Merge branch 'master' into firedrake

.gitignore

@@ -80,7 +80,6 @@ docs/exampleconcepts
 docs/faq.html
 docs/installation.html
 docs/linearsolvertable.html
-docs/manconcepts
 docs/manual.pdf
 docs/developers.pdf
 docs/troubleshooting.html

.gitmessage

@@ -1,6 +1,6 @@
 
 
-Commit-type: i.e. bug-fix, portability-fix, testing-fix, style-fix, feature, documentation, example
+Commit-type: i.e. optimization, bug-fix, portability-fix, testing-fix, style-fix, feature, documentation, example
 Funded-by:
 Project:
 Time:     hours

.hgignore

@@ -80,7 +80,6 @@ docs/exampleconcepts
 docs/faq.html
 docs/installation.html
 docs/linearsolvertable.html
-docs/manconcepts
 docs/manual.pdf
 docs/developers.pdf
 docs/troubleshooting.html

.travis.yml

@@ -96,7 +96,7 @@ before_install:
   - if [[ -n "$MPI" ]]; then export CC=mpicc CXX=mpicxx FC=mpifort; fi
   - export NBUILD=`getconf _NPROCESSORS_ONLN`
 install:
-  - ./configure --with-cc=$CC --with-cxx=$CXX --with-fc=$FC --with-clanguage=${LANGUAGE:-C} --with-64-bit-indices=${INT64:-0} --with-scalar-type=${SCALAR:-real} --with-precision=${PRECISION:-double} --with-mpi=${MPI:-0} $BLASLAPACK COPTFLAGS="$OPTFLAGS" CXXOPTFLAGS="$OPTFLAGS" FOPTFLAGS="$OPTFLAGS"
+  - ./configure --with-cc=$CC --with-cxx=$CXX --with-fc=$FC --with-clanguage=${LANGUAGE:-C} --with-64-bit-indices=${INT64:-0} --with-scalar-type=${SCALAR:-real} --with-precision=${PRECISION:-double} --with-mpi=${MPI:-0} $BLASLAPACK COPTFLAGS="$OPTFLAGS" CXXOPTFLAGS="$OPTFLAGS" FOPTFLAGS="$OPTFLAGS" --with-cxx-dialect=0
   - make -j$NBUILD CPPFLAGS=-DPETSC_USE_CXX_COMPLEX_FLOAT_WORKAROUND
 
 script:

config/BuildSystem/config/base.py

@@ -226,6 +226,10 @@ def getExecutable(self, names, path = [], getFullPath = 0, useDefaultPath = 0, r
        - If found, the path is stored in the variable "name", or "resultName" if given
        - By default, a make macro "resultName" will hold the path'''
     found = 0
+    if isinstance(names,str) and names.startswith('/'):
+      path = os.path.dirname(names)
+      names = os.path.basename(names)
+
     if isinstance(names, str):
       names = [names]
     if isinstance(path, str):

config/BuildSystem/config/compilerFlags.py

@@ -77,6 +77,11 @@ def configureCompilerFlags(self):
       bopts.append('g')
     else:
       bopts.append('O')
+
+    # According to gcc doc, gcov does not require -g, so we do it alone
+    if self.argDB['with-gcov']:
+      bopts.append('gcov')
+
     options = self.getOptionsObject()
     if not options:
       return
@@ -96,17 +101,18 @@ def configureCompilerFlags(self):
       try:
         self.rejected[language] = []
         for bopt in bopts:
-          if not bopt == '' and self.getOptionalFlagsName(language) in self.argDB:
+          if bopt in ['g','O'] and self.getOptionalFlagsName(language) in self.argDB: # check --COPTFLAGS etc
             # treat user supplied options as single option - as it could include options separated by spaces '-tp k8-64'
             flags = [self.argDB[self.getOptionalFlagsName(language)]]
-          elif not bopt == '' and self.hasOptFlags(getattr(self.setCompilers,flagsName)):
+          elif bopt in ['g','O'] and self.hasOptFlags(getattr(self.setCompilers,flagsName)): # check --CFLAGS etc
             self.logPrint('Optimization options found in '+flagsName+ '. Skipping setting defaults')
             flags = []
           elif bopt == '' and flagsName in self.argDB:
             self.logPrint('Ignoring default options which were overridden using --'+flagsName+ ' ' + self.argDB[flagsName])
             flags = []
           else:
             flags = options.getCompilerFlags(language, self.setCompilers.getCompiler(), bopt)
+
           for testFlag in flags:
             if isinstance(testFlag,tuple):
               testFlag = ' '.join(testFlag)

config/BuildSystem/config/compilerOptions.py

@@ -33,9 +33,9 @@ def getCFlags(self, compiler, bopt):
         if not nargs.ArgBool('with-errorchecking', arg if arg is not None else '1', isTemporary=True).getValue():
           flags.extend(['-Wno-unused-but-set-variable'])
       elif bopt == 'g':
-        if self.argDB['with-gcov']:
-          flags.extend(['-fprofile-arcs', '-ftest-coverage'])
         flags.append('-g3')
+      elif bopt == 'gcov':
+        flags.extend(['--coverage','-Og']) # --coverage is equal to -fprofile-arcs -ftest-coverage. Use -Og to have accurate coverage result and fine performance
       elif bopt == 'O':
         flags.append('-g')
         if config.setCompilers.Configure.isClang(compiler, self.log):
@@ -119,10 +119,10 @@ def getCxxFlags(self, compiler, bopt):
         if not nargs.ArgBool('with-errorchecking', arg if arg is not None else '1', isTemporary=True).getValue():
           flags.extend(['-Wno-unused-but-set-variable'])
       elif bopt in ['g']:
-        if self.argDB['with-gcov']:
-          flags.extend(['-fprofile-arcs', '-ftest-coverage'])
         # -g3 causes an as SEGV on OSX
         flags.append('-g')
+      elif bopt == 'gcov':
+        flags.extend(['--coverage','-Og'])
       elif bopt in ['O']:
         flags.append('-g')
         if 'USER' in os.environ:
@@ -204,12 +204,12 @@ def getFortranFlags(self, compiler, bopt):
         if not config.setCompilers.Configure.isGfortran47plus(compiler, self.log):
           flags.extend(['-Wno-unused-variable']) # older gfortran warns about unused common block constants
         if config.setCompilers.Configure.isGfortran45x(compiler, self.log):
-          flags.extend(['-Wno-line-truncation']) # Work around bug in this series, fixed in 4.6: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=42852
+          flags.extend(['-Wno-line-truncation']) # Work around bug in this series, fixed in 4.6: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=42852
       elif bopt == 'g':
-        if self.argDB['with-gcov']:
-          flags.extend(['-fprofile-arcs', '-ftest-coverage'])
         # g77 3.2.3 preprocesses the file into nothing if we give -g3
         flags.append('-g')
+      elif bopt == 'gcov':
+        flags.extend(['--coverage','-Og'])
       elif bopt == 'O':
         flags.append('-g')
         flags.extend(['-O'])
@@ -257,6 +257,8 @@ def getFortranFlags(self, compiler, bopt):
     return flags
 
   def getCompilerFlags(self, language, compiler, bopt):
+    if bopt == 'gcov' and not config.setCompilers.Configure.isGNU(compiler, self.log) and not config.setCompilers.Configure.isClang(compiler, self.log):
+      raise RuntimeError('Having --with-gcov but the compiler is neither GCC nor Clang, we do not know how to do gcov')
     flags = ''
     if language == 'C' or language == 'CUDA':
       flags = self.getCFlags(compiler, bopt)
@@ -300,4 +302,5 @@ def getCompilerVersion(self, language, compiler):
     except RuntimeError as e:
       self.logWrite('Could not determine compiler version: '+str(e))
     self.logWrite('getCompilerVersion: '+str(compiler)+' '+str(version)+'\n')
+    self.framework.addMakeMacro(language+'_VERSION',version)
     return version