--- trunk/SConstruct	2008/11/15 12:43:11	2040
+++ trunk/SConstruct	2010/08/19 01:40:52	3096
@@ -1,7 +1,7 @@
 
 ########################################################
 #
-# Copyright (c) 2003-2008 by University of Queensland
+# Copyright (c) 2003-2010 by University of Queensland
 # Earth Systems Science Computational Center (ESSCC)
 # http://www.uq.edu.au/esscc
 #
@@ -15,7 +15,9 @@
 EnsureSConsVersion(0,96,91)
 EnsurePythonVersion(2,3)
 
-import sys, os, re, socket
+import sys, os, re, socket, platform, stat
+# For copy()
+import shutil
 
 # Add our extensions
 if os.path.isdir('scons'): sys.path.append('scons')
@@ -33,22 +35,46 @@
 
 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)
+#Holds names of variables from the calling environment which need to be passed
+#to tools
+env_export=[]
+
+#Determine where to read options from use:
+#1. command line
+#2. scons/<hostname>_options.py
+#3. name as part of a cluster
+options_file=ARGUMENTS.get('options_file', None)
+effective_hostname=socket.gethostname().split('.')[0]
+if not options_file:
+  mangledhostname = re.sub("[^0-9a-zA-Z]", "_", effective_hostname)
+  options_file = os.path.join("scons",mangledhostname+"_options.py")
+  #If there is no options file with that name see if there is a substitute
+  if not os.path.isfile(options_file):
+    effective_hostname = scons_extensions.effectiveName(effective_hostname)
+    mangledhostname = re.sub("[^0-9a-zA-Z]", "_", effective_hostname)
+    options_file = os.path.join("scons",mangledhostname+"_options.py")
+
 if not os.path.isfile(options_file):
+  print "Options file not found (expected '%s')" % 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)
+#Does our scons support the newer Variables class or do we need to use Options?
+
+try:
+   dummyvar=Variables
+   opts = Variables(options_file, ARGUMENTS)
+   adder = opts.AddVariables
+except:
+   opts = Options(options_file, ARGUMENTS)
+   adder = opts.AddOptions
+   BoolVariable = BoolOption
 
 ############ Load build options ################################
 
-opts.AddOptions(
+adder(
+#opts.AddOptions(
 # Where to install esys stuff
   ('prefix', 'where everything will be installed',                       Dir('#.').abspath),
   ('incinstall', 'where the esys headers will be installed',             os.path.join(Dir('#.').abspath,'include')),
@@ -56,25 +82,30 @@
   ('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', 'For backwards compatibility', 'no'),
-  BoolOption('usedebug', 'Do you want a debug build?', 'no'),
-  BoolOption('usevtk', 'Do you want to use VTK?', 'yes'),
+  BoolVariable('dodebug', 'For backwards compatibility', 'no'),
+  BoolVariable('usedebug', 'Do you want a debug build?', 'no'),
+  BoolVariable('usevtk', 'Do you want to use VTK?', 'yes'),
   ('options_file', 'File of paths/options. Default: scons/<hostname>_options.py', options_file),
+  ('cc', 'path to C compiler', 'DEFAULT'),
+  ('cxx', 'path to C++ compiler', 'DEFAULT'),
   ('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'),
+  ('cc_flags', 'C/C++ compiler flags to use', '-DEFAULT_1'),
+  ('cc_optim', 'C/C++ optimization flags to use', '-DEFAULT_2'),
+  ('cc_debug', 'C/C++ 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', ''),
+  ('cc_extra', 'Extra C compiler flags', ''),
+  ('cxx_extra', 'Extra C++ compiler 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', 'yes'),
-  BoolOption('usepedantic', 'Compile with -pedantic if using gcc', 'no'),
-  BoolOption('usewarnings','Compile with warnings as errors if using gcc','yes'),
+  BoolVariable('useopenmp', 'Compile parallel version using OpenMP', 'no'),
+  BoolVariable('usepedantic', 'Compile with -pedantic if using gcc', 'no'),
+  BoolVariable('usewarnings','Compile with warnings as errors if using gcc','yes'),
+  ('forcelazy','for testing use only - set the default value for autolazy','leave_alone'),
+  ('forcecollres','for testing use only - set the default value for force resolving collective ops','leave_alone'),
 # Python
   ('python_path', 'Path to Python includes', '/usr/include/'+python_version),
   ('python_lib_path', 'Path to Python libs', usr_lib),
@@ -85,40 +116,50 @@
   ('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'),
+  BoolVariable('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'),
+  BoolVariable('useMPI', 'For backwards compatibility', 'no'),
+  BoolVariable('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']),
+  ('mpi_libs', 'MPI libraries to link with (needs to be shared!)', []),
+  ('mpi_flavour','Type of MPI execution environment','none'), 
 # ParMETIS
-  BoolOption('useparmetis', 'Compile parallel version using ParMETIS', 'yes'),
+  BoolVariable('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
-  BoolOption('usepapi', 'switch on/off the usage of PAPI', 'no'),
+  BoolVariable('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),
+  BoolVariable('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'),
+  BoolVariable('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'),
+  BoolVariable('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
+  BoolVariable('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']),
+# VisIt
+  BoolVariable('usevisit', 'switch on/off the usage of the VisIt sim library', 'no'),
+  ('visit_path', 'Path to VisIt libsim includes', '/usr/include'),
+  ('visit_lib_path', 'Path to VisIt sim library', usr_lib),
 # AMD (used by UMFPACK)
   ('amd_path', 'Path to AMD includes', '/usr/include/suitesparse'),
   ('amd_lib_path', 'Path to AMD libs', usr_lib),
@@ -127,10 +168,43 @@
   ('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']),
+#Lapack options
+  BoolVariable('uselapack','switch on/off use of Lapack','no'),
+  ('lapack_path', 'Path to Lapack includes','/usr/include'),
+  ('lapack_lib_path', 'Path to Lapack libs', usr_lib),
+  ('lapack_libs', 'Lapack libraries to link with', []),
+  ('lapack_type', '{clapack,mkl}','clapack'),
 # An option for specifying the compiler tools set (see windows branch).
-  ('tools_names', 'allow control over the tools in the env setup', ['intelc'])
+  ('tools_names', 'allow control over the tools in the env setup', ['default']),
+# 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),
+  ('env_export','Environment variables to be passed to children',[]),
+#To enable passing function pointers through python
+  BoolVariable('iknowwhatimdoing','allow nonstandard C',False)
 )
 
+
+###################
+
+# This is only to support old versions of scons which don't accept
+# the variant_dir parameter (older than 0.98 I think).
+# Once these are no longer an issue we can go back to a direct call
+# to obj.SConscript
+import SCons
+vs=SCons.__version__.split('.')
+cantusevariantdir=float(vs[0]+'.'+vs[1])<0.98
+
+
+def CallSConscript(obj, **kw):
+    if cantusevariantdir:
+	    if 'variant_dir' in kw:
+		kw['build_dir']=kw['variant_dir']
+		del kw['variant_dir'] 
+    obj.SConscript(**kw)
+
+
 ############ Specify which compilers to use ####################
 
 # intelc uses regular expressions improperly and emits a warning about
@@ -141,16 +215,35 @@
       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':
+   if 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)
+      if env['tools_names']!='default':
+	env=Environment(tools = ['default'] +env['tools_names'], options=opts)
+
+# Override compiler choice if provided
+if env['cc'] != 'DEFAULT': env['CC']=env['cc']
+if env['cxx'] != 'DEFAULT': env['CXX']=env['cxx']
+
 Help(opts.GenerateHelpText(env))
 
+############ Make sure target directories exist ################
+
+if not os.path.isdir(env['bininstall']):
+    os.makedirs(env['bininstall'])
+if not os.path.isdir(env['libinstall']):
+    os.makedirs(env['libinstall'])
+if not os.path.isdir(env['pyinstall']):
+    os.makedirs(env['pyinstall'])
+
+########## Copy required environment vars ######################
+
+for i in env['env_export']:
+   env.Append(ENV = {i:os.environ[i]})
+ 
 ############ Fill in compiler options if not set above #########
 
 # Backwards compatibility: allow dodebug=yes and useMPI=yes
@@ -160,9 +253,18 @@
 # 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.
+
+cc_flags = ""
+cc_optim = ""
+cc_debug = ""
+omp_optim = ""
+omp_debug = ""
+omp_libs = []
+
 if env["CC"] == "icc":
   # Intel compilers
-  cc_flags		= "-fPIC -ansi -wd161 -w1 -vec-report0 -DBLOCKTIMER -DCORE_ID1"
+  cc_flags		= "-std=c99 -fPIC -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"
@@ -170,18 +272,19 @@
   omp_libs		= ['guide', 'pthread']
   pedantic		= ""
   fatalwarning		= ""		# Switch to turn warnings into errors
-elif env["CC"] == "gcc":
+  sysheaderopt		= ""
+elif env["CC"][:3] == "gcc":
   # GNU C on any system
-  cc_flags		= "-pedantic -Wall -fPIC -ansi -ffast-math -Wno-unknown-pragmas -DBLOCKTIMER -isystem " + env['boost_path'] + " -isystem " + env['python_path'] + " -Wno-sign-compare -Wno-system-headers -Wno-strict-aliasing"
-#the strict aliasing warning is triggered by some type punning in the boost headers for version 1.34
-#isystem does not seem to prevent this
+  cc_flags		= "-pedantic -Wall -fPIC -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		= ""
-  omp_debug		= ""
+  omp_optim		= "-fopenmp"
+  omp_debug		= "-fopenmp"
   omp_libs		= []
   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"
@@ -192,10 +295,13 @@
   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
@@ -205,6 +311,27 @@
 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'])
+
+#set up the colective resolve values
+if env['forcecollres']    != "leave_alone":
+  print env['forcecollres']
+  if env['forcecollres'] == 'on':
+	env.Append(CPPDEFINES=['FRESCOLLECTON'])
+  else:
+     if env['forcecollres'] == 'off':
+	env.Append(CPPDEFINES=['FRESCOLLECTOFF'])
+ 
+
+if env['iknowwhatimdoing']:
+	env.Append(CPPDEFINES=['IKNOWWHATIMDOING'])
+
 # OpenMP is disabled if useopenmp=no or both variables omp_optim and omp_debug are empty
 if not env["useopenmp"]:
   env['omp_optim'] = ""
@@ -213,11 +340,29 @@
 
 if env['omp_optim'] == "" and env['omp_debug'] == "": env["useopenmp"] = 0
 
+# Windows doesn't use LD_LIBRARY_PATH but PATH instead
+if IS_WINDOWS_PLATFORM:
+    LD_LIBRARY_PATH_KEY='PATH'
+    env['ENV']['LD_LIBRARY_PATH']=''
+else:
+    LD_LIBRARY_PATH_KEY='LD_LIBRARY_PATH'
 ############ 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']['ESCRIPT_NUM_THREADS'] = os.environ['ESCRIPT_NUM_THREADS']
+except KeyError: pass
+
+try: env['ENV']['ESCRIPT_NUM_PROCS'] = os.environ['ESCRIPT_NUM_PROCS']
+except KeyError: env['ENV']['ESCRIPT_NUM_PROCS']=1
+
+try: env['ENV']['ESCRIPT_NUM_NODES'] = os.environ['ESCRIPT_NUM_NODES']
+except KeyError: env['ENV']['ESCRIPT_NUM_NODES']=1
+
+try: env['ENV']['ESCRIPT_HOSTFILE'] = os.environ['ESCRIPT_HOSTFILE']
+except KeyError: pass
+
 try: env['ENV']['PATH'] = os.environ['PATH']
 except KeyError: pass
 
@@ -230,7 +375,7 @@
 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']
+try: env.PrependENVPath(LD_LIBRARY_PATH_KEY,os.environ['LD_LIBRARY_PATH'])
 except KeyError: pass
 
 try: env['ENV']['LIBRARY_PATH'] = os.environ['LIBRARY_PATH']
@@ -246,9 +391,10 @@
 except KeyError: pass
 
 # Configure for test suite
-env.PrependENVPath('PYTHONPATH', prefix)
-env.PrependENVPath('LD_LIBRARY_PATH', env['libinstall'])
 
+
+env.PrependENVPath(LD_LIBRARY_PATH_KEY, env['libinstall'])
+env.PrependENVPath('PYTHONPATH', prefix)
 env['ENV']['ESCRIPT_ROOT'] = prefix
 
 ############ Set up paths for Configure() ######################
@@ -265,19 +411,23 @@
 # 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['cc_extra'] != '': env.Append(CFLAGS = env['cc_extra'])
+if env['cxx_extra'] != '': env.Append(CXXFLAGS = env['cxx_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']])
-  env.Append(CPPDEFINES = ['ESYSUTILS_STATIC_LIB'])
+  env.AppendENVPath('PATH',	[env['boost_lib_path']])
+  env.AppendENVPath('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.AppendENVPath('PATH',	[env['netCDF_lib_path']])
 
 env.Append(ARFLAGS = env['ar_flags'])
 
@@ -291,12 +441,12 @@
 if global_revision == "": global_revision="-2"
 env.Append(CPPDEFINES = ["SVN_VERSION="+global_revision])
 
-############ numarray (required) ###############################
+############ numpy (required) ###############################
 
 try:
-  from numarray import identity
+  from numpy import identity
 except ImportError:
-  print "Cannot import numarray, you need to set your PYTHONPATH"
+  print "Cannot import numpy, you need to set your PYTHONPATH"
   sys.exit(1)
 
 ############ C compiler (required) #############################
@@ -306,41 +456,64 @@
 
 # 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)
+   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) #######################
 
-conf.env.AppendUnique(CPPPATH		= [env['python_path']])
+
+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_KEY, env['python_lib_path'])	# The wrapper script needs to find these libs
+conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_Main'):
+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) ##################################
 
-conf.env.AppendUnique(CPPPATH		= [env['boost_path']])
+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
+conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, env['libinstall'])
+
+
+#Yep we still cant figure this one out. - working on it.
+if not IS_WINDOWS_PLATFORM:
+  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)
 
-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()
@@ -366,7 +539,10 @@
   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
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, 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
@@ -387,7 +563,10 @@
   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
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, 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
@@ -408,10 +587,14 @@
   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
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, 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
+if env['usemkl'] and not conf.CheckFunc('pardiso'): env['usemkl'] = 0
+
 
 # Add MKL to environment env if it was found
 if env['usemkl']:
@@ -436,12 +619,16 @@
   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
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, env['umf_lib_path'])	# The wrapper script needs to find these libs
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, env['amd_lib_path'])	# The wrapper script needs to find these libs
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, env['libinstall'])
 
 if env['useumfpack'] and not conf.CheckCHeader('umfpack.h'): env['useumfpack'] = 0
 if env['useumfpack'] and not conf.CheckFunc('umfpack_di_symbolic'): 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']:
@@ -450,6 +637,47 @@
 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
+# weipa library and tools.
+if env['usesilo']:
+  env.AppendUnique(CPPPATH = [env['silo_path']])
+  env.AppendUnique(LIBPATH = [env['silo_lib_path']])
+
+############ VisIt (optional) ###################################
+
+if env['usevisit']:
+  env.AppendUnique(CPPPATH = [env['visit_path']])
+  env.AppendUnique(LIBPATH = [env['visit_lib_path']])
+
+########### Lapack (optional) ##################################
+
+if env['uselapack']:
+	env.AppendUnique(CPPDEFINES='USE_LAPACK')
+	env.AppendUnique(CPPPATH = [env['lapack_path']])
+	env.AppendUnique(LIBPATH =[env['lapack_lib_path']])
+
+	env.Append(LIBPATH = '/usr/lib/atlas')
+	env.Append(LIBS = [env['lapack_libs']])
+	if env['lapack_type']=='mkl':
+	   if not env['usemkl']:
+		env['uselapack']=0
+		print "mkl_lapack requires mkl"
+	   else:
+	   	env.AppendUnique(CPPDEFINES='MKL_LAPACK')
+	   
+
 ############ Add the compiler flags ############################
 
 # Enable debug by choosing either cc_debug or cc_optim
@@ -464,7 +692,22 @@
 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});
+
+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});
+
+epstopdfbuilder = Builder(action = scons_extensions.eps2pdf, suffix=".pdf", src_suffix=".eps", single_source=True)
+env.Append(BUILDERS = {'EpsToPDF' : epstopdfbuilder});
+
 ############ MPI (optional) ####################################
+if not env['usempi']: env['mpi_flavour']='none'
 
 # Create a modified environment for MPI programs (identical to env if usempi=no)
 env_mpi = clone_env(env)
@@ -473,18 +716,29 @@
 conf = Configure(clone_env(env_mpi))
 
 if env_mpi['usempi']:
+  VALID_MPIs=[ "MPT", "MPICH", "MPICH2", "OPENMPI", "INTELMPI" ]
+  if not env_mpi['mpi_flavour'] in VALID_MPIs: 
+      raise ValueError,"MPI is enabled but mpi_flavour = %s is not a valid key from %s."%( env_mpi['mpi_flavour'],VALID_MPIs)
   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
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, 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
+# 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']])
+  # NetCDF 4.1 defines MPI_Comm et al. if MPI_INCLUDED is not defined!
+  # On the other hand MPT and OpenMPI don't define the latter so we have to
+  # do that here
+  if env['usenetcdf'] and env_mpi['mpi_flavour'] in ["MPT","OPENMPI"]:
+    env_mpi.Append(CPPDEFINES = ['MPI_INCLUDED'])
 else:
   conf.Finish()
 
@@ -501,7 +755,10 @@
   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
+  conf.env.PrependENVPath(LD_LIBRARY_PATH_KEY, 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_KEY, 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
@@ -515,37 +772,35 @@
 
 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 numpy"
 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['usevisit']: print "	Using VisIt"
+else: print "	Not using VisIt"
 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"
+if env['usempi']: print "	Using MPI (flavour = %s)"%env['mpi_flavour']
 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['uselapack']: print "	Using Lapack"
+else: print "	Not using Lapack"
 if env['usedebug']: print "	Compiling for debug"
 else: print "	Not compiling for debug"
 print "	Installing in", prefix
@@ -555,59 +810,139 @@
 
 ############ 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"))
-if not env['usempi']: Execute(Delete(env['libinstall'] + "/pythonMPI"))
+Execute(Delete(os.path.join(env['libinstall'],"Compiled.with.debug")))
+Execute(Delete(os.path.join(env['libinstall'],"Compiled.with.mpi")))
+Execute(Delete(os.path.join(env['libinstall'],"Compiled.with.openmp")))
+Execute(Delete(os.path.join(env['libinstall'],"pyversion")))
+Execute(Delete(os.path.join(env['libinstall'],"buildvars")))
+if not env['usempi']: Execute(Delete(os.path.join(env['libinstall'],"pythonMPI")))
 
-############ 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});
+############ Build the subdirectories ##########################
 
-runUnitTest_builder = Builder(action = scons_extensions.runUnitTest, suffix = '.passed', src_suffix=env['PROGSUFFIX'], single_source=True)
-env.Append(BUILDERS = {'RunUnitTest' : runUnitTest_builder});
+if env['usepedantic']: env_mpi.Append(CCFLAGS = pedantic)
 
-runPyUnitTest_builder = Builder(action = scons_extensions.runPyUnitTest, suffix = '.passed', src_suffic='.py', single_source=True)
-env.Append(BUILDERS = {'RunPyUnitTest' : runPyUnitTest_builder});
 
-############ Build the subdirectories ##########################
+from grouptest import *
+
+TestGroups=[]
+
+dodgy_env=clone_env(env_mpi)	# Environment without pedantic options
+
+############ 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)
+
 
 Export(
   ["env",
    "env_mpi",
    "clone_env",
-   "IS_WINDOWS_PLATFORM"
+   "dodgy_env",
+   "IS_WINDOWS_PLATFORM",
+   "TestGroups",
+   "CallSConscript",
+   "cantusevariantdir"
    ]
   )
 
-env.SConscript(dirs = ['tools/CppUnitTest/src'], build_dir='build/$PLATFORM/tools/CppUnitTest', duplicate=0)
-env.SConscript(dirs = ['paso/src'], build_dir='build/$PLATFORM/paso', 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/$PLATFORM/scripts', duplicate=0)
+CallSConscript(env, dirs = ['tools/CppUnitTest/src'], variant_dir='build/$PLATFORM/tools/CppUnitTest', duplicate=0)
+CallSConscript(env, dirs = ['tools/escriptconvert'], variant_dir='build/$PLATFORM/tools/escriptconvert', duplicate=0)
+CallSConscript(env, dirs = ['paso/src'], variant_dir='build/$PLATFORM/paso', duplicate=0)
+CallSConscript(env, dirs = ['weipa/src'], variant_dir='build/$PLATFORM/weipa', duplicate=0)
+CallSConscript(env, dirs = ['escript/src'], variant_dir='build/$PLATFORM/escript', duplicate=0)
+CallSConscript(env, dirs = ['esysUtils/src'], variant_dir='build/$PLATFORM/esysUtils', duplicate=0)
+CallSConscript(env, dirs = ['finley/src'], variant_dir='build/$PLATFORM/finley', duplicate=0)
+CallSConscript(env, dirs = ['modellib/py_src'], variant_dir='build/$PLATFORM/modellib', duplicate=0)
+CallSConscript(env, dirs = ['doc'], variant_dir='build/$PLATFORM/doc', duplicate=0)
+CallSConscript(env, dirs = ['pyvisi/py_src'], variant_dir='build/$PLATFORM/pyvisi', duplicate=0)
+CallSConscript(env, dirs = ['pycad/py_src'], variant_dir='build/$PLATFORM/pycad', duplicate=0)
+CallSConscript(env, dirs = ['pythonMPI/src'], variant_dir='build/$PLATFORM/pythonMPI', duplicate=0)
+CallSConscript(env, dirs = ['scripts'], variant_dir='build/$PLATFORM/scripts', duplicate=0)
+CallSConscript(env, dirs = ['paso/profiling'], variant_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('$TARGET'))
+  remember_list += env.Command(os.path.join(env['libinstall'],"Compiled.with.debug"), None, Touch('$TARGET'))
 
 if env['usempi']:
-  remember_list += env.Command(env['libinstall'] + "/Compiled.with.mpi", None, Touch('$TARGET'))
+  remember_list += env.Command(os.path.join(env['libinstall'],"Compiled.with.mpi"), None, Touch('$TARGET'))
 
-if env['omp_optim'] != '':
-  remember_list += env.Command(env['libinstall'] + "/Compiled.with.openmp", None, Touch('$TARGET'))
+if env['useopenmp']:
+  remember_list += env.Command(os.path.join(env['libinstall'],"Compiled.with.openmp"), None, Touch('$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])
+  if sys.version_info[4] >0 : versionstring+="rc%s"%sys.version_info[4]
+  os.system("echo "+versionstring+" > "+os.path.join(env['libinstall'],"pyversion"))
+
+############## Populate the buildvars file #####################
+
+buildvars=open(os.path.join(env['libinstall'],'buildvars'),'w')
+buildvars.write('python='+str(sys.version_info[0])+"."+str(sys.version_info[1])+"."+str(sys.version_info[2])+'\n')
+
+# Find the boost version by extracting it from version.hpp
+boosthpp=open(os.path.join(env['boost_path'],'boost','version.hpp'))
+boostversion='unknown'
+try:
+    for line in boosthpp:
+        ver=re.match(r'#define BOOST_VERSION (\d+)',line)
+        if ver:
+            boostversion=ver.group(1)
+except StopIteration: 
+    pass
+buildvars.write("boost="+boostversion+"\n")
+buildvars.write("svn_revision="+str(global_revision)+"\n")
+out="usedebug="
+if env['usedebug']:
+    out+="y"
+else:
+    out+="n"
+out+="\nusempi="
+if env['usempi']:
+    out+="y"
+else:
+    out+="n"
+out+="\nuseopenmp="
+if env['useopenmp']:
+    out+="y"
+else:
+    out+="n"
+buildvars.write(out+"\n")
+buildvars.write("mpi_flavour="+env['mpi_flavour']+'\n')
+out="lapack="
+if env['uselapack']:
+   out+="y"
+else:
+   out+="n"
+out+="\nsilo="
+if env['usesilo']:
+   out+="y"
+else:
+   out+="n"
+out+="\nusevisit="
+if env['usevisit']:
+   out+="y"
+else:
+   out+="n"
+buildvars.write(out+"\n")
+buildvars.close()
+
+
 ############ Targets to build and install libraries ############
 
 target_init = env.Command(env['pyinstall']+'/__init__.py', None, Touch('$TARGET'))
@@ -620,6 +955,13 @@
 env.Alias('build_paso', ['target_install_paso_headers', 'target_paso_a'])
 env.Alias('install_paso', ['build_paso', 'target_install_paso_a'])
 
+env.Alias('build_weipa', ['target_install_weipa_headers', 'target_weipa_so', 'target_weipacpp_so'])
+env.Alias('install_weipa', ['build_weipa', 'target_install_weipa_so', 'target_install_weipacpp_so', 'target_install_weipa_py'])
+
+
+env.Alias('build_escriptreader', ['target_install_weipa_headers', 'target_escriptreader_a'])
+env.Alias('install_escriptreader', ['build_escriptreader', 'target_install_escriptreader_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'])
 
@@ -630,23 +972,27 @@
 build_all_list = []
 build_all_list += ['build_esysUtils']
 build_all_list += ['build_paso']
+build_all_list += ['build_weipa']
 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_finley_wrapper']
+#if not IS_WINDOWS_PLATFORM:	build_all_list += ['target_escript_wrapper']
+build_all_list += ['target_escriptconvert']
 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_weipa']
 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_finley_wrapper']
+#if not IS_WINDOWS_PLATFORM:	install_all_list += ['target_install_escript_wrapper']
+if env['usesilo']:	install_all_list += ['target_install_escriptconvert']
 install_all_list += ['remember_options']
 env.Alias('install_all', install_all_list)
 
@@ -659,8 +1005,40 @@
 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'])
+env.Alias('api_epydoc','install_all')
+
+env.Alias('docs', ['examples_tarfile', 'examples_zipfile', 'api_epydoc', 'api_doxygen', 'guide_pdf', 'guide_html','install_pdf', 'cookbook_pdf'])
+
+build_platform=os.name
+
+if not IS_WINDOWS_PLATFORM:
+   try:
+   	utest=open("utest.sh","w")
+	#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)
+
+   #Make sure that the escript wrapper is in place
+   if not os.path.isfile(os.path.join(env['bininstall'],'escript')):
+       print "Copying escript wrapper"
+       shutil.copy("bin/escript",os.path.join(env['bininstall'],'escript'))
+
+############ Targets to build PasoTests suite ################
+
+env.Alias('build_PasoTests','build/'+build_platform+'/paso/profiling/PasoTests')
 
+env.Alias('release_prep', ['docs', 'install_all'])