Merge commit 'v2.0.1-826-g347c1e3'

This commit is contained in:
Test User 2017-08-01 23:27:48 +02:00
commit 719949fb17
10 changed files with 130 additions and 227 deletions

97
DAMASK_prerequisits.sh Executable file
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@ -0,0 +1,97 @@
#!/usr/bin/env bash
OUTFILE="system_report.txt"
echo date +"%m-%d-%y" >$OUTFILE
# redirect STDOUT and STDERR to logfile
# https://stackoverflow.com/questions/11229385/redirect-all-output-in-a-bash-script-when-using-set-x^
exec > $OUTFILE 2>&1
# directory, file is not a symlink by definition
# https://stackoverflow.com/questions/59895/getting-the-source-directory-of-a-bash-script-from-within
DAMASK_ROOT="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
echo ==============================================================================================
echo DAMASK settings
echo ==============================================================================================
echo DAMASK_ROOT:
echo $DAMASK_ROOT
echo
echo Version:
cat VERSION
echo
echo Settings in CONFIG:
cat CONFIG
echo
echo ==============================================================================================
echo System
echo ==============================================================================================
uname -a
echo
echo ==============================================================================================
echo Python
echo ==============================================================================================
DEFAULT_PYTHON=python2.7
for executable in python python2 python3 python2.7; do
if [[ "$(which $executable)x" != "x" ]]; then
echo $executable version: $($executable --version 2>&1)
else
echo $executable does not exist
fi
done
echo Location of $DEFAULT_PYTHON: $(ls -la $(which $DEFAULT_PYTHON))
echo
for module in numpy scipy;do
echo ----------------------------------------------------------------------------------------------
echo $module
echo ----------------------------------------------------------------------------------------------
$DEFAULT_PYTHON -c "import $module; \
print('Version: {}'.format($module.__version__)); \
print('Location: {}'.format($module.__file__))"
done
echo ----------------------------------------------------------------------------------------------
echo vtk
echo ----------------------------------------------------------------------------------------------
$DEFAULT_PYTHON -c "import vtk; \
print('Version: {}'.format(vtk.vtkVersion.GetVTKVersion())); \
print('Location: {}'.format(vtk.__file__))"
echo ----------------------------------------------------------------------------------------------
echo h5py
echo ----------------------------------------------------------------------------------------------
$DEFAULT_PYTHON -c "import h5py; \
print('Version: {}'.format(h5py.version.version)); \
print('Location: {}'.format(h5py.__file__))"
echo
echo ==============================================================================================
echo GCC
echo ==============================================================================================
for executable in gcc g++ gfortran ;do
if [[ "$(which $executable)x" != "x" ]]; then
echo $(which $executable) version: $($executable --version 2>&1)
else
echo $executable does not exist
fi
done
echo
echo ==============================================================================================
echo Intel Compiler Suite
echo ==============================================================================================
for executable in icc icpc ifort ;do
if [[ "$(which $executable)x" != "x" ]]; then
echo $(which $executable) version: $($executable --version 2>&1)
else
echo $executable does not exist
fi
done
echo
echo ==============================================================================================
echo MPI Wrappers
echo ==============================================================================================
for executable in mpicc mpiCC mpicxx mpicxx mpifort mpif90 mpif77; do
if [[ "$(which $executable)x" != "x" ]]; then
echo $(which $executable) version: $($executable --show 2>&1)
else
echo $executable does not exist
fi
done

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@ -1 +1 @@
v2.0.1-810-g68493a0 v2.0.1-825-g734bc69

14
env/DAMASK.csh vendored
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@ -26,15 +26,11 @@ if ( "x$DAMASK_NUM_THREADS" == "x" ) then
set DAMASK_NUM_THREADS=1 set DAMASK_NUM_THREADS=1
endif endif
# according to http://software.intel.com/en-us/forums/topic/501500 # currently, there is no information that unlimited causes problems
# this seems to make sense for the stack size # still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
if ( `which free` != "free: Command not found." ) then # http://superuser.com/questions/220059/what-parameters-has-ulimit
set freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'` limit datasize unlimited # maximum heap size (kB)
set heap=` expr $freeMem / 2` limit stacksize unlimited # maximum stack size (kB)
set stack=`expr $freeMem / $DAMASK_NUM_THREADS / 2`
# http://superuser.com/questions/220059/what-parameters-has-ulimit
limit datasize $heap # maximum heap size (kB)
limit stacksize $stack # maximum stack size (kB)
endif endif
if ( `limit | grep memoryuse` != "" ) then if ( `limit | grep memoryuse` != "" ) then
limit memoryuse unlimited # maximum physical memory size limit memoryuse unlimited # maximum physical memory size

21
env/DAMASK.sh vendored
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@ -5,7 +5,6 @@ function canonicalPath {
python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $1 python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $1
} }
if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then if [ "$OSTYPE" == "linux-gnu" ] || [ "$OSTYPE" == 'linux' ]; then
DAMASK_ROOT=$(dirname $BASH_SOURCE) DAMASK_ROOT=$(dirname $BASH_SOURCE)
else else
@ -42,19 +41,13 @@ PROCESSING=$(type -p postResults || true 2>/dev/null)
[ "x$DAMASK_NUM_THREADS" == "x" ] && DAMASK_NUM_THREADS=1 [ "x$DAMASK_NUM_THREADS" == "x" ] && DAMASK_NUM_THREADS=1
# according to http://software.intel.com/en-us/forums/topic/501500 # currently, there is no information that unlimited causes problems
# this seems to make sense for the stack size # still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
FREE=$(type -p free 2>/dev/null) # http://superuser.com/questions/220059/what-parameters-has-ulimit
if [ "x$FREE" != "x" ]; then ulimit -d unlimited 2>/dev/null # maximum heap size (kB)
freeMem=$(free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}') ulimit -s unlimited 2>/dev/null # maximum stack size (kB)
# http://superuser.com/questions/220059/what-parameters-has-ulimit ulimit -v unlimited 2>/dev/null # maximum virtual memory size
ulimit -d unlimited 2>/dev/null \ ulimit -m unlimited 2>/dev/null # maximum physical memory size
|| ulimit -d $(expr $freeMem / 2) 2>/dev/null # maximum heap size (kB)
ulimit -s unlimited 2>/dev/null \
|| ulimit -s $(expr $freeMem / $DAMASK_NUM_THREADS / 2) 2>/dev/null # maximum stack size (kB)
fi
ulimit -v unlimited 2>/dev/null # maximum virtual memory size
ulimit -m unlimited 2>/dev/null # maximum physical memory size
# disable output in case of scp # disable output in case of scp
if [ ! -z "$PS1" ]; then if [ ! -z "$PS1" ]; then

36
env/DAMASK.zsh vendored
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@ -1,6 +1,10 @@
# sets up an environment for DAMASK on zsh # sets up an environment for DAMASK on zsh
# usage: source DAMASK.zsh # usage: source DAMASK.zsh
function canonicalPath {
python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $1
}
# transition compatibility (renamed $DAMASK_ROOT/DAMASK_env.zsh to $DAMASK_ROOT/env/DAMASK.zsh) # transition compatibility (renamed $DAMASK_ROOT/DAMASK_env.zsh to $DAMASK_ROOT/env/DAMASK.zsh)
if [ ${0:t:r} = 'DAMASK' ]; then if [ ${0:t:r} = 'DAMASK' ]; then
DAMASK_ROOT=${0:a:h}'/..' DAMASK_ROOT=${0:a:h}'/..'
@ -21,21 +25,21 @@ unset -f set
# add DAMASK_BIN if present # add DAMASK_BIN if present
[ "x$DAMASK_BIN" != "x" ] && PATH=$DAMASK_BIN:$PATH [ "x$DAMASK_BIN" != "x" ] && PATH=$DAMASK_BIN:$PATH
SOLVER=`which DAMASK_spectral || True 2>/dev/null` SOLVER=$(type -p DAMASK_spectral || true 2>/dev/null)
PROCESSING=`which postResults || True 2>/dev/null` [ "x$SOLVER" == "x" ] && SOLVER='Not found!'
[ "x$DAMASK_NUM_THREADS" = "x" ] && DAMASK_NUM_THREADS=1
# according to http://software.intel.com/en-us/forums/topic/501500 PROCESSING=$(type -p postResults || true 2>/dev/null)
# this seems to make sense for the stack size [ "x$PROCESSING" == "x" ] && PROCESSING='Not found!'
if [ "`which free 2>/dev/null`" != "free not found" ]; then
freeMem=`free -k | grep -E '(Mem|Speicher):' | awk '{print $4;}'`
# http://superuser.com/questions/220059/what-parameters-has-ulimit [ "x$DAMASK_NUM_THREADS" == "x" ] && DAMASK_NUM_THREADS=1
#ulimit -d `expr $freeMem / 2` 2>/dev/null # maximum heap size (kB)
ulimit -s `expr $freeMem / $DAMASK_NUM_THREADS / 2` 2>/dev/null # maximum stack size (kB) # currently, there is no information that unlimited causes problems
fi # still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
ulimit -v unlimited 2>/dev/null # maximum virtual memory size # http://superuser.com/questions/220059/what-parameters-has-ulimit
ulimit -m unlimited 2>/dev/null # maximum physical memory size ulimit -d unlimited 2>/dev/null # maximum heap size (kB)
ulimit -s unlimited 2>/dev/null # maximum stack size (kB)
ulimit -v unlimited 2>/dev/null # maximum virtual memory size
ulimit -m unlimited 2>/dev/null # maximum physical memory size
# disable output in case of scp # disable output in case of scp
if [ ! -z "$PS1" ]; then if [ ! -z "$PS1" ]; then
@ -51,8 +55,8 @@ if [ ! -z "$PS1" ]; then
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 ]] \ [[ $(canonicalPath "$PETSC_DIR") == $PETSC_DIR ]] \
|| echo " ~~> "$(python -c "import os,sys; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" "$PETSC_DIR") || echo " ~~> "$(canonicalPath "$PETSC_DIR")
fi fi
[[ "x$PETSC_ARCH" == "x" ]] \ [[ "x$PETSC_ARCH" == "x" ]] \
|| echo "PETSc architecture $PETSC_ARCH" || echo "PETSc architecture $PETSC_ARCH"
@ -79,7 +83,7 @@ fi
export DAMASK_NUM_THREADS export DAMASK_NUM_THREADS
export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH export PYTHONPATH=$DAMASK_ROOT/lib:$PYTHONPATH
for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN MATCH; do for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN; do
unset "${var}" unset "${var}"
done done
for var in DAMASK MSC; do for var in DAMASK MSC; do

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@ -1,177 +0,0 @@
#
# System-Wide Abaqus Environment File
# -------------------------------------
standard_parallel = ALL
mp_mode = MPI
mp_file_system = (DETECT,DETECT)
mp_num_parallel_ftps = (4, 4)
mp_environment_export = ('MPI_PROPAGATE_TSTP',
'ABA_CM_BUFFERING',
'ABA_CM_BUFFERING_LIMIT',
'ABA_ITERATIVE_SOLVER_VERBOSE',
'ABA_DMPSOLVER_BWDPARALLELOFF',
'ABA_ELP_SURFACE_SPLIT',
'ABA_ELP_SUSPEND',
'ABA_HOME',
'ABA_MEMORY_MODE',
'ABA_MPI_MESSAGE_TRACKING',
'ABA_MPI_VERBOSE_LEVEL',
'ABA_PATH',
'ABAQUS_CSE_RELTIMETOLERANCE',
'ABA_RESOURCE_MONITOR',
'ABA_RESOURCE_USEMALLINFO',
'ABAQUS_LANG',
'ABAQUS_CSE_CURRCONFIGMAPPING',
'ABAQUS_MPF_DIAGNOSTIC_LEVEL',
'ABAQUSLM_LICENSE_FILE',
'ABQ_CRTMALLOC',
'ABQ_DATACHECK',
'ABQ_RECOVER',
'ABQ_RESTART',
'ABQ_SPLITFILE',
'ABQ_XPL_WINDOWDUMP',
'ABQ_XPL_PARTITIONSIZE',
'ABQLMHANGLIMIT',
'ABQLMQUEUE',
'ABQLMUSER',
'CCI_RENDEZVOUS',
'DOMAIN',
'DOMAIN_CPUS',
'DOUBLE_PRECISION',
'FLEXLM_DIAGNOSTICS',
'FOR0006',
'FOR0064',
'FOR_IGNORE_EXCEPTIONS',
'FOR_DISABLE_DIAGNOSTIC_DISPLAY',
'LD_PRELOAD',
'MP_NUMBER_OF_THREADS',
'MPC_GANG',
'MPI_FLAGS',
'MPI_FLUSH_FCACHE',
'MPI_RDMA_NENVELOPE',
'MPI_SOCKBUFSIZE',
'MPI_USE_MALLOPT_MMAP_MAX',
'MPI_USE_MALLOPT_MMAP_THRESHOLD',
'MPI_USE_MALLOPT_SBRK_PROTECTION',
'MPI_WORKDIR',
'MPCCI_DEBUG',
'MPCCI_CODEID',
'MPCCI_JOBID',
'MPCCI_NETDEVICE',
'MPCCI_TINFO',
'MPCCI_SERVER',
'ABAQUS_CCI_DEBUG',
'NCPUS',
'OMP_DYNAMIC',
'OMP_NUM_THREADS',
'OUTDIR',
'PAIDUP',
'PARALLEL_METHOD',
'RAIDEV_NDREG_LAZYMEM',
'ABA_SYMBOLIC_GENERALCOLLAPSE',
'ABA_SYMBOLIC_GENERAL_MAXCLIQUERANK',
'ABA_ADM_MINIMUMINCREASE',
'ABA_ADM_MINIMUMDECREASE',
'IPATH_NO_CPUAFFINITY',
'MALLOC_MMAP_THRESHOLD_',
'ABA_EXT_SIMOUTPUT',
'SMA_WS',
'SMA_PARENT',
'SMA_PLATFORM',
'ABA_PRE_DECOMPOSITION',
'ACML_FAST_MALLOC',
'ACML_FAST_MALLOC_CHUNK_SIZE',
'ACML_FAST_MALLOC_MAX_CHUNKS',
'ACML_FAST_MALLOC_DEBUG')
import driverUtils, os
#-*- mode: python -*-
# #
# Compile and Link command settings for the Windows 64 Platform #
# ( AMD Opteron / Intel EM64T ) #
# #
compile_fortran=['ifort',
'/c','/DABQ_WIN86_64', '/u',
'/iface:cref', '/recursive', '/Qauto-scalar',
'/QxSSE3', '/QaxAVX',
'/heap-arrays:1',
# '/Od', '/Ob0' # <-- Optimization
# '/Zi', # <-- Debugging
'/include:%I', '/free', '/O1', '/fpp', '/openmp', '/Qmkl']
link_sl=['LINK',
'/nologo', '/NOENTRY', '/INCREMENTAL:NO', '/subsystem:console', '/machine:AMD64',
'/NODEFAULTLIB:LIBC.LIB', '/NODEFAULTLIB:LIBCMT.LIB',
'/DEFAULTLIB:OLDNAMES.LIB', '/DEFAULTLIB:LIBIFCOREMD.LIB', '/DEFAULTLIB:LIBIFPORTMD', '/DEFAULTLIB:LIBMMD.LIB',
'/DEFAULTLIB:kernel32.lib', '/DEFAULTLIB:user32.lib', '/DEFAULTLIB:advapi32.lib',
'/FIXED:NO', '/dll',
'/def:%E', '/out:%U', '%F', '%A', '%L', '%B',
'oldnames.lib', 'user32.lib', 'ws2_32.lib', 'netapi32.lib', 'advapi32.lib']
link_exe=['LINK',
'/nologo', '/INCREMENTAL:NO', '/subsystem:console', '/machine:AMD64', '/STACK:20000000',
'/NODEFAULTLIB:LIBC.LIB', '/NODEFAULTLIB:LIBCMT.LIB', '/DEFAULTLIB:OLDNAMES.LIB', '/DEFAULTLIB:LIBIFCOREMD.LIB',
'/DEFAULTLIB:LIBIFPORTMD', '/DEFAULTLIB:LIBMMD.LIB', '/DEFAULTLIB:kernel32.lib',
'/DEFAULTLIB:user32.lib', '/DEFAULTLIB:advapi32.lib',
'/FIXED:NO', '/LARGEADDRESSAWARE',
'/out:%J', '%F', '%M', '%L', '%B', '%O',
'oldnames.lib', 'user32.lib', 'ws2_32.lib', 'netapi32.lib', 'advapi32.lib']
# Link command to be used for MAKE w/o fortran compiler.
# remove the pound signs in order to remove the comments and have the file take effect.
#
#link_exe=['LINK', '/nologo', 'INCREMENTAL:NO', '/subsystem:console', '/machine:AMD64', '/NODEFAULTLIB:LIBC.LIB', '/NODEFAULTLIB:LIBCMT.LIB',
# '/DEFAULTLIB:OLDNAMES.LIB', '/DEFAULTLIB:MSVCRT.LIB', '/DEFAULTLIB:kernel32.lib', 'DEFAULTLIB:user32.lib', '/DEFAULTLIB:advapi32.lib',
# '/FIXED:NO', '/LARGEADDRESSAWARE', '/DEBUG', '/out:%J', '%F', '%M', '%L', '%B', '%O', 'oldnames.lib', 'user32.lib', 'ws2_32.lib',
# 'netapi32.lib', 'advapi32.lib]
# MPI Configuration
mp_mode = THREADS
mp_mpi_implementation = NATIVE
mp_rsh_command = 'dummy %H -l %U -n %C'
mp_mpirun_path = {}
mpirun = ''
progDir = os.environ.get('ProgramFiles','C:\\Program Files')
for mpiDir in ('Microsoft HPC Pack', 'Microsoft HPC Pack 2008 R2', 'Microsoft HPC Pack 2008', 'Microsoft HPC Pack 2008 SDK'):
mpirun = progDir + os.sep + mpiDir + os.sep + 'bin' + os.sep + 'mpiexec.exe'
if os.path.exists(mpirun):
mp_mpirun_path[NATIVE] = mpirun
mp_mpirun_path[MSSDK] = os.path.join(progDir, mpiDir)
break
if os.environ.has_key('CCP_HOME'):
from queueCCS import QueueCCS
queues['default'] = QueueCCS(queueName='share')
queues['share'] = QueueCCS(queueName='share')
queues['local'] = QueueCCS(queueName='local')
queues['genxmlshare'] = QueueCCS(queueName='genxmlshare')
queues['genxmllocal'] = QueueCCS(queueName='genxmllocal')
del QueueCCS
mpirun = os.path.join(os.environ['CCP_HOME'], 'bin', 'mpiexec.exe')
if os.path.exists(mpirun):
mp_mpirun_path[NATIVE] = mpirun
run_mode=BATCH
if mp_mpirun_path:
mp_mode=MPI
del progDir, mpiDir, mpirun
graphicsEnv = driverUtils.locateFile(os.environ['ABA_PATH'],'site','graphicsConfig','env')
if graphicsEnv:
execfile(graphicsEnv)
else:
raise 'Cannot find the graphics configuration environment file (graphicsConfig.env)'
del driverUtils, os, graphicsEnv
license_server_type=FLEXNET
abaquslm_license_file=""
doc_root="
doc_root_type="html"
academic=RESEARCH

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@ -14,12 +14,6 @@ except(NameError):
class ASCIItable(): class ASCIItable():
"""Read and write to ASCII tables""" """Read and write to ASCII tables"""
__slots__ = ['__IO__',
'info',
'labeled',
'data',
]
tmpext = '_tmp' # filename extension for in-place access tmpext = '_tmp' # filename extension for in-place access
# ------------------------------------------------------------------ # ------------------------------------------------------------------

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@ -101,8 +101,6 @@ class Texture(Section):
class Material(): class Material():
"""Reads, manipulates and writes material.config files""" """Reads, manipulates and writes material.config files"""
__slots__ = ['data']
def __init__(self,verbose=True): def __init__(self,verbose=True):
"""Generates ordered list of parts""" """Generates ordered list of parts"""
self.parts = [ self.parts = [

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@ -61,7 +61,6 @@ for name in filenames:
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
table.data_readArray(options.pos) table.data_readArray(options.pos)
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data.shape[1] < 3: if table.data.shape[1] < 3:
table.data = np.hstack((table.data, table.data = np.hstack((table.data,
np.zeros((table.data.shape[0], np.zeros((table.data.shape[0],

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@ -70,7 +70,6 @@ for name in filenames:
# --------------- figure out size and grid --------------------------------------------------------- # --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray(options.pos) table.data_readArray(options.pos)
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data.shape[1] < 3: if table.data.shape[1] < 3:
table.data = np.hstack((table.data, table.data = np.hstack((table.data,
np.zeros((table.data.shape[0], np.zeros((table.data.shape[0],