Merge branch 'firedrake' into barral/allinone

config/BuildSystem/config/base.py

@@ -302,12 +302,10 @@ def getExecutables(self, names, path = '', getFullPath = 0, useDefaultPath = 0,
   # Preprocessor, Compiler, and Linker Operations
   def pushLanguage(self, language):
     if language == 'C++': language = 'Cxx'
-    self.logPrint('Pushing language '+language)
     self.language.append(language)
     return self.language[-1]
 
   def popLanguage(self):
-    self.logPrint('Popping language '+self.language[-1])
     self.language.pop()
     return self.language[-1]
 
@@ -457,7 +455,7 @@ def report(command, status, output, error):
     f = open(self.compilerSource, 'w')
     f.write(self.getCode(codeStr))
     f.close()
-    (out, err, ret) = Configure.executeShellCommand(command, checkCommand = report, timeout = timeout, log = self.log, lineLimit = 100000)
+    (out, err, ret) = Configure.executeShellCommand(command, checkCommand = report, timeout = timeout, log = self.log, logOutputflg = False, lineLimit = 100000)
     if self.cleanup:
       for filename in [self.compilerDefines, self.compilerFixes, self.compilerSource]:
         if os.path.isfile(filename): os.remove(filename)

config/BuildSystem/config/compilers.py

@@ -4,6 +4,12 @@
 import os
 import shutil
 
+def remove_xcode_verbose(buf):
+  retbuf =[]
+  for line in buf.splitlines():
+    if not line.startswith('ld: warning: text-based stub file'): retbuf.append(line)
+  return ('\n').join(retbuf)
+
 class MissingProcessor(AttributeError):
   pass
 
@@ -242,6 +248,7 @@ def checkCLibraries(self):
     self.setCompilers.LDFLAGS = oldFlags
     self.popLanguage()
 
+    output = remove_xcode_verbose(output)
     # PGI: kill anything enclosed in single quotes
     if output.find('\'') >= 0:
       # Cray has crazy non-matching single quotes so skip the removal
@@ -552,6 +559,7 @@ def checkCxxLibraries(self):
     self.setCompilers.LDFLAGS = oldFlags
     self.popLanguage()
 
+    output = remove_xcode_verbose(output)
     # PGI: kill anything enclosed in single quotes
     if output.find('\'') >= 0:
       if output.count('\'')%2: raise RuntimeError('Mismatched single quotes in C library string')
@@ -939,6 +947,7 @@ def checkFortranLibraries(self):
     self.setCompilers.LDFLAGS = oldFlags
     self.popLanguage()
 
+    output = remove_xcode_verbose(output)
     # replace \CR that ifc puts in each line of output
     output = output.replace('\\\n', '')
 

config/BuildSystem/config/framework.py

@@ -413,6 +413,7 @@ def filterCompileOutput(self, output):
     if output.find('warning #264: floating-point value does not fit in required floating-point type') >= 0: return output
     if output.find('warning: ISO C90 does not support') >= 0: return output
     if output.find('warning: ISO C does not support') >= 0: return output
+    if output.find('warning #2650: attributes ignored here') >= 0: return output
     if output.find('Warning: attribute visibility is unsupported and will be skipped') >= 0: return output
     if output.find('(E) Invalid statement found within an interface block. Executable statement, statement function or syntax error encountered.') >= 0: return output
     elif self.argDB['ignoreCompileOutput']:

config/BuildSystem/config/package.py

@@ -213,6 +213,13 @@ def getPointerSizeFlag(self,cflags):
       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():
@@ -356,7 +363,7 @@ def getIncludeDirs(self, prefix, includeDir):
   def generateGuesses(self):
     d = self.checkDownload()
     if d:
-      if not self.liblist or self.builtafterpetsc :
+      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.libdir, self.altlibdir]:
         libdirpath = os.path.join(d, libdir)
@@ -394,6 +401,9 @@ def generateGuesses(self):
                            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.libdir, self.altlibdir]:
         libdirpath = os.path.join(d, libdir)
         if not os.path.isdir(libdirpath):
@@ -409,7 +419,7 @@ def generateGuesses(self):
       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[0]:
+      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:
@@ -418,7 +428,7 @@ def generateGuesses(self):
         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[0]:
+      if self.liblist and self.liblist[0]:
         libs  = self.argDB['with-'+self.package+'-lib']
         slibs = str(self.argDB['with-'+self.package+'-lib'])
       else:

config/BuildSystem/config/packages/BlasLapack.py

@@ -28,14 +28,20 @@ def setupDependencies(self, framework):
     return
 
   def __str__(self):
-    return 'BLAS/LAPACK: '+self.libraries.toString(self.lib)+'\n'
+    output  = config.package.Package.__str__(self)
+    if self.has64bitindices:
+      output += '  uses 64 bit integers\n'
+    else:
+      output += '  uses 32 bit integers\n'
+    return output
 
   def setupHelp(self, help):
     config.package.Package.setupHelp(self,help)
     import nargs
     help.addArgument('BLAS/LAPACK', '-with-blas-lib=<libraries: e.g. [/Users/..../libblas.a,...]>',    nargs.ArgLibrary(None, None, 'Indicate the library(s) containing BLAS'))
     help.addArgument('BLAS/LAPACK', '-with-lapack-lib=<libraries: e.g. [/Users/..../liblapack.a,...]>',nargs.ArgLibrary(None, None, 'Indicate the library(s) containing LAPACK'))
     help.addArgument('BLAS/LAPACK', '-with-blaslapack-suffix=<string>',nargs.ArgLibrary(None, None, 'Indicate a suffix for BLAS/LAPACK subroutine names.'))
+    help.addArgument('BLAS/LAPACK', '-with-64-bit-blas-indices', nargs.ArgBool(None, 0, 'Try to use 64 bit integers for BLAS/LAPACK; will error if not available'))
 #    help.addArgument('BLAS/LAPACK', '-known-64-bit-blas-indices=<bool>', nargs.ArgBool(None, 0, 'Indicate if using 64 bit integer BLAS'))
     return
 
@@ -208,8 +214,7 @@ def generateGuesses(self):
       self.log.write('Looking for BLAS/LAPACK in user specified directory: '+dir+'\n')
       self.log.write('Files and directories in that directory:\n'+str(os.listdir(dir))+'\n')
 
-      # If using 64 bit indices then look for 64 bit integer MKL
-      if self.defaultIndexSize == 64: ILP64 = '_ilp64'
+      if self.argDB['with-64-bit-blas-indices']: ILP64 = '_ilp64'
       else: ILP64 = '_lp64'
 
       # Look for Multi-Threaded MKL for MKL_C/Pardiso
@@ -250,6 +255,7 @@ def generateGuesses(self):
       self.setCompilers.LDFLAGS += '-Wl,-rpath,'+os.path.join(dir,'bin','maci64')
       yield ('User specified MATLAB [ILP64] MKL MacOS lib dir', None, [os.path.join(dir,'bin','maci64','mkl.dylib'), os.path.join(dir,'sys','os','maci64','libiomp5.dylib'), 'pthread'])
       self.setCompilers.LDFLAGS = oldFlags
+      yield ('User specified MKL11/12 and later', None, [os.path.join(dir,'libmkl_intel'+ILP64+'.a'),'mkl_sequential','mkl_core','pthread'])
       # Some new MKL 11/12 variations
       for libdir in [os.path.join('lib','32'),os.path.join('lib','ia32'),'32','ia32','']:
         if not os.path.exists(os.path.join(dir,libdir)):
@@ -260,7 +266,8 @@ def generateGuesses(self):
         if not os.path.exists(os.path.join(dir,libdir)):
           self.logPrint('MKL Path not found.. skipping: '+os.path.join(dir,libdir))
         else:
-          yield ('User specified MKL11/12 Linux64', None, [os.path.join(dir,libdir,'libmkl_intel'+ILP64+'.a'),'mkl_sequential','mkl_core','pthread'])
+          yield ('User specified MKL11+ Linux64', None, [os.path.join(dir,libdir,'libmkl_intel'+ILP64+'.a'),'mkl_sequential','mkl_core','mkl_def','pthread'])
+          yield ('User specified MKL11+ Mac-64', None, [os.path.join(dir,libdir,'libmkl_intel'+ILP64+'.a'),'mkl_sequential','mkl_core','pthread'])
       # Older Linux MKL checks
       yield ('User specified MKL Linux lib dir', None, [os.path.join(dir, 'libmkl_lapack.a'), 'mkl', 'guide', 'pthread'])
       for libdir in ['32','64','em64t']:
@@ -430,6 +437,8 @@ def configureLibrary(self):
     self.executeTest(self.checkRuntimeIssues)
     if self.mkl and self.has64bitindices:
       self.addDefine('HAVE_LIBMKL_INTEL_ILP64',1)
+    if self.argDB['with-64-bit-blas-indices'] and not self.has64bitindices:
+      raise RuntimeError('You requested 64 bit integer BLAS/LAPACK using --with-64-bit-blas-indices but they are not available given your other BLAS/LAPACK options')
 
   def checkESSL(self):
     '''Check for the IBM ESSL library'''
@@ -466,8 +475,9 @@ def checkMKL(self):
               break
 
           if not found:
-            raise RuntimeError('Unable to find MKL include directory. Please source the mklvars-script to set up the MKL environment.\n')
-        self.logPrint('MKL include path set to ' + str(self.include))
+            self.logPrint('Unable to find MKL include directory!')
+          else:
+            self.logPrint('MKL include path set to ' + str(self.include))
     self.logWrite(self.libraries.restoreLog())
     return
 

config/BuildSystem/config/packages/MFEM.py

@@ -13,6 +13,12 @@ def __init__(self, framework):
     self.noMPIUni               = 1
     return
 
+  def setupHelp(self, help):
+    import nargs
+    config.package.Package.setupHelp(self, help)
+    help.addArgument('MFEM', '-download-mfem-ghv-cxx=<prog>', nargs.Arg(None, None, 'CXX Front-end compiler to compile get_hypre_version'))
+    return
+
   def setupDependencies(self, framework):
     config.package.Package.setupDependencies(self, framework)
     self.hypre = framework.require('config.packages.hypre',self)
@@ -44,10 +50,15 @@ def Install(self):
     cxxflags = self.setCompilers.getCompilerFlags()
     cxxflags = cxxflags.replace('-fvisibility=hidden','') # MFEM is currently broken with -fvisibility=hidden
     self.setCompilers.popLanguage()
+    if 'download-mfem-ghv-cxx' in self.argDB and self.argDB['download-mfem-ghv-cxx']:
+      ghv = self.argDB['download-mfem-ghv-cxx']
+    else:
+      ghv = cxx
 
     with open(os.path.join(configDir,'user.mk'),'w') as g:
       g.write('PREFIX = '+prefix+'\n')
       g.write('MPICXX = '+cxx+'\n')
+      g.write('export GHV_CXX = '+ghv+'\n')
       g.write('CXXFLAGS = '+cxxflags+'\n')
       if self.argDB['with-shared-libraries']:
         g.write('SHARED = YES\n')
@@ -57,6 +68,7 @@ def Install(self):
         g.write('STATIC = YES\n')
       g.write('AR = '+self.setCompilers.AR+'\n')
       g.write('ARFLAGS = '+self.setCompilers.AR_FLAGS+'\n')
+      g.write('LDFLAGS = '+self.setCompilers.LDFLAGS+'\n')
       g.write('MFEM_USE_MPI = YES\n')
       g.write('MFEM_MPIEXEC = '+self.mpi.mpiexec+'\n')
       g.write('MFEM_USE_METIS_5 = YES\n')

config/BuildSystem/config/packages/ctetgen.py

@@ -50,7 +50,11 @@ def postProcess(self):
     try:
       self.logPrintBox('Compiling Ctetgen; this may take several minutes')
       # uses the regular PETSc library builder and then moves result 
-      output,err,ret  = config.package.GNUPackage.executeShellCommand(self.make.make+' PETSC_DIR='+self.petscdir.dir+' clean lib',timeout=1000, log = self.log, cwd=self.packageDir)
+      # turn off any compiler optimizations as they may break CTETGEN
+      self.setCompilers.pushLanguage('C')
+      cflags = self.checkNoOptFlag()+' '+self.getSharedFlag(self.setCompilers.getCompilerFlags())+' '+self.getPointerSizeFlag(self.setCompilers.getCompilerFlags())+' '+self.getWindowsNonOptFlags(self.setCompilers.getCompilerFlags())+' '+self.getDebugFlags(self.setCompilers.getCompilerFlags())
+      self.setCompilers.popLanguage()
+      output,err,ret  = config.package.GNUPackage.executeShellCommand(self.make.make+' PETSC_DIR='+self.petscdir.dir+' clean lib PCC_FLAGS="'+cflags+'"',timeout=1000, log = self.log, cwd=self.packageDir)
       self.log.write(output+err)
       self.logPrintBox('Installing Ctetgen; this may take several minutes')
       self.installDirProvider.printSudoPasswordMessage(1)

config/BuildSystem/config/packages/cuda.py

@@ -11,18 +11,12 @@ def __init__(self, framework):
     self.precisions       = ['single','double']
     self.cxx              = 0
     self.complex          = 1
-    self.cudaArch         = ''
     self.CUDAVersion      = 0
     self.CUDAMinVersion   = (7, 5)
     self.hastests         = 0
     self.hastestsdatafiles= 0
     return
 
-  def __str__(self):
-    output  = config.package.Package.__str__(self)
-    output += '  Arch:     '+self.cudaArch+'\n'
-    return output
-
   def setupHelp(self, help):
     import nargs
     config.package.Package.setupHelp(self, help)
@@ -80,8 +74,6 @@ def checkSizeofVoidP(self):
 
   def configureTypes(self):
     import config.setCompilers
-    if not config.setCompilers.Configure.isGNU(self.setCompilers.CC, self.log):
-      raise RuntimeError('Must use GNU compilers with CUDA')
     if not self.getDefaultPrecision() in ['double', 'single']:
       raise RuntimeError('Must use either single or double precision with CUDA')
     self.checkSizeofVoidP()

config/BuildSystem/config/packages/fftw.py

@@ -4,8 +4,8 @@ class Configure(config.package.GNUPackage):
   def __init__(self, framework):
     config.package.GNUPackage.__init__(self, framework)
     # host locally as fftw.org url can expire after new release.
-    self.download   = ['http://www.fftw.org/fftw-3.3.7.tar.gz',
-                       'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/fftw-3.3.7.tar.gz']
+    self.download   = ['http://www.fftw.org/fftw-3.3.8.tar.gz',
+                       'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/fftw-3.3.8.tar.gz']
     self.functions  = ['fftw_malloc','fftw_mpi_cleanup']
     self.includes   = ['fftw3-mpi.h']
     self.liblist    = [['libfftw3_mpi.a','libfftw3.a']]

config/BuildSystem/config/packages/mpi4py.py

@@ -3,16 +3,16 @@
 class Configure(config.package.Package):
   def __init__(self, framework):
     config.package.Package.__init__(self, framework)
-    self.download          = ['https://mpi4py.googlecode.com/files/mpi4py-1.3.1.tar.gz',
-                              'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/mpi4py-1.3.1.tar.gz']
+    self.download          = ['https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-3.0.1.tar.gz',
+                              'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/mpi4py-3.0.1.tar.gz']
     self.functions         = []
     self.includes          = []
     self.useddirectly      = 0
     return
 
   def setupDependencies(self, framework):
     config.package.Package.setupDependencies(self, framework)
-    self.numpy           = framework.require('config.packages.Numpy',self)
+    self.python          = framework.require('config.packages.python',self)
     self.setCompilers    = framework.require('config.setCompilers',self)
     self.sharedLibraries = framework.require('PETSc.options.sharedLibraries', self)
     self.installdir      = framework.require('PETSc.options.installDir',self)
@@ -37,16 +37,16 @@ def Install(self):
     self.addMakeRule('mpi4pybuild','', \
                        ['@echo "*** Building mpi4py ***"',\
                           '@(MPICC=${PCC} && export MPICC && cd '+self.packageDir+' && \\\n\
-           python setup.py clean --all && \\\n\
-           '+archflags+'python setup.py build ) > ${PETSC_ARCH}/lib/petsc/conf/mpi4py.log 2>&1 || \\\n\
+           '+self.python.pyexe+' setup.py clean --all && \\\n\
+           '+archflags+self.python.pyexe+' setup.py build ) > ${PETSC_ARCH}/lib/petsc/conf/mpi4py.log 2>&1 || \\\n\
              (echo "**************************ERROR*************************************" && \\\n\
              echo "Error building mpi4py. Check ${PETSC_ARCH}/lib/petsc/conf/mpi4py.log" && \\\n\
              echo "********************************************************************" && \\\n\
              exit 1)'])
     self.addMakeRule('mpi4pyinstall','', \
                        ['@echo "*** Installing mpi4py ***"',\
                           '@(MPICC=${PCC} && export MPICC && cd '+self.packageDir+' && \\\n\
-           '+archflags+'python setup.py install --install-lib='+os.path.join(self.installDir,'lib')+') >> ${PETSC_ARCH}/lib/petsc/conf/mpi4py.log 2>&1 || \\\n\
+           '+archflags+self.python.pyexe+' setup.py install --install-lib='+os.path.join(self.installDir,'lib')+') >> ${PETSC_ARCH}/lib/petsc/conf/mpi4py.log 2>&1 || \\\n\
              (echo "**************************ERROR*************************************" && \\\n\
              echo "Error building mpi4py. Check ${PETSC_ARCH}/lib/petsc/conf/mpi4py.log" && \\\n\
              echo "********************************************************************" && \\\n\
@@ -67,6 +67,8 @@ def configureLibrary(self):
     self.checkDownload()
     if not self.sharedLibraries.useShared:
         raise RuntimeError('mpi4py requires PETSc be built with shared libraries; rerun with --with-shared-libraries')
+    if not self.python.numpy:
+        raise RuntimeError('mpi4py requires Python with numpy module installed')
 
   def alternateConfigureLibrary(self):
     self.addMakeRule('mpi4py-build','')

config/BuildSystem/config/packages/openblas.py

@@ -36,7 +36,7 @@ def Install(self):
       raise RuntimeError('Cannot request OpenBLAS without Fortran compiler, use --download-f2cblaslapack intead')
 
     cmdline = 'CC='+self.compilers.CC+' FC='+self.compilers.FC
-    if self.argDB['download-openblas-64-bit-blas-indices']:
+    if self.argDB['download-openblas-64-bit-blas-indices'] or self.argDB['with-64-bit-blas-indices']:
       cmdline += " INTERFACE64=1 "
     if 'download-openblas-make-options' in self.argDB and self.argDB['download-openblas-make-options']:
       cmdline+=" "+self.argDB['download-openblas-make-options']