fixed installation, will test now

DAMASK_env.sh

@@ -2,13 +2,12 @@
 # usage:  source DAMASK_env.sh
 
 if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]
-  then LOCATION=$(readlink -f "`dirname $BASH_SOURCE`")
+  then DAMASK_ROOT=$(readlink -f "`dirname $BASH_SOURCE`")
 else
   STAT=$(stat "`dirname $BASH_SOURCE`")
-  LOCATION=${STAT##* }
+  DAMASK_ROOT=${STAT##* }
 fi
-export DAMASK_ROOT=${LOCATION}
+
-source $DAMASK_ROOT/installation/options
 if [ "x$DAMASK_NUM_THREADS" != "x" ] 
   then export DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS
 fi
@@ -27,6 +26,9 @@ fi
 if [ "x$F90" != "x" ] 
   then export F90=$F90
 fi
+if [ "x$DAMASK_BIN" == "x" ] 
+  then DAMASK_BIN=$DAMASK_ROOT/bin
+fi
 
 # disable output in case of scp
 if [ ! -z "$PS1" ]; then
@@ -36,7 +38,7 @@ if [ ! -z "$PS1" ]; then
   echo http://damask.mpie.de
   echo
   echo Preparing environment ...
-  echo "DAMASK_ROOT=$DAMASK_ROOT"
+  echo "DAMASK installation in $DAMASK_ROOT"
   echo "DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
   echo "F90=$F90"
   echo "prepending to LD_LIBRARY_PATH: $LD_NEW"
@@ -45,7 +47,5 @@ ulimit -s unlimited
 ulimit -c 0
 ulimit -v unlimited
 ulimit -m unlimited
-export DAMASK_BIN=$DAMASK_ROOT/bin
-export PATH=$PATH:$DAMASK_BIN
 export PYTHONPATH=$PYTHONPATH:$DAMASK_ROOT/lib
 export LD_LIBRARY_PATH=$LD_NEW:$LD_LIBRARY_PATH

Makefile

@@ -2,12 +2,12 @@ SHELL = /bin/sh
 ########################################################################################
 # Makefile for the installation of DAMASK
 ########################################################################################
-.PHONY : spectral
+.PHONY: spectral
 spectral:
 	@$(MAKE) clean -C code >/dev/null
 	$(MAKE) -C code
 
-.PHONY : marc
+.PHONY: marc
 marc:
 	@./installation/mods_MarcMentat/apply_DAMASK_modifications.sh ${MAKEFLAGS}
 
@@ -16,15 +16,15 @@ processing:
 	@$(MAKE) tidy -C code >/dev/null
 	@./installation/compile_CoreModule.py ${MAKEFLAGS}
 
-.PHONY : tidy
+.PHONY: tidy
 tidy: 
 	@$(MAKE) tidy -C code >/dev/null
 
-.PHONY : clean
+.PHONY: clean
 clean: 
 	@$(MAKE) clean -C code >/dev/null
 
-.PHONY : install
+.PHONY: install
 install:
 	@./installation/symlink_Code.py ${MAKEFLAGS}
 	@./installation/symlink_Processing.py ${MAKEFLAGS}

code/Makefile

@@ -35,11 +35,18 @@ SHELL = /bin/sh
 # SUFFIX         = arbitrary suffix (after file to compile)
 # STANDARD_CHECK = checking for Fortran 2008, compiler dependend
 ########################################################################################
-include ../installation/options
+ifeq ($(wildcard "${HOME}/.damask/damask.conf"),)
+	include ${HOME}/.damask/damask.conf
+else
+	include /etc/damask.conf
+endif  
+
 
 COMPILERNAME ?= $(F90)
 
-INCLUDE_DIRS +=-I$(DAMASK_ROOT)/lib
+INCLUDE_DIRS :=-I../lib
+LIBRARIES :=-lfftw3
+LIB_DIRS  :=-L$(FFTWROOT)/lib
 
 ifeq "$(FASTBUILD)" "YES"
 OPENMP := OFF
@@ -75,7 +82,22 @@ ifeq  "$(PORTABLE)" "FALSE"
 PORTABLE_SWITCH =-msse3
 endif
 
+# settings for multicore support
+ifeq "$(OPENMP)" "ON"
+OPENMP_FLAG_ifort =-openmp -openmp-report0 -parallel
+OPENMP_FLAG_gfortran =-fopenmp
+ACML_ARCH =_mp
+IMKL_ARCH =_intel_thread
+LIBRARIES +=-lfftw3_threads -lpthread
+else
+IMKL_ARCH =_sequential
+endif
 
+ifneq  "x$(IMKLROOT)" "x"
+LIB_DIRS  :=-L$(IMKLROOT)/lib/intel64
+INCLUDE_DIRS +=-I$(IMKLROOT)/include
+LIBRARIES +=-lmkl_intel_lp64 -lmkl_core -lmkl$(ACML_ARCH) -lm -lpthread -liomp5
+else
 ifneq  "x$(ACMLROOT)" "x"
 LIB_DIRS  +=-L$(ACMLROOT)/$(F90)64$(ACML_ARCH)/lib
 LIBRARIES +=-lacml$(ACML_ARCH)
@@ -85,26 +107,10 @@ LIB_DIRS  +=-L$(LAPACKROOT)/lib64 -L$(LAPACKROOT)/lib
 LIBRARIES +=-llapack
 endif
 endif
-
-COMPILE_OPTIONS_ifort :=
-ifeq "$(F90)" "ifort"
-ifneq  "x$(IMKLROOT)" "x"
-COMPILE_OPTIONS_ifort +=-I$(IMKLROOT)/include -mkl=sequential
-LIBRARIES :=-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lm
-LIB_DIRS  :=-L$(IMKLROOT)/lib/intel64
-endif
 endif
 
-# settings for multicore support
-ifeq "$(OPENMP)" "ON"
-OPENMP_FLAG_ifort =-openmp -openmp-report0 -parallel
-OPENMP_FLAG_gfortran =-fopenmp
-ACML_ARCH =_mp
-LIBRARIES +=-lfftw3_threads -lpthread
-endif
 
-LIBRARIES +=-lfftw3
+
-LIB_DIRS  +=-L$(FFTWROOT)/lib
 
 #hdf5
 ifeq "$(HDF5)" "ON"
@@ -139,7 +145,7 @@ OPTIMIZATION_AGGRESSIVE_ifort    :=-O3 $(PORTABLE_SWITCH) -no-prec-div -fp-model
 OPTIMIZATION_AGGRESSIVE_gfortran :=-O3 $(PORTABLE_SWITCH) -ffast-math -funroll-loops -ftree-vectorize 
 
 
-COMPILE_OPTIONS_ifort    +=-fpp\
+COMPILE_OPTIONS_ifort    :=-fpp\
                            -ftz\
                            -assume byterecl
 ifneq "$(FASTBUILD)" "YES"
@@ -464,12 +470,14 @@ endif
 %.o : %.f90
 	$(PREFIX) $(COMPILERNAME) $(COMPILE) -c $< $(SUFFIX)
 
-.PHONY : tidy 
+.PHONY: tidy
+tidy:
 	@rm -rf *.o
 	@rm -rf *.mod
 
 
-.PHONY : clean
+.PHONY: clean
+clean:
 	@rm -rf *.o
 	@rm -rf *.mod
 	@rm -rf *.exe

configure

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-import os,re,sys,string,subprocess
+import os,re,sys,string,subprocess,shutil
 
 from optparse import OptionParser, Option
 
@@ -28,67 +28,225 @@ class extendableOption(Option):
 ########################################################
 
 parser = OptionParser(option_class=extendableOption, usage='%prog options', description = """
-Sets up the pre and post processing tools of DAMASK
+Configures the compilation and installation of DAMASK
 
 """ + string.replace('$Id$','\n','\\n')
 )
 
-compilers = ['ifort','gfortran']
+#--- determine default compiler ----------------------------------------------------------------------
-blastypes = ['LAPACK','ACML','IMKL']
-
-parser.add_option('--with-fc',               dest='compiler', type='string',
-                                             help='F90 compiler [%default]')
-parser.add_option('--with-marc-dir',         dest='marcdir', type='string',
-                                             help='root directory of MSC.Marc [%default]')
-parser.add_option('--with-fftw-dir',         dest='fftwdir', type='string',
-                                             help='root directory of FFTW [%default]')
-parser.add_option('--with-blas-lapack-dir',  dest='blasdir', type='string',
-                                             help='root directory of LAPACK [%default]')
-parser.add_option('--with-blas-type',        dest='blastype', type='string',
-                                             help='type of BLAS/LAPACK library [%default]')
-parser.add_option('--with-spectral-options', dest='spectraloptions', type='string', action='extend',
-                                             help='options for spectral solver %default')
-
 compiler = os.getenv('F90')
 if compiler == None: compiler ={True:'ifort',False:'gfortran'}[\
                                 subprocess.call(['which', 'ifort'],\
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0]
-parser.set_defaults(compiler = compiler)
+
-parser.set_defaults(blastype = 'LAPACK')
+#--- default option values  --------------------------------------------------------------------------
-parser.set_defaults(fftwdir =  '/usr/local')
+defaults={'F90':compiler,\
-parser.set_defaults(blasdir =  '/usr')
+          'FFTW_ROOT':'/usr/local',\
-parser.set_defaults(marcdir =  '/msc')
+          'MARC_ROOT':'/msc',\
+          'HDF5_ROOT':'/usr/local',\
+          'DAMASK_NUM_THREADS':4,\
+          'blasType':'LAPACK',\
+          'blasRoot':{'LAPACK':'/usr',\
+                      'ACML'  :'/opt/acml5.3.1',\
+                      'IMKL'  :{True:'/opt/intel/composerxe/mkl',False:os.getenv('MKLROOT')}\
+                               [os.getenv('MKLROOT')==None]},\
+          'spectralOptions':{}}
+
+#--- if local config file exists, read, otherwise assume global config file  ------------------------
+if os.path.isfile(os.path.join(os.getenv('HOME'),'.damask/damask.conf')):
+  configFile = os.path.join(os.getenv('HOME'),'.damask/damask.conf')
+else:
+  configFile = '/etc/damask.conf'
+
+#--- set default values according to read in values  ------------------------------------------------
+try:
+  with open(configFile,'r') as f:
+    print('\n-----\n reading default values from %s\n-----'%configFile)
+    for line in f:
+      items = re.split('[= ]',line)
+    
+      if (not line.strip() or items[0].startswith('#')):
+        pass
+      elif items[0] == 'F90':
+        defaults['F90']=items[1].rstrip()
+      elif items[0] == 'FFTW_ROOT': 
+        defaults['FFTW_ROOT']=items[1].rstrip()
+      elif items[0] == 'MARC_ROOT': 
+        defaults['MARC_ROOT']=items[1].rstrip()
+      elif items[0] == 'HDF5_ROOT': 
+        defaults['HDF5_ROOT']=items[1].rstrip()
+      elif items[0] == 'DAMASK_NUM_THREADS': 
+        defaults['DAMASK_NUM_THREADS']=int(items[1])
+      elif items[0] in [name+'_ROOT' for name in defaults['blasRoot']]:
+        defaults['blasType']=items[0][:-5]
+        defaults['blasRoot'][items[0][:-5]] =items[1].rstrip()
+      else:
+        defaults['spectralOptions'][items[0]]=items[1].rstrip()
+except IOError:
+  pass
+
+
+parser.add_option('--with-fc',               dest='compiler', type='string', metavar='string', \
+                                             help='F90 compiler [%default]')
+parser.add_option('--with-fftw-dir',         dest='fftwRoot', type='string', metavar='string', \
+                                             help='root directory of FFTW [%default]')
+parser.add_option('--with-marc-dir',         dest='marcRoot', type='string', metavar='string', \
+                                             help='root directory of MSC.Marc [%default]')
+parser.add_option('--with-HDF5-dir',         dest='hdf5Root', type='string', metavar='string', \
+                                             help='root directory of HDF5 [%default]')
+parser.add_option('--with-OMP-threads',      dest='threads', type='int', metavar='int',\
+                                             help='number of openMP threads [%default]')
+parser.add_option('--with-blas-type',        dest='blasType', type='string', metavar='string', \
+                                             help='type of BLAS/LAPACK library [%default]')
+parser.add_option('--with-blas-dir',         dest='blasRoot', type='string', metavar='string', \
+                                             help='root directory of BLAS/LAPACK library [%default]')
+parser.add_option('--with-spectral-options', dest='spectraloptions', type='string', action='extend', metavar='<string LIST>', \
+                                             help='options for compilation of spectral solver')
+
+parser.set_defaults(compiler = defaults['F90'])
+parser.set_defaults(fftwRoot = defaults['FFTW_ROOT'])
+parser.set_defaults(marcRoot = defaults['MARC_ROOT'])
+parser.set_defaults(hdf5Root = defaults['HDF5_ROOT'])
+parser.set_defaults(threads  = defaults['DAMASK_NUM_THREADS'])
+parser.set_defaults(blasType = defaults['blasType'])
+
+#--- set default for blasRoot depending on current option (or default) for blasType  --------------------
+
+blasType = defaults['blasType'].upper()
+for i, arg in enumerate(sys.argv):
+  if arg.startswith('--with-blas-type'):
+    if arg.endswith('--with-blas-type'): 
+      blasType = sys.argv[i+1].upper()
+    else:
+      blasType = sys.argv[i][17:].upper()
+if blasType not in ['LAPACK','ACML','IMKL']:
+  blasType='LAPACK'
+
+parser.set_defaults(blasRoot = [defaults['blasRoot'][blasType]][0])
 parser.set_defaults(spectraloptions = [])
 
 (options,filenames) = parser.parse_args()
 
-options.blastype = options.blastype.upper()
+#--- consistency checks --------------------------------------------------------------------------------
-options.compiler = options.compiler.lower()
+options.compiler=options.compiler.lower()
+options.blasType=options.blasType.upper() 
+options.fftwRoot=options.fftwRoot.rstrip('/')
+options.marcRoot=options.marcRoot.rstrip('/')
+options.hdf5Root=options.hdf5Root.rstrip('/') 
+options.blasRoot=options.blasRoot.rstrip('/') 
 
-if options.blastype not in blastypes: print('Unknown BLAS type selected')
+if options.compiler not in ['ifort','gfortran']: 
-if options.compiler not in compilers: print('Unknown compiler type selected')
+  print('Error: Unknown compiler option: %s'%options.compiler)
+  sys.exit(1)
 
+if not subprocess.call(['which', options.compiler],stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
+  print('Compiler Warning: executable %s not found!'%options.compiler)
+
+for lib in ['libfftw3.a','libfftw3.a']:
+  if not os.path.isfile(os.path.join(options.fftwRoot,'lib/%s'%lib)):
+    print('FFTW Warning: %s not found in %s!'%(lib,os.path.join(options.fftwRoot,'lib')))
+
+if not os.path.isdir(options.marcRoot):
+  print('MSC.Marc Warning: Root directory %s not found!'%options.marcRoot)
+
+if options.blasType == 'LAPACK':
+  if os.path.isdir(os.path.join(options.blasRoot,'lib64')): 
+    blasLocation = os.path.join(options.blasRoot,'lib64')
+  else:
+    blasLocation=os.path.join(options.blasRoot,'lib')
+  for lib in ['liblapack.a','liblapack.a']:
+    if not os.path.isfile(os.path.join(blasLocation,lib)): 
+      print('LAPACK Warning: %s not found in %s!'%(lib,blasLocation))
+elif options.blasType == 'ACML':
+  blasLocationSerial=os.path.join(options.blasRoot,'%s64/lib'%options.compiler)
+  for lib in ['libacml.a','libacml.a']:
+    if not os.path.isfile(os.path.join(blasLocationSerial,lib)): 
+      print('ACML Warning: %s not found in %s!'%(lib,blasLocationSerial))
+  blasLocationParallel=os.path.join(options.blasRoot,'%s64_mp/lib'%options.compiler)
+  for lib in ['libacml_mp.a','libacml_mp.a']:
+    if not os.path.isfile(os.path.join(blasLocationParallel,lib)): 
+      print('ACML Warning: %s not found in %s!'%(lib,blasLocationParallel))
+elif options.blasType == 'IMKL':
+  if options.compiler == 'gfortran':
+    print('Error: IMKL does not support gfortran')
+    sys.exit(1)
+  blasLocation=os.path.join(options.blasRoot,'lib/intel64')
+  for lib in ['libmkl_core.so','libmkl_core.a',\
+              'libmkl_sequential.so','libmkl_sequential.a',\
+              'libmkl_intel_lp64.so','libmkl_intel_lp64.a']:
+    if not os.path.isfile(os.path.join(blasLocation,lib)): 
+      print('IMKL Warning: %s not found in %s!'%(lib,blasLocation))
+else:
+  print('Error: Unknown BLAS/LAPACK library: %s'%options.blasType)
+  sys.exit(1)
+
+
+#--- try to read config file (to keep comments and order) ----------------------------------------------
 output = []
-with open('installation/options','r') as f:
+try: 
+  with open(configFile,'r') as f:
     for line in f:
       items = re.split('[= ]',line)
     
-    if items[0] == 'F90':      line = '%s=%s\n'%(items[0],options.compiler)
+      if (not line.strip() or items[0].startswith('#')):
-    if items[0] == 'FFTW_ROOT': line = '%s=%s\n'%(items[0],options.fftwdir.rstrip('/'))
+        pass
-    if items[0] == 'MSC_ROOT':  line = '%s=%s\n'%(items[0],options.marcdir.rstrip('/'))
+      if items[0] == 'F90':
-    for blastype in blastypes:
+        line = '%s=%s\n'%(items[0],options.compiler)
-      if options.blastype == blastype and items[0] == '%s_ROOT'%blastype:
+        options.compiler =''
-        line = '%s=%s\n'%(items[0],options.blasdir.rstrip('/'))
+      if items[0] == 'FFTW_ROOT':
+        line = '%s=%s\n'%(items[0],options.fftwRoot)
+        options.fftwRoot =''
+      if items[0] == 'MARC_ROOT':
+        line = '%s=%s\n'%(items[0],options.marcRoot)
+        options.marcRoot =''
+      if items[0] == 'HDF5_ROOT':
+        line = '%s=%s\n'%(items[0],options.hdf5Root)
+        options.hdf5Root =''
+      if items[0] == 'DAMASK_NUM_THREADS':
+        line = '%s=%s\n'%(items[0],options.threads)
+        options.threads =''
+      for blasType in defaults['blasRoot'].keys():
+        if items[0] == '%s_ROOT'%blasType and items[0] == '%s_ROOT'%options.blasType:
+          line = '%s=%s\n'%(items[0],options.blasRoot)
+          options.blasType=''
+        elif items[0] == '%s_ROOT'%blasType: line = '#'+line
       for spectralOption in options.spectraloptions:
         [key,value] = re.split('[= ]',spectralOption)[0:2]
         if key == items[0]:
           line = '%s=%s\n'%(items[0],value)
           options.spectraloptions.remove(spectralOption)
-
       output.append(line)
+except IOError:
+  pass
+
+#--- write remaining options --------------------------------------------------------------------------
+for opt, value in options.__dict__.items():
+  if opt == 'compiler' and value !='':
+    output.append('F90=%s\n'%value)
+  if opt == 'fftwRoot' and value !='':
+    output.append('FFTW_ROOT=%s\n'%value)
+  if opt == 'marcRoot' and value !='':
+    output.append('MARC_ROOT=%s\n'%value)
+  if opt == 'hdf5Root' and value !='':
+    output.append('HDF5_ROOT=%s\n'%value)
+  if opt == 'threads' and value !='':
+    output.append('DAMASK_NUM_THREADS=%s\n'%value)
+  if opt == 'blasType' and value !='':
+    output.append('%s_ROOT=%s\n'%(blasType,options.blasRoot))
+
 for spectralOption in options.spectraloptions:
   output.append(spectralOption+'\n')
 
-with open('installation/options','w') as f:
+#--- decide where do save the data ----------------------------------------------------------------------
+root=os.access('/etc/', os.W_OK)
+if root:
+  configFileNew = '/etc/damask.conf'
+else:
+  configFileNew = os.path.join(os.getenv('HOME'),'.damask/damask.conf')
+  if not os.path.isdir(os.path.join(os.getenv('HOME'),'.damask')):
+    os.mkdir(os.path.join(os.getenv('HOME'),'.damask'))
+
+print('\n-----\n writing values to %s\n-----'%configFileNew)
+with open(configFileNew,'w') as f:
   for line in output:
     f.write(line)

installation/compile_CoreModule.py

@@ -32,7 +32,7 @@ compileCommand = {
 
 # see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
 if   options['IMKL_ROOT'] != '' and options['F90'] != 'gfortran':
-  lib_lapack = '-L%s/lib/intel64 -I%s/include -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -liomp5 -lm'%(options['IMKL_ROOT'],options['IMKL_ROOT'])
+  lib_lapack = '-L%s/lib/intel64 -I%s/include -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -liomp5'%(options['IMKL_ROOT'],options['IMKL_ROOT'])
 elif options['ACML_ROOT'] != '':
   lib_lapack = '-L%s/%s64/lib -lacml'%(options['ACML_ROOT'],options['F90'])
 elif options['LAPACK_ROOT'] != '':

installation/mods_MarcMentat/apply_DAMASK_modifications.sh

@@ -4,7 +4,11 @@ DEFAULT_VERSION='2013.1'
 
 WORKINGDIR="$( cd "$( dirname "$0" )" && pwd )"
 
-source $WORKINGDIR/../options
+if [ -f $HOME/.damask/damask.conf ] then
+   source $HOME/.damask/damask.conf
+else
+   source /etc/damask.conf
+fi
 
 while [ ! -d "$WORKINGDIR/$VERSION" ] || [ -z "$VERSION" ]
 do

installation/options

@@ -1,18 +0,0 @@
-# $Id: pathinfo 2176 2013-02-19 13:35:38Z MPIE\p.eisenlohr $
-# possible options are
-# IMKL_ROOT      base installation directory of Intel Math Kernel Library
-# ACML_ROOT      base installation directory of AMD Core Math Library
-# LAPAC_KROOT    base installation directory of (system) LAPACK Library
-# MSC_ROOT           base installation directory of MSC.Marc/Mentat
-# FFTW_ROOT      base installation directory of Fastest Fourier Transform in the West library
-# Do NOT add any trailing /lib/ to the end
-#  of the base installation path---this will be done automatically
-
-FFTW_ROOT=
-LAPACK_ROOT=
-ACML_ROOT=
-IMKL_ROOT=
-MSC_ROOT=
-F90=
-DAMASK_NUM_THREADS=2
-

installation/symlink_Code.py

@@ -10,14 +10,21 @@ bin_link = { \
 
 MarcReleases =[2011,2012,2013,2013.1]
 
-damaskEnv = damask.Environment('../../')          # script location relative to root
+baseDir = damask.Environment('../../').relPath('code/')
-baseDir = damaskEnv.relPath('code/')
+
+root=os.access('/usr/local/bin', os.W_OK)
+if root:
+  binDir = '/usr/local/bin'
+else:
+  binDir = os.path.join(os.getenv('HOME'),'bin')
+  if not os.path.isdir(binDir):
+    os.mkdir(binDir)
 
 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(),\
+      sym_link = os.path.abspath(os.path.join(binDir,\
                                               {True: dir,
                                                False:os.path.splitext(file)[0]}[file == '']))
       if os.path.lexists(sym_link): os.remove(sym_link)

installation/symlink_Processing.py

@@ -5,7 +5,7 @@ import os
 from damask import Environment
 
 damaskEnv = Environment()
-baseDir = damaskEnv.relPath('processing/')
+baseDir = damaskEnv.relPath('installation/')
 codeDir = damaskEnv.relPath('code/')
 
 #define ToDo list
@@ -82,13 +82,21 @@ bin_link = { \
                 ],
             }
 
+root=os.access('/usr/local/bin', os.W_OK)
+if root:
+  binDir = '/usr/local/bin'
+else:
+  binDir = os.path.join(os.getenv('HOME'),'bin')
+  if not os.path.isdir(binDir):
+    os.mkdir(binDir)
+            
 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))
+      sym_link = os.path.abspath(os.path.join(binDir,dir))
     else:
-      sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),os.path.splitext(file)[0]))
+      sym_link = os.path.abspath(os.path.join(binDir,os.path.splitext(file)[0]))
     print sym_link,'-->',src
     if os.path.lexists(sym_link):
       os.remove(sym_link)    

lib/damask/environment.py

@@ -17,21 +17,8 @@ class Environment():
     return os.path.join(self.rootDir(),relative)
 
   def rootDir(self):
-    damask_root = os.getenv('DAMASK_ROOT')
+    return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
-    if damask_root == '' or damask_root == None:            # env not set
-      if sys.argv[0] == '':                                 # no caller path
-        cwd = os.getcwd()
-      else:
-        cwd = sys.argv[0] if os.path.isdir(sys.argv[0]) else os.path.dirname(sys.argv[0])
 
-      damask_root = os.path.normpath(os.path.join(os.path.realpath(cwd),self.rootRelation))
-
-    return damask_root
-
-  def binDir(self):
-    damask_bin  = os.getenv('DAMASK_BIN')
-    if damask_bin == '' or damask_bin  == None: damask_bin = self.relPath('bin/')
-    return damask_bin
 
   def get_options(self):
     with open(self.relPath('installation/options')) as file: