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DAMASK_EICMD
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clarified fixed expression

This commit is contained in:
Martin Diehl 2016-09-16 03:23:59 +02:00
parent 1180c8bb88
commit 4a627161d5
2 changed files with 46 additions and 60 deletions
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99
DAMASK_env.zsh
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@ -1,87 +1,74 @@
# sets up an environment for DAMASK on zsh # sets up an environment for DAMASK on bash
# usage: source DAMASK_env.zsh # usage: source DAMASK_env.sh
DAMASK_ROOT=${0:a:h} if [ "$OSTYPE" = "linux-gnu" ] || [ "$OSTYPE" = 'linux' ]; then
DAMASK_ROOT=$(readlink -f "`dirname ${(%):-%N}`")
# defining set() allows to source the same file for tcsh and zsh, with and without space around = else
set() { print 'Not done yet'
export $1$2$3
}
source $DAMASK_ROOT/CONFIG
unset -f set
# add DAMASK_BIN if present but not yet in $PATH
MATCH=`echo ":$PATH:" | grep $DAMASK_BIN:`
if [[ ( "x$DAMASK_BIN" != "x" ) && ( "x$MATCH" = "x" ) ]]; then
export PATH=$DAMASK_BIN:$PATH
fi fi
[[ -f $HOME/.damask/damask.conf ]] && source $HOME/.damask/damask.conf || source /etc/damask.conf
# if DAMASK_BIN is present and not in $PATH, add it
#if [[ [[ "x$DAMASK_BIN" != "x" ]] && ! `echo ":$PATH:" | grep $DAMASK_BIN:` ]]; then
export PATH=$DAMASK_BIN:$PATH
#fi
SOLVER=`which DAMASK_spectral 2>/dev/null` SOLVER=`which DAMASK_spectral 2>/dev/null`
if [ "x$SOLVER" = "x" ]; then
export SOLVER='Not found!'
fi
PROCESSING=`which postResults 2>/dev/null` PROCESSING=`which postResults 2>/dev/null`
if [ "x$DAMASK_NUM_THREADS" = "x" ]; then if [ "x$PROCESSING" = "x" ]; then
DAMASK_NUM_THREADS=1 export PROCESSING='Not found!'
fi fi
# according to http://software.intel.com/en-us/forums/topic/501500 # according to http://software.intel.com/en-us/forums/topic/501500
# this seems to make sense for the stack size # this seems to make sense for the stack size
if [ "`which free 2>/dev/null`" != "free not found" ]; then #FREE=`which free 2>/dev/null`
freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'` #if [ "x$FREE" != "x" ]; then
# freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
# http://superuser.com/questions/220059/what-parameters-has-ulimit # heap=`expr $freeMem / 2`
ulimit -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB) # stack=`expr $freeMem / 2`
ulimit -d `expr $freeMem / 2` 2>/dev/null # maximum heap size (kB) #
fi # # http://superuser.com/questions/220059/what-parameters-has-ulimit
ulimit -v unlimited 2>/dev/null # maximum virtual memory size # ulimit -s $stack 2>/dev/null # maximum stack size (kB)
# ulimit -d $heap 2>/dev/null # maximum heap size (kB)
#fi
#ulimit -c 2000 2>/dev/null # core file size (512-byte blocks)
#ulimit -v unlimited 2>/dev/null # maximum virtual memory size
ulimit -m unlimited 2>/dev/null # maximum physical memory size ulimit -m unlimited 2>/dev/null # maximum physical memory size
# disable output in case of scp # disable output in case of scp
if [ ! -z "$PS1" ]; then if [ ! -z "$PS1" ]; then
echo echo
echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK echo Düsseldorf Advanced Materials Simulation Kit - DAMASK
echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf echo Max-Planck-Institut für Eisenforschung, Düsseldorf
echo https://damask.mpie.de echo http://damask.mpie.de
echo echo
echo "Using environment with ..." echo Using environment with ...
echo "DAMASK $DAMASK_ROOT" echo "DAMASK $DAMASK_ROOT"
echo "Spectral Solver $SOLVER" [[ "x$SOLVER" != "x" ]] && echo "Spectral Solver $SOLVER"
echo "Post Processing $PROCESSING" [[ "x$PROCESSING" != "x" ]] && echo "Post Processing $PROCESSING"
echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS" echo "Multithreading DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
if [ "x$PETSC_DIR" != "x" ]; then if [ "x$PETSC_DIR" != "x" ]; then
echo "PETSc location $PETSC_DIR" echo "PETSc location $PETSC_DIR"
[[ $(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") == $PETSC_DIR ]] \ [[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo " ~~> "`readlink -f $PETSC_DIR`
|| echo " ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR")
fi fi
[[ "x$PETSC_ARCH" == "x" ]] \ [[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
|| echo "PETSc architecture $PETSC_ARCH"
echo "MSC.Marc/Mentat $MSC_ROOT" echo "MSC.Marc/Mentat $MSC_ROOT"
echo echo
echo -n "heap size " echo -n "heap size/MiB "; echo "`ulimit -d`/1024" | bc
[[ "$(ulimit -d)" == "unlimited" ]] \ echo -n "stack size/MiB "; echo "`ulimit -s`/1024" | bc
&& echo "unlimited" \
|| echo $(python -c \
"import math; \
size=$(( 1024*$(ulimit -d) )); \
print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
echo -n "stack size "
[[ "$(ulimit -s)" == "unlimited" ]] \
&& echo "unlimited" \
|| echo $(python -c \
"import math; \
size=$(( 1024*$(ulimit -s) )); \
print('{:.4g} {}'.format(size / (1 << ((int(math.log(size,2) / 10) if size else 0) * 10)), \
['bytes','KiB','MiB','GiB','TiB','EiB','ZiB'][int(math.log(size,2) / 10) if size else 0]))")
fi fi
export DAMASK_NUM_THREADS export DAMASK_NUM_THREADS
export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do for var in BASE STAT SOLVER PROCESSING FREE; do
unset "${var}" unset "${var}"
done done
for var in DAMASK MSC; do for var in DAMASK IMKL ACML LAPACK MSC FFTW HDF5; do
unset "${var}_ROOT" unset "${var}_ROOT"
done done
for var in ABAQUS MARC; do
unset "${var}_VERSION"
done

5
processing/pre/geom_grainGrowth.py
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@ -99,15 +99,14 @@ for name in filenames:
for smoothIter in xrange(options.N): for smoothIter in xrange(options.N):
boundary = np.zeros(microstructure.shape) interfaceEnergy = np.zeros(microstructure.shape)
for i in (-1,0,1): for i in (-1,0,1):
for j in (-1,0,1): for j in (-1,0,1):
for k in (-1,0,1): for k in (-1,0,1):
# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood) # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
boundary = np.maximum(boundary, interfaceEnergy = np.maximum(interfaceEnergy,
interfacialEnergy(microstructure,np.roll(np.roll(np.roll( interfacialEnergy(microstructure,np.roll(np.roll(np.roll(
microstructure,i,axis=0), j,axis=1), k,axis=2))) microstructure,i,axis=0), j,axis=1), k,axis=2)))
interfaceEnergy = boundary
# periodically extend interfacial energy array by half a grid size in positive and negative directions # periodically extend interfacial energy array by half a grid size in positive and negative directions
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,