def try_io_operation(io_fn):
if cfg.options.on_io_error in [1, 2]:
max_tries = 100
else:
max_tries = 0
wait_time = 6
tries = 0
done = False
while not done:
try:
io_fn()
break
except RuntimeError: # e.g., generated by C++ code
tries += 1
if tries > max_tries:
logger.error("I/O operation failed, giving up after %s tries.",
max_tries)
raise
logger.warn(
"I/O operation failed, retrying in %s seconds. (Tries left: %s)",
wait_time, max_tries - tries)
time.sleep(wait_time)
except: # any other exception bails out
raise
def create_controller(run, params, *args, **kwargs):
"""
Create a controller object, depending on the environment in which the script was executed:
TODO: Explain.
"""
# Case 1: Report to stdout, then exit, if requested by command line options.
print_num_params = cfg.options.print_num_params_requested
print_all_params = cfg.options.print_all_params_requested
if print_num_params or print_all_params:
return PrintParametersController(run, params, print_num_params, print_all_params, *args, **kwargs)
# Case 2: Use environment variable to select parameter set
env = kwargs.pop("env", None)
env_offset = kwargs.pop("env_offset", 0)
if env:
if env in os.environ:
return EnvironmentVariableController(run, params, env, env_offset, *args, **kwargs)
else:
logger.warn("Environment variable '%s' not found, ignoring 'env' parameter in controller creation" % env)
# Case 3: Sun grid engine controller
sge = kwargs.pop("sun_grid_engine", False)
if sge:
if "SGE_TASK_ID" in os.environ:
return SunGridEngineController(run, params, *args, **kwargs)
else:
logger.warn("Environment variable 'SGE_TASK_ID' not found, ignoring 'sun_grid_engine' parameter in controller creation")
# Case 4: This controller is used when the script was executed locally. It optionally uses the -p argument passed to the sim script.
return LocalController(run, params, *args, **kwargs)
def cpu_count():
try:
import multiprocessing
return multiprocessing.cpu_count()
except:
from magnum.logger import logger
logger.warn("Could not find out number of processors")
return 1
def cpu_count():
try:
import multiprocessing
return multiprocessing.cpu_count()
except:
from magnum.logger import logger
logger.warn("Could not find out number of processors")
return 1
def assign_VectorField(field, val, mask):
mesh = field.mesh
# initialize from lambda?
from_lambda = hasattr(val, "__call__")
# initialize from other VectorField ???
from_field = isinstance(val, VectorField)
# initialize from a numerical value?
from_value = not from_lambda and not from_field and isinstance(
val, tuple) and len(val) == 3
# fill entire field?
fill_everywhere = (mask is None) or (len(mask) == mesh.total_nodes)
# Do the initialization (modify field)
if from_value:
if fill_everywhere:
# Fill complete field with a single value
field.fill(val)
else:
# Masked fill with a single value
for c in mask:
field.set(c, val)
elif from_field:
src_field = val
# Automatic field interpolation if meshes do not match.
# XXX Is this a good idea?
if not field.mesh.isCompatible(src_field.mesh):
src_field = src_field.interpolate(field.mesh)
logger.warn(
"Field initialized by linear interpolation of other field (their meshes were different sizes!)"
)
if fill_everywhere:
# Fill field by copying values from init field
field.assign(src_field)
else:
# Fill some parts of the field using values from field
for c in mask:
field.set(c, src_field.get(c))
elif from_lambda:
fn = val
# Fill some parts of the field using an initialization function
for c in mask or range(mesh.total_nodes):
field.set(c, fn(field, mesh.getPosition(c)))
else:
raise ValueError(
"Don't know how to assign to vector field using the expression %s"
% val)
return field
def __init__(self, run, params, env, offset=0, *args, **kwargs):
super(EnvironmentVariableController, self).__init__(run, params, *args, **kwargs)
try:
task_id = int(os.environ[env]) - offset
except:
logger.error("Could not read environment variable '%s'." % env)
raise
if task_id >= len(self.all_params):
logger.warn("SGE task id is greater than the number of parameter sets.")
self.my_params = []
else:
self.my_params = [(task_id, self.all_params[task_id])]
def __init__(self, run, params, env, offset=0, *args, **kwargs):
super(EnvironmentVariableController,
self).__init__(run, params, *args, **kwargs)
try:
task_id = int(os.environ[env]) - offset
except:
logger.error("Could not read environment variable '%s'." % env)
raise
if task_id >= len(self.all_params):
logger.warn(
"SGE task id is greater than the number of parameter sets.")
self.my_params = []
else:
self.my_params = [(task_id, self.all_params[task_id])]
def assign_VectorField(field, val, mask):
mesh = field.mesh
# initialize from lambda?
from_lambda = hasattr(val, "__call__")
# initialize from other VectorField ???
from_field = isinstance(val, VectorField)
# initialize from a numerical value?
from_value = not from_lambda and not from_field and isinstance(val, tuple) and len(val) == 3
# fill entire field?
fill_everywhere = (mask is None) or (len(mask) == mesh.total_nodes)
# Do the initialization (modify field)
if from_value:
if fill_everywhere:
# Fill complete field with a single value
field.fill(val)
else:
# Masked fill with a single value
for c in mask: field.set(c, val)
elif from_field:
src_field = val
# Automatic field interpolation if meshes do not match.
# XXX Is this a good idea?
if not field.mesh.isCompatible(src_field.mesh):
src_field = src_field.interpolate(field.mesh)
logger.warn("Field initialized by linear interpolation of other field (their meshes were different sizes!)")
if fill_everywhere:
# Fill field by copying values from init field
field.assign(src_field)
else:
# Fill some parts of the field using values from field
for c in mask: field.set(c, src_field.get(c))
elif from_lambda:
fn = val
# Fill some parts of the field using an initialization function
for c in mask or range(mesh.total_nodes):
field.set(c, fn(field, mesh.getPosition(c)))
else:
raise ValueError("Don't know how to assign to vector field using the expression %s" % val)
return field
def __init__(self, run, params, **options):
ControllerBase.__init__(self, run, params)
if hasattr(cfg.options, 'prange'):
prange = cfg.options.prange
else:
prange = range(len(self.getAllParameters()))
self.__prange = []
for i in prange:
if i < len(self.getAllParameters()):
self.__prange.append(i)
else:
logger.warn("Ignoring parameter id %s (no such parameter set!)" % i)
if len(self.__prange) == 0:
logger.warn("Controller: No parameter sets selected!")
def __init__(self, run, params, *args, **kwargs):
super(LocalController, self).__init__(run, params, *args, **kwargs)
if hasattr(cfg.options, 'prange'):
prange = cfg.options.prange
else:
prange = range(self.num_params)
self.my_params = []
for i in prange:
if i < self.num_params:
self.my_params.append((i, self.all_params[i]))
else:
logger.warn("Ignoring parameter id %s (no such parameter set!)" % i)
if len(self.my_params) == 0:
logger.warn("Controller: No parameter sets selected!")
def __init__(self, run, params, *args, **kwargs):
super(LocalController, self).__init__(run, params, *args, **kwargs)
if hasattr(cfg.options, 'prange'):
prange = cfg.options.prange
else:
prange = range(self.num_params)
self.my_params = []
for i in prange:
if i < self.num_params:
self.my_params.append((i, self.all_params[i]))
else:
logger.warn(
"Ignoring parameter id %s (no such parameter set!)" % i)
if len(self.my_params) == 0:
logger.warn("Controller: No parameter sets selected!")
def try_io_operation(io_fn):
if cfg.options.on_io_error in [1, 2]:
max_tries = 100
else:
max_tries = 0
wait_time = 6
tries = 0
done = False
while not done:
try:
io_fn()
break
except RuntimeError: # e.g., generated by C++ code
tries += 1
if tries > max_tries:
logger.error("I/O operation failed, giving up after %s tries.", max_tries)
raise
logger.warn("I/O operation failed, retrying in %s seconds. (Tries left: %s)", wait_time, max_tries - tries)
time.sleep(wait_time)
except: # any other exception is an immediate error
raise
def createImage(*args, **kwargs):
logger.warn(_msg)
def parseCommandLine(self, argv):
from optparse import OptionParser, OptionValueError, OptionGroup
parser = OptionParser(version="MagNum v.0.1")
hw_group = OptionGroup(parser,
"Hardware options",
"Options that control which hardware is used.",
)
hw_group.add_option("-g",
type = "string",
help = "enable GPU processing (using 32-bit accuracy) on cuda device GPU_ID. The simulator will fall back to CPU mode if it was not compiled with CUDA support or when no CUDA capable graphics cards were detected.",
metavar = "GPU_ID",
dest = "gpu32",
default = None
)
hw_group.add_option("-G",
type = "string",
help = "enable GPU processing (using 64-bit accuracy) on cuda device GPU_ID. TODO: Describe fallback behaviour.",
metavar = "GPU_ID",
dest = "gpu64",
default = None
)
hw_group.add_option("-t", "--threads",
help = "enable CPU multithreading with NUM_THREADS (1..64) threads. This parameter instructs the fftw library to use NUM_THREADS threads for computing FFTs.",
metavar = "NUM_THREADS",
dest = "num_fftw_threads",
type = "int",
default = 1
)
#hw_group.add_option("-f", "--fftw-mode",
# help = "set fftw plan creation mode (0:Estimate, 1:Measure, 2:Exhaustive), default is Measure (1).",
# dest = "fftw_plan",
# default = 1,
# type = "int",
# metavar = "FFTW_MODE"
#)
parser.add_option_group(hw_group)
log_group = OptionGroup(parser,
"Logging options",
"Options related to logging and benchmarking."
)
log_group.add_option("--loglevel", "-l",
type = "int",
help = "set log level (0:Debug, 1:Info, 2:Warn, 4:Error, 5:Critical), default is Debug (0).",
metavar = "LEVEL",
dest = "loglevel",
default = 1
)
log_group.add_option("--prof",
help = "Log profiling info at program exit.",
dest = "profiling_enabled",
action = "store_true",
default = False
)
parser.add_option_group(log_group)
def prange_callback(option, opt_str, value, parser, *args, **kwargs):
# e.g.: ./script.py --prange=0,64 -> xrange(0,64) object
match = re.match("^(\d+),(\d+)$", value)
if match:
p0, p1 = int(match.group(1)), int(match.group(2))
else:
match = re.match("^(\d+)$", value)
if match:
p0 = int(match.group(1))
p1 = p0 + 1
else:
raise OptionValueError("Invalid --prange format.")
if not p0 < p1:
raise OptionValueError("Invalid --prange specified: second value must be greater than first value")
setattr(parser.values, "prange", range(p0, p1))
ctrl_group = OptionGroup(parser,
"Parameter sweep options",
"These options have only an effect when the simulation script uses a Controller object to sweep through a parameter range."
)
ctrl_group.add_option("--param-range", "-p",
type = "string",
help = "set parameter range to run, e.g. --prange=0,64. ",
metavar = "RANGE",
action = "callback",
callback= prange_callback,
default = None
)
ctrl_group.add_option("--print-num-params",
help = "print number of sweep parameters to stdout and exit.",
action = "store_true",
dest = "print_num_params_requested",
default = False
)
ctrl_group.add_option("--print-all-params",
action = "store_true",
help = "print all sweep parameters to stdout and exit.",
dest = "print_all_params_requested",
default = False,
)
parser.add_option_group(ctrl_group)
misc_group = OptionGroup(parser,
"Miscellanous options"
)
misc_group.add_option("--on_io_error",
type = "int",
help = "Specifies what to do when an i/o error occurs when writing an .omf/.vtk file. 0: Abort (default), 1: Retry a few times, then abort, 2: Retry a few times, then pause and ask for user intervention",
metavar = "MODE",
dest = "on_io_error",
default = 0
)
parser.add_option_group(misc_group)
options, rest_args = parser.parse_args(argv)
self.options = options
### Process the options ###
# --loglevel, -l
import logging
ll_map = [logging.DEBUG, logging.INFO, logging.WARN, logging.ERROR, logging.CRITICAL]
logger.setLevel(ll_map[options.loglevel])
logger.info("MicroMagnum 0.2 Copyright (C) 2012 by the MicroMagnum team.")
logger.info("This program comes with ABSOLUTELY NO WARRANTY.")
logger.info("This is free software, and you are welcome to redistribute it")
logger.info("under certain conditions; see the file COPYING in the distribution package.")
logger.info("----------")
# -g, -G
def parse_gpu_id(arg):
if arg == "auto": return -1
return int(arg)
cuda_mode = MagnumConfig.CUDA_DISABLED
cuda_dev = -1
if options.gpu32 is not None:
cuda_mode = MagnumConfig.CUDA_32
cuda_dev = parse_gpu_id(options.gpu32)
if options.gpu64 is not None:
if options.gpu32 is not None: logger.warn("Ignoring -g argument because -G was specified")
cuda_mode = MagnumConfig.CUDA_64
cuda_dev = parse_gpu_id(options.gpu64)
self.enableCuda(cuda_mode, cuda_dev)
# --prof
if options.profiling_enabled:
self.enableProfiling(True)
# enable fftw threads...
self.setFFTWThreads(options.num_fftw_threads)
def createImage(*args, **kwargs):
logger.warn(_msg)
def Co(**params):
"""
Return a material object for the material 'Cobalt'.
"""
logger.warn("Warning: The Co material parameters are not verified!")
return Material.fromDB("Co", **params)
def Ni(**params):
"""
Return a material object for the material 'Nickel'.
"""
logger.warn("Warning: The Ni material parameters are not verified!")
return Material.fromDB("Ni", **params)
def Fe(**params):
"""
Return a material object for the material 'Iron'.
"""
logger.warn("Warning: The Fe material parameters are not verified!")
return Material.fromDB("Fe", **params)
def Ni(**params):
"""
Return a material object for the material 'Nickel'.
"""
logger.warn("Warning: The Ni material parameters are not verified!")
return Material.fromDB("Ni", **params)
from .shape import Shape
from magnum.logger import logger
from magnum.mesh import RectangularMesh
try:
import Image
_found_image_lib = True
except:
_found_image_lib = False
logger.warn("Python Imaging Library not found!")
logger.warn("-> This means that the ImageShapeCreator and related classes are not available!")
class ImageShape(Shape):
"""
This class can create a shape with an image. The image defines the shape between the x-y-axes and z is filled in the whole world.
To use the ImageShape take the *ImageShapeCreator*. For example:
.. code-block:: python
isc = ImageShapeCreator("phi.png", mesh)
world = World(mesh, Body("phi", Material.Py(), isc.pick("black")))
You can use the following colors:
*black, green, blue, red, yellow, grey, white.*
It is not necessary to use a color exactly. Every pixel is interpreted as the nearest color.
"""
def __init__(self, isc, color):
#
# You should have received a copy of the GNU General Public License
# along with magnum.fd. If not, see <http://www.gnu.org/licenses/>.
from magnum.micromagnetics.world.shape import Shape
from magnum.logger import logger
from magnum.mesh import RectangularMesh
from math import log, floor
try:
import gmshpy
_found_gmsh_lib = True
except:
_found_gmsh_lib = False
logger.warn("Python wrappers for Gmsh not found!")
logger.warn("-> This means that the GmshShape class is not available!")
class GmshShape(Shape):
"""
This class can create a shape from a number of gemetry/mesh files that are supported by Gmsh.
The Python wrappers for Gmsh have to be installed on the system.
"""
def __init__(self, model, shift = (0.0, 0.0, 0.0), scale = 1.0):
if not _found_gmsh_lib: raise NotImplementedError("GmshShape class can not be used because the Python wrappers for GMSH could not be loaded ('import gmshpy')")
super(GmshShape, self).__init__()
self.__model = model
self.__shift = shift
self.__scale = scale
#
# You should have received a copy of the GNU General Public License
# along with magnum.fd. If not, see <http://www.gnu.org/licenses/>.
from magnum.micromagnetics.world.shape import Shape
from magnum.logger import logger
from magnum.mesh import RectangularMesh
from math import log, floor
try:
import gmshpy
_found_gmsh_lib = True
except:
_found_gmsh_lib = False
logger.warn("Python wrappers for Gmsh not found!")
logger.warn("-> This means that the GmshShape class is not available!")
class GmshShape(Shape):
"""
This class can create a shape from a number of gemetry/mesh files that are supported by Gmsh.
The Python wrappers for Gmsh have to be installed on the system.
"""
def __init__(self, model, shift=(0.0, 0.0, 0.0), scale=1.0):
if not _found_gmsh_lib:
raise NotImplementedError(
"GmshShape class can not be used because the Python wrappers for GMSH could not be loaded ('import gmshpy')"
)
super(GmshShape, self).__init__()
def Co(**params):
"""
Return a material object for the material 'Cobalt'.
"""
logger.warn("Warning: The Co material parameters are not verified!")
return Material.fromDB("Co", **params)
def writeImage(*args, **kwargs):
logger.warn(_msg)
def writeImage(*args, **kwargs):
logger.warn(_msg)
def Controller(run, params, *args, **kwargs):
logger.warn("The 'Controller' function is deprecated, please use 'create_controller' instead.")
return create_controller(run, params, *args, **kwargs)
def Fe(**params):
"""
Return a material object for the material 'Iron'.
"""
logger.warn("Warning: The Fe material parameters are not verified!")
return Material.fromDB("Fe", **params)
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with magnum.fd. If not, see <http://www.gnu.org/licenses/>.
from magnum.logger import logger
from magnum.mesh import RectangularMesh
from magnum.micromagnetics.world.shape import Shape
try:
import Image
_found_image_lib = True
except:
_found_image_lib = False
logger.warn("Python Imaging Library not found!")
logger.warn(
"-> This means that the ImageShapeCreator and related classes are not available!"
)
class ImageShape(Shape):
"""
This class can create a shape from an graphical image using a color mask. In order to use this class,
the Python Imaging Library has to be installed ('import Image').
ImageShape objects are usually created by the *pick* method of an *ImageShapeCreator* object:
.. code-block:: python
isc = ImageShapeCreator("image.png", mesh) # load the image, stretching it over the xy-axes of the mesh.
def parseCommandLine(self, argv):
import magnum
parser = OptionParser(version="MicroMagnum " + magnum.__version__)
hw_group = OptionGroup(
parser,
"Hardware options",
"Options that control which hardware is used.",
)
hw_group.add_option(
"-g",
type="string",
help=
"enable GPU processing (using 32-bit accuracy) on cuda device GPU_ID. The simulator will fall back to CPU mode if it was not compiled with CUDA support or when no CUDA capable graphics cards were detected.",
metavar="GPU_ID",
dest="gpu32",
default=None)
hw_group.add_option(
"-G",
type="string",
help=
"enable GPU processing (using 64-bit accuracy) on cuda device GPU_ID. TODO: Describe fallback behaviour.",
metavar="GPU_ID",
dest="gpu64",
default=None)
hw_group.add_option(
"-t",
"--threads",
help=
"enable CPU multithreading with NUM_THREADS (1..64) threads. This parameter instructs the fftw library to use NUM_THREADS threads for computing FFTs.",
metavar="NUM_THREADS",
dest="num_fftw_threads",
type="int",
default=1)
parser.add_option_group(hw_group)
log_group = OptionGroup(
parser, "Logging options",
"Options related to logging and benchmarking.")
log_group.add_option(
"--loglevel",
"-l",
type="int",
help=
"set log level (0:Debug, 1:Info, 2:Warn, 4:Error, 5:Critical), default is Debug (0).",
metavar="LEVEL",
dest="loglevel",
default=1)
log_group.add_option("--prof",
help="Log profiling info at program exit.",
dest="profiling_enabled",
action="store_true",
default=False)
parser.add_option_group(log_group)
def prange_callback(option, opt_str, value, parser, *args, **kwargs):
# e.g.: ./script.py --prange=0,64 -> xrange(0,64) object
match = re.match("^(\d+),(\d+)$", value)
if match:
p0, p1 = int(match.group(1)), int(match.group(2))
else:
match = re.match("^(\d+)$", value)
if match:
p0 = int(match.group(1))
p1 = p0 + 1
else:
raise OptionValueError(
"Invalid --param-range / -p format.")
if not p0 < p1:
raise OptionValueError(
"Invalid --param-range / -p specified: second value must be greater than first value"
)
setattr(parser.values, "prange", range(p0, p1))
ctrl_group = OptionGroup(
parser, "Parameter sweep options",
"These options have only an effect when the simulation script uses a Controller object to sweep through a parameter range."
)
ctrl_group.add_option(
"--param-range",
"-p",
type="string",
help=
"select parameter set to run, e.g. --param-range=0,64 to run sets 0 to 63.",
metavar="RANGE",
action="callback",
callback=prange_callback,
default=None)
ctrl_group.add_option(
"--print-num-params",
help="print number of sweep parameters to stdout and exit.",
action="store_true",
dest="print_num_params_requested",
default=False)
ctrl_group.add_option(
"--print-all-params",
action="store_true",
help="print all sweep parameters to stdout and exit.",
dest="print_all_params_requested",
default=False,
)
parser.add_option_group(ctrl_group)
misc_group = OptionGroup(parser, "Miscellanous options")
misc_group.add_option(
"--on_io_error",
type="int",
help=
"Specifies what to do when an i/o error occurs when writing an .omf/.vtk file. 0: Abort (default), 1: Retry a few times, then abort, 2: Retry a few times, then pause and ask for user intervention",
metavar="MODE",
dest="on_io_error",
default=0)
parser.add_option_group(misc_group)
options, rest_args = parser.parse_args(argv)
self.options = options
### Process the options ###
# --loglevel, -l
ll_map = [
logging.DEBUG, logging.INFO, logging.WARN, logging.ERROR,
logging.CRITICAL
]
logger.setLevel(ll_map[options.loglevel])
logger.info(
"----------------------------------------------------------------------"
)
logger.info("MicroMagnum %s" % magnum.__version__)
logger.info("Copyright (C) 2012 by the MicroMagnum team.")
logger.info("This program comes with ABSOLUTELY NO WARRANTY.")
logger.info(
"This is free software, and you are welcome to redistribute it under"
)
logger.info(
"certain conditions; see the file COPYING in the distribution package."
)
logger.info(
"----------------------------------------------------------------------"
)
# -g, -G
if options.gpu32 and options.gpu64:
logger.warn("Ignoring -g argument because -G was specified")
def parse_gpu_id(arg):
return -1 if arg == "auto" else int(arg)
if options.gpu64:
cuda_mode, cuda_dev = MagnumConfig.CUDA_64, parse_gpu_id(
options.gpu64)
elif options.gpu32:
cuda_mode, cuda_dev = MagnumConfig.CUDA_32, parse_gpu_id(
options.gpu32)
else:
cuda_mode, cuda_dev = MagnumConfig.CUDA_DISABLED, -1
self.enableCuda(cuda_mode, cuda_dev)
# --prof
if options.profiling_enabled:
self.enableProfiling(True)
# enable fftw threads...
self.setFFTWThreads(options.num_fftw_threads)
