--- trunk/SConstruct	2006/03/30 11:35:55	694
+++ trunk/SConstruct	2009/03/11 08:17:57	2300
@@ -1,358 +1,789 @@
-#          Copyright 2006 by ACcESS MNRF                   
-#                                                          
-#              http://www.access.edu.au                    
-#       Primary Business: Queensland, Australia            
-#  Licensed under the Open Software License version 3.0    
-#     http://www.opensource.org/licenses/osl-3.0.php       
-#                                                          
+
+########################################################
+#
+# Copyright (c) 2003-2008 by University of Queensland
+# Earth Systems Science Computational Center (ESSCC)
+# http://www.uq.edu.au/esscc
 #
+# Primary Business: Queensland, Australia
+# Licensed under the Open Software License version 3.0
+# http://www.opensource.org/licenses/osl-3.0.php
 #
+########################################################
+
 
-# top-level Scons configuration file for all esys13 modules
-# Begin initialisation Section
-# all of this section just intialises default environments and helper 
-# scripts. You shouldn't need to modify this section.
 EnsureSConsVersion(0,96,91)
 EnsurePythonVersion(2,3)
 
-import sys, os
+import sys, os, re, socket, platform, stat
+
 # Add our extensions
-if sys.path.count('scons')==0: sys.path.append('scons')
+if os.path.isdir('scons'): sys.path.append('scons')
 import scons_extensions
 
-# Default options and options help text
-# These are defaults and can be overridden using command line arguments or an options file.
-# if the options_file or ARGUMENTS do not exist then the ones listed as default here are used
-# DO NOT CHANGE THEM HERE
-if ARGUMENTS.get('options_file',0):
-   options_file = ARGUMENTS.get('options_file',0)
-else:
-   import socket
-   from string import ascii_letters,digits
-   hostname=""
-   for s in socket.gethostname().split('.')[0]:
-      if s in ascii_letters+digits:
-         hostname+=s
-      else:
-         hostname+="_"
-   options_file = "scons/"+hostname+"_options.py"
+# Use /usr/lib64 if available, else /usr/lib
+usr_lib = '/usr/lib'
+if os.path.isfile('/usr/lib64/libc.so'): usr_lib = '/usr/lib64'
+
+# The string python2.4 or python2.5
+python_version = 'python%s.%s' % (sys.version_info[0], sys.version_info[1])
+
+# MS Windows support, many thanks to PH
+IS_WINDOWS_PLATFORM = (os.name== "nt")
+
+prefix = ARGUMENTS.get('prefix', Dir('#.').abspath)
+
+# Read configuration options from file scons/<hostname>_options.py
+hostname = re.sub("[^0-9a-zA-Z]", "_", socket.gethostname().split('.')[0])
+tmp = os.path.join("scons",hostname+"_options.py")
+options_file = ARGUMENTS.get('options_file', tmp)
+if not os.path.isfile(options_file):
+  options_file = False
+  print "Options file not found (expected '%s')" % tmp
+else:
+  print "Options file is", options_file
 
+# Load options file and command-line arguments
 opts = Options(options_file, ARGUMENTS)
+
+############ Load build options ################################
+
 opts.AddOptions(
 # Where to install esys stuff
-  ('incinstall', 'where the esys headers will be installed', Dir('#.').abspath+'/include'), 
-  ('libinstall', 'where the esys libraries will be installed', Dir('#.').abspath+'/lib'), 
-  ('pyinstall', 'where the esys python modules will be installed', Dir('#.').abspath), 
+  ('prefix', 'where everything will be installed',                       Dir('#.').abspath),
+  ('incinstall', 'where the esys headers will be installed',             os.path.join(Dir('#.').abspath,'include')),
+  ('bininstall', 'where the esys binaries will be installed',            os.path.join(prefix,'bin')),
+  ('libinstall', 'where the esys libraries will be installed',           os.path.join(prefix,'lib')),
+  ('pyinstall', 'where the esys python modules will be installed',       os.path.join(prefix,'esys')),
 # Compilation options
-  BoolOption('dodebug', 'Do you want a debug build?', 'yes'),
-  ('options_file', "Optional file containing preferred options. Ignored if it doesn't exist (default: scons/hostname_options.py)", options_file),
-  ('cc_defines','C/C++ defines to use', None),
-  ('cc_flags','C compiler flags to use (Release build)', None),
-  ('cc_flags_debug', 'C compiler flags to use (Debug build)', None),
-  ('cxx_flags', 'C++ compiler flags to use (Release build)', None),
-  ('cxx_flags_debug', 'C++ compiler flags to use (Debug build)', None),
-  ('ar_flags', 'Static library archiver flags to use', None),
-  ('sys_libs', 'System libraries to link with', None),
-# MKL
-  PathOption('mkl_path', 'Path to MKL includes', None), 
-  PathOption('mkl_lib_path', 'Path to MKL libs', None), 
-  ('mkl_libs', 'MKL libraries to link with', None),
-# SCSL
-  PathOption('scsl_path', 'Path to SCSL includes', None), 
-  PathOption('scsl_lib_path', 'Path to SCSL libs', None), 
-  ('scsl_libs', 'SCSL libraries to link with', None),
-# UMFPACK 
-  PathOption('umf_path', 'Path to UMF includes', None), 
-  PathOption('umf_lib_path', 'Path to UMF libs', None), 
-  ('umf_libs', 'UMF libraries to link with', None),
+  BoolOption('dodebug', 'For backwards compatibility', 'no'),
+  BoolOption('usedebug', 'Do you want a debug build?', 'no'),
+  BoolOption('usevtk', 'Do you want to use VTK?', 'yes'),
+  ('options_file', 'File of paths/options. Default: scons/<hostname>_options.py', options_file),
+  ('win_cc_name', 'windows C compiler name if needed', 'msvc'),
+  # The strings -DDEFAULT_ get replaced by scons/<hostname>_options.py or by defaults below
+  ('cc_flags', 'C compiler flags to use', '-DEFAULT_1'),
+  ('cc_optim', 'C compiler optimization flags to use', '-DEFAULT_2'),
+  ('cc_debug', 'C compiler debug flags to use', '-DEFAULT_3'),
+  ('omp_optim', 'OpenMP compiler flags to use (Release build)', '-DEFAULT_4'),
+  ('omp_debug', 'OpenMP compiler flags to use (Debug build)', '-DEFAULT_5'),
+  ('omp_libs', 'OpenMP compiler libraries to link with', '-DEFAULT_6'),
+  ('cc_extra', 'Extra C/C++ flags', ''),
+  ('ld_extra', 'Extra linker flags', ''),
+  ('sys_libs', 'System libraries to link with', []),
+  ('ar_flags', 'Static library archiver flags to use', ''),
+  BoolOption('useopenmp', 'Compile parallel version using OpenMP', 'no'),
+  BoolOption('usepedantic', 'Compile with -pedantic if using gcc', 'no'),
+  BoolOption('usewarnings','Compile with warnings as errors if using gcc','yes'),
+  ('forcelazy','for testing use only - set the default value for autolazy','leave_alone'),
 # Python
-# locations of include files for python
-  PathOption('python_path', 'Path to Python includes', '/usr/include/python%s.%s'%(sys.version_info[0],sys.version_info[1])), 
-  PathOption('python_lib_path', 'Path to Python libs', '/usr/lib'), 
-  ('python_lib', 'Python libraries to link with', ["python%s.%s"%(sys.version_info[0],sys.version_info[1]),]),
+  ('python_path', 'Path to Python includes', '/usr/include/'+python_version),
+  ('python_lib_path', 'Path to Python libs', usr_lib),
+  ('python_libs', 'Python libraries to link with', [python_version]),
+  ('python_cmd', 'Python command', 'python'),
 # Boost
-  PathOption('boost_path', 'Path to Boost includes', '/usr/include'), 
-  PathOption('boost_lib_path', 'Path to Boost libs', '/usr/lib'), 
-  ('boost_lib', 'Boost libraries to link with', ['boost_python',]),
-# CppUnit
-  PathOption('cppunit_path', 'Path to CppUnit includes', Dir('#.').abspath+'/tools/CppUnitTest/inc'), 
-  PathOption('cppunit_lib_path', 'Path to CppUnit libs', Dir('#.').abspath+'/lib'), 
-  ('cppunit_lib', 'CppUnit libraries to link with', ['CppUnitTest',]),
-# Doc building
-  PathOption('doxygen_path', 'Path to Doxygen executable', None), 
-  PathOption('epydoc_path', 'Path to Epydoc executable', None), 
-  PathOption('epydoc_pythonpath', 'Path to Epydoc python files', None), 
+  ('boost_path', 'Path to Boost includes', '/usr/include'),
+  ('boost_lib_path', 'Path to Boost libs', usr_lib),
+  ('boost_libs', 'Boost libraries to link with', ['boost_python']),
+# NetCDF
+  BoolOption('usenetcdf', 'switch on/off the usage of netCDF', 'yes'),
+  ('netCDF_path', 'Path to netCDF includes', '/usr/include'),
+  ('netCDF_lib_path', 'Path to netCDF libs', usr_lib),
+  ('netCDF_libs', 'netCDF C++ libraries to link with', ['netcdf_c++', 'netcdf']),
+# MPI
+  BoolOption('useMPI', 'For backwards compatibility', 'no'),
+  BoolOption('usempi', 'Compile parallel version using MPI', 'no'),
+  ('MPICH_IGNORE_CXX_SEEK', 'name of macro to ignore MPI settings of C++ SEEK macro (for MPICH)' , 'MPICH_IGNORE_CXX_SEEK'),
+  ('mpi_path', 'Path to MPI includes', '/usr/include'),
+  ('mpi_run', 'mpirun name' , 'mpiexec -np 1'),
+  ('mpi_lib_path', 'Path to MPI libs (needs to be added to the LD_LIBRARY_PATH)', usr_lib),
+  ('mpi_libs', 'MPI libraries to link with (needs to be shared!)', ['mpich' , 'pthread', 'rt']),
+# ParMETIS
+  BoolOption('useparmetis', 'Compile parallel version using ParMETIS', 'yes'),
+  ('parmetis_path', 'Path to ParMETIS includes', '/usr/include'),
+  ('parmetis_lib_path', 'Path to ParMETIS library', usr_lib),
+  ('parmetis_libs', 'ParMETIS library to link with', ['parmetis', 'metis']),
 # PAPI
-  PathOption('papi_path', 'Path to PAPI includes', None), 
-  PathOption('papi_lib_path', 'Path to PAPI libs', None), 
-  ('papi_libs', 'PAPI libraries to link with', None),
+  BoolOption('usepapi', 'switch on/off the usage of PAPI', 'no'),
+  ('papi_path', 'Path to PAPI includes', '/usr/include'),
+  ('papi_lib_path', 'Path to PAPI libs', usr_lib),
+  ('papi_libs', 'PAPI libraries to link with', ['papi']),
+  BoolOption('papi_instrument_solver', 'use PAPI in Solver.c to instrument each iteration of the solver', False),
+# MKL
+  BoolOption('usemkl', 'switch on/off the usage of MKL', 'no'),
+  ('mkl_path', 'Path to MKL includes', '/sw/sdev/cmkl/10.0.2.18/include'),
+  ('mkl_lib_path', 'Path to MKL libs', '/sw/sdev/cmkl/10.0.2.18/lib/em64t'),
+  ('mkl_libs', 'MKL libraries to link with', ['mkl_solver', 'mkl_em64t', 'guide', 'pthread']),
+# UMFPACK
+  BoolOption('useumfpack', 'switch on/off the usage of UMFPACK', 'no'),
+  ('ufc_path', 'Path to UFconfig includes', '/usr/include/suitesparse'),
+  ('umf_path', 'Path to UMFPACK includes', '/usr/include/suitesparse'),
+  ('umf_lib_path', 'Path to UMFPACK libs', usr_lib),
+  ('umf_libs', 'UMFPACK libraries to link with', ['umfpack']),
+# Silo
+  BoolOption('usesilo', 'switch on/off the usage of Silo', 'yes'),
+  ('silo_path', 'Path to Silo includes', '/usr/include'),
+  ('silo_lib_path', 'Path to Silo libs', usr_lib),
+  ('silo_libs', 'Silo libraries to link with', ['siloh5', 'hdf5']),
+# AMD (used by UMFPACK)
+  ('amd_path', 'Path to AMD includes', '/usr/include/suitesparse'),
+  ('amd_lib_path', 'Path to AMD libs', usr_lib),
+  ('amd_libs', 'AMD libraries to link with', ['amd']),
+# BLAS (used by UMFPACK)
+  ('blas_path', 'Path to BLAS includes', '/usr/include/suitesparse'),
+  ('blas_lib_path', 'Path to BLAS libs', usr_lib),
+  ('blas_libs', 'BLAS libraries to link with', ['blas']),
+# An option for specifying the compiler tools set (see windows branch).
+  ('tools_names', 'allow control over the tools in the env setup', ['intelc']),
+# finer control over library building, intel aggressive global optimisation
+# works with dynamic libraries on windows.
+  ('share_esysUtils', 'control static or dynamic esysUtils lib', False),
+  ('share_paso', 'control static or dynamic paso lib', False)
 )
 
-# Initialise Scons Build Environment
-# check for user environment variables we are interested in
-try:
-   python_path = os.environ['PYTHONPATH']
-except KeyError:
-   python_path = ''
-try:
-   path = os.environ['PATH']
-except KeyError:
-   path = ''
-try:
-   ld_library_path = os.environ['LD_LIBRARY_PATH']
-except KeyError:
-   ld_library_path = ''
-
-# Note: On the Altix the intel compilers are not automatically
-# detected by scons intelc.py script. The Altix has a different directory
-# path and in some locations the "modules" facility is used to support
-# multiple compiler versions. This forces the need to import the users PATH
-# environment which isn't the "scons way"
-# This doesn't impact linux and windows which will use the default compiler (g++ or msvc, or the intel compiler if it is installed on both platforms)
-# FIXME: Perhaps a modification to intelc.py will allow better support for ia64 on altix
- 
-if os.name != "nt" and os.uname()[4]=='ia64':
-   env = Environment(ENV = {'PATH':path}, tools = ['default', 'intelc'], options = opts)
-   env['ENV']['PATH'] = path
-   env['ENV']['LD_LIBRARY_PATH'] = ld_library_path
-   env['ENV']['PYTHONPATH'] = python_path
-   if env['CXX'] == 'icpc':
-      env['LINK'] = env['CXX'] # version >=9 of intel c++ compiler requires use of icpc to link in C++ runtimes (icc does not). FIXME: this behaviour could be directly incorporated into scons intelc.py
-elif os.name == "nt":
-   # FIXME: Need to implement equivalent of ld library path for windoze
-   env = Environment(tools = ['default', 'intelc'], options = opts)
-   env['ENV']['PYTHONPATH'] = python_path
-else:
-   env = Environment(tools = ['default'], options = opts)
-   env['ENV']['PATH'] = path
-   env['ENV']['LD_LIBRARY_PATH'] = ld_library_path
-   env['ENV']['PYTHONPATH'] = python_path
+############ Specify which compilers to use ####################
 
-# Setup help for options
+# intelc uses regular expressions improperly and emits a warning about
+# failing to find the compilers.  This warning can be safely ignored.
+
+if IS_WINDOWS_PLATFORM:
+      env = Environment(options = opts)
+      env = Environment(tools = ['default'] + env['tools_names'],
+                        options = opts)
+else:
+   if socket.gethostname().split('.')[0] == 'service0':
+      env = Environment(tools = ['default', 'intelc'], options = opts)
+   elif os.uname()[4]=='ia64':
+      env = Environment(tools = ['default', 'intelc'], options = opts)
+      if env['CXX'] == 'icpc':
+         env['LINK'] = env['CXX'] # version >=9 of intel c++ compiler requires use of icpc to link in C++ runtimes (icc does not)
+   else:
+      env = Environment(tools = ['default'], options = opts)
 Help(opts.GenerateHelpText(env))
 
-# Add some customer builders
+############ Fill in compiler options if not set above #########
+
+# Backwards compatibility: allow dodebug=yes and useMPI=yes
+if env['dodebug']: env['usedebug'] = 1
+if env['useMPI']: env['usempi'] = 1
+
+# Default compiler options (override allowed in hostname_options.py, but should not be necessary)
+# For both C and C++ you get: cc_flags and either the optim flags or debug flags
+
+sysheaderopt = ""		# how do we indicate that a header is a system header. Use "" for no action.
+
+if env["CC"] == "icc":
+  # Intel compilers
+  cc_flags		= "-fPIC -ansi -wd161 -w1 -vec-report0 -DBLOCKTIMER -DCORE_ID1"
+  cc_optim		= "-O3 -ftz -IPF_ftlacc- -IPF_fma -fno-alias"
+  cc_debug		= "-g -O0 -DDOASSERT -DDOPROF -DBOUNDS_CHECK"
+  omp_optim		= "-openmp -openmp_report0"
+  omp_debug		= "-openmp -openmp_report0"
+  omp_libs		= ['guide', 'pthread']
+  pedantic		= ""
+  fatalwarning		= ""		# Switch to turn warnings into errors
+  sysheaderopt		= ""
+elif env["CC"] == "gcc":
+  # GNU C on any system
+  cc_flags		= "-pedantic -Wall -fPIC -ansi -ffast-math -Wno-unknown-pragmas -DBLOCKTIMER  -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing"
+#the long long warning occurs on the Mac
+  cc_optim		= "-O3"
+  cc_debug		= "-g -O0 -DDOASSERT -DDOPROF -DBOUNDS_CHECK"
+  omp_optim		= "-fopenmp"
+  omp_debug		= "-fopenmp"
+  omp_libs		= ['gomp']
+  pedantic		= "-pedantic-errors -Wno-long-long"
+  fatalwarning		= "-Werror"
+  sysheaderopt		= "-isystem "
+elif env["CC"] == "cl":
+  # Microsoft Visual C on Windows
+  cc_flags		= "/FD /EHsc /GR /wd4068 -D_USE_MATH_DEFINES -DDLL_NETCDF"
+  cc_optim		= "/O2 /Op /MT /W3"
+  cc_debug		= "/Od /RTC1 /MTd /ZI -DBOUNDS_CHECK"
+  omp_optim		= ""
+  omp_debug		= ""
+  omp_libs		= []
+  pedantic		= ""
+  fatalwarning		= ""
+  sysheaderopt		= ""
+elif env["CC"] == "icl":
+  # intel C on Windows, see windows_intelc_options.py for a start
+  pedantic		= ""
+  fatalwarning		= ""
+  sysheaderopt		= ""
+
+
+# If not specified in hostname_options.py then set them here
+if env["cc_flags"]	== "-DEFAULT_1": env['cc_flags'] = cc_flags
+if env["cc_optim"]	== "-DEFAULT_2": env['cc_optim'] = cc_optim
+if env["cc_debug"]	== "-DEFAULT_3": env['cc_debug'] = cc_debug
+if env["omp_optim"]	== "-DEFAULT_4": env['omp_optim'] = omp_optim
+if env["omp_debug"]	== "-DEFAULT_5": env['omp_debug'] = omp_debug
+if env["omp_libs"]	== "-DEFAULT_6": env['omp_libs'] = omp_libs
+
+#set up the autolazy values
+if env['forcelazy']    != "leave_alone":
+  if env['forcelazy'] == 'on':
+	env.Append(CPPDEFINES='FAUTOLAZYON')
+  else:
+     if env['forcelazy'] == 'off':
+	env.Append(CPPDEFINES='FAUTOLAZYOFF')
+
+# OpenMP is disabled if useopenmp=no or both variables omp_optim and omp_debug are empty
+if not env["useopenmp"]:
+  env['omp_optim'] = ""
+  env['omp_debug'] = ""
+  env['omp_libs'] = []
+
+if env['omp_optim'] == "" and env['omp_debug'] == "": env["useopenmp"] = 0
+
+############ Copy environment variables into scons env #########
+
+try: env['ENV']['OMP_NUM_THREADS'] = os.environ['OMP_NUM_THREADS']
+except KeyError: env['ENV']['OMP_NUM_THREADS'] = 1
+
+try: env['ENV']['PATH'] = os.environ['PATH']
+except KeyError: pass
+
+try: env['ENV']['PYTHONPATH'] = os.environ['PYTHONPATH']
+except KeyError: pass
+
+try: env['ENV']['C_INCLUDE_PATH'] = os.environ['C_INCLUDE_PATH']
+except KeyError: pass
+
+try: env['ENV']['CPLUS_INCLUDE_PATH'] = os.environ['CPLUS_INCLUDE_PATH']
+except KeyError: pass
+
+try: env['ENV']['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH']
+except KeyError: pass
+
+try: env['ENV']['LIBRARY_PATH'] = os.environ['LIBRARY_PATH']
+except KeyError: pass
+
+try: env['ENV']['DISPLAY'] = os.environ['DISPLAY']
+except KeyError: pass
+
+try: env['ENV']['XAUTHORITY'] = os.environ['XAUTHORITY']
+except KeyError: pass
+
+try: env['ENV']['HOME'] = os.environ['HOME']
+except KeyError: pass
+
+# Configure for test suite
+env.PrependENVPath('PYTHONPATH', prefix)
+env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+env['ENV']['ESCRIPT_ROOT'] = prefix
+
+############ Set up paths for Configure() ######################
+
+# Make a copy of an environment
+# Use env.Clone if available, but fall back on env.Copy for older version of scons
+def clone_env(env):
+  if 'Clone' in dir(env): return env.Clone()	# scons-0.98
+  else:                   return env.Copy()	# scons-0.96
+
+# Add cc option -I<Escript>/trunk/include
+env.Append(CPPPATH		= [Dir('include')])
+
+# Add cc option -L<Escript>/trunk/lib
+env.Append(LIBPATH		= [Dir(env['libinstall'])])
+
+if env['cc_extra'] != '': env.Append(CCFLAGS = env['cc_extra'])
+if env['ld_extra'] != '': env.Append(LINKFLAGS = env['ld_extra'])
+
+if env['usepedantic']: env.Append(CCFLAGS = pedantic)
+
+# MS Windows
+if IS_WINDOWS_PLATFORM:
+  env.PrependENVPath('PATH',	[env['boost_lib_path']])
+  env.PrependENVPath('PATH',	[env['libinstall']])
+  if not env['share_esysUtils'] :
+    env.Append(CPPDEFINES = ['ESYSUTILS_STATIC_LIB'])
+  if not env['share_paso'] :
+    env.Append(CPPDEFINES = ['PASO_STATIC_LIB'])
+
+  if env['usenetcdf']:
+    env.PrependENVPath('PATH',	[env['netCDF_lib_path']])
+
+env.Append(ARFLAGS = env['ar_flags'])
+
+# Get the global Subversion revision number for getVersion() method
+try:
+   global_revision = os.popen("svnversion -n .").read()
+   global_revision = re.sub(":.*", "", global_revision)
+   global_revision = re.sub("[^0-9]", "", global_revision)
+except:
+   global_revision="-1"
+if global_revision == "": global_revision="-2"
+env.Append(CPPDEFINES = ["SVN_VERSION="+global_revision])
+
+############ numarray (required) ###############################
+
+try:
+  from numarray import identity
+except ImportError:
+  print "Cannot import numarray, you need to set your PYTHONPATH"
+  sys.exit(1)
+
+############ C compiler (required) #############################
+
+# Create a Configure() environment for checking existence of required libraries and headers
+conf = Configure(clone_env(env))
+
+# Test that the compiler is working
+if not conf.CheckFunc('printf'):
+   print "Cannot run C compiler '%s' (or libc is missing)" % (env['CC'])
+   sys.exit(1)
+
+if conf.CheckFunc('gethostname'):
+  conf.env.Append(CPPDEFINES = ['HAVE_GETHOSTNAME'])
+
+############ python libraries (required) #######################
+
+
+if not sysheaderopt =="":
+  conf.env.Append(CCFLAGS=sysheaderopt+env['python_path'])
+else:
+  conf.env.AppendUnique(CPPPATH		= [env['python_path']])
+
+conf.env.AppendUnique(LIBPATH		= [env['python_lib_path']])
+conf.env.AppendUnique(LIBS		= [env['python_libs']])
+
+conf.env.PrependENVPath('LD_LIBRARY_PATH', env['python_lib_path'])	# The wrapper script needs to find these libs
+conf.env.PrependENVPath('PYTHONPATH', prefix)
+conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if not conf.CheckCHeader('Python.h'):
+  print "Cannot find python include files (tried 'Python.h' in directory %s)" % (env['python_path'])
+  sys.exit(1)
+if not conf.CheckFunc('Py_Exit'):
+  print "Cannot find python library method Py_Main (tried lib %s in directory %s)" % (env['python_libs'], env['python_lib_path'])
+  sys.exit(1)
+
+############ boost (required) ##################################
+
+if not sysheaderopt =="":
+# This is required because we can't -isystem /usr/system because it breaks std includes
+  if os.path.normpath(env['boost_path']) =="/usr/include":
+    conf.env.Append(CCFLAGS=sysheaderopt+os.path.join(env['boost_path'],'boost'))
+  else:
+    conf.env.Append(CCFLAGS=sysheaderopt+env['boost_path'])
+else:
+  conf.env.AppendUnique(CPPPATH		= [env['boost_path']])
+
+conf.env.AppendUnique(LIBPATH		= [env['boost_lib_path']])
+conf.env.AppendUnique(LIBS		= [env['boost_libs']])
+
+conf.env.PrependENVPath('LD_LIBRARY_PATH', env['boost_lib_path'])	# The wrapper script needs to find these libs
+#ensure that our path entries remain at the front
+conf.env.PrependENVPath('PYTHONPATH', prefix)
+conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if not conf.CheckCXXHeader('boost/python.hpp'):
+  print "Cannot find boost include files (tried boost/python.hpp in directory %s)" % (env['boost_path'])
+  sys.exit(1)
+
+if not conf.CheckFunc('PyObject_SetAttr'):
+  print "Cannot find boost library method PyObject_SetAttr (tried method PyObject_SetAttr in library %s in directory %s)" % (env['boost_libs'], env['boost_lib_path'])
+  sys.exit(1)
+
+# Commit changes to environment
+env = conf.Finish()
+
+############ VTK (optional) ####################################
+
+if env['usevtk']:
+  try:
+    import vtk
+    env['usevtk'] = 1
+  except ImportError:
+    env['usevtk'] = 0
+
+# Add VTK to environment env if it was found
+if env['usevtk']:
+  env.Append(CPPDEFINES = ['USE_VTK'])
+
+############ NetCDF (optional) #################################
+
+conf = Configure(clone_env(env))
+
+if env['usenetcdf']:
+  conf.env.AppendUnique(CPPPATH	= [env['netCDF_path']])
+  conf.env.AppendUnique(LIBPATH	= [env['netCDF_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env['netCDF_libs']])
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['netCDF_lib_path'])	# The wrapper script needs to find these libs
+  #ensure that our path entries remain at the front
+  conf.env.PrependENVPath('PYTHONPATH', prefix)
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if env['usenetcdf'] and not conf.CheckCHeader('netcdf.h'): env['usenetcdf'] = 0
+if env['usenetcdf'] and not conf.CheckFunc('nc_open'): env['usenetcdf'] = 0
+
+# Add NetCDF to environment env if it was found
+if env['usenetcdf']:
+  env = conf.Finish()
+  env.Append(CPPDEFINES = ['USE_NETCDF'])
+else:
+  conf.Finish()
+
+############ PAPI (optional) ###################################
+
+# Start a new configure environment that reflects what we've already found
+conf = Configure(clone_env(env))
+
+if env['usepapi']:
+  conf.env.AppendUnique(CPPPATH	= [env['papi_path']])
+  conf.env.AppendUnique(LIBPATH	= [env['papi_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env['papi_libs']])
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['papi_lib_path'])	# The wrapper script needs to find these libs
+  #ensure that our path entries remain at the front
+  conf.env.PrependENVPath('PYTHONPATH', prefix)
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if env['usepapi'] and not conf.CheckCHeader('papi.h'): env['usepapi'] = 0
+if env['usepapi'] and not conf.CheckFunc('PAPI_start_counters'): env['usepapi'] = 0
+
+# Add PAPI to environment env if it was found
+if env['usepapi']:
+  env = conf.Finish()
+  env.Append(CPPDEFINES = ['BLOCKPAPI'])
+else:
+  conf.Finish()
+
+############ MKL (optional) ####################################
+
+# Start a new configure environment that reflects what we've already found
+conf = Configure(clone_env(env))
+
+if env['usemkl']:
+  conf.env.AppendUnique(CPPPATH	= [env['mkl_path']])
+  conf.env.AppendUnique(LIBPATH	= [env['mkl_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env['mkl_libs']])
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['mkl_lib_path'])	# The wrapper script needs to find these libs
+  #ensure that our path entries remain at the front
+  conf.env.PrependENVPath('PYTHONPATH', prefix)
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if env['usemkl'] and not conf.CheckCHeader('mkl_solver.h'): env['usemkl'] = 0
+if env['usemkl'] and not conf.CheckFunc('pardiso_'): env['usemkl'] = 0
+
+# Add MKL to environment env if it was found
+if env['usemkl']:
+  env = conf.Finish()
+  env.Append(CPPDEFINES = ['MKL'])
+else:
+  conf.Finish()
+
+############ UMFPACK (optional) ################################
+
+# Start a new configure environment that reflects what we've already found
+conf = Configure(clone_env(env))
+
+if env['useumfpack']:
+  conf.env.AppendUnique(CPPPATH	= [env['ufc_path']])
+  conf.env.AppendUnique(CPPPATH	= [env['umf_path']])
+  conf.env.AppendUnique(LIBPATH	= [env['umf_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env['umf_libs']])
+  conf.env.AppendUnique(CPPPATH	= [env['amd_path']])
+  conf.env.AppendUnique(LIBPATH	= [env['amd_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env['amd_libs']])
+  conf.env.AppendUnique(CPPPATH	= [env['blas_path']])
+  conf.env.AppendUnique(LIBPATH	= [env['blas_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env['blas_libs']])
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['umf_lib_path'])	# The wrapper script needs to find these libs
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['amd_lib_path'])	# The wrapper script needs to find these libs
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['blas_lib_path'])	# The wrapper script needs to find these libs
+  #ensure that our path entries remain at the front
+  conf.env.PrependENVPath('PYTHONPATH', prefix)
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if env['useumfpack'] and not conf.CheckFunc('umfpack_di_symbolic'): env['useumfpack'] = 0
+if env['useumfpack'] and not conf.CheckCHeader('umfpack.h'): env['useumfpack'] = 0
+# if env['useumfpack'] and not conf.CheckFunc('daxpy'): env['useumfpack'] = 0 # this does not work on shake73?
+
+# Add UMFPACK to environment env if it was found
+if env['useumfpack']:
+  env = conf.Finish()
+  env.Append(CPPDEFINES = ['UMFPACK'])
+else:
+  conf.Finish()
+
+############ Silo (optional) ###################################
+
+if env['usesilo']:
+  conf = Configure(clone_env(env))
+  conf.env.AppendUnique(CPPPATH = [env['silo_path']])
+  conf.env.AppendUnique(LIBPATH = [env['silo_lib_path']])
+  conf.env.AppendUnique(LIBS = [env['silo_libs']])
+  if not conf.CheckCHeader('silo.h'): env['usesilo'] = 0
+  if not conf.CheckFunc('DBMkDir'): env['usesilo'] = 0
+  conf.Finish()
+
+# Add the path to Silo to environment env if it was found.
+# Note that we do not add the libs since they are only needed for the
+# escriptreader library and tools.
+if env['usesilo']:
+  env.AppendUnique(CPPPATH = [env['silo_path']])
+  env.AppendUnique(LIBPATH = [env['silo_lib_path']])
+  env.Append(CPPDEFINES = ['HAVE_SILO'])
+
+############ Add the compiler flags ############################
+
+# Enable debug by choosing either cc_debug or cc_optim
+if env['usedebug']:
+  env.Append(CCFLAGS		= env['cc_debug'])
+  env.Append(CCFLAGS		= env['omp_debug'])
+else:
+  env.Append(CCFLAGS		= env['cc_optim'])
+  env.Append(CCFLAGS		= env['omp_optim'])
+
+# Always use cc_flags
+env.Append(CCFLAGS		= env['cc_flags'])
+env.Append(LIBS			= [env['omp_libs']])
+
+
+############ Add some custom builders ##########################
+
 py_builder = Builder(action = scons_extensions.build_py, suffix = '.pyc', src_suffix = '.py', single_source=True)
 env.Append(BUILDERS = {'PyCompile' : py_builder});
 
-if env['PLATFORM'] == "win32":
-   runUnitTest_builder = Builder(action = scons_extensions.runUnitTest, suffix = '.passed', src_suffix='.exe', single_source=True)
-else:
-   runUnitTest_builder = Builder(action = scons_extensions.runUnitTest, suffix = '.passed', single_source=True)
+runUnitTest_builder = Builder(action = scons_extensions.runUnitTest, suffix = '.passed', src_suffix=env['PROGSUFFIX'], single_source=True)
 env.Append(BUILDERS = {'RunUnitTest' : runUnitTest_builder});
 
 runPyUnitTest_builder = Builder(action = scons_extensions.runPyUnitTest, suffix = '.passed', src_suffic='.py', single_source=True)
 env.Append(BUILDERS = {'RunPyUnitTest' : runPyUnitTest_builder});
 
-# Convert the options which are held in environment variable into python variables for ease of handling and configure compilation options
-try:
-   incinstall = env['incinstall']
-   env.Append(CPPPATH = [incinstall,])
-except KeyError:
-   incinstall = None  
-try:
-   libinstall = env['libinstall']
-   env.Append(LIBPATH = [libinstall,])
-   env.PrependENVPath('LD_LIBRARY_PATH', libinstall)
-except KeyError:
-   libinstall = None  
-try:
-   pyinstall = env['pyinstall']+'/esys' # all targets will install into pyinstall/esys but PYTHONPATH points at straight pyinstall so you go import esys.escript etc
-   env.PrependENVPath('PYTHONPATH', env['pyinstall'])
-except KeyError:
-   pyinstall = None  
-try:
-   dodebug = env['dodebug']
-except KeyError:
-   dodebug = None  
-try:
-   cc_defines = env['cc_defines']
-   env.Append(CPPDEFINES = [cc_defines,])
-except KeyError:
-   pass
-if dodebug:
-   try:
-      flags = env['cc_flags_debug']
-      env.Append(CCFLAGS = flags)
-   except KeyError:
-      pass
+############ MPI (optional) ####################################
+
+# Create a modified environment for MPI programs (identical to env if usempi=no)
+env_mpi = clone_env(env)
+
+# Start a new configure environment that reflects what we've already found
+conf = Configure(clone_env(env_mpi))
+
+if env_mpi['usempi']:
+  conf.env.AppendUnique(CPPPATH	= [env_mpi['mpi_path']])
+  conf.env.AppendUnique(LIBPATH	= [env_mpi['mpi_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env_mpi['mpi_libs']])
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['mpi_lib_path'])	# The wrapper script needs to find these libs
+  #ensure that our path entries remain at the front
+  conf.env.PrependENVPath('PYTHONPATH', prefix)
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if env_mpi['usempi'] and not conf.CheckCHeader('mpi.h'): env_mpi['usempi'] = 0
+if env_mpi['usempi'] and not conf.CheckFunc('MPI_Init'): env_mpi['usempi'] = 0
+
+# Add MPI to environment env_mpi if it was found
+if env_mpi['usempi']:
+  env_mpi = conf.Finish()
+  env_mpi.Append(CPPDEFINES = ['PASO_MPI', 'MPI_NO_CPPBIND', env_mpi['MPICH_IGNORE_CXX_SEEK']])
 else:
-   try:
-      flags = env['cc_flags']
-      env.Append(CCFLAGS = flags)
-   except KeyError:
-      pass
+  conf.Finish()
 
-if dodebug:
-   try:
-      flags = env['cxx_flags_debug']
-      env.Append(CXXFLAGS = flags)
-   except KeyError:
-      pass
+env['usempi'] = env_mpi['usempi']
+
+############ ParMETIS (optional) ###############################
+
+# Start a new configure environment that reflects what we've already found
+conf = Configure(clone_env(env_mpi))
+
+if not env_mpi['usempi']: env_mpi['useparmetis'] = 0
+
+if env_mpi['useparmetis']:
+  conf.env.AppendUnique(CPPPATH	= [env_mpi['parmetis_path']])
+  conf.env.AppendUnique(LIBPATH	= [env_mpi['parmetis_lib_path']])
+  conf.env.AppendUnique(LIBS	= [env_mpi['parmetis_libs']])
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['parmetis_lib_path'])	# The wrapper script needs to find these libs
+  #ensure that our path entries remain at the front
+  conf.env.PrependENVPath('PYTHONPATH', prefix)
+  conf.env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
+
+if env_mpi['useparmetis'] and not conf.CheckCHeader('parmetis.h'): env_mpi['useparmetis'] = 0
+if env_mpi['useparmetis'] and not conf.CheckFunc('ParMETIS_V3_PartGeomKway'): env_mpi['useparmetis'] = 0
+
+# Add ParMETIS to environment env_mpi if it was found
+if env_mpi['useparmetis']:
+  env_mpi = conf.Finish()
+  env_mpi.Append(CPPDEFINES = ['USE_PARMETIS'])
 else:
-   try:
-      flags = env['cxx_flags']
-      env.Append(CXXFLAGS = flags)
-   except KeyError:
-      pass
+  conf.Finish()
 
-try:
-   flags = env['ar_flags']
-   env.Append(ARFLAGS = flags)
-except KeyError:
-   ar_flags = None  
-try:
-   sys_libs = env['sys_libs']
-except KeyError:
-   sys_libs = '' 
+env['useparmetis'] = env_mpi['useparmetis']
+
+############ Now we switch on Warnings as errors ###############
+
+#this needs to be done after configuration because the scons test files have warnings in them
+
+if ((fatalwarning != "") and (env['usewarnings'])):
+  env.Append(CCFLAGS		= fatalwarning)
+  env_mpi.Append(CCFLAGS		= fatalwarning)
+
+############ Summarize our environment #########################
+
+print ""
+print "Summary of configuration (see ./config.log for information)"
+print "	Using python libraries"
+print "	Using numarray"
+print "	Using boost"
+if env['usenetcdf']: print "	Using NetCDF"
+else: print "	Not using NetCDF"
+if env['usevtk']: print "	Using VTK"
+else: print "	Not using VTK"
+if env['usemkl']: print "	Using MKL"
+else: print "	Not using MKL"
+if env['useumfpack']: print "	Using UMFPACK"
+else: print "	Not using UMFPACK"
+if env['usesilo']: print "	Using Silo"
+else: print "	Not using Silo"
+if env['useopenmp']: print "	Using OpenMP"
+else: print "	Not using OpenMP"
+if env['usempi']: print "	Using MPI"
+else: print "	Not using MPI"
+if env['useparmetis']: print "	Using ParMETIS"
+else: print "	Not using ParMETIS (requires MPI)"
+if env['usepapi']: print "	Using PAPI"
+else: print "	Not using PAPI"
+if env['usedebug']: print "	Compiling for debug"
+else: print "	Not compiling for debug"
+print "	Installing in", prefix
+if ((fatalwarning != "") and (env['usewarnings'])): print "	Treating warnings as errors"
+else: print "	Not treating warnings as errors"
+print ""
+
+############ Delete option-dependent files #####################
+
+Execute(Delete(env['libinstall'] + "/Compiled.with.debug"))
+Execute(Delete(env['libinstall'] + "/Compiled.with.mpi"))
+Execute(Delete(env['libinstall'] + "/Compiled.with.openmp"))
+Execute(Delete(env['libinstall'] + "pyversion"))
+if not env['usempi']: Execute(Delete(env['libinstall'] + "/pythonMPI"))
+
+
+############ Build the subdirectories ##########################
+
+from grouptest import *
+
+TestGroups=[]
+
+Export(
+  ["env",
+   "env_mpi",
+   "clone_env",
+   "IS_WINDOWS_PLATFORM",
+   "TestGroups"
+   ]
+  )
 
-try:
-   includes = env['mkl_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['mkl_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   mkl_libs = env['mkl_libs']
-except KeyError:
-   mkl_libs = ''
-try:
-   includes = env['scsl_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['scsl_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   scsl_libs = env['scsl_libs']
-except KeyError:
-   scsl_libs = ''
-try:
-   includes = env['umf_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['umf_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   umf_libs = env['umf_libs']
-except KeyError:
-   umf_libs = ''
-try:
-   includes = env['boost_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['boost_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   boost_lib = env['boost_lib']
-except KeyError:
-   boost_lib = None  
-try:
-   includes = env['cppunit_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['cppunit_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   cppunit_lib = env['cppunit_lib']
-except KeyError:
-   boost_lib = None  
-try:
-   includes = env['python_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['python_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   python_lib = env['python_lib']
-except KeyError:
-   python_lib = None  
-try:
-   doxygen_path = env['doxygen_path']
-except KeyError:
-   doxygen_path = None  
-try:
-   epydoc_path = env['epydoc_path']
-except KeyError:
-   epydoc_path = None  
-try:
-   epydoc_pythonpath = env['epydoc_pythonpath']
-except KeyError:
-   epydoc_pythonpath = None  
-try:
-   includes = env['papi_path']
-   env.Append(CPPPATH = [includes,])
-except KeyError:
-   pass
-try:
-   lib_path = env['papi_lib_path']
-   env.Append(LIBPATH = [lib_path,])
-except KeyError:
-   pass
-try:
-   papi_libs = env['papi_libs']
-except KeyError:
-   papi_libs = None  
-
-# Targets
-env.Default(libinstall)
-env.Default(incinstall)
-env.Default(pyinstall)
-env.Alias('build_tests')
-env.Alias('run_tests')
-env.Alias('py_tests')
-env.Alias('basic_py_tests')
-env.Alias('all_tests', ['run_tests', 'py_tests'])
-
-# Python install - esys __init__.py
-# This is just an empty file but stills need to be touched so add a special target and Command. Note you can't use the scons Touch() function as it will not
-# create the file if it doesn't exist
-env.Command(pyinstall+'/__init__.py', None, 'touch $TARGET')
-
-# Allow sconscripts to see the env
-Export(["env", "incinstall", "libinstall", "pyinstall", "dodebug", "mkl_libs", "scsl_libs", "umf_libs",
-	"boost_lib", "python_lib", "doxygen_path", "epydoc_path", "epydoc_pythonpath", "papi_libs", "cppunit_lib", "sys_libs" ])
-
-# End initialisation section
-# Begin configuration section
-# Insert new components to be build here
-# FIXME: might be nice to replace this verbosity with a list of targets and some
-# FIXME: nifty python to create the lengthy but very similar env.Sconscript lines
-# Third Party libraries
 env.SConscript(dirs = ['tools/CppUnitTest/src'], build_dir='build/$PLATFORM/tools/CppUnitTest', duplicate=0)
-# C/C++ Libraries
+env.SConscript(dirs = ['tools/libescriptreader/src'], build_dir='build/$PLATFORM/tools/libescriptreader', duplicate=0)
 env.SConscript(dirs = ['paso/src'], build_dir='build/$PLATFORM/paso', duplicate=0)
-env.SConscript(dirs = ['bruce/src'], build_dir='build/$PLATFORM/bruce', duplicate=0)
 env.SConscript(dirs = ['escript/src'], build_dir='build/$PLATFORM/escript', duplicate=0)
 env.SConscript(dirs = ['esysUtils/src'], build_dir='build/$PLATFORM/esysUtils', duplicate=0)
 env.SConscript(dirs = ['finley/src'], build_dir='build/$PLATFORM/finley', duplicate=0)
 env.SConscript(dirs = ['modellib/py_src'], build_dir='build/$PLATFORM/modellib', duplicate=0)
+env.SConscript(dirs = ['doc'], build_dir='build/$PLATFORM/doc', duplicate=0)
 env.SConscript(dirs = ['pyvisi/py_src'], build_dir='build/$PLATFORM/pyvisi', duplicate=0)
+env.SConscript(dirs = ['pycad/py_src'], build_dir='build/$PLATFORM/pycad', duplicate=0)
+env.SConscript(dirs = ['pythonMPI/src'], build_dir='build/$PLATFORM/pythonMPI', duplicate=0)
+env.SConscript(dirs = ['scripts'], build_dir='build/$PLATFORM/scripts', duplicate=0)
+env.SConscript(dirs = ['paso/profiling'], build_dir='build/$PLATFORM/paso/profiling', duplicate=0)
+
+
+############ Remember what optimizations we used ###############
+
+remember_list = []
+
+if env['usedebug']:
+  remember_list += env.Command(env['libinstall'] + "/Compiled.with.debug", None, Touch('$TARGET'))
+
+if env['usempi']:
+  remember_list += env.Command(env['libinstall'] + "/Compiled.with.mpi", None, Touch('$TARGET'))
+
+if env['omp_optim'] != '':
+  remember_list += env.Command(env['libinstall'] + "/Compiled.with.openmp", None, Touch('$TARGET'))
+
+env.Alias('remember_options', remember_list)
+
+
+############### Record python interpreter version ##############
+
+if not IS_WINDOWS_PLATFORM:
+  versionstring="Python "+str(sys.version_info[0])+"."+str(sys.version_info[1])+"."+str(sys.version_info[2])
+  os.system("echo "+versionstring+" > "+env['libinstall']+"/pyversion")
+
+############ Targets to build and install libraries ############
+
+target_init = env.Command(env['pyinstall']+'/__init__.py', None, Touch('$TARGET'))
+env.Alias('target_init', [target_init])
+
+# The headers have to be installed prior to build in order to satisfy #include <paso/Common.h>
+env.Alias('build_esysUtils', ['target_install_esysUtils_headers', 'target_esysUtils_a'])
+env.Alias('install_esysUtils', ['build_esysUtils', 'target_install_esysUtils_a'])
+
+env.Alias('build_paso', ['target_install_paso_headers', 'target_paso_a'])
+env.Alias('install_paso', ['build_paso', 'target_install_paso_a'])
+
+env.Alias('build_escript', ['target_install_escript_headers', 'target_escript_so', 'target_escriptcpp_so'])
+env.Alias('install_escript', ['build_escript', 'target_install_escript_so', 'target_install_escriptcpp_so', 'target_install_escript_py'])
+
+env.Alias('build_finley', ['target_install_finley_headers', 'target_finley_so', 'target_finleycpp_so'])
+env.Alias('install_finley', ['build_finley', 'target_install_finley_so', 'target_install_finleycpp_so', 'target_install_finley_py'])
+
+# Now gather all the above into a couple easy targets: build_all and install_all
+build_all_list = []
+build_all_list += ['build_esysUtils']
+build_all_list += ['build_paso']
+build_all_list += ['build_escript']
+build_all_list += ['build_finley']
+if env['usempi']:		build_all_list += ['target_pythonMPI_exe']
+if not IS_WINDOWS_PLATFORM:	build_all_list += ['target_escript_wrapper']
+if env['usesilo']:	build_all_list += ['target_escript2silo']
+env.Alias('build_all', build_all_list)
+
+install_all_list = []
+install_all_list += ['target_init']
+install_all_list += ['install_esysUtils']
+install_all_list += ['install_paso']
+install_all_list += ['install_escript']
+install_all_list += ['install_finley']
+install_all_list += ['target_install_pyvisi_py']
+install_all_list += ['target_install_modellib_py']
+install_all_list += ['target_install_pycad_py']
+if env['usempi']:		install_all_list += ['target_install_pythonMPI_exe']
+if not IS_WINDOWS_PLATFORM:	install_all_list += ['target_install_escript_wrapper']
+if env['usesilo']:	install_all_list += ['target_install_escript2silo']
+install_all_list += ['remember_options']
+env.Alias('install_all', install_all_list)
+
+# Default target is install
+env.Default('install_all')
+
+############ Targets to build and run the test suite ###########
+
+env.Alias('build_cppunittest', ['target_install_cppunittest_headers', 'target_cppunittest_a'])
+env.Alias('install_cppunittest', ['build_cppunittest', 'target_install_cppunittest_a'])
+env.Alias('run_tests', ['install_all', 'target_install_cppunittest_a'])
+env.Alias('all_tests', ['install_all', 'target_install_cppunittest_a', 'run_tests', 'py_tests'])
+env.Alias('build_full',['install_all','build_tests','build_py_tests'])
+
+############ Targets to build the documentation ################
+
+env.Alias('docs', ['examples_tarfile', 'examples_zipfile', 'api_epydoc', 'api_doxygen', 'guide_pdf', 'guide_html'])
+
+if not IS_WINDOWS_PLATFORM:
+   try:
+   	utest=open("utest.sh","w")
+	build_platform=os.name		#Sometimes Mac python says it is posix
+	if (build_platform=='posix') and platform.system()=="Darwin":
+		build_platform='darwin'
+	utest.write(GroupTest.makeHeader(build_platform))
+	for tests in TestGroups:
+	    utest.write(tests.makeString())
+	utest.close()
+	os.chmod("utest.sh",stat.S_IRWXU|stat.S_IRGRP|stat.S_IXGRP|stat.S_IROTH|stat.S_IXOTH)
+	print "utest.sh written"
+   except IOError:
+	print "Error attempting to write unittests file."
+	sys.exit(1)
 
-# FIXME:need to be incorporated into build system
-# FIXME: 'pyvisi/SConstruct']
-# FIXME: 'doc/SConstruct']
-# FIXME: 'doc/SConstruct']