Merge branch 'master' into barry/wirth-fusion-materials

bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
	src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

.mailmap

@@ -8,6 +8,7 @@
 
 Andy Terrel <aterrel@uchicago.edu>
 Aron Ahmadia <aron@ahmadia.net>                 <ahmadia@harley.mcs.anl.gov>
+Barry Smith <bsmith@mcs.anl.gov>                BarryFSmith
 Blaise Bourdin <bourdin@lsu.edu>
 Brad Aagaard <baagaard@usgs.gov>                <baagaard at usgs.gov>
 Ethan Coon <ecoon@lanl.gov>

bin/TOPSInstaller.py → bin/FASTMathInstaller.py

@@ -1,6 +1,15 @@
 #!/usr/bin/env python
 """
-TOPS software installer. This is written using the EasyGui.py python module
+FASTMath software installer.
+
+This can be run from the command line with:
+
+curl --silent https://bitbucket.org/petsc/petsc/raw/60658920ec66ea33cc584d568c1da6e3ed8d2bf9/bin/FASTMathInstaller.py | python
+
+I still cannot come up with a simple portable browser-based click to install to have this run due to people's security concerns.
+
+
+This is written using the EasyGui.py python module
 which is, for simplicity, included in this file
 
 EasyGui provides an easy-to-use interface for simple GUI interaction
@@ -1260,24 +1269,23 @@ def _test():
 
 if __name__ == '__main__':
         args = []
-        title = "TOPS Software Installer"
-        message1 = """SciDAC TOPS Software Installer"""
-        message2 = """The DOE Mathematics SciDAC TOPS ISIC develops software for the
-scalable solution of optimizations, eigenvalues and algebraic systems. More
-information on TOPS may be found at http://www.tops-scidac.org. \n\n
+        title = "FASTMat Software Installer"
+        message1 = """SciDAC FASTMath Software Installer"""
+        message2 = """The DOE Mathematics SciDAC FASTMath develops software for the
+scalable solution of optimizations, eigenvalues and algebraic systems.  \n\n
 The software installed is covered by a variety of licenses, please refer to
 each package's license information before redistributing it. This installer
-can also install additional packages that are used by the TOPS packages."""
+can also install additional packages that are used by the FASTMath packages."""
 
-	result = buttonbox(message=message1, title="TOPS Software Installer", choices = ["Cancel", "Continue"],fontSize = 20,message2=message2)
+	result = buttonbox(message=message1, title="FASTMath Software Installer", choices = ["Cancel", "Continue"],fontSize = 20,message2=message2)
         if result == "Cancel": sys.exit()
 
-	result = buttonbox(message='This preview version of the installer uses\nthe nightly snapshot of the development\nversion of PETSc.\n\nShould you encounter problems please send email\nto petsc-maint@mcs.anl.gov with all output\n', title="TOPS Software Installer", choices = ["Cancel", "Continue"])
+	result = buttonbox(message='Should you encounter problems please send email\nto petsc-maint@mcs.anl.gov with all output\n', title="FASTMath Software Installer", choices = ["Cancel", "Continue"])
         if result == "Cancel": sys.exit()
 
         options = []
         packages = ["hypre (parallel preconditioners)","SuperLU_dist (parallel sparse direct solver)", "SuperLU","Sundials (parallel ODE integrators)"]
-        reply = multchoicebox("Pick the optional TOPS packages to install. PETSc will \nalways be installed. \n\nNote: many of these packages are not portable\nfor all machines, hence select only the packages you truly need.",title, packages)
+        reply = multchoicebox("Pick the optional FASTMath packages to install. PETSc will \nalways be installed. \n\nNote: many of these packages are not portable\nfor all machines, hence select only the packages you truly need.",title, packages)
         for i in reply:
              i = i.lower().replace(' ','')
              f = i.find('(')
@@ -1292,12 +1300,18 @@ def _test():
              if f > 0: i = i[0:f]
              args.append('--download-'+i+'=1')
 
-        reply = indexbox('Compiler to use for PETSc?',title,['C','C++'])
-        if reply == 1: args.append( '--with-clanguage=c++')
+        result = buttonbox('Compiler to use for compiling PETSc?\n\nC is recommended even if you plan to program in C++',title,choices = ['C','C++'])
+        args.append( '--with-clanguage='+result)
+
+        reply = indexbox('Use complex numbers; select only if needed',title,['Yes','No'])
+        if reply == 1: args.append( '--with-scalar-type=complex')
+        else: args.append( '--with-scalar-type=real')
+
+        result = buttonbox('Precision of floating point numbers',title,choices = ['double','__float128','single'])
+        args.append( '--with-precision='+result)
 
         reply = ynbox('Compile libraries so they may be used from Fortran?',title)
-        if reply: args.append( '--with-fortran=1')
-        else: args.append('--with-fc=0')
+        if not reply: args.append( '--with-fc=0')
 
         reply = ynbox('Compile libraries so they may be used from Python?',title)
         if reply:
@@ -1312,7 +1326,7 @@ def _test():
              if '--with-clanguage=c++' in args:
                  reply = fileopenbox("Location of C++ compiler","Location of C++ compiler")
                  args.append('--with-cxx='+reply)
-             if '--with-fortran=1' in args:
+             if not '--with-fc=0' in args:
                  reply = fileopenbox("Location of Fortran compiler","Location of Fortran compiler")
                  args.append('--with-fc='+reply)
 
@@ -1321,7 +1335,7 @@ def _test():
 
         reply = indexbox('Which version of BLAS and LAPACK do you wish to use?',title,['Have installer locate it', 'Install it',"I'll indicate its location"])
         if reply == 1:
-             if '--with-fortran=1' in args: args.append('--download-f-blas-lapack')
+             if not '--with-fc=0' in args: args.append('--download-f-blas-lapack')
              else: args.append('--download-f2cblaslapack')
         elif reply == 2:
            reply = diropenbox("Directory of BLAS and LAPACK libraries","Directory of BLAS and LAPACK libraries")
@@ -1337,52 +1351,64 @@ def _test():
            if not reply: sys.exit()
            args.append('--with-mpi-dir='+reply)
 
-        reply = buttonbox('Install TOPS Solver Components?',title,['Yes','No'],message2="You must have CCAFE and BABEL\n already installed to use them.")
-        if reply == 'Yes':
-           reply = diropenbox("Directory of Babel","Directory of Babel")
-           if not reply: sys.exit()
-           args.append('--with-babel-dir='+reply)
-           reply = diropenbox("Directory of CCafe","Directory of CCAFE")
-           if not reply: sys.exit()
-           args.append('--with-ccafe-dir='+reply)
-
-
-        reply = ynbox('Do MPI jobs need to be submitted with a batch system?',title)
-        if reply: args.append('--with-batch=1')
+        if reply == 4:
+          reply = ynbox('Do MPI jobs need to be submitted with a batch system?',title)
+          if reply: args.append('--with-batch=1')
 
         arch = ''
         while not arch:
-           arch = enterbox("Name of this configuration",title)
+           arch = enterbox("Name of this configuration",title,"arch-")
         args.append('-PETSC_ARCH='+arch)
 
-        reply = diropenbox("Location to compile and install packages","Location to compile and install packages")
+        reply = diropenbox("Location of PETSc directory or where to download and compile packages","Location of PETSc directory or where to download and compile andpackages")
         if not reply: sys.exit()
 
         import os.path
         import sys
 
-
-        petscroot = os.path.join(reply,'petsc-dev')
-        if not os.path.isfile(os.path.join(petscroot,'include','petscsys.h')):
-          y = ynbox('Could not locate PETSc directory, should I download it?',title)
-          if not y: sys.exit()
-          # download PETSc
-          import urllib
-          try:
-            urllib.urlretrieve('http://ftp.mcs.anl.gov/pub/petsc/petsc-dev.tar.gz', os.path.join(reply,'petsc.tar.gz'))
-          except Exception, e:
-            raise RuntimeError('Unable to download PETSc')
-          import commands
-          try:
-            commands.getoutput('cd '+reply+'; gunzip petsc.tar.gz ; tar xf petsc.tar')
-          except RuntimeError, e:
-            raise RuntimeError('Error unzipping petsc.tar.gz'+str(e))
-          os.unlink(os.path.join(reply, 'petsc.tar'))
+        petscroot = None
+        if os.path.isfile(os.path.join(reply,'include','petscsys.h')):
+          petscroot = os.path.join(reply,'petsc')
+        else:
+          ldir = os.listdir(reply)
+          for i in ldir:
+            if i.startswith('petsc') and os.path.isfile(os.path.join(reply,i,'include','petscsys.h')):
+              y = ynbox('There is a subdirectory called '+os.path.join(reply,i)+'.Do you wish to use that?',title)
+              if y: 
+                petscroot = os.path.join(reply,i)
+                break
+          if not petscroot:
+            y = ynbox('Could not locate PETSc directory, should I download it\nand install it in the directory '+reply+'?',title)
+            if not y: sys.exit()
+
+            result = buttonbox('Which version of PETSc should I download?\n\nPlease be patient after making your selection\nthis may take several minutes.'+reply,title,choices = ['Release','Development'])
+            if result == 'Release':
+              # download PETSc
+              import urllib
+              try:
+                urllib.urlretrieve('http://ftp.mcs.anl.gov/pub/petsc/petsc.tar.gz', os.path.join(reply,'petsc.tar.gz'))
+              except Exception, e:
+                raise RuntimeError('Unable to download PETSc')
+              import commands
+              try:
+                commands.getoutput('cd '+reply+'; gunzip petsc.tar.gz ; tar xf petsc.tar')
+              except RuntimeError, e:
+                raise RuntimeError('Error unzipping petsc.tar.gz'+str(e))
+              os.unlink(os.path.join(reply, 'petsc.tar'))
+            else:
+              import commands
+              try:
+                commands.getoutput('cd '+reply+'; git clone https://bitbucket.org/petsc/petsc.git')
+              except RuntimeError, e:
+                raise RuntimeError('Error trying to obtain development version of PETSc with git'+str(e))
+            ldir = os.listdir(reply)
+            for i in ldir:
+              # wrong because will pick up old petsc directories in this directory
+              if i.startswith('petsc') and os.path.isfile(os.path.join(reply,i,'include','petscsys.h')): petscroot = os.path.join(reply,i)
 
 
         args.append('--with-shared-libraries=1')
-        args.append('--with-dynamic-loading=1')
-        args.append('--with-external-packages-dir='+reply)
+        args.append('--with-external-packages-dir='+os.path.join(petscroot,arch,'externalpackages'))
         args = multenterbox("Configure options you have selected.", title, None, args)
         if not args: sys.exit()
 
@@ -1398,3 +1424,6 @@ def _test():
         f.close()
         os.chmod(configfile,0755)
         msgbox('After hitting OK run\n\n cd '+petscroot+'\npython config-'+arch+'.py\n\nto continue the install')
+        print("Execute the following two commands and follow the directions")
+        print('cd '+petscroot)
+        print('python config-'+arch+'.py')

bin/maint/asterix-test.sh

@@ -4,10 +4,10 @@ set -x
 # basic gcc tests
 ./config/examples/asterix/asterix64.py
 make PETSC_ARCH=asterix64 all alltests tests_DATAFILESPATH DATAFILESPATH=/home/balay/datafiles
-./config/configure.py  CC=gcc FC=gfortran CXX=g++ PETSC_ARCH=asterix64-cxx-sieve --with-clanguage=cxx \
---with-sieve=1 --download-mpich=1 --download-boost=1 --download-chaco=1 \
+./config/configure.py  CC=gcc FC=gfortran CXX=g++ PETSC_ARCH=asterix64-cxx --with-clanguage=cxx \
+--download-mpich=1 --download-boost=1 --download-chaco=1 \
 --download-plapack=1 --download-tetgen=1 --download-triangle=1 --download-hdf5=1
-make PETSC_ARCH=asterix64-cxx-sieve all alltests tests_DATAFILESPATH DATAFILESPATH=/home/balay/datafiles
+make PETSC_ARCH=asterix64-cxx all alltests tests_DATAFILESPATH DATAFILESPATH=/home/balay/datafiles
 ./config/examples/asterix/asterix64-openmpi.py
 make PETSC_ARCH=asterix64-openmpi all alltests tests_DATAFILESPATH DATAFILESPATH=/home/balay/datafiles
 ./config/examples/asterix/asterix64.py --with-clanguage=cxx -PETSC_ARCH=asterix64-cxx-opt --with-debugging=0 --with-log=0
@@ -26,7 +26,7 @@ make PETSC_ARCH=asterix64-c89 all test alltests tests_DATAFILESPATH DATAFILESPAT
 # basic sun tests
 ./config/examples/asterix/asterix64-sun.py
 make PETSC_ARCH=asterix64-sun all test
-./config/examples/asterix/asterix64-sun.py --with-shared-libraries=1 --with-dynamic-loading=1 -PETSC_ARCH=asterix64-sun-dynamic
+./config/examples/asterix/asterix64-sun.py --with-shared-libraries=1 -PETSC_ARCH=asterix64-sun-dynamic
 make PETSC_ARCH=asterix64-sun-dynamic all alltests tests_DATAFILESPATH DATAFILESPATH=/home/balay/datafiles
 ./config/examples/asterix/asterix64-sun.py --with-clanguage=cxx -PETSC_ARCH=asterix64-sun-cxx  --with-debugging=0 --with-pic=0 \
 --download-f-blaslapack=1 --download-spooles=1 --download-superlu=1 \
@@ -35,7 +35,7 @@ make PETSC_ARCH=asterix64-sun-dynamic all alltests tests_DATAFILESPATH DATAFILES
 make PETSC_ARCH=asterix64-sun-cxx all
 make PETSC_ARCH=asterix64-sun-cxx CLINKER=sun-cc shared
 make PETSC_ARCH=asterix64-sun-cxx test
-./config/examples/asterix/asterix64-sun.py --with-shared-libraries=1 --with-dynamic-loading=1 --with-scalar-type=complex --with-clanguage=cxx -PETSC_ARCH=asterix64-sun-complex-dynamic
+./config/examples/asterix/asterix64-sun.py --with-shared-libraries=1 --with-scalar-type=complex --with-clanguage=cxx -PETSC_ARCH=asterix64-sun-complex-dynamic
 make PETSC_ARCH=asterix64-sun-complex-dynamic all
 make PETSC_ARCH=asterix64-sun-complex-dynamic CLINKER=sun-cc shared
 make PETSC_ARCH=asterix64-sun-complex-dynamic test

bin/maint/builddist

@@ -89,7 +89,7 @@ version_subminor=`grep '^#define PETSC_VERSION_SUBMINOR ' include/petscversion.h
 
 #generated a couple of more values
 version_date=`date +"%b, %d, %Y"`
-version_git=`git log -1 --pretty=format:%H`
+version_git=`git describe`
 version_date_git=`git log -1 --pretty=format:%ci`
 if [ ${version}foo = foo ]; then
   if  [ ${version_release} = 0 ]; then

bin/maint/buildtest

@@ -73,10 +73,10 @@ if ( $? ) then
 else
   set BUILDER="yes"
 endif
+set GCOV=`grep PETSC_USE_GCOV $nPETSC_DIR/$PETSC_ARCH/include/petscconf.h`
 
-if ( "${BUILDER}" == "yes" ) then
-  env PETSC_ARCH=$PETSC_ARCH PETSC_DIR=$nPETSC_DIR ./config/builder2.py clean >>& build.log
-  env PETSC_ARCH=$PETSC_ARCH PETSC_DIR=$nPETSC_DIR ./config/builder2.py build >>& build.log
+if ( "${GCOV}" != "" ) then
+  make PETSC_ARCH=$PETSC_ARCH PETSC_DIR=$nPETSC_DIR  all-legacy test >>& build.log
 else
   make PETSC_ARCH=$PETSC_ARCH PETSC_DIR=$nPETSC_DIR  all test >>& build.log
 endif
@@ -100,6 +100,7 @@ if ( $? ) then
   set VALGRIND='DUMMYARGUMENT=foobar'
 else
   set VALGRIND=`echo MPIEXEC="${PETSC_DIR}/bin/petscmpiexec -valgrind"`
+  setenv PETSCVALGRIND_OPTIONS "--suppressions=${PETSC_DIR}/bin/maint/petsc-val.supp"
 endif
 rm -f examples.log
 echo "Build on $MACH $PETSC_ARCH TESTMODE=$TESTMODE ${VALGRIND}  `date` " > examples.log
@@ -110,7 +111,6 @@ else
 endif
 echo '******************************************************' >>& $nPETSC_DIR/examples.log
 
-set GCOV=`grep PETSC_USE_GCOV $nPETSC_DIR/$PETSC_ARCH/include/petscconf.h`
 if ( "${GCOV}" != "" ) then
   make PETSC_ARCH=$PETSC_ARCH PETSC_DIR=$nPETSC_DIR gcov  >>& examples.log
 endif

bin/maint/confignightly/churn2

@@ -3,4 +3,4 @@
 set MACH=churn
 set USR=petsc
 set LOC=/sandbox/petsc/${RNAME}-2
-set CONF=arch-linux-cxx-sieve
+set CONF=arch-linux-cxx

bin/maint/confignightly/crush3

@@ -3,4 +3,4 @@
 set MACH=crush
 set USR=petsc
 set LOC=/sandbox/petsc/${RNAME}-3
-set CONF=arch-linux-cxx-sieve-gcov
+set CONF=arch-linux-cxx-gcov

bin/maint/dos/makecpp.tcl

@@ -55,7 +55,6 @@ proc updatemakefile { makefile } {
         #
         regsub  -all  "\ninclude" $databuff  "\n!include" databuff
         #
-        # Change -D__SDIR__='"${LOCDIR}"' to /D__SDIR__="\"${LOCDIR}\""
         # Change -DPETSC_DIR='"${PETSC_DIR}"' to /DPETSC_DIR="\"${PETSC_DIR}\""
         #
         regsub -all  "\\\-D" $databuff "/D" databuff

bin/maint/dos/rules_win32

@@ -25,9 +25,6 @@ OBJS	       = $(OBJSC) $(OBJSF)
 PETSC_INCLUDE  = /I$(PETSC_DIR) /I$(PETSC_DIR)\include $(MPI_INCLUDE) \
                  /I$(PETSC_DIR)\bmake\$(PETSC_ARCH) $(AMS_INCLUDE) $(PETSC_BLASLAPACK_FLAGS)
 CCPPFLAGS      = $(PETSC_INCLUDE) $(PCONF) $(PETSCFLAGS) $(CPPFLAGS)
-# __SDIR__ is not required as, on NT, the absolute path is used when compiling a
-# source file (which already includes the __SDIR__ information
-#		/D__SDIR__="\"$(LOCDIR)\""
 FCPPFLAGS      = $(PETSC_INCLUDE) $(PCONF) $(PETSCFLAGS) $(FPPFLAGS)
 PETSC_SYS_LIB  = libpetsc.lib $(EXTERNAL_LIB) $(BLASLAPACK_LIB) \
                  $(MPE_LIB) $(MPI_LIB) $(X11_LIB) $(SYS_LIB)

bin/maint/gcov.py

@@ -89,18 +89,17 @@ def make_tarball(dirname):
     print """Tarball created in %s"""%(PETSC_DIR)
     return
 
-def make_htmlpage(LOC,tarballs):
+def make_htmlpage(gcov_dir,LOC,tarballs):
 
     # Create index_gcov webpages using information processed from
     # running gcov
     # This is done in four stages
-    # Stage 1: Extract tar balls,merge files and dump .lines files in /tmp/gcov
+    # Stage 1: Extract tar balls,merge files and dump .lines files in gcov_dir
     # Stage 2: Process .lines files
     # Stage 3: Create marked HTML source code files
     # Stage 4: Create HTML pages having statistics and hyperlinks to HTML source code           files (files are sorted by filename and percentage code tested)
     #  Stores the main HTML pages in LOC if LOC is defined via command line argument o-wise it uses the default PETSC_DIR
 
-    gcov_dir = os.path.join('/tmp','gcov')
     if os.path.isdir(gcov_dir):
         shutil.rmtree(gcov_dir)
     os.makedirs(gcov_dir)
@@ -387,7 +386,7 @@ def make_htmlpage(LOC,tarballs):
 
 def main():
 
-    USER = os.environ>['USER']
+    USER = os.environ['USER']
     gcov_dir = "/tmp/gcov-"+USER
 
     if (sys.argv[1] == "-run_gcov"):
@@ -406,7 +405,7 @@ def main():
             LOC = PETSC_DIR
             tarballs = sys.argv[2:]
 
-        make_htmlpage(LOC,tarballs)
+        make_htmlpage(gcov_dir,LOC,tarballs)
     else:
         print "No or invalid option specified:"
         print "Usage: To run gcov and create tarball"

bin/maint/generatefortranstubs.py

@@ -13,8 +13,8 @@ def FixFile(filename):
   ff.close()
 
   # gotta be a better way to do this
-  data = re.subn('\nvoid ','\nvoid PETSC_STDCALL ',data)[0]
-  data = re.subn('\nPetscErrorCode ','\nvoid PETSC_STDCALL ',data)[0]
+  data = re.subn('\nvoid ','\nPETSC_EXTERN void PETSC_STDCALL ',data)[0]
+  data = re.subn('\nPetscErrorCode ','\nPETSC_EXTERN void PETSC_STDCALL ',data)[0]
   data = re.subn('Petsc([ToRm]*)Pointer\(int\)','Petsc\\1Pointer(void*)',data)[0]	
   data = re.subn('PetscToPointer\(a\) \(a\)','PetscToPointer(a) (*(long *)(a))',data)[0]
   data = re.subn('PetscFromPointer\(a\) \(int\)\(a\)','PetscFromPointer(a) (long)(a)',data)[0]
@@ -161,7 +161,10 @@ def processDir(arg,dirname,names):
     (status,output) = commands.getstatusoutput(cmd)
     if status:
       raise RuntimeError('Error running bfort\n'+cmd+'\n'+output)
-    FixDir(petscdir,outdir,verbose)
+    try:
+      FixDir(petscdir,outdir,verbose)
+    except:
+      print 'Error! with FixDir('+outdir+')'
 
   # remove from list of subdirectories all directories without source code
   rmnames=[]

bin/maint/getinterfaces.py

@@ -244,7 +244,6 @@ def main(args):
   classes['PetscBinary'] = {}
   classes['PetscOptions'] = {}
   classes['PetscMalloc'] = {}
-  classes['PetscHMPI'] = {}
   classes['PetscToken'] = {}
   for i in args:
     getclasses(i)

bin/maint/package-test.sh

@@ -2,8 +2,8 @@
 set -x
 ECHO=
 
-OPT1='--with-shared-libraries=1 --with-dynamic-loading=1 --with-debugging=0'
-OPT2='--with-clanguage=cxx --with-sieve=1 --with-log=0'
+OPT1='--with-shared-libraries=1 --with-debugging=0'
+OPT2='--with-clanguage=cxx --with-log=0'
 OPT3='--with-scalar-type=complex --with-clanguage=cxx --with-pic=0 --with-log=0'
 
 DATAFILESPATH=/home/petsc/datafiles

bin/maint/petsc-val.supp

@@ -0,0 +1,10 @@
+{
+   <petsc-nightlybuild-with-gfortran>
+   Memcheck:Cond
+   fun:fd_to_stream
+   fun:_gfortrani_init_units
+   fun:init
+   fun:call_init.part.0
+   fun:_dl_init
+   obj:/lib/x86_64-linux-gnu/ld-2.15.so
+}