fixed DAMASK_env.sh to work with linux and Mac, started to reorganize installation to be consistent for all solvers
This commit is contained in:
Martin Diehl
parent
2ba3c11879
commit
e025ac5952
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@ -1,9 +1,32 @@
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# sets up an environment for DAMASK on bash
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# usage: source DAMASK_env.sh
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STAT=$(stat "`dirname $BASH_SOURCE`")
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LOCATION=${STAT##* }
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FFTWROOT=/usr/local
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LAPACKROOT=/usr
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ACMLROOT=
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IMKLROOT=
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if [ "$OSTYPE" == "linux-gnu" ]
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then LOCATION=$(readlink -f "`dirname $BASH_SOURCE`")
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else
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STAT=$(stat "`dirname $BASH_SOURCE`")
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LOCATION=${STAT##* }
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fi
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export DAMASK_ROOT=${LOCATION}
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export DAMASK_NUM_THREADS=2
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export FFTWROOT=${FFTWROOT}
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LD_NEW=$FFTWROOT/lib
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if [ "x$LAPACKROOT" != "x" ]
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then export LAPACKROOT=$LAPACKROOT
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LD_NEW=$LD_NEW:$LAPACKROOT/lib:$LAPACKROOT/lib64
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fi
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if [ "x$ACMLROOT" != "x" ]
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then export ACMLROOT=$ACMLROOT
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LD_NEW=$LD_NEW:$ACMLROOT/ifort64_mp/lib:$ACMLROOT/ifort64/lib:$ACMLROOT/gfortran64_mp/lib:$ACMLROOT/gfortran64/lib
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fi
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if [ "x$IMKLROOT" != "x" ]
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then export IMKLROOT=${IMKLROOT}
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fi
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# disable output in case of scp
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if [ ! -z "$PS1" ]; then
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echo
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@ -14,12 +37,13 @@ if [ ! -z "$PS1" ]; then
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echo Preparing environment ...
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echo "DAMASK_ROOT=$DAMASK_ROOT"
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echo "DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
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echo "prepending to LD_LIBRARY_PATH: $LD_NEW"
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fi
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ulimit -s unlimited
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ulimit -c 0
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ulimit -v unlimited
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ulimit -m unlimited
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export DAMASK_BIN=${DAMASK_ROOT}/bin
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export PATH=${PATH}:${DAMASK_BIN}
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export PYTHONPATH=${PYTHONPATH}:${DAMASK_ROOT}/lib
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
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export DAMASK_BIN=$DAMASK_ROOT/bin
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export PATH=$PATH:$DAMASK_BIN
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export PYTHONPATH=$PYTHONPATH:$DAMASK_ROOT/lib
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export LD_LIBRARY_PATH=$LD_NEW:$LD_LIBRARY_PATH
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@ -0,0 +1,31 @@
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SHELL = /bin/sh
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########################################################################################
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# Makefile for the installation of DAMASK
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########################################################################################
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.PHONY : spectral
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spectral:
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@$(MAKE) clean -C code >/dev/null
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$(MAKE) -C code
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.PHONY : marc
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marc:
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@./installation/mods_Marc/apply_DAMASK_modifcation.py
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.PHONY : processing
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processing:
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@$(MAKE) tidy -C code >/dev/null
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@./installation/compile_CoreModule.py
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.PHONY : tidy
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tidy:
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@$(MAKE) tidy -C code >/dev/null
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.PHONY : clean
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clean:
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@$(MAKE) clean -C code >/dev/null
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.PHONY : install
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install:
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@./installation/symlink_Code.py
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@./installation/symlink_Processing.py
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@ -0,0 +1,18 @@
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#!/usr/bin/env python
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import os,re,subprocess,sys
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import damask
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damaskEnv = damask.Environment() # script location relative to root
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baseDir = damaskEnv.relPath('code/')
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# basic idea: try to get the specific locations from:
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# 1) command line option
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# 2) envinronment variable
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# 3) for F90: autodetect
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# then call the respective scripts with their options
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# changing dirs and compiler in makefile
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compiler ={True:'ifort',False:'gfortran'}[\
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subprocess.call(['which', 'ifort'],\
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stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0]
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@ -0,0 +1,126 @@
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#!/usr/bin/env python
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# Makes postprocessing routines acessible from everywhere.
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import os,sys,glob,string,subprocess
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from damask import Environment
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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########################################################
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# MAIN
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########################################################
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parser = OptionParser(option_class=extendableOption, usage='%prog options', description = """
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Sets up the pre and post processing tools of DAMASK
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""" + string.replace('$Id$','\n','\\n')
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)
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compilers = ['ifort','gfortran']
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parser.add_option('F90', dest='compiler', type='string', \
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help='name of F90 [%default]')
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parser.add_option('LAPACKROOT', dest='lapackroot', type='string', \
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help='name of F90 [%default]')
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parser.add_option('ACMLROOT', dest='acmlroot', type='string', \
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help='name of F90 [%default]')
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parser.add_option('IMKLROOT', dest='imklroot', type='string', \
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help='name of F90 [%default]')
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parser.add_option('FFTWROOT', dest='fftwroot', type='string', \
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help='name of F90 [%default]')
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(options,filenames) = parser.parse_args()
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if options.compiler not in compilers:
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parser.error('compiler switch "F90" has to be one out of: %s'%(', '.join(compilers)))
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f2py_compiler = {
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'gfortran': 'gnu95 --f90flags="-fPIC -fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics -DSpectral -fdefault-real-8 -fdefault-double-8 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
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'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"',
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}[options.compiler]
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damaskEnv = Environment()
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baseDir = damaskEnv.relPath('installation/')
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codeDir = damaskEnv.relPath('code/')
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if options.imklroot= '' and options.compiler != 'gfortran':
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lib_lapack = '-L%s/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -liomp5 -lpthread -lm'%(options.imklroot)
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elif options.acmlroot= '':
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lib_lapack = '-L%s/%s64/lib -lacml'%(options.acmlroot,compiler)
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elif options.lapackroot != '':
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lib_lapack = '-L%s -llapack'%(options.lapack) # see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
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execute = { \
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'coreModule' : [
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'make tidy',
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# The following command is used to compile the fortran files and make the functions defined
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# in damask.core.pyf available for python in the module core.so
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# It uses the fortran wrapper f2py that is included in the numpy package to construct the
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# module core.so out of the fortran code in the f90 files
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# For the generation of the pyf file use the following lines:
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###########################################################################
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#'f2py -h damask.core.pyf' +\
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#' --overwrite-signature --no-lower prec.f90 DAMASK_spectral_interface.f90 math.f90 mesh.f90',
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###########################################################################
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'rm `readlink -f %s`' %(os.path.join(damaskEnv.relPath('lib/damask'),'core.so')),
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'f2py damask.core.pyf' +\
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' --build-dir ./' +\
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' -c --no-lower --fcompiler=%s'%(f2py_compiler) +\
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' %s'%'prec.f90'+\
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' %s'%'DAMASK_spectral_interface.f90'+\
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' %s'%'IO.f90'+\
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' %s'%'libs.f90'+\
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' %s'%'numerics.f90'+\
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' %s'%'debug.f90'+\
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' %s'%'math.f90'+\
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' %s'%'FEsolving.f90'+\
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' %s'%'mesh.f90'+\
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' %s'%'core_quit.f90'+\
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' -L%s/lib -lfftw3'%(options.fftwroot)+\
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' %s'%lib_lapack,
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'mv %s `readlink -f %s`' %(os.path.join(codeDir,'core.so'),os.path.join(damaskEnv.relPath('lib/damask'),'core.so')),
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]
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}
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os.chdir(codeDir) # needed for compilation with gfortran and f2py
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for tasks in execute:
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for cmd in execute[tasks]:
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try:
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print 'executing...:',cmd
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os.system(cmd)
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except:
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print 'failed..!'
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pass
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modules = glob.glob('*.mod')
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for module in modules:
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print 'removing', module
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os.remove(module)
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#check if compilation of core module was successful
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try:
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with open(damaskEnv.relPath('lib/damask/core.so')) as f: pass
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except IOError as e:
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print '*********\n* core.so not found, compilation of core modules was not successful\n*********'
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sys.exit()
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f.close
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@ -0,0 +1,34 @@
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#!/usr/bin/env python
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import os
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import damask
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bin_link = { \
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'.' : [
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'DAMASK_spectral.exe',
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],
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}
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MarcReleases =[2011,2012,2013,2013.1]
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damaskEnv = damask.Environment('../../') # script location relative to root
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baseDir = damaskEnv.relPath('code/')
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for dir in bin_link:
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for file in bin_link[dir]:
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src = os.path.abspath(os.path.join(baseDir,dir,file))
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if os.path.exists(src):
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sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),\
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{True: dir,
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False:os.path.splitext(file)[0]}[file == '']))
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if os.path.lexists(sym_link): os.remove(sym_link)
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os.symlink(src,sym_link)
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print sym_link,'-->',src
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for version in MarcReleases:
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src = os.path.abspath(os.path.join(baseDir,'DAMASK_marc.f90'))
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if os.path.exists(src):
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sym_link = os.path.abspath(os.path.join(baseDir,'DAMASK_marc'+str(version)+'.f90'))
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if os.path.lexists(sym_link): os.remove(sym_link)
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os.symlink(src,sym_link)
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print sym_link,'-->',src
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@ -0,0 +1,97 @@
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#!/usr/bin/env python
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# Makes postprocessing routines acessible from everywhere.
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import os
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from damask import Environment
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damaskEnv = Environment()
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baseDir = damaskEnv.relPath('processing/')
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codeDir = damaskEnv.relPath('code/')
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#define ToDo list
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bin_link = { \
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'pre' : [
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'marc_addUserOutput.py',
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'mentat_pbcOnBoxMesh.py',
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'mentat_spectralBox.py',
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'OIMang_hex2cub.py',
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'patchFromReconstructedBoundaries.py',
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'randomSeeding.py',
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'seed_check.py',
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'geom_fromAng.py',
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'geom_fromVPSC.py',
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'geom_fromEuclideanDistance.py',
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'geom_fromMinimalSurface.py',
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'geom_fromVoronoiTessellation.py',
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'geom_fromOsteonGeometry.py',
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'geom_canvas.py',
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'geom_check.py',
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'geom_rescale.py',
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'geom_pack.py',
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'geom_unpack.py',
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'geom_translate.py',
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'geom_vicinityOffset.py',
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'geom_grainGrowth.py',
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'geom_poke.py',
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],
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'post' : [
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'3Dvisualize.py',
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'permuteData.py',
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'addCalculation.py',
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'addCauchy.py',
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'addCompatibilityMismatch.py',
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'addCurl.py',
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'addDeformedConfiguration.py',
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'addDeterminant.py',
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'addDeviator.py',
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'addDivergence.py',
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'addEhkl.py',
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'addEuclideanDistance.py',
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'addGrainID.py',
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'addMises.py',
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'addNorm.py',
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'addOrientations.py',
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'addIPFcolor.py',
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'addPK2.py',
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'addSchmidfactors.py',
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'addSpectralDecomposition.py',
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'addStrainTensors.py',
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'averageDown.py',
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'binXY.py',
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'blowUp.py',
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'stddevDown.py',
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'deleteColumn.py',
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'deleteInfo.py',
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'filterTable.py',
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'sortTable.py',
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'marc_deformedGeometry.py',
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'marc_extractData.py',
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'mentat_colorMap.py',
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'nodesFromCentroids.py',
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'perceptualUniformColorMap.py',
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'postResults.py',
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'showTable.py',
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'tagLabel.py',
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'vtk2ang.py',
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'vtk_addData.py',
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'vtk_pointcloud.py',
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'vtk_addPointcloudData.py',
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'vtk_voxelcloud.py',
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'vtk_addVoxelcloudData.py',
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],
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}
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for dir in bin_link:
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for file in bin_link[dir]:
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src = os.path.abspath(os.path.join(baseDir,dir,file))
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if (file == ''):
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sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),dir))
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else:
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sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),os.path.splitext(file)[0]))
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print sym_link,'-->',src
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if os.path.lexists(sym_link):
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os.remove(sym_link)
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os.symlink(src,sym_link)
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