more modifications, only configure needs modifications

code/setup/symlink_Code.py

@@ -1,34 +0,0 @@
-#!/usr/bin/env python
-import os
-import damask
-
-bin_link = { \
-            '.' : [
-                    'DAMASK_spectral.exe',
-                  ],
-           }
-
-MarcReleases =[2011,2012,2013,2013.1]
-
-damaskEnv = damask.Environment('../../')          # script location relative to root
-baseDir = damaskEnv.relPath('code/')
-
-for dir in bin_link:
-  for file in bin_link[dir]:
-    src = os.path.abspath(os.path.join(baseDir,dir,file))
-    if os.path.exists(src): 
-      sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),\
-                                              {True: dir,
-                                               False:os.path.splitext(file)[0]}[file == '']))
-      if os.path.lexists(sym_link): os.remove(sym_link)
-      os.symlink(src,sym_link)
-      print sym_link,'-->',src
-
-
-for version in MarcReleases:
-  src = os.path.abspath(os.path.join(baseDir,'DAMASK_marc.f90'))
-  if os.path.exists(src): 
-    sym_link = os.path.abspath(os.path.join(baseDir,'DAMASK_marc'+str(version)+'.f90'))                    
-    if os.path.lexists(sym_link): os.remove(sym_link)
-    os.symlink(src,sym_link)
-    print sym_link,'-->',src

installation/compile_CoreModule.py

@@ -59,7 +59,6 @@ elif lapackroot != '':
 
 execute = { \
           'coreModule' : [ 
-                        'make tidy',
                         # The following command is used to compile the fortran files and make the functions defined
                         # in damask.core.pyf available for python in the module core.so
                         # It uses the fortran wrapper f2py that is included in the numpy package to construct the

installation/mods_MarcMentat/apply_DAMASK_modifications

@@ -4,6 +4,8 @@ DEFAULT_VERSION='2013.1'
 
 WORKINGDIR=`dirname $0`
 
+source ../options
+
 while [ ! -d "$WORKINGDIR/$VERSION" ] || [ -z "$VERSION" ]
 do
   echo "Input version of MARC/MENTAT installation: [${DEFAULT_VERSION}]"
@@ -14,9 +16,8 @@ do
 done
 echo "MSC version: $VERSION"
 
-INSTALLDIR=''
+if [ "x$MSCROOT" != "x" ] 
-if [ -f $WORKINGDIR/../../lib/pathinfo ]; then
+  then INSTALLDIR=$MSCROOT
-  INSTALLDIR=`grep -vE "^[[:space:]]*#|^$" $WORKINGDIR/../../lib/pathinfo | grep -i msc | head -n1 | awk 'BEGIN { FS = "[ \t]+" } ; { print $2 }'`
 fi
 
 while [ ! -d "$INSTALLDIR" ] || [ -z "$INSTALLDIR" ]
@@ -30,20 +31,17 @@ echo "MSC installation path: $INSTALLDIR"
 
 BLASDIR=''
 BLASTYPE=''
-if [ -f $WORKINGDIR/../../lib/pathinfo ]; then
+if [ "x$LAPACKROOT" != "x" ] 
-  IMKLDIR=`grep -vE "^[[:space:]]*#|^$" $WORKINGDIR/../../lib/pathinfo | grep -i imkl | head -n1 | awk 'BEGIN { FS = "[ \t]+" } ; { print $2 }'`
+  BLASDIR=$LAPACKROOT
-  ACMLDIR=`grep -vE "^[[:space:]]*#|^$" $WORKINGDIR/../../lib/pathinfo | grep -i acml | head -n1 | awk 'BEGIN { FS = "[ \t]+" } ; { print $2 }'`
-  LAPACKDIR=`grep -vE "^[[:space:]]*#|^$" $WORKINGDIR/../../lib/pathinfo | grep -i lapack | head -n1 | awk 'BEGIN { FS = "[ \t]+" } ; { print $2 }'`
-  if [ -d "$IMKLDIR" ]; then
-    BLASDIR=$IMKLDIR
-    BLASTYPE='IMKL'
-  elif [ -d "$ACMLDIR" ]; then
-    BLASDIR=$ACMLDIR
-    BLASTYPE='ACML'
-  elif [ -d "$LAPACKDIR" ]; then
-    BLASDIR=$LAPACKDIR
   BLASTYPE='LAPACK'
-  fi
+fi
+if [ "x$ACMLROOT" != "x" ] 
+  BLASDIR=$ACMLROOT
+  BLASTYPE='ACML'
+fi
+if [ "x$IMKLROOT" != "x" ] 
+  BLASDIR=$IMKLROOT
+  BLASTYPE='IMKL'
 fi
 
 while [ ! -d "$BLASDIR" ] || [ -z "$BLASDIR" ]

installation/options

@@ -13,3 +13,4 @@ LAPACKROOT=/usr
 ACMLROOT=
 IMKLROOT=
 F90=gfortran
+MSCROOT=/msc

installation/setup_env.py

@@ -1,166 +0,0 @@
-#!/usr/bin/env python
-
-import os,sys,string,re,platform
-from optparse import OptionParser
-
-validShell = {\
-             'bash':    'DAMASK_env.sh' ,
-             'csh':     'DAMASK_env.csh',
-             'windows': 'DAMASK_env.bat',
-              }
-
-env_order = ['DAMASK_ROOT','DAMASK_BIN','PATH','PYTHONPATH','LD_LIBRARY_PATH']
-environment = { 'DAMASK_ROOT':
-                              [{'delete':'',
-                                'substitute':'[DamaskRoot]',
-                                'append': False,
-                               },
-                              ],
-                'DAMASK_BIN':
-                              [{'delete':'',
-                                'substitute':'[os.path.join(DamaskRoot,"bin")]',
-                                'append': False,
-                               },
-                              ],
-                'PATH':
-                              [{'delete':'"${DAMASK_BIN}"',
-                                'substitute':'["${DAMASK_BIN}"]',
-                                'append': True,
-                               },
-                              ],
-                'PYTHONPATH':
-                              [{'delete':'"${DAMASK_ROOT}/lib"',
-                                'substitute':'["${DAMASK_ROOT}/lib"]',
-                                'append': True,
-                               },
-                              ], 
-                'LD_LIBRARY_PATH':
-                              [{'activate':  'pathInfo["acml"]',
-                                'delete':    '"acml"',                                             # what keywords trigger item deletion from existing path 
-                                'substitute':'[os.path.join(pathInfo["acml"],"ifort64_mp/lib"),\
-                                               os.path.join(pathInfo["acml"],"ifort64/lib"),\
-                                               os.path.join(pathInfo["acml"],"gfortran64_mp/lib"),\
-                                               os.path.join(pathInfo["acml"],"gfortran64/lib")]',  # what to substitute for deleted path items
-                                'append': True,                                                    # whether new entries append to existing ${env}
-                               },
-                               {'activate':  'pathInfo["lapack"]',
-                                'delete':    '[os.path.join(pathInfo["lapack"],"lib"),\
-                                               os.path.join(pathInfo["lapack"],"lib64")]',         # deleted current (same) entry
-                                'substitute':'[os.path.join(pathInfo["lapack"],"lib"),\
-                                               os.path.join(pathInfo["lapack"],"lib64")]',         # what to substitute for deleted path
-                                'append': True,                                                    # whether new entries append to existing ${env}
-                               },
-                               {'activate':  'pathInfo["fftw"]',
-                                'delete':    '[os.path.join(pathInfo["fftw"],"lib")]',             # deleted current (same) entry
-                                'substitute':'[os.path.join(pathInfo["fftw"],"lib")]',             # what to substitute for deleted path items
-                                'append': True,                                                    # whether new entries append to existing ${env}
-                               },
-                              ],
-               }
-
-parser = OptionParser(usage="%prog [options]", description = """
-Sets up your shell resource to be compatible with DAMASK. 
-""" + string.replace('$Id: setup_shellrc.py 2126 2013-02-01 13:22:40Z MPIE\m.diehl $','\n','\\n')
-)
-
-parser.add_option("-s","--shell", type="string", 
-                  dest = "shell", \
-                  help = "type of shell, e.g. "+', '.join(validShell.keys())+" [%default]")
-
-parser.set_defaults(shell = 'windows' if platform.system() == 'Windows' else 'bash')
-(options, args) = parser.parse_args()
-
-pathInfo = {}
-
-DamaskRoot = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])),'../'))
-try:                                                                                              # check for user-defined pathinfo
-  file = open(os.path.join(DamaskRoot,'lib/pathinfo'))
-  content = map(lambda string: string.strip(),file.readlines())
-  file.close()
-  for line in content:
-    if not (line.startswith('#') or line == ''):
-      items = line.split() + ['','']
-      pathInfo[items[0].lower()] = {False: os.path.normpath(os.path.join(DamaskRoot,'lib/',items[1])),
-                                    True: items[1]}[items[1] == '']
-except:
-  pass
-
-theShell = options.shell.lower()
-if theShell not in validShell:
-  print('invalid shell %s, assuming bash', theShell)
-  theShell='bash'
-
-theSourceFile = validShell[theShell]
-thePath = os.path.join(DamaskRoot,theSourceFile)
-if os.path.exists(thePath):
-  print('parsing existing %s'%thePath)
-
-  currentSourceFile = open(thePath)
-  content = map(string.strip,currentSourceFile.readlines())
-  currentSourceFile.close()
-
-  match = {}
-  for var in env_order: match[var] = False
-  
-  output = []
-      
-  for line in content:
-    for var in env_order:
-      m = re.search(\
-                    {\
-                     'bash':    r'^(.*? %s=)([^;]*)(.*)$'%var,
-                     'csh':     r'^(\s*setenv\s+%s\s+)([^;]*)(.*)$'%var,
-                     'windows': r'^(\s*SET\s+%s\s+)([^;]*)(.*)$'%var                              #case insesitiv search + second % sign
-                    }[theShell],line)
-      if m:
-        n = re.search(r'(%s)'%var, line)
-        o = re.search(r'(#)', line)
-        if o:
-          if o.start() < n.start():
-            print 'skipped potential comment line, please check!'
-            continue
-        match[var] = True
-        items = m.group(2).split(':')
-        for piece in environment[var]:
-          try:
-            if 'activate' not in piece or eval(piece['activate']) != '':
-              if piece['append']:
-                if 'delete' in piece:
-                  killer = eval(piece['delete'])
-                  if type(killer) == str:
-                    items = [path for path in items if killer not in path]
-                  if type(killer) == list:
-                    items = [path for path in items if path not in killer]
-                items += eval(piece['substitute'])
-              else:
-                items = eval(piece['substitute'])
-          except:
-            pass
-        line = m.group(1)+':'.join(items)+m.group(3)
-
-    output.append(line)
-
-for var in env_order:
-  if not match[var]:
-    items = ['${%s}'%var]
-    for piece in environment[var]:
-      try:
-        if 'activate' not in piece or eval(piece['activate']) != '':
-          if piece['append']:
-            items += eval(piece['substitute'])
-          else:
-            items =  eval(piece['substitute'])
-      except:
-        pass
-    output.append({\
-       'bash':    'export %s=%s'%(var,':'.join(items)),
-       'csh':     'setenv %s %s'%(var,':'.join(items)),
-       'windows': 'SET %s %s'%(var,':'.join(items)),
-      }[theShell])
-
-print('writing to %s'%thePath)
-newSourceFile = open(thePath,'w')
-newSourceFile.write('\n'.join(output)+'\n')
-newSourceFile.close()
-
-

installation/setup_shellrc.py

@@ -1,168 +0,0 @@
-#!/usr/bin/env python
-
-import os,sys,string,re
-from optparse import OptionParser
-
-validShellRC = {\
-               'bash':['.bashrc','.bash_profile','.bash_login','.profile','new'],
-               'csh': ['.cshrc','new'],
-              }
-
-env_order = ['DAMASK_ROOT','DAMASK_BIN','PATH','PYTHONPATH','LD_LIBRARY_PATH']
-environment = { 'DAMASK_ROOT':
-                              [{'delete':'',
-                                'substitute':'[DamaskRoot]',
-                                'append': False,
-                               },
-                              ],
-                'DAMASK_BIN':
-                              [{'delete':'',
-                                'substitute':'[os.path.join(DamaskRoot,"bin")]',
-                                'append': False,
-                               },
-                              ],
-                'PATH':
-                              [{'delete':'"${DAMASK_BIN}"',
-                                'substitute':'["${DAMASK_BIN}"]',
-                                'append': True,
-                               },
-                              ],
-                'PYTHONPATH':
-                              [{'delete':'"${DAMASK_ROOT}/lib"',
-                                'substitute':'["${DAMASK_ROOT}/lib"]',
-                                'append': True,
-                               },
-                              ], 
-                'LD_LIBRARY_PATH':
-                              [{'activate':  'pathInfo["acml"]',
-                                'delete':    '"acml"',                                             # what keywords trigger item deletion from existing path 
-                                'substitute':'[os.path.join(pathInfo["acml"],"ifort64_mp/lib"),\
-                                               os.path.join(pathInfo["acml"],"ifort64/lib"),\
-                                               os.path.join(pathInfo["acml"],"gfortran64_mp/lib"),\
-                                               os.path.join(pathInfo["acml"],"gfortran64/lib")]',  # what to substitute for deleted path items
-                                'append': True,                                                    # whether new entries append to existing ${env}
-                               },
-                               {'activate':  'pathInfo["lapack"]',
-                                'delete':    '[os.path.join(pathInfo["lapack"],"lib"),\
-                                               os.path.join(pathInfo["lapack"],"lib64")]',         # deleted current (same) entry
-                                'substitute':'[os.path.join(pathInfo["lapack"],"lib"),\
-                                               os.path.join(pathInfo["lapack"],"lib64")]',         # what to substitute for deleted path
-                                'append': True,                                                    # whether new entries append to existing ${env}
-                               },
-                               {'activate':  'pathInfo["fftw"]',
-                                'delete':    '[os.path.join(pathInfo["fftw"],"lib")]',             # deleted current (same) entry
-                                'substitute':'[os.path.join(pathInfo["fftw"],"lib")]',             # what to substitute for deleted path items
-                                'append': True,                                                    # whether new entries append to existing ${env}
-                               },
-                              ],
-               }
-
-parser = OptionParser(usage="%prog [options]", description = """
-Sets up your shell resource to be compatible with DAMASK. 
-""" + string.replace('$Id$','\n','\\n')
-)
-
-parser.add_option("-s","--shell", type="string", 
-                  dest = "shell", \
-                  help = "type of shell, e.g. "+', '.join(validShellRC.keys())+" [%default]")
-
-parser.set_defaults(shell = 'bash')
-
-(options, args) = parser.parse_args()
-
-pathInfo = {}
-hitSomething = False
-
-DamaskRoot = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])),'../'))
-try:                                        # check for user-defined pathinfo
-  file = open(os.path.join(DamaskRoot,'lib/pathinfo'))
-  content = map(lambda string: string.strip(),file.readlines())
-  file.close()
-  for line in content:
-    if not (line.startswith('#') or line == ''):
-      items = line.split() + ['','']
-      pathInfo[items[0].lower()] = {False: os.path.normpath(os.path.join(DamaskRoot,'lib/',items[1])),
-                                    True: items[1]}[items[1] == '']
-except:
-  pass
-
-theShell = options.shell.lower()
-theHome = os.getenv('USERPROFILE') or os.getenv('HOME')
-
-for theRC in validShellRC[theShell]:
-  if theRC == 'new' and not hitSomething:
-    theRC = validShellRC[theShell][0]
-    print 'Could not find a file to store bash information, creating "%s" in home directory'%theRC
-    open(os.path.join(theHome,theRC), 'w').close()
-  thePath = os.path.join(theHome,theRC)
-  if os.path.exists(thePath):
-    print thePath
-    hitSomething = True
-    rc = open(os.path.join(theHome,theRC))
-    content = map(string.strip,rc.readlines())
-    rc.close()
-
-    match = {}
-    for var in env_order: match[var] = False
-  
-    output = []
-      
-    for line in content:
-      for var in env_order:
-        m = re.search(\
-                      {\
-                       'bash': r'^(.*? %s=)([^;]*)(.*)$'%var,
-                       'csh':  r'^(\s*setenv\s+%s\s+)([^;]*)(.*)$'%var 
-                      }[theShell],line)
-        if m:
-          n = re.search(r'(%s)'%var, line)
-          o = re.search(r'(#)', line)
-          if o:
-            if o.start() < n.start():
-              print 'skipped potential comment line, please check!'
-              continue
-          match[var] = True
-          items = m.group(2).split(':')
-          for piece in environment[var]:
-            try:
-              if 'activate' not in piece or eval(piece['activate']) != '':
-                if piece['append']:
-                  if 'delete' in piece:
-                    killer = eval(piece['delete'])
-                    if type(killer) == str:
-                      items = [path for path in items if killer not in path]
-                    if type(killer) == list:
-                      items = [path for path in items if path not in killer]
-                  items += eval(piece['substitute'])
-                else:
-                  items = eval(piece['substitute'])
-            except:
-              pass
-          line = m.group(1)+':'.join(items)+m.group(3)
-
-      output.append(line)
-
-    for var in env_order:
-      if not match[var]:
-        items = ['${%s}'%var]
-        for piece in environment[var]:
-          try:
-            if 'activate' not in piece or eval(piece['activate']) != '':
-              if piece['append']:
-                items += eval(piece['substitute'])
-              else:
-                items =  eval(piece['substitute'])
-          except:
-            pass
-        output.append({\
-           'bash':'export %s=%s'%(var,':'.join(items)),
-           'csh': 'setenv %s %s'%(var,':'.join(items)),
-          }[theShell])
-
-    rc = open(os.path.join(theHome,theRC),'w')
-    rc.write('\n'.join(output)+'\n')
-    rc.close()
-
-
-if not hitSomething: print 'none of %s found..!'%(', '.join(validShellRC[theShell]))
-

lib/pathinfo

@@ -10,8 +10,8 @@
 #  of the base installation path---this will be done automatically
 # Out of IMKL, ACML, LAPACK the first defined value is used to access BLAS functionality
 
-#IMKL    /opt/intel/composerxe/mkl
+IMKL
-#ACML    /opt/acml4.4.0
+ACML    /opt/acml5.3.0
 LAPACK  /usr
 FFTW    /usr/local
-MSC     /msc
+#MSC     /msc

processing/setup/compile_CoreModule.py

@@ -1,131 +0,0 @@
-#!/usr/bin/env python
-
-# Makes postprocessing routines acessible from everywhere.
-
-import os,sys,glob,string,subprocess
-from damask import Environment
-from optparse import OptionParser, Option
-
-
-# -----------------------------
-class extendableOption(Option):
-# -----------------------------
-# used for definition of new option parser action 'extend', which enables to take multiple option arguments
-# taken from online tutorial http://docs.python.org/library/optparse.html
-  
-  ACTIONS = Option.ACTIONS + ("extend",)
-  STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
-  TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
-  ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
-
-  def take_action(self, action, dest, opt, value, values, parser):
-    if action == "extend":
-      lvalue = value.split(",")
-      values.ensure_value(dest, []).extend(lvalue)
-    else:
-      Option.take_action(self, action, dest, opt, value, values, parser)
-
-      
-      
-########################################################
-# MAIN
-########################################################
-
-parser = OptionParser(option_class=extendableOption, usage='%prog options', description = """
-Sets up the pre and post processing tools of DAMASK
-
-""" + string.replace('$Id$','\n','\\n')
-)
-
-compilers = ['intel','ifort','intel32','gfortran','gnu95']
-
-parser.add_option('--F90', '--f90',     dest='compiler', type='string', \
-                                        help='name of F90 [%default]')
-parser.set_defaults(compiler  = {True:'ifort',False:'gfortran'}[\
-                                 subprocess.call(['which', 'ifort'],\
-                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0])
-(options,filenames) = parser.parse_args()
-
-if options.compiler not in compilers:
-  parser.error('compiler switch "--F90" has to be one out of: %s'%(', '.join(compilers)))
-
-f2py_compiler = {
-                  'gfortran': 'gnu95   --f90flags="-fPIC -fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics -DSpectral -fdefault-real-8 -fdefault-double-8 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
-                  'gnu95':    'gnu95   --f90flags="-fPIC -fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics -DSpectral -fdefault-real-8 -fdefault-double-8 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
-                  'intel32':  'intel   --f90flags="-fPIC -fpp -stand f08 -diag-disable 5268 -assume byterecl -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
-                  'intel':    'intelem --f90flags="-fPIC -fpp -stand f08 -diag-disable 5268 -assume byterecl -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
-                  'ifort':    'intelem --f90flags="-fPIC -fpp -stand f08 -diag-disable 5268 -assume byterecl -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
-                }[options.compiler]
-compiler = {
-                  'gfortran': 'gfortran',
-                  'gnu95':    'gfortran',
-                  'intel32':  'ifort',
-                  'intel':    'ifort',
-                  'ifort':    'ifort',
-                }[options.compiler]
-
-damaskEnv = Environment()
-baseDir = damaskEnv.relPath('processing/')
-codeDir = damaskEnv.relPath('code/')
-
-if   'imkl' in damaskEnv.pathInfo and damaskEnv.pathInfo['imkl'] != '' and options.compiler != 'gfortran':
-  lib_lapack = '-L%s/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -liomp5 -lpthread -lm'%(os.path.join(damaskEnv.pathInfo['imkl']))
-elif 'acml' in damaskEnv.pathInfo and damaskEnv.pathInfo['acml'] != '':
-  lib_lapack = '-L%s/%s64/lib -lacml'%(os.path.join(damaskEnv.pathInfo['acml']),compiler)
-elif 'lapack' in damaskEnv.pathInfo and damaskEnv.pathInfo['lapack'] != '':
-  lib_lapack = '-L%s -llapack'%(damaskEnv.pathInfo['lapack'])                                     # see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
-
-execute = { \
-          'coreModule' : [ 
-                        'make tidy',
-                        # The following command is used to compile the fortran files and make the functions defined
-                        # in damask.core.pyf available for python in the module core.so
-                        # It uses the fortran wrapper f2py that is included in the numpy package to construct the
-                        # module core.so out of the fortran code in the f90 files
-                        # For the generation of the pyf file use the following lines:
-                        ###########################################################################
-                        #'f2py -h damask.core.pyf' +\
-                        #' --overwrite-signature --no-lower prec.f90 DAMASK_spectral_interface.f90 math.f90 mesh.f90',
-                        ###########################################################################
-                        'rm `readlink -f %s`' %(os.path.join(damaskEnv.relPath('lib/damask'),'core.so')),
-                        'f2py damask.core.pyf' +\
-                        ' --build-dir ./' +\
-                        ' -c --no-lower --fcompiler=%s'%(f2py_compiler) +\
-                        ' %s'%'prec.f90'+\
-                        ' %s'%'DAMASK_spectral_interface.f90'+\
-                        ' %s'%'IO.f90'+\
-                        ' %s'%'libs.f90'+\
-                        ' %s'%'numerics.f90'+\
-                        ' %s'%'debug.f90'+\
-                        ' %s'%'math.f90'+\
-                        ' %s'%'FEsolving.f90'+\
-                        ' %s'%'mesh.f90'+\
-                        ' %s'%'core_quit.f90'+\
-                        ' -L%s/lib -lfftw3'%(damaskEnv.pathInfo['fftw'])+\
-                        ' %s'%lib_lapack,
-                        'mv %s `readlink -f %s`' %(os.path.join(codeDir,'core.so'),os.path.join(damaskEnv.relPath('lib/damask'),'core.so')),
-                        ]
-            }
-
-os.chdir(codeDir)                   # needed for compilation with gfortran and f2py
-for tasks in execute:
-  for cmd in execute[tasks]:
-    try:
-      print 'executing...:',cmd
-      os.system(cmd)
-    except:
-      print 'failed..!'
-      pass
-
-modules = glob.glob('*.mod')
-for module in modules:
-  print 'removing', module
-  os.remove(module)
-
-#check if compilation of core module was successful
-try:
-  with open(damaskEnv.relPath('lib/damask/core.so')) as f: pass
-except IOError as e:
-  print '*********\n* core.so not found, compilation of core modules was not successful\n*********'
-  sys.exit()
-f.close

processing/setup/setup_processing.sh

@@ -1,5 +0,0 @@
-#!/usr/bin/env sh
-
-${DAMASK_ROOT}/processing/setup/symLink_Processing.py
-${DAMASK_ROOT}/processing/setup/compile_CoreModule.py $@
-

processing/setup/symLink_Processing.py

@@ -1,97 +0,0 @@
-#!/usr/bin/env python
-
-# Makes postprocessing routines acessible from everywhere.
-import os
-from damask import Environment
-
-damaskEnv = Environment()
-baseDir = damaskEnv.relPath('processing/')
-codeDir = damaskEnv.relPath('code/')
-
-#define ToDo list
-bin_link = { \
-        'pre' : [
-                'marc_addUserOutput.py',
-                'mentat_pbcOnBoxMesh.py',
-                'mentat_spectralBox.py',
-                'OIMang_hex2cub.py',
-                'patchFromReconstructedBoundaries.py',
-                'randomSeeding.py',
-                'seed_check.py',
-                'geom_fromAng.py',
-                'geom_fromVPSC.py',
-                'geom_fromEuclideanDistance.py',
-                'geom_fromMinimalSurface.py',
-                'geom_fromVoronoiTessellation.py',
-                'geom_fromOsteonGeometry.py',
-                'geom_canvas.py',
-                'geom_check.py',
-                'geom_rescale.py',
-                'geom_pack.py',
-                'geom_unpack.py',
-                'geom_translate.py',
-                'geom_vicinityOffset.py',
-                'geom_grainGrowth.py',
-                'geom_poke.py',
-                ],
-        'post' : [
-                '3Dvisualize.py',
-                'permuteData.py',
-                'addCalculation.py',
-                'addCauchy.py',
-                'addCompatibilityMismatch.py',
-                'addCurl.py',
-                'addDeformedConfiguration.py',
-                'addDeterminant.py',
-                'addDeviator.py',
-                'addDivergence.py',
-                'addEhkl.py',
-                'addEuclideanDistance.py',
-                'addGrainID.py',
-                'addMises.py',
-                'addNorm.py',
-                'addOrientations.py',
-                'addIPFcolor.py',
-                'addPK2.py',
-                'addSchmidfactors.py',
-                'addSpectralDecomposition.py',
-                'addStrainTensors.py',
-                'averageDown.py',
-                'binXY.py',
-                'blowUp.py',
-                'stddevDown.py',
-                'deleteColumn.py',
-                'deleteInfo.py',
-                'filterTable.py',
-                'sortTable.py',
-                'marc_deformedGeometry.py',
-                'marc_extractData.py',
-                'mentat_colorMap.py',
-                'nodesFromCentroids.py',
-                'perceptualUniformColorMap.py',
-                'postResults.py',
-                'showTable.py',
-                'tagLabel.py',
-                'vtk2ang.py',
-                'vtk_addData.py',
-                'vtk_pointcloud.py',
-                'vtk_addPointcloudData.py',
-                'vtk_voxelcloud.py',
-                'vtk_addVoxelcloudData.py',
-                ],
-            }
-            
-for dir in bin_link:
-  for file in bin_link[dir]:
-    src = os.path.abspath(os.path.join(baseDir,dir,file))
-    if (file == ''):
-      sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),dir))
-    else:
-      sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),os.path.splitext(file)[0]))
-    print sym_link,'-->',src
-    if os.path.lexists(sym_link):
-      os.remove(sym_link)    
-    os.symlink(src,sym_link)            
-
-
-