PACKAGE, d, l, includedir)
      else:
        includedir = ''
        for l in self.generateLibList(d): # d = '' i.e search compiler libraries
            yield('Compiler specific search '+self.PACKAGE, d, l, includedir)

    if not self.lookforbydefault or ('with-'+self.package in self.framework.clArgDB and self.argDB['with-'+self.package]):
      mesg = 'Unable to find '+self.package+' in default locations!\nPerhaps you can specify with --with-'+self.package+'-dir=<directory>\nIf you do not want '+self.name+', then give --with-'+self.package+'=0'
      if self.download: mesg +='\nYou might also consider using --download-'+self.package+' instead'
      if self.alternativedownload: mesg +='\nYou might also consider using --download-'+self.alternativedownload+' instead'
      raise RuntimeError(mesg)

  def checkDownload(self):
    '''Check if we should download the package, returning the install directory or the empty string indicating installation'''
    if not self.download:
      return ''
    if self.argDB['with-batch'] and self.argDB['download-'+self.package] and not (hasattr(self.setCompilers,'cross_cc') or self.installwithbatch): raise RuntimeError('--download-'+self.name+' cannot be used on batch systems. You must either\n\
    1) load the appropriate module on your system and use --with-'+self.name+' or \n\
    2) locate its installation on your machine or install it yourself and use --with-'+self.name+'-dir=path\n')

    if self.argDB['download-'+self.package] and 'package-prefix-hash' in self.argDB and self.argDB['package-prefix-hash'] == 'reuse' and not hasattr(self,'postProcess') and not self.builtafterpetsc: # package already built in prefix hash location so reuse it
      self.installDir = self.defaultInstallDir
      return self.defaultInstallDir
    if self.argDB['download-'+self.package]:
      if self.license and not os.path.isfile('.'+self.package+'_license'):
        self.logClear()
        self.logPrint("**************************************************************************************************", debugSection='screen')
        self.logPrint('Please register to use '+self.downloadname+' at '+self.license, debugSection='screen')
        self.logPrint("**************************************************************************************************\n", debugSection='screen')
        fd = open('.'+self.package+'_license','w')
        fd.close()
      return self.getInstallDir()
    else:
      # check if download option is set for MPI dependent packages - if so flag an error.
      mesg=''
      if hasattr(self,'mpi') and self.mpi in self.deps:
        if 'download-mpich' in self.argDB and self.argDB['download-mpich'] or 'download-openmpi' in self.argDB and self.argDB['download-openmpi']:
          mesg+='Cannot use --download-mpich or --download-openmpi when not using --download-%s. Perhaps you want --download-%s.\n' % (self.package,self.package)
      if mesg:
        raise RuntimeError(mesg)
    return ''

  def installNeeded(self, mkfile):
    makefile       = os.path.join(self.packageDir, mkfile)
    makefileSaved  = os.path.join(self.confDir, 'lib','petsc','conf','pkg.conf.'+self.package)
    gcommfileSaved = os.path.join(self.confDir,'lib','petsc','conf', 'pkg.gitcommit.'+self.package)
    if self.downloaded:
      self.log.write(self.PACKAGE+' was just downloaded, forcing a rebuild because cannot determine if package has changed\n')
      return 1
    if not os.path.isfile(makefileSaved) or not (self.getChecksum(makefileSaved) == self.getChecksum(makefile)):
      self.log.write('Have to rebuild '+self.PACKAGE+', '+makefile+' != '+makefileSaved+'\n')
      return 1
    else:
      self.log.write('Makefile '+makefileSaved+' has correct checksum\n')
    if self.gcommfile and os.path.isfile(self.gcommfile):
      if not os.path.isfile(gcommfileSaved) or not (self.getChecksum(gcommfileSaved) == self.getChecksum(self.gcommfile)):
        self.log.write('Have to rebuild '+self.PACKAGE+', '+self.gcommfile+' != '+gcommfileSaved+'\n')
        return 1
      else:
        self.log.write('Commit file '+gcommfileSaved+' has correct checksum\n')
    self.log.write('Do not need to rebuild '+self.PACKAGE+'\n')
    return 0

  def postInstall(self, output, mkfile):
    '''Dump package build log into configure.log - also copy package config to prevent unnecessary rebuild'''
    self.log.write('********Output of running make on '+self.PACKAGE+' follows *******\n')
    self.log.write(output)
    self.log.write('********End of Output of running make on '+self.PACKAGE+' *******\n')
    subconfDir = os.path.join(self.confDir, 'lib', 'petsc', 'conf')
    if not os.path.isdir(subconfDir):
      os.makedirs(subconfDir)
    makefile       = os.path.join(self.packageDir, mkfile)
    makefileSaved  = os.path.join(subconfDir, 'pkg.conf.'+self.package)
    gcommfileSaved = os.path.join(subconfDir, 'pkg.gitcommit.'+self.package)
    import shutil
    shutil.copyfile(makefile,makefileSaved)
    if self.gcommfile and os.path.exists(self.gcommfile):
      shutil.copyfile(self.gcommfile,gcommfileSaved)
    self.framework.actions.addArgument(self.PACKAGE, 'Install', 'Installed '+self.PACKAGE+' into '+self.installDir)

  def matchExcludeDir(self,dir):
    '''Check is the dir matches something in the excluded directory list'''
    for exdir in self.excludedDirs:
      if dir.lower().startswith(exdir.lower()):
        return 1
    return 0

  def gitPreReqCheck(self):
    '''Some packages may need addition prerequisites if the package comes from a git repository'''
    return 1

  def updatehgDir(self):
    '''Checkout the correct hash'''
    if hasattr(self.sourceControl, 'hg') and (self.packageDir == os.path.join(self.externalPackagesDir,'hg.'+self.package)):
      if hasattr(self,'hghash'):
        config.base.Configure.executeShellCommand([self.sourceControl.hg, 'update', '-c', self.hghash], cwd=self.packageDir, log = self.log)

  def updateGitDir(self):
    '''Checkout the correct gitcommit for the gitdir - and update pkg.gitcommit'''
    if hasattr(self.sourceControl, 'git') and (self.packageDir == os.path.join(self.externalPackagesDir,'git.'+self.package)):
      if not (hasattr(self, 'gitcommit') and self.gitcommit):
        if hasattr(self, 'download_git'):
          self.gitcommit = 'HEAD'
        else:
          raise RuntimeError('Trying to update '+self.package+' package source directory '+self.packageDir+' which is supposed to be a git repository, but no gitcommit is set for this package.\n\
Try to delete '+self.packageDir+' and rerun configure.\n\
If the problem persists, please send your configure.log to petsc-maint@mcs.anl.gov')
      # verify that packageDir is actually a git clone
      if not os.path.isdir(os.path.join(self.packageDir,'.git')):
        raise RuntimeError(self.packageDir +': is not a git repository! '+os.path.join(self.packageDir,'.git')+' not found!')
      gitdir,err,ret = config.base.Configure.executeShellCommand([self.sourceControl.git, 'rev-parse','--git-dir'], cwd=self.packageDir, log = self.log)
      if gitdir != '.git':
        raise RuntimeError(self.packageDir +': is not a git repository! "git rev-parse --gitdir" gives: '+gitdir)

      prefetch = 0
      if self.gitcommit.startswith('origin/'):
        prefetch = self.gitcommit.replace('origin/','')
      else:
        try:
          config.base.Configure.executeShellCommand([self.sourceControl.git, 'cat-file', '-e', self.gitcommit+'^{commit}'], cwd=self.packageDir, log = self.log)
          gitcommit_hash,err,ret = config.base.Configure.executeShellCommand([self.sourceControl.git, 'rev-parse', self.gitcommit], cwd=self.packageDir, log = self.log)
          if self.gitcommit != 'HEAD':
            # check if origin/branch exists - if so warn user that we are using the remote branch
            try:
              rbranch = 'origin/'+self.gitcommit
              config.base.Configure.executeShellCommand([self.sourceControl.git, 'cat-file', '-e', rbranch+'^{commit}'], cwd=self.packageDir, log = self.log)
              gitcommit_hash,err,ret = config.base.Configure.executeShellCommand([self.sourceControl.git, 'rev-parse', self.gitcommit], cwd=self.packageDir, log = self.log)
              self.logPrintWarning('Branch "%s" is specified, however remote branch "%s" also exists! Proceeding with using the remote branch. \
To use the local branch (manually checkout local branch and) - rerun configure with option --download-%s-commit=HEAD)' % (self.gitcommit, rbranch, self.name))
              prefetch = self.gitcommit
            except:
              pass
        except:
          prefetch = self.gitcommit
      if prefetch:
        fetched = 0
        self.logPrintBox('Attempting a "git fetch" commit/branch/tag: %s from Git repositor%s: %s' % (str(self.gitcommit), str('ies' if len(self.retriever.git_urls) > 1 else 'y'), str(self.retriever.git_urls)))
        for git_url in self.retriever.git_urls:
          try:
            config.base.Configure.executeShellCommand([self.sourceControl.git, 'fetch', '--tags', git_url, prefetch], cwd=self.packageDir, log = self.log)
            gitcommit_hash,err,ret = config.base.Configure.executeShellCommand([self.sourceControl.git, 'rev-parse', 'FETCH_HEAD'], cwd=self.packageDir, log = self.log)
            fetched = 1
            break
          except:
            continue
        if not fetched:
          raise RuntimeError('The above "git fetch" failed! Check if the specified "commit/branch/tag" is present in the remote git repo.\n\
To use currently downloaded (local) git snapshot - use: --download-'+self.package+'-commit=HEAD')
      if self.gitcommit != 'HEAD':
        try:
          config.base.Configure.executeShellCommand([self.sourceControl.git, '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'], cwd=self.packageDir, log = self.log)
          config.base.Configure.executeShellCommand([self.sourceControl.git, 'clean', '-f', '-d', '-x'], cwd=self.packageDir, log = self.log)
        except RuntimeError as e:
          if str(e).find("Unknown option: -c") >= 0:
            self.logPrintWarning('Unable to "git stash". Likely due to antique Git version (<1.8). Proceeding without stashing!')
          else:
            raise RuntimeError('Unable to run git stash/clean in repository: '+self.packageDir+'.\nPerhaps its a git error!')
        try:
          if self.gitsubmodules:
            config.base.Configure.executeShellCommand([self.sourceControl.git, 'checkout', '--recurse-submodules', '-f', gitcommit_hash], cwd=self.packageDir, log = self.log)
          else:
            config.base.Configure.executeShellCommand([self.sourceControl.git, 'checkout', '-f', gitcommit_hash], cwd=self.packageDir, log = self.log)
        except:
          raise RuntimeError('Unable to checkout commit: '+self.gitcommit+' in repository: '+self.packageDir+'.\nPerhaps its a git error!')
      # write a commit-tag file
      self.gcommfile = os.path.join(self.packageDir,'pkg.gitcommit')
      with open(self.gcommfile,'w') as fd:
        fd.write(gitcommit_hash)
    return

  def getDir(self):
    '''Find the directory containing the package'''
    packages = self.externalPackagesDir
    if not os.path.isdir(packages):
      os.makedirs(packages)
      self.framework.actions.addArgument('Framework', 'Directory creation', 'Created the external packages directory: '+packages)
    Dir = []
    pkgdirs = os.listdir(packages)
    gitpkg  = 'git.'+self.package
    hgpkg  = 'hg.'+self.package
    self.logPrint('Looking for '+self.PACKAGE+' at '+gitpkg+ ', '+hgpkg+' or a directory starting with '+str(self.downloaddirnames))
    if hasattr(self.sourceControl, 'git') and gitpkg in pkgdirs:
      Dir.append(gitpkg)
    if hasattr(self.sourceControl, 'hg') and hgpkg in pkgdirs:
      Dir.append(hgpkg)
    for d in pkgdirs:
      for j in self.downloaddirnames:
        if d.lower().startswith(j.lower()) and os.path.isdir(os.path.join(packages, d)) and not self.matchExcludeDir(d):
          Dir.append(d)

    if len(Dir) > 1:
      raise RuntimeError('Located multiple directories with package '+self.package+' '+str(Dir)+'\nDelete directory '+self.arch+' and rerun ./configure')

    if Dir:
      self.logPrint('Found a copy of '+self.PACKAGE+' in '+str(Dir[0]))
      return os.path.join(packages, Dir[0])
    else:
      self.logPrint('Could not locate an existing copy of '+self.PACKAGE+':')
      self.logPrint('  '+str(pkgdirs))
      return

  def setupDownload(self):
    import retrieval
    self.retriever = retrieval.Retriever(self.sourceControl, argDB = self.argDB)
    self.retriever.setup()
    self.retriever.ver = self.petscdir.version
    self.retriever.setupURLs(self.package,self.download,self.gitsubmodules,self.gitPreReqCheck())

  def downLoad(self):
    '''Downloads a package; using hg or ftp; opens it in the with-packages-build-dir directory'''
    retriever = self.retriever
    retriever.saveLog()
    self.logPrint('Downloading '+self.name)
    # now attempt to download each url until any one succeeds.
    err =''
    for proto, url in retriever.generateURLs():
      self.logPrintBox('Trying to download '+url+' for '+self.PACKAGE)
      try:
        retriever.genericRetrieve(proto, url, self.externalPackagesDir)
        self.logWrite(retriever.restoreLog())
        retriever.saveLog()
        pkgdir = self.getDir()
        if not pkgdir:
          raise RuntimeError('Could not locate downloaded package ' +self.PACKAGE +' in '+self.externalPackagesDir)
        self.framework.actions.addArgument(self.PACKAGE, 'Download', 'Downloaded '+self.PACKAGE+' into '+pkgdir)
        retriever.restoreLog()
        self.downloaded = 1
        return pkgdir
      except RuntimeError as e:
        self.logPrint('ERROR: '+str(e))
        err += str(e)
    self.logWrite(retriever.restoreLog())
    raise RuntimeError('Error during download/extract/detection of '+self.PACKAGE+':\n'+err)

  def Install(self):
    raise RuntimeError('No custom installation implemented for package '+self.package+'\n')

  def checkInclude(self, incl, hfiles, otherIncludes = [], timeout = 600.0):
    self.headers.pushLanguage(self.buildLanguages[0]) # default is to use the first language in checking
    self.headers.saveLog()
    ret = self.executeTest(self.headers.checkInclude, [incl, hfiles], {'otherIncludes' : otherIncludes, 'macro' : None, 'timeout': timeout})
    self.logWrite(self.headers.restoreLog())
    self.headers.popLanguage()
    return ret

  def checkMacros(self, timeout = 600.0):
    if not len(self.macros):
      return
    self.headers.pushLanguage(self.buildLanguages[0]) # default is to use the first language in checking
    self.logPrint('Checking for macros ' + str(self.macros) + ' in ' + str(self.includes))
    self.headers.saveLog()
    for macro in self.macros:
      self.executeTest(self.headers.checkInclude, [self.include, self.includes], {'macro' : macro, 'timeout' : timeout})
    self.logWrite(self.headers.restoreLog())
    self.headers.popLanguage()
    return

  def checkPackageLink(self, includes, body, cleanup = 1, codeBegin = None, codeEnd = None, shared = 0):
    flagsArg = self.getPreprocessorFlagsArg()
    oldFlags = getattr(self.compilers, flagsArg)
    oldLibs  = self.compilers.LIBS
    setattr(self.compilers, flagsArg, oldFlags+' '+self.headers.toString(self.include))
    self.compilers.LIBS = self.libraries.toString(self.lib)+' '+self.compilers.LIBS
    if 'FC' in self.buildLanguages:
      self.compilers.LIBS = ' '.join([self.libraries.getLibArgument(lib) for lib in self.compilers.flibs])+' '+self.setCompilers.LIBS
    if 'Cxx' in self.buildLanguages:
      self.compilers.LIBS = ' '.join([self.libraries.getLibArgument(lib) for lib in self.compilers.cxxlibs])+' '+self.setCompilers.LIBS
    result = self.checkLink(includes, body, cleanup, codeBegin, codeEnd, shared)
    setattr(self.compilers, flagsArg,oldFlags)
    self.compilers.LIBS = oldLibs
    return result

  @staticmethod
  def sortPackageDependencies(startnode):
    '''Create a dependency graph for all deps, and sort them'''
    import graph
    depGraph = graph.DirectedGraph()

    def addGraph(Graph,node,nodesAdded=[]):
      '''Recursively traverse the dependency graph - and add them as graph edges.'''
      if not hasattr(node,'deps'): return
      Graph.addVertex(node)
      nodesAdded.append(node)
      deps = list(node.deps)
      for odep in node.odeps:
        if odep.found: deps.append(odep)
      if deps:
        Graph.addEdges(node,outputs=deps)
      for dep in deps:
        if dep not in nodesAdded:
          addGraph(Graph,dep,nodesAdded)
      return

    addGraph(depGraph,startnode)
    return [sortnode for sortnode in graph.DirectedGraph.topologicalSort(depGraph,start=startnode)]

  def checkDependencies(self):
    '''Loop over declared dependencies of package and error if any are missing'''
    for package in self.deps:
      if not hasattr(package, 'found'):
        raise RuntimeError('Package '+package.name+' does not have found attribute!')
      if not package.found:
        if self.argDB['with-'+package.package] == 1:
          raise RuntimeError('Package '+package.PACKAGE+' needed by '+self.name+' failed to configure.\nMail configure.log to petsc-maint@mcs.anl.gov.')
        else:
          str = ''
          if package.download: str = ' or --download-'+package.package
          raise RuntimeError('Did not find package '+package.PACKAGE+' needed by '+self.name+'.\nEnable the package using --with-'+package.package+str)
    for package in self.odeps:
      if not hasattr(package, 'found'):
        raise RuntimeError('Package '+package.name+' does not have found attribute!')
      if not package.found:
        if 'with-'+package.package in self.framework.clArgDB and self.framework.clArgDB['with-'+package.package] == 1:
          raise RuntimeError('Package '+package.PACKAGE+' needed by '+self.name+' failed to configure.\nMail configure.log to petsc-maint@mcs.anl.gov.')

    dpkgs = Package.sortPackageDependencies(self)
    dpkgs.remove(self)
    for package in dpkgs:
      if hasattr(package, 'lib'):     self.dlib += package.lib
      if hasattr(package, 'include'): self.dinclude += package.include
    return

  def configureLibrary(self):
    '''Find an installation and check if it can work with PETSc'''
    self.log.write('==================================================================================\n')
    self.logPrint('Checking for a functional '+self.name)
    foundLibrary = 0
    foundHeader  = 0

    for location, directory, lib, incl in self.generateGuesses():
      #  directory is not used in the search, it is used only in logging messages about where the
      #  searching is taking place. It has to already be embedded inside the lib argument
      if self.builtafterpetsc:
        self.found = 1
        return

      if directory and not os.path.isdir(directory):
        self.logPrint('Directory does not exist: %s (while checking "%s" for "%r")' % (directory,location,lib))
        continue
      if lib == '': lib = []
      elif not isinstance(lib, list): lib = [lib]
      if incl == '': incl = []
      elif not isinstance(incl, list): incl = [incl]
      testedincl = list(incl)
      # weed out duplicates when adding fincs
      for loc in self.compilers.fincs:
        if not loc in incl:
          incl.append(loc)
      if self.functions:
        self.logPrint('Checking for library in '+location+': '+str(lib))
        if directory:
          self.logPrint('Contents of '+directory+': '+str(os.listdir(directory)))
          for libdir in self.libDirs:
            flibdir = os.path.join(directory, libdir)
            if os.path.isdir(flibdir):
              self.logPrint('Contents '+flibdir+': '+str(os.listdir(flibdir)))
      else:
        self.logPrint('Not checking for library in '+location+': '+str(lib)+' because no functions given to check for')

      otherlibs = self.dlib
      if 'FC' in self.buildLanguages:
        otherlibs.extend(self.compilers.flibs)
      if 'Cxx' in self.buildLanguages:
        otherlibs.extend(self.compilers.cxxlibs)
      self.libraries.saveLog()
      if self.executeTest(self.libraries.check,[lib, self.functions],{'otherLibs' : self.dlib, 'fortranMangle' : self.functionsFortran, 'cxxMangle' : self.functionsCxx[0], 'prototype' : self.functionsCxx[1], 'call' : self.functionsCxx[2], 'cxxLink': 'Cxx' in self.buildLanguages}):
        self.lib = lib
        if self.functionsDefine:
          self.executeTest(self.libraries.check,[lib, self.functionsDefine],{'otherLibs' : self.dlib, 'fortranMangle' : self.functionsFortran, 'cxxMangle' : self.functionsCxx[0], 'prototype' : self.functionsCxx[1], 'call' : self.functionsCxx[2], 'cxxLink': 'Cxx' in self.buildLanguages, 'functionDefine': 1})
        self.logWrite(self.libraries.restoreLog())
        self.logPrint('Checking for headers '+str(self.includes)+' in '+location+': '+str(incl))
        if (not self.includes) or self.checkInclude(incl, self.includes, self.dinclude, timeout = 60.0):
          if self.includes:
            self.include = testedincl
          self.found     = 1
          self.dlib      = self.lib+self.dlib
          dinc = []
          [dinc.append(inc) for inc in incl+self.dinclude if inc not in dinc]
          self.dinclude = dinc
          self.checkMacros(timeout = 60.0)
          if not hasattr(self.framework, 'packages'):
            self.framework.packages = []
          self.directory = directory
          self.framework.packages.append(self)
          return
      else:
        self.logWrite(self.libraries.restoreLog())
    if not self.lookforbydefault or ('with-'+self.package in self.framework.clArgDB and self.argDB['with-'+self.package]):
      raise RuntimeError('Could not find a functional '+self.name+'\n')
    if self.lookforbydefault and 'with-'+self.package not in self.framework.clArgDB:
      self.argDB['with-'+self.package] = 0

  def checkSharedLibrary(self):
    '''By default we don\'t care about checking if the library is shared'''
    return 1

  def alternateConfigureLibrary(self):
    '''Called if --with-packagename=0; does nothing by default'''
    pass

  def consistencyChecks(self):
    '''Checks run on the system and currently installed packages that need to be correct for the package now being configured'''
    def inVersionRange(myRange,reqRange):
      # my minimum needs to be less than the maximum and my maximum must be greater than
      # the minimum
      return (myRange[0].lower() <= reqRange[1].lower()) and (myRange[1].lower() >= reqRange[0].lower())

    self.printTest(self.consistencyChecks)
    if 'with-'+self.package+'-dir' in self.argDB and ('with-'+self.package+'-include' in self.argDB or 'with-'+self.package+'-lib' in self.argDB):
      raise RuntimeError('Specify either "--with-'+self.package+'-dir" or "--with-'+self.package+'-lib --with-'+self.package+'-include". But not both!')

    blaslapackconflict = 0
    for pkg in self.deps:
      if pkg.package == 'blaslapack':
        if pkg.has64bitindices and self.requires32bitintblas:
          blaslapackconflict = 1

    cxxVersionRange = (self.minCxxVersion,self.maxCxxVersion)
    cxxVersionConflict = not inVersionRange(cxxVersionRange,self.setCompilers.cxxDialectRange[self.getDefaultLanguage()])
    # if user did not request option, then turn it off if conflicts with configuration
    if self.lookforbydefault and 'with-'+self.package not in self.framework.clArgDB:
      mess = None
      if 'Cxx' in self.buildLanguages and not hasattr(self.compilers, 'CXX'):
        mess = 'requires C++ but C++ compiler not set'
      if 'FC'  in self.buildLanguages and not hasattr(self.compilers, 'FC'):
        mess = 'requires Fortran but Fortran compiler not set'
      if self.noMPIUni and self.mpi.usingMPIUni:
        mess = 'requires real MPI but MPIUNI is being used'
      if cxxVersionConflict:
        mess = 'cannot work with C++ version being used'
      if not self.defaultPrecision.lower() in self.precisions:
        mess = 'does not support the current precision '+ self.defaultPrecision.lower()
      if not self.complex and self.defaultScalarType.lower() == 'complex':
        mess = 'does not support complex numbers but PETSc being build with complex'
      if self.defaultIndexSize == 64 and self.requires32bitint:
        mess = 'does not support 64-bit indices which PETSc is configured for'
      if blaslapackconflict:
        mess = 'requires 32-bit BLAS/LAPACK indices but configure is building with 64-bit'

      if mess:
        self.logPrint('Turning off default package '+ self.package + ' because package ' + mess)
        self.argDB['with-'+self.package] = 0

    if self.argDB['with-'+self.package]:
      if blaslapackconflict:
        raise RuntimeError('Cannot use '+self.name+' with 64-bit BLAS/LAPACK indices')
      if 'Cxx' in self.buildLanguages and not hasattr(self.compilers, 'CXX'):
        raise RuntimeError('Cannot use '+self.name+' without C++, make sure you do NOT have --with-cxx=0')
      if 'FC'  in self.buildLanguages and not hasattr(self.compilers, 'FC'):
        raise RuntimeError('Cannot use '+self.name+' without Fortran, make sure you do NOT have --with-fc=0')
      if self.noMPIUni and self.mpi.usingMPIUni:
        raise RuntimeError('Cannot use '+self.name+' with MPIUNI, you need a real MPI')
      if cxxVersionConflict:
        raise RuntimeError('Cannot use '+self.name+' as it requires -std=['+','.join(map(str,cxxVersionRange))+'], while your compiler seemingly only supports -std=['+','.join(map(str,self.setCompilers.cxxDialectRange[self.getDefaultLanguage()]))+']')
      if self.download and self.argDB.get('download-'+self.downloadname.lower()) and not self.downloadonWindows and (self.setCompilers.CC.find('win32fe') >= 0):
        raise RuntimeError('External package '+self.name+' does not support --download-'+self.downloadname.lower()+' with Microsoft compilers')
      if not self.defaultPrecision.lower() in self.precisions:
        raise RuntimeError('Cannot use '+self.name+' with '+self.defaultPrecision.lower()+', it is not available in this precision')
      if not self.complex and self.defaultScalarType.lower() == 'complex':
        raise RuntimeError('Cannot use '+self.name+' with complex numbers it is not coded for this capability')
      if self.defaultIndexSize == 64 and self.requires32bitint:
        raise RuntimeError('Cannot use '+self.name+' with 64-bit integers, it is not coded for this capability')
    if not self.download and 'download-'+self.downloadname.lower() in self.argDB and self.argDB['download-'+self.downloadname.lower()]:
      raise RuntimeError('External package '+self.name+' does not support --download-'+self.downloadname.lower())
    return

  def versionToStandardForm(self,version):
    '''Returns original string'''
    '''This can be overloaded by packages that have their own unique representation of versions; for example CUDA'''
    return version

  def versionToTuple(self,version):
    '''Converts string of the form x.y to (x,y)'''
    if not version: return ()
    vl = version.split('.')
    if len(vl) > 2:
      vl[-1] = re.compile(r'^[0-9]+').search(vl[-1]).group(0)
    return tuple(map(int,vl))

  def checkVersion(self):
    '''Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version'''
    def dropPatch(str):
      '''Drops the patch version number in a version if it exists'''
      if str.find('.') == str.rfind('.'): return str
      return str[0:str.rfind('.')]
    def zeroPatch(str):
      '''Replaces the patch version number in a version if it exists with 0'''
      if str.find('.') == str.rfind('.'): return str
      return str[0:str.rfind('.')]+'.0'
    def infinitePatch(str):
      '''Replaces the patch version number in a version if it exists with a very large number'''
      if str.find('.') == str.rfind('.'): return str
      return str[0:str.rfind('.')]+'.100000'

    if not self.version and not self.minversion and not self.maxversion and not self.versionname: return
    if not self.versioninclude:
      if not self.includes:
        self.log.write('For '+self.package+' unable to find version information since includes and version includes are missing skipping version check\n')
        self.version = ''
        return
      self.versioninclude = self.includes[0]
    self.pushLanguage(self.buildLanguages[0]) # default is to use the first language in checking
    flagsArg = self.getPreprocessorFlagsArg()
    oldFlags = getattr(self.compilers, flagsArg)
    if self.language[-1] == 'HIP':
      extraFlags = ' -o -' # Force 'hipcc -E' to output to stdout, instead of *.cui files (as of hip-4.0. hip-4.1+ does not need it, but does not get hurt either).
    else:
      extraFlags = ''
    setattr(self.compilers, flagsArg, oldFlags+extraFlags+' '+self.headers.toString(self.dinclude))
    self.compilers.saveLog()

    # X.py uses a weird list of two headers.
    if not isinstance(self.versioninclude,list):
      headerList = [self.versioninclude]
    else:
      headerList = self.versioninclude

    includeLines = ''
    for header in headerList:
      includeLines += '#include "'+header+'"\n'
    try:
      # We once used '#include "'+self.versioninclude+'"\npetscpkgver('+self.versionname+');\n',
      # but some preprocessors are picky (ex. dpcpp -E), reporting errors on the code above even
      # it is just supposed to do preprocessing:
      #
      #  error: C++ requires a type specifier for all declarations
      #  petscpkgver(__SYCL_COMPILER_VERSION);
      #  ^
      #
      # So we instead use this compilable code.
      output = self.outputPreprocess(
'''
{x}
#define  PetscXstr_(s) PetscStr_(s)
#define  PetscStr_(s)  #s
const char *ver = "petscpkgver(" PetscXstr_({y}) ")";
'''.format(x=includeLines, y=self.versionname))
       # Ex. char *ver = "petscpkgver(" "20211206" ")";
       # But after stripping spaces, quotes etc below, it becomes char*ver=petscpkgver(20211206);
      self.logWrite(self.compilers.restoreLog())
    except:
      self.log.write('For '+self.package+' unable to run preprocessor to obtain version information, skipping version check\n')
      self.logWrite(self.compilers.restoreLog())
      self.popLanguage()
      setattr(self.compilers, flagsArg,oldFlags)
      self.version = ''
      return
    self.popLanguage()
    setattr(self.compilers, flagsArg,oldFlags)
    # the preprocessor output might be very long, but the petscpkgver line should be at the end. Therefore, we partition it backwards
    [mid, right] = output.rpartition('petscpkgver')[1:]
    version = ''
    if mid: # if mid is not empty, then it should be 'petscpkgver', meaning we found the version string
      verLine = right.split(';',1)[0] # get the string before the first ';'. Preprocessor might dump multiline result.
      self.log.write('Found the raw version string: ' + verLine +'\n')
      # strip backslashes, spaces, and quotes. Note MUMPS' version macro has "" around it, giving output: (" "\"5.4.1\"" ")";
      for char in ['\\', ' ', '"']:
          verLine = verLine.replace(char, '')
      # get the string between the outer ()
      version = verLine.split('(', 1)[-1].rsplit(')',1)[0]
      self.log.write('This is the processed version string: ' + version +'\n')
    if not version:
      self.log.write('For '+self.package+' unable to find version information: output below, skipping version check\n')
      self.log.write(output)
      if self.requiresversion:
        raise RuntimeError('Configure must be able to determined the version information for '+self.name+'. It was unable to, please send configure.log to petsc-maint@mcs.anl.gov')
      return
    try:
      self.foundversion = self.versionToStandardForm(version)
    except:
      self.log.write('For '+self.package+' unable to convert version information ('+version+') to standard form, skipping version check\n')
      if self.requiresversion:
        raise RuntimeError('Configure must be able to determined the version information for '+self.name+'. It was unable to, please send configure.log to petsc-maint@mcs.anl.gov')
      return

    self.log.write('For '+self.package+' need '+self.minversion+' <= '+self.foundversion+' <= '+self.maxversion+'\n')

    try:
      self.version_tuple = self.versionToTuple(self.foundversion)
    except:
      self.log.write('For '+self.package+' unable to convert version string to tuple, skipping version check\n')
      if self.requiresversion:
        raise RuntimeError('Configure must be able to determined the version information for '+self.name+'; it appears to be '+self.foundversion+'. It was unable to, please send configure.log to petsc-maint@mcs.anl.gov')
      self.foundversion = ''
      return

    suggest = ''
    if self.download:
      suggest = '. Suggest using --download-'+self.package+' for a compatible '+self.name
      if self.argDB['download-'+self.package]:
        rmdir = None
        try:
          rmdir = self.getDir()
        except:
          pass
        if rmdir:
          # this means that --download-package was requested, the package was not rebuilt, but there are newer releases of the package so it should be rebuilt
          suggest += ' after running "rm -rf ' + self.getDir() +'"\n'
          suggest += 'DO NOT DO THIS if you rely on the exact version of the currently installed ' + self.name
    if self.minversion:
      if self.versionToTuple(self.minversion) > self.version_tuple:
        raise RuntimeError(self.PACKAGE+' version is '+self.foundversion+', this version of PETSc needs at least '+self.minversion+suggest+'\n')
    elif self.version:
      if self.versionToTuple(zeroPatch(self.version)) > self.version_tuple:
        self.logPrintWarning('Using version '+self.foundversion+' of package '+self.PACKAGE+', PETSc is tested with '+dropPatch(self.version)+suggest)
    if self.maxversion:
      if self.versionToTuple(self.maxversion) < self.version_tuple:
        raise RuntimeError(self.PACKAGE+' version is '+self.foundversion+', this version of PETSc needs at most '+self.maxversion+suggest+'\n')
    elif self.version:
      if self.versionToTuple(infinitePatch(self.version)) < self.version_tuple:
        self.logPrintWarning('Using version '+self.foundversion+' of package '+self.PACKAGE+', PETSc is tested with '+dropPatch(self.version)+suggest)
    return

  def configure(self):
    if hasattr(self, 'download_solaris') and config.setCompilers.Configure.isSolaris(self.log):
      self.download = self.download_solaris
    if hasattr(self, 'download_darwin') and config.setCompilers.Configure.isDarwin(self.log):
      self.download = self.download_darwin
    if hasattr(self, 'download_mingw') and config.setCompilers.Configure.isMINGW(self.framework.getCompiler(), self.log):
      self.download = self.download_mingw
    if self.download and self.argDB['download-'+self.downloadname.lower()] and (not self.framework.batchBodies or self.installwithbatch):
      self.argDB['with-'+self.package] = 1
      downloadPackageVal = self.argDB['download-'+self.downloadname.lower()]
      if isinstance(downloadPackageVal, str):
        self.download = [downloadPackageVal]
    if self.download and self.argDB['download-'+self.downloadname.lower()+'-commit']:
      self.gitcommit = self.argDB['download-'+self.downloadname.lower()+'-commit']
      if hasattr(self, 'download_git'):
        self.download = self.download_git
    elif self.gitcommitmain and not self.petscdir.versionRelease:
      self.gitcommit = self.gitcommitmain
    if not 'with-'+self.package in self.argDB:
      self.argDB['with-'+self.package] = 0
    if 'with-'+self.package+'-dir' in self.argDB or 'with-'+self.package+'-include' in self.argDB or 'with-'+self.package+'-lib' in self.argDB:
      self.argDB['with-'+self.package] = 1
    if 'with-'+self.package+'-pkg-config' in self.argDB:
      self.argDB['with-'+self.package] = 1

    self.consistencyChecks()
    if self.argDB['with-'+self.package]:
      # If clanguage is c++, test external packages with the c++ compiler
      self.libraries.pushLanguage(self.defaultLanguage)
      self.executeTest(self.checkDependencies)
      self.executeTest(self.configureLibrary)
      if not self.builtafterpetsc:
        self.executeTest(self.checkVersion)
      self.executeTest(self.checkSharedLibrary)
      self.libraries.popLanguage()
    else:
      self.executeTest(self.alternateConfigureLibrary)
    return

  def updateCompilers(self, installDir, mpiccName, mpicxxName, mpif77Name, mpif90Name):
    '''Check if mpicc, mpicxx etc binaries exist - and update setCompilers() database.
    The input arguments are the names of the binaries specified by the respective packages
    This should really be part of compilers.py but it also uses compilerFlags.configure() so
    I am putting it here and Matt can fix it'''

    # Both MPICH and MVAPICH now depend on LD_LIBRARY_PATH for sharedlibraries.
    # So using LD_LIBRARY_PATH in configure - and -Wl,-rpath in makefiles
    if self.argDB['with-shared-libraries']:
      config.setCompilers.Configure.addLdPath(os.path.join(installDir,'lib'))
    # Initialize to empty
    mpicc=''
    mpicxx=''
    mpifc=''

    mpicc = os.path.join(installDir,"bin",mpiccName)
    if not os.path.isfile(mpicc): raise RuntimeError('Could not locate installed MPI compiler: '+mpicc)
    try:
      self.logPrint('Showing compiler and options used by newly built MPI')
      self.executeShellCommand(mpicc + ' -show', log = self.log)[0]
    except:
      pass
    if hasattr(self.compilers, 'CXX'):
      mpicxx = os.path.join(installDir,"bin",mpicxxName)
      if not os.path.isfile(mpicxx): raise RuntimeError('Could not locate installed MPI compiler: '+mpicxx)
      try:
        self.executeShellCommand(mpicxx + ' -show', log = self.log)[0]
      except:
        pass
    if hasattr(self.compilers, 'FC'):
      if self.fortran.fortranIsF90:
        mpifc = os.path.join(installDir,"bin",mpif90Name)
      else:
        mpifc = os.path.join(installDir,"bin",mpif77Name)
      if not os.path.isfile(mpifc): raise RuntimeError('Could not locate installed MPI compiler: '+mpifc)
      try:
        self.executeShellCommand(mpifc + ' -show', log = self.log)[0]
      except:
        pass
    # redo compiler detection, copy the package cxx dialect restrictions though
    oldPackageRanges = self.setCompilers.cxxDialectPackageRanges
    self.setCompilers.updateMPICompilers(mpicc,mpicxx,mpifc)
    self.setCompilers.cxxDialectPackageRanges = oldPackageRanges
    self.compilers.__init__(self.framework)
    self.compilers.headerPrefix = self.headerPrefix
    self.compilers.setup()
    self.compilerFlags.saveLog()
    self.compilerFlags.configure()
    self.logWrite(self.compilerFlags.restoreLog())
    self.compilers.saveLog()
    self.compilers.configure()
    self.logWrite(self.compilers.restoreLog())
    if self.cuda.found:
      self.cuda.configureLibrary()
    return

  def checkSharedLibrariesEnabled(self):
    if self.havePETSc:
      useShared = self.sharedLibraries.useShared
    else:
      useShared = True
    if 'download-'+self.package+'-shared' in self.framework.clArgDB and self.argDB['download-'+self.package+'-shared']:
      raise RuntimeError(self.package+' cannot use download-'+self.package+'-shared=1. This flag can only be used to disable '+self.package+' shared libraries')
    if not useShared or ('download-'+self.package+'-shared' in self.framework.clArgDB and not self.argDB['download-'+self.package+'-shared']):
      return False
    else:
      return True

  def compilePETSc(self):
    try:
      self.logPrintBox('Compiling PETSc; this may take several minutes')
      output,err,ret  = config.package.Package.executeShellCommand(self.make.make+' all PETSC_DIR='+self.petscdir.dir+' PETSC_ARCH='+self.arch, cwd=self.petscdir.dir, timeout=1000, log = self.log)
      self.log.write(output+err)
    except RuntimeError as e:
      raise RuntimeError('Error running make all on PETSc: '+str(e))
    if self.framework.argDB['prefix']:
      try:
        self.logPrintBox('Installing PETSc; this may take several minutes')
        output,err,ret  = config.package.Package.executeShellCommand(self.make.make+' install PETSC_DIR='+self.petscdir.dir+' PETSC_ARCH='+self.arch, cwd=self.petscdir.dir, timeout=60, log = self.log)
        self.log.write(output+err)
      except RuntimeError as e:
        raise RuntimeError('Error running make install on PETSc: '+str(e))
    elif not self.argDB['with-batch']:
      try:
        self.logPrintBox('Testing PETSc; this may take several minutes')
        output,err,ret  = config.package.Package.executeShellCommand(self.make.make+' test PETSC_DIR='+self.petscdir.dir+' PETSC_ARCH='+self.arch, cwd=self.petscdir.dir, timeout=60, log = self.log)
        output = output+err
        self.log.write(output)
        if output.find('error') > -1 or output.find('Error') > -1:
          raise RuntimeError('Error running make check on PETSc: '+output)
      except RuntimeError as e:
        raise RuntimeError('Error running make check on PETSc: '+str(e))
    self.installedpetsc = 1


'''
config.package.GNUPackage is a helper class whose intent is to simplify writing configure modules
for GNU-style packages that are installed using the "configure; make; make install" idiom.

Brief overview of how BuildSystem\'s configuration of packages works.
---------------------------------------------------------------------
    Configuration is carried out by "configure objects": instances of classes desendant from config.base.Configure.
  These configure objects implement the "configure()" method, and are inserted into a "framework" object,
  which makes the "configure()" calls according to the dependencies between the configure objects.
    config.package.Package extends config.base.Configure and adds instance variables and methods that facilitate
  writing classes that configure packages.  Customized package configuration classes are written by subclassing
  config.package.Package -- the "parent class".

    Packages essentially encapsulate libraries, that either
    (A) are already (prefix-)installed already somewhere on the system or
    (B) need to be downloaded, built and installed first
  If (A), the parent class provides a generic mechanism for locating the installation, by looking in user-specified and standard locations.
  If (B), the parent class provides a generic mechanism for determining whether a download is necessary, downloading and unpacking
  the source (if the download is, indeed, required), determining whether the package needs to be built, providing the build and
  installation directories, and a few other helper tasks.  The package subclass is responsible for implementing the "Install" hook,
  which is called by the parent class when the actual installation (building the source code, etc.) is done.  As an aside, BuildSystem-
  controlled build and install of a package at configuration time has a much better chance of guaranteeing language, compiler and library
  (shared or not) consistency among packages.
    No matter whether (A) or (B) is realized, the parent class control flow demands that the located or installed package
  be checked to ensure it is functional.  Since a package is conceptualized as a library, the check consists in testing whether
  a specified set of libraries can be linked against, and ahat the specified headers can be located.  The libraries and headers are specified
  by name, and the corresponding paths are supplied as a result of the process of locating or building the library.  The verified paths and
  library names are then are stored by the configure object as instance variables.  These can be used by other packages dependent on the package
  being configured; likewise, the package being configured will use the information from the packages it depends on by examining their instance
  variables.

    Thus, the parent class provides for the overall control and data flow, which goes through several configuration stages:
  "init", "setup", "location/installation", "testing".  At each stage, various "hooks" -- methods -- are called.
  Some hooks (e.g., Install) are left unimplemented by the parent class and must be implemented by the package subclass;
  other hooks are implemented by the parent class and provide generic functionality that is likely to suit most packages,
  but can be overridden for custom purposes.  Each hook typically prepares the state -- instance variables -- of the configure object
  for the next phase of configuration.  Below we describe the stages, some of the more typically-used hooks and instance variables in some
  detail.


  init:
  ----
  The init stage constructs the configure object; it is implemented by its __init__ method.
  Parent package class sets up the following useful state variables:
    self.name             - derived from module name                      [string]
    self.package          - lowercase name                                [string]
    self.PACKAGE          - uppercase name                                [string]
    self.downloadname     - same as self.name (usage a bit inconsistent)  [string]
    self.downloaddirnames - same as self.name (usage a bit inconsistent)  [string]
  Package subclass typically sets up the following state variables:
    self.download         - url to download source from                   [string]
    self.includes         - names of header files to locate               [list of strings]
    self.liblist          - names of library files to locate              [list of lists of strings]
    self.functions        - names of functions to locate in libraries     [list of strings]
    self.cxx              - whether C++ compiler, (this does not require that PETSc be built with C++, should it?) is required for this package      [bool]
    self.functionsFortran - whether to mangle self.functions symbols      [bool]
  Most of these instance variables determine the behavior of the location/installation and the testing stages.
  Ideally, a package subclass would extend only the __init__ method and parameterize the remainder of
  the configure process by the appropriate variables.  This is not always possible, since some
  of the package-specific choices depend on


  setup:
  -----
  The setup stage follows init and is accomplished by the configure framework calling each configure objects
  setup hooks:

    setupHelp:
    ---------
    This is used to define the command-line arguments expected by this configure object.
    The parent package class sets up generic arguments:
      --with-<package>         [bool]
      --with-<package>-dir     [string: directory]
      --download-<package>     [string:"yes","no","filename"]
      --with-<package>-include [string: directory]
      --with-<package>-lib     [string: directory]
    Here <package> is self.package defined in the init stage.
    The package subclass can add to these arguments.  These arguments\' values are set
    from the defaults specified in setupHelp or from the user-supplied command-line arguments.
    Their values can be queried at any time during the configure process.

    setupDependencies:
    -----------------
    This is used to specify other configure objects that the package being configured depends on.
    This is done via the configure framework\'s "require" mechanism:
      self.framework.require(<dependentObject>, self)
    dependentObject is a string -- the name of the configure module this package depends on.

    The parent package class by default sets up some of the common dependencies:
      config.compilers, config.types, config.headers, config.libraries, config.packages.MPI,
    among others.
    The package subclass should add package-specific dependencies via the "require" mechanism,
    as well as list them in self.deps [list].  This list is used during the location/installation
    stage to ensure that the package\'s dependencies have been configured correctly.

  Location/installation:
  ---------------------
  These stages (somewhat mutually-exclusive), as well as the testing stage are carried out by the code in
  configureLibrary.  These stages calls back to certain hooks that allow the user to control the
  location/installation process by overriding these hooks in the package subclass.

  Location:
  --------
  [Not much to say here, yet.]

  Installation:
  ------------
  This stage is carried out by configure and functions called from it, most notably, configureLibrary
  The essential difficulty here is that the function calls are deeply nested (A-->B-->C--> ...),
  as opposed to a single driver repeatedly calling small single-purpose callback hooks.  This means that any
  customization would not be able to be self-contained by would need to know to call further down the chain.
  Moreover, the individual functions on the call stack combine generic code with the code that is naturally meant
  for customization by a package subclass.  Thus, a customization would have to reproduce this generic code.
  Some of the potentially customizable functionality is split between different parts of the code below
  configure (see, e.g., the comment at the end of this paragraph).
    Because of this, there are few opportunities for customization in the installation stage, without a substantial
  restructuring of configure, configureLibrary and/or its callees. Here we mention the main customizable callback
  Install along with two generic services, installNeeded and postInstall, which are provided by the parent class and
  can be used in implementing a custom Install.
    Comment: Note that configure decides whether to configure the package, in part, based on whether
             self.download is a non-empty list at the beginning of configure.
             This means that resetting self.download cannot take place later than this.
             On the other hand, constructing the correct self.download here might be premature, as it might result
             in unnecessary prompts for user input, only to discover later that a download is not required.
             Because of this a package configure class must always have at least dummy string for self.download, if
             a download is possible.

  Here is a schematic description of the main point on the call chain:

  configure:
    check whether to configure the package:
    package is configured only if
      self.download is not an empty string list and the command-line download flag is on
      OR if
      the command-line flag "-with-"self.package is present, prompting a search for the package on the system
      OR if
      the command-line flag(s) pointing to a package installation "-with-"self.package+"-dir or ...-lib, ...-include are present
    ...
    configureLibrary:
      consistencyChecks:
        ...
        check that appropriate language support is on:
          self.cxx            == 1 implies C++ compiler must be present
          self.fc             == 1 implies Fortran compiler must be present
          self.noMPIUni       == 1 implies real MPI must be present
      ...
      generateGuesses:
        ...
        checkDownload:
          ...
          check val = argDB[\'download-\'self.downloadname.tolower()\']
          /*
           note the inconsistency with setupHelp: it declares \'download-\'self.package
           Thus, in order for the correct variable to be queried here, we have to have
           self.downloadname.tolower() == self.package
          */
          if val is a string, set self.download = [val]
          check the package license
          getInstallDir:
            ...
            set the following instance variables, creating directories, if necessary:
            self.installDir   /* This is where the package will be installed, after it is built. */
            self.includeDir   /* subdir of self.installDir */
            self.libDir       /* subdir of self.installDir, defined as self.installDir + self.libDirs[0] */
            self.confDir      /* where packages private to the configure/build process are built, such as --download-make */
                              /* The subdirectory of this 'conf' is where the configuration information will be stored for the package */
            self.packageDir = /* this dir is where the source is unpacked and built */
            self.getDir():
              ...
              if a package dir starting with self.downloadname does not exist already
                create the package dir
                downLoad():
                  ...
                  download and unpack the source to self.packageDir,
            Install():
            /* This must be implemented by a package subclass */

    Install:
    ------
    Note that it follows from the above pseudocode, that the package source is already in self.packageDir
    and the dir instance variables (e.g., installDir, confDir) already point to existing directories.
    The user can implement whatever actions are necessary to configure, build and install
    the package.  Typically, the package is built using GNU\'s "configure; make; make install"
    idiom, so the customized Install forms GNU configure arguments using the compilers,
    system libraries and dependent packages (their locations, libs and includes) discovered
    by configure up to this point.

    It is important to check whether the package source in self.packageDir needs rebuilding, since it might
    have been downloaded in a previous configure run, as is checked by getDir() above.
    However, the package might now need to be built with different options.  For that reason,
    the parent class provides a helper method
      installNeeded(self, mkfile):
        This method compares two files: the file with name mkfile in self.packageDir and
        the file with name self.name in self.confDir (a subdir of the installation dir).
        If the former is absent or differs from the latter, this means the source has never
        been built or was built with different arguments, and needs to be rebuilt.
        This helper method should be run at the beginning of an Install implementation,
        to determine whether an install is actually needed.
    The other useful helper method provided by the parent class is
       postInstall(self, output,mkfile):
         This method will simply save string output in the file with name mkfile in self.confDir.
         Storing package configuration parameters there will enable installNeeded to do its job
         next time this package is being configured.

  testing:
  -------
  The testing is carried out by part of the code in config.package.configureLibrary,
  after the package library has been located or installed.
  The library is considered functional if two conditions are satisfied:
   (1) all of the symbols in self.functions have been resolved when linking against the libraries in self.liblist,
       either located on the system or newly installed;
   (2) the headers in self.includes have been located.
  If no symbols are supplied in self.functions, no link OR header testing is done.



  Extending package class:
  -----------------------
  Generally, extending the parent package configure class is done by overriding some
  or all of its methods (see config/BuildSystem/config/packages/hdf5.py, for example).
  Because convenient (i.e., localized) hooks are available onto to some parts of the
  configure process, frequently writing a custom configure class amounts to overriding
  configureLibrary so that pre- and post-code can be inserted before calling to
  config.package.Package.configureLibrary.

  In any event, Install must be implemented anew for any package configure class extending
  config.package.Package.  Naturally, instance variables have to be set appropriately
  in __init__ (or elsewhere), package-specific help options and dependencies must be defined.
  Therefore, the general pattern for package configure subclassing is this:
    - override __init__ and set package-specific instance variables
    - override setupHelp and setupDependencies hooks to set package-specific command-line
      arguments and dependencies on demand
    - override Install, making use of the parent class\'s installNeeded and postInstall
    - override configureLibrary, if necessary, to insert pre- and post-configure fixup code.

  GNUPackage class:
  ----------------
  This class is an attempt at making writing package configure classes easier for the packages
  that use the "configure; make; make install" idiom for the installation -- "GNU packages".
  The main contribution is in the implementation of a generic Install method, which attempts
  to automate the building of a package based on the mostly standard instance variables.


  Besides running GNU configure, GNUPackage.Install runs installNeeded, make and postInstall
  at the appropriate times, automatically determining whether a rebuild is necessary, saving
  a GNU configure arguments stamp to perform the check in the future, etc.

  setupHelp:
  ---------
  This method extends config.Package.setupHelp by adding two command-line arguments:
    "-download-"+self.package+"-version" with self.downloadversion as default or None, if it does not exist
    "-download-"+self.package+"-shared" with False as the default.

  Summary:
  -------
  In order to customize GNUPackage:
    - set up the usual instance variables in __init__, plus the following instance variables, if necessary/appropriate:
        self.downloadpath
        self.downloadext
        self.downloadversion
    - override setupHelp to declare command-line arguments that can be used anywhere below
      (GNUPackage takes care of some of the basic args, including the download version)
    - override setupDependencies to process self.odeps and enable this optional package feature in the current externalpackage.
    - override setupDownload to control the precise download URL and/or
    - override setupDownloadVersion to control the self.downloadversion string inserted into self.download between self.downloadpath and self.downloadext
'''

class GNUPackage(Package):
  def __init__(self, framework):
    Package.__init__(self,framework)
    self.builddir = 'no' # requires build be done in a subdirectory, not in the directory tree
    self.configureName = 'configure'
    return

  def setupHelp(self, help):
    config.package.Package.setupHelp(self,help)
    import nargs
    help.addArgument(self.PACKAGE, '-download-'+self.package+'-shared=<bool>',     nargs.ArgBool(None, 0, 'Install '+self.PACKAGE+' with shared libraries'))
    help.addArgument(self.PACKAGE, '-download-'+self.package+'-configure-arguments=string', nargs.ArgString(None, 0, 'Additional GNU autoconf configure arguments for the build of '+self.name))

  def formGNUConfigureArgs(self):
    '''This sets up the prefix, compiler flags, shared flags, and other generic arguments
       that are fed into the configure script supplied with the package.
       Override this to set options needed by a particular package'''
    args=[]
    ## prefix
    args.append('--prefix='+self.installDir)
    args.append('MAKE='+self.make.make)
    args.append('--libdir='+self.libDir)
    ## compiler args
    self.pushLanguage('C')
    if not self.installwithbatch and hasattr(self.setCompilers,'cross_cc'):
      args.append('CC="'+self.setCompilers.cross_cc+'"')
    else:
      args.append('CC="'+self.getCompiler()+'"')
    args.append('CFLAGS="'+self.updatePackageCFlags(self.getCompilerFlags())+'"')
    args.append('AR="'+self.setCompilers.AR+'"')
    args.append('ARFLAGS="'+self.setCompilers.AR_FLAGS+'"')
    if not self.installwithbatch and hasattr(self.setCompilers,'cross_LIBS'):
      args.append('LIBS="'+self.setCompilers.cross_LIBS+'"')
    if self.setCompilers.LDFLAGS:
      args.append('LDFLAGS="'+self.setCompilers.LDFLAGS+'"')
    self.popLanguage()
    if hasattr(self.compilers, 'CXX'):
      self.pushLanguage('Cxx')
      if not self.installwithbatch and hasattr(self.setCompilers,'cross_CC'):
        args.append('CXX="'+self.setCompilers.cross_CC+'"')
      else:
        args.append('CXX="'+self.getCompiler()+'"')
      args.append('CXXFLAGS="'+self.updatePackageCxxFlags(self.getCompilerFlags())+'"')
      self.popLanguage()
    else:
      args.append('--disable-cxx')
    if hasattr(self.compilers, 'FC'):
      self.pushLanguage('FC')
      fc = self.getCompiler()
      if self.fortran.fortranIsF90:
        try:
          output, error, status = self.executeShellCommand(fc+' -v', log = self.log)
          output += error
        except:
          output = ''
        if output.find('IBM') >= 0:
          fc = os.path.join(os.path.dirname(fc), 'xlf')
          self.log.write('Using IBM f90 compiler, switching to xlf for compiling ' + self.PACKAGE + '\n')
        # now set F90
        if not self.installwithbatch and hasattr(self.setCompilers,'cross_fc'):
          args.append('F90="'+self.setCompilers.cross_fc+'"')
        else:
          args.append('F90="'+fc+'"')
        args.append('F90FLAGS="'+self.updatePackageFFlags(self.getCompilerFlags())+'"')
      else:
        args.append('--disable-f90')
      args.append('FFLAGS="'+self.updatePackageFFlags(self.getCompilerFlags())+'"')
      if not self.installwithbatch and hasattr(self.setCompilers,'cross_fc'):
        args.append('FC="'+self.setCompilers.cross_fc+'"')
        args.append('F77="'+self.setCompilers.cross_fc+'"')
      else:
        args.append('FC="'+fc+'"')
        args.append('F77="'+fc+'"')
      args.append('FCFLAGS="'+self.updatePackageFFlags(self.getCompilerFlags())+'"')
      self.popLanguage()
    else:
      args.append('--disable-fortran')
      args.append('--disable-fc')
      args.append('--disable-f77')
      args.append('--disable-f90')
    if self.checkSharedLibrariesEnabled():
      args.append('--enable-shared')
    else:
      args.append('--disable-shared')

    cuda_module = self.framework.findModule(self, config.packages.cuda)
    if cuda_module and cuda_module.found:
      with self.Language('CUDA'):
        args.append('CUDAC='+self.getCompiler())
        args.append('CUDAFLAGS="'+self.updatePackageCUDAFlags(self.getCompilerFlags())+'"')
    return args

  def preInstall(self):
    '''Run pre-install steps like generate configure script'''
    if not os.path.isfile(os.path.join(self.packageDir,self.configureName)):
      if not self.programs.autoreconf:
        raise RuntimeError('autoreconf required for ' + self.PACKAGE+' not found (or broken)! Use your package manager to install autoconf')
      if not self.programs.libtoolize:
        raise RuntimeError('libtoolize required for ' + self.PACKAGE+' not found! Use your package manager to install libtool')
      try:
        self.logPrintBox('Running libtoolize on ' +self.PACKAGE+'; this may take several minutes')
        output,err,ret  = config.base.Configure.executeShellCommand([self.programs.libtoolize, '--install'], cwd=self.packageDir, timeout=100, log=self.log)
        if ret:
          raise RuntimeError('Error in libtoolize: ' + output+err)
      except RuntimeError as e:
        raise RuntimeError('Error running libtoolize on ' + self.PACKAGE+': '+str(e))
      try:
        self.logPrintBox('Running autoreconf on ' +self.PACKAGE+'; this may take several minutes')
        output,err,ret  = config.base.Configure.executeShellCommand([self.programs.autoreconf, '--force', '--install'], cwd=self.packageDir, timeout=200, log = self.log)
        if ret:
          raise RuntimeError('Error in autoreconf: ' + output+err)
      except RuntimeError as e:
        raise RuntimeError('Error running autoreconf on ' + self.PACKAGE+': '+str(e))


  def Install(self):
    ##### getInstallDir calls this, and it sets up self.packageDir (source download), self.confDir and self.installDir
    args = self.formGNUConfigureArgs()  # allow package to change self.packageDir
    if self.download and self.argDB['download-'+self.downloadname.lower()+'-configure-arguments']:
       args.append(self.argDB['download-'+self.downloadname.lower()+'-configure-arguments'])
    args = ' '.join(args)
    conffile = os.path.join(self.packageDir,self.package+'.petscconf')
    fd = open(conffile, 'w')
    fd.write(args)
    fd.close()
    ### Use conffile to check whether a reconfigure/rebuild is required
    if not self.installNeeded(conffile):
      return self.installDir

    self.preInstall()

    if self.builddir == 'yes':
      folder = os.path.join(self.packageDir, 'petsc-build')
      if os.path.isdir(folder):
        import shutil
        shutil.rmtree(folder)
      os.mkdir(folder)
      self.packageDir = folder
      dot = '..'
    else:
      dot = '.'

    ### Configure and Build package
    try:
      self.logPrintBox('Running configure on ' +self.PACKAGE+'; this may take several minutes')
      output1,err1,ret1  = config.base.Configure.executeShellCommand(os.path.join(dot, self.configureName)+' '+args, cwd=self.packageDir, timeout=2000, log = self.log)
    except RuntimeError as e:
      self.logPrint('Error running configure on ' + self.PACKAGE+': '+str(e))
      try:
        with open(os.path.join(self.packageDir,'config.log')) as fd:
          conf = fd.read()
          fd.close()
          self.logPrint('Output in config.log for ' + self.PACKAGE+': '+conf)
      except:
        pass
      raise RuntimeError('Error running configure on ' + self.PACKAGE)
    try:
      self.logPrintBox('Running make on '+self.PACKAGE+'; this may take several minutes')
      if self.parallelMake: pmake = self.make.make_jnp+' '+self.makerulename+' '
      else: pmake = self.make.make+' '+self.makerulename+' '

      output2,err2,ret2  = config.base.Configure.executeShellCommand(self.make.make+' clean', cwd=self.packageDir, timeout=200, log = self.log)
      output3,err3,ret3  = config.base.Configure.executeShellCommand(pmake, cwd=self.packageDir, timeout=6000, log = self.log)
      self.logPrintBox('Running make install on '+self.PACKAGE+'; this may take several minutes')
      output4,err4,ret4  = config.base.Configure.executeShellCommand(self.make.make+' install', cwd=self.packageDir, timeout=1000, log = self.log)
    except RuntimeError as e:
      self.logPrint('Error running make; make install on '+self.PACKAGE+': '+str(e))
      raise RuntimeError('Error running make; make install on '+self.PACKAGE)
    self.postInstall(output1+err1+output2+err2+output3+err3+output4+err4, conffile)
    return self.installDir

  def Bootstrap(self,command):
    '''check for configure script - and run bootstrap - if needed'''
    import os
    if not os.path.isfile(os.path.join(self.packageDir,self.configureName)):
      if not self.programs.libtoolize:
        raise RuntimeError('Could not bootstrap '+self.PACKAGE+' using autotools: libtoolize not found')
      if not self.programs.autoreconf:
        raise RuntimeError('Could not bootstrap '+self.PACKAGE+' using autotools: autoreconf not found')
      self.logPrintBox('Bootstrapping '+self.PACKAGE+' using autotools; this may take several minutes')
      try:
        self.executeShellCommand(command,cwd=self.packageDir,log=self.log)
      except RuntimeError as e:
        raise RuntimeError('Could not bootstrap '+self.PACKAGE+': maybe autotools (or recent enough autotools) could not be found?\nError: '+str(e))

class CMakePackage(Package):
  def __init__(self, framework):
    Package.__init__(self, framework)
    self.minCmakeVersion = (2,0,0)
    return

  def setupHelp(self, help):
    config.package.Package.setupHelp(self,help)
    import nargs
    help.addArgument(self.PACKAGE, '-download-'+self.package+'-shared=<bool>',     nargs.ArgBool(None, 0, 'Install '+self.PACKAGE+' with shared libraries'))
    help.addArgument(self.PACKAGE, '-download-'+self.package+'-cmake-arguments=string', nargs.ArgString(None, 0, 'Additional CMake arguments for the build of '+self.name))

  def setupDependencies(self, framework):
    Package.setupDependencies(self, framework)
    self.cmake = framework.require('config.packages.cmake',self)
    if self.argDB['download-'+self.downloadname.lower()]:
      self.cmake.maxminCmakeVersion = max(self.minCmakeVersion,self.cmake.maxminCmakeVersion)
    return

  def formCMakeConfigureArgs(self):
    import os
    import shlex
    #  If user has set, for example, CMAKE_GENERATOR Ninja then CMake calls from configure will generate the wrong external package tools for building
    try:
      del os.environ['CMAKE_GENERATOR']
    except:
      pass

    args = ['-DCMAKE_INSTALL_PREFIX='+self.installDir]
    args.append('-DCMAKE_INSTALL_NAME_DIR:STRING="'+self.libDir+'"')
    args.append('-DCMAKE_INSTALL_LIBDIR:STRING="lib"')
    args.append('-DCMAKE_VERBOSE_MAKEFILE=1')
    if self.compilerFlags.debugging:
      args.append('-DCMAKE_BUILD_TYPE=Debug')
    else:
      args.append('-DCMAKE_BUILD_TYPE=Release')
    args.append('-DCMAKE_AR="'+self.setCompilers.AR+'"')
    self.framework.pushLanguage('C')
    args.append('-DCMAKE_C_COMPILER="'+self.framework.getCompiler()+'"')
    # bypass CMake findMPI() bug that can find compilers later in the PATH before the first one in the PATH.
    # relevant lines of findMPI() begins with if(_MPI_BASE_DIR)
    self.getExecutable(self.framework.getCompiler(), getFullPath=1, resultName='mpi_C',setMakeMacro=0)
    args.append('-DMPI_C_COMPILER="'+self.mpi_C+'"')
    ranlib = shlex.split(self.setCompilers.RANLIB)[0]
    args.append('-DCMAKE_RANLIB='+ranlib)
    cflags = self.updatePackageCFlags(self.setCompilers.getCompilerFlags())
    args.append('-DCMAKE_C_FLAGS:STRING="'+cflags+'"')
    args.append('-DCMAKE_C_FLAGS_DEBUG:STRING="'+cflags+'"')
    args.append('-DCMAKE_C_FLAGS_RELEASE:STRING="'+cflags+'"')
    self.framework.popLanguage()
    if hasattr(self.compilers, 'CXX'):
      lang = self.framework.pushLanguage('Cxx')
      args.append('-DCMAKE_CXX_COMPILER="'+self.framework.getCompiler()+'"')
      # bypass CMake findMPI() bug that can find compilers later in the PATH before the first one in the PATH.
      # relevant lines of findMPI() begins with if(_MPI_BASE_DIR)
      self.getExecutable(self.framework.getCompiler(), getFullPath=1, resultName='mpi_CC',setMakeMacro=0)
      args.append('-DMPI_CXX_COMPILER="'+self.mpi_CC+'"')
      cxxFlags = self.updatePackageCxxFlags(self.framework.getCompilerFlags())

      cxxFlags = cxxFlags.split(' ')
      # next line is needed because CMAKE passes CXX flags even when linking an object file!
      cxxFlags = self.rmArgs(cxxFlags,['-TP'])
      cxxFlags = ' '.join(cxxFlags)

      args.append('-DCMAKE_CXX_FLAGS:STRING="{cxxFlags}"'.format(cxxFlags=cxxFlags))
      args.append('-DCMAKE_CXX_FLAGS_DEBUG:STRING="{cxxFlags}"'.format(cxxFlags=cxxFlags))
      args.append('-DCMAKE_CXX_FLAGS_RELEASE:STRING="{cxxFlags}"'.format(cxxFlags=cxxFlags))
      langdialect = getattr(self.setCompilers,lang+'dialect',None)
      if langdialect:
        # langdialect is only set as an attribute if the user specifically chose a dialect
        # (see config/setCompilers.py::checkCxxDialect())
        args.append('-DCMAKE_CXX_STANDARD={stdver}'.format(stdver=langdialect[-2:])) # extract '17' from c++17
      self.framework.popLanguage()

    if hasattr(self.compilers, 'FC'):
      self.framework.pushLanguage('FC')
      args.append('-DCMAKE_Fortran_COMPILER="'+self.framework.getCompiler()+'"')
      # bypass CMake findMPI() bug that can find compilers later in the PATH before the first one in the PATH.
      # relevant lines of findMPI() begins with if(_MPI_BASE_DIR)
      self.getExecutable(self.framework.getCompiler(), getFullPath=1, resultName='mpi_FC',setMakeMacro=0)
      args.append('-DMPI_Fortran_COMPILER="'+self.mpi_FC+'"')
      args.append('-DCMAKE_Fortran_FLAGS:STRING="'+self.updatePackageFFlags(self.framework.getCompilerFlags())+'"')
      args.append('-DCMAKE_Fortran_FLAGS_DEBUG:STRING="'+self.updatePackageFFlags(self.framework.getCompilerFlags())+'"')
      args.append('-DCMAKE_Fortran_FLAGS_RELEASE:STRING="'+self.updatePackageFFlags(self.framework.getCompilerFlags())+'"')
      self.framework.popLanguage()

    if self.setCompilers.LDFLAGS:
      ldflags = self.setCompilers.LDFLAGS.replace('"','\\"') # escape double quotes (") in LDFLAGS
      args.append('-DCMAKE_EXE_LINKER_FLAGS:STRING="'+ldflags+'"')

    if not config.setCompilers.Configure.isWindows(self.setCompilers.CC, self.log) and self.checkSharedLibrariesEnabled():
      args.append('-DBUILD_SHARED_LIBS:BOOL=ON')
      args.append('-DBUILD_STATIC_LIBS:BOOL=OFF')
    else:
      args.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
      args.append('-DBUILD_STATIC_LIBS:BOOL=ON')

    if 'MSYSTEM' in os.environ:
      args.append('-G "MSYS Makefiles"')
    for package in self.deps + self.odeps:
      if package.found and package.name == 'cuda':
        with self.Language('CUDA'):
          args.append('-DCMAKE_CUDA_COMPILER='+self.getCompiler())
          cuda_flags = self.updatePackageCUDAFlags(self.getCompilerFlags())
          args.append('-DCMAKE_CUDA_FLAGS:STRING="{}"'.format(cuda_flags))
          args.append('-DCMAKE_CUDA_FLAGS_DEBUG:STRING="{}"'.format(cuda_flags))
          args.append('-DCMAKE_CUDA_FLAGS_RELEASE:STRING="{}"'.format(cuda_flags))
          if hasattr(self.setCompilers,'CUDA_CXX'): # CUDA_CXX is set in cuda.py and might be mpicxx.
            args.append('-DCMAKE_CUDA_HOST_COMPILER="{}"'.format(self.setCompilers.CUDA_CXX))
          else:
            with self.Language('C++'):
              args.append('-DCMAKE_CUDA_HOST_COMPILER="{}"'.format(self.getCompiler()))
        break
    return args

  def updateControlFiles(self):
    # Override to change build control files
    return

  def Install(self):
    import os
    args = self.formCMakeConfigureArgs()
    if self.download and 'download-'+self.downloadname.lower()+'-cmake-arguments' in self.framework.clArgDB:
       args.append(self.argDB['download-'+self.downloadname.lower()+'-cmake-arguments'])
    args = ' '.join(args)
    conffile = os.path.join(self.packageDir,self.package+'.petscconf')
    fd = open(conffile, 'w')
    fd.write(args)
    fd.close()

    if self.installNeeded(conffile):

      if not self.cmake.found:
        raise RuntimeError('CMake not found, needed to build '+self.PACKAGE+'. Rerun configure with --download-cmake.')

      self.updateControlFiles()

      # effectively, this is 'make clean'
      folder = os.path.join(self.packageDir, self.cmakelistsdir, 'petsc-build')
      if os.path.isdir(folder):
        import shutil
        shutil.rmtree(folder)
      os.mkdir(folder)

      try:
        self.logPrintBox('Configuring '+self.PACKAGE+' with CMake; this may take several minutes')
        output1,err1,ret1  = config.package.Package.executeShellCommand(self.cmake.cmake+' .. '+args, cwd=folder, timeout=900, log = self.log)
      except RuntimeError as e:
        self.logPrint('Error configuring '+self.PACKAGE+' with CMake '+str(e))
        try:
          with open(os.path.join(folder, 'CMakeFiles', 'CMakeOutput.log')) as fd:
            conf = fd.read()
            fd.close()
            self.logPrint('Output in CMakeOutput.log for ' + self.PACKAGE+':\n'+conf)
        except:
          pass
        raise RuntimeError('Error configuring '+self.PACKAGE+' with CMake')
      try:
        self.logPrintBox('Compiling and installing '+self.PACKAGE+'; this may take several minutes')
        output2,err2,ret2  = config.package.Package.executeShellCommand(self.make.make_jnp+' '+self.makerulename, cwd=folder, timeout=3000, log = self.log)
        output3,err3,ret3  = config.package.Package.executeShellCommand(self.make.make+' install', cwd=folder, timeout=3000, log = self.log)
      except RuntimeError as e:
        self.logPrint('Error running make on  '+self.PACKAGE+': '+str(e))
        raise RuntimeError('Error running make on  '+self.PACKAGE)
      self.postInstall(output1+err1+output2+err2+output3+err3,conffile)
      # CMake has no option to set the library name to .lib instead of .a so rename libraries
      if config.setCompilers.Configure.isWindows(self.setCompilers.AR, self.log):
        import pathlib
        path = pathlib.Path(os.path.join(self.installDir,'lib'))
        self.logPrint('Changing .a files to .lib files in'+str(path))
        for f in path.iterdir():
          if f.is_file() and f.suffix in ['.a']:
            self.logPrint('Changing '+str(f)+' to '+str(f.with_suffix('.lib')))
            f.rename(f.with_suffix('.lib'))
    return self.installDir
