def _census_memory_requirement(self):
"""
Guesstimate the memory required for this simulator.
Guesstimate is based on a census of the dominant arrays after the
simulator has been configured.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
#magic_number = 8.0 # Bytes
memreq = self.history.nbytes
#LOG.info("Memory required by this simulatin will be approximately %s Bytes" % (memreq))
try:
memreq += self.surface.triangles.nbytes * 2 # normals
memreq += self.surface.vertices.nbytes * 2 # normals
memreq += self.surface.vertex_mapping.nbytes * 4 #vertex_mapping, region_average, region_sum
memreq += self.surface.eeg_projection.nbytes
memreq += self.surface.local_connectivity.matrix.nnz * 8
except AttributeError:
pass
for monitor in self.monitors:
memreq += monitor._stock.nbytes
if isinstance(monitor, monitors_module.Bold):
memreq += monitor._interim_stock.nbytes
if psutil and memreq > psutil.virtual_memory().total:
LOG.error("This is gonna get ugly...")
self._memory_requirement_census = magic_number * memreq
#import pdb; pdb.set_trace()
msg = "Memory requirement census: simulation will need about %.1f MB"
LOG.info(msg % (self._memory_requirement_census / 1048576.0))
def _census_memory_requirement(self):
"""
Guesstimate the memory required for this simulator.
Guesstimate is based on a census of the dominant arrays after the
simulator has been configured.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
#magic_number = 8.0 # Bytes
memreq = self.history.nbytes
#LOG.info("Memory required by this simulatin will be approximately %s Bytes" % (memreq))
try:
memreq += self.surface.triangles.nbytes * 2 # normals
memreq += self.surface.vertices.nbytes * 2 # normals
memreq += self.surface.vertex_mapping.nbytes * 4 #vertex_mapping, region_average, region_sum
memreq += self.surface.eeg_projection.nbytes
memreq += self.surface.local_connectivity.matrix.nnz * 8
except AttributeError:
pass
for monitor in self.monitors:
memreq += monitor._stock.nbytes
if isinstance(monitor, monitors_module.Bold):
memreq += monitor._interim_stock.nbytes
if psutil and memreq > psutil.virtual_memory().total:
LOG.error("This is gonna get ugly...")
self._memory_requirement_census = magic_number * memreq
#import pdb; pdb.set_trace()
msg = "Memory requirement census: simulation will need about %.1f MB"
LOG.info(msg % (self._memory_requirement_census / 1048576.0))
def _guesstimate_memory_requirement(self):
"""
Guestimate the memroy required for this simulator.
Guesstimate is based on the shape of the dominant arrays, and as such
can operate before configuration.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
if self.surface:
number_of_nodes = self.surface.number_of_vertices
else:
number_of_nodes = self.connectivity.number_of_regions
number_of_regions = self.connectivity.number_of_regions
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
bits_64 = 8.0 # Bytes
bits_32 = 4.0 # Bytes
#NOTE: The speed hack for getting the first element of hist shape should
# partially resolves calling of this method with a non-configured
# connectivity, there remains the less common issue if no tract_lengths...
hist_shape = (self.connectivity.tract_lengths.max() / (self.conduction_speed or self.connectivity.speed or 3.0) / self.integrator.dt, #self.connectivity.delays.max()
self.model.nvar, number_of_nodes,
self.model.number_of_modes)
memreq = numpy.prod(hist_shape) * bits_64
if self.surface:
memreq += self.surface.number_of_triangles * 3 * bits_32 * 2 # normals
memreq += self.surface.number_of_vertices * 3 * bits_64 * 2 # normals
memreq += number_of_nodes * number_of_regions * bits_64 * 4 #vertex_mapping, region_average, region_sum
#???memreq += self.surface.local_connectivity.matrix.nnz * 8
if not isinstance(self.monitors, (list, tuple)):
monitors = [self.monitors]
else:
monitors = self.monitors
for monitor in monitors:
if not isinstance(monitor, monitors_module.Bold):
stock_shape = (monitor.period / self.integrator.dt,
self.model.variables_of_interest.shape[0],
number_of_nodes,
self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
if hasattr(monitor, "sensors"):
try:
memreq += number_of_nodes * monitor.sensors.number_of_sensors * bits_64 #projection_matrix
except AttributeError:
LOG.debug("No sensors specified, guessing memory based on default EEG.")
memreq += number_of_nodes * 62.0 * bits_64
else:
stock_shape = (monitor.hrf_length * monitor._stock_sample_rate,
self.model.variables_of_interest.shape[0],
number_of_nodes,
self.model.number_of_modes)
interim_stock_shape = (1.0 / (2.0**-2 * self.integrator.dt),
self.model.variables_of_interest.shape[0],
number_of_nodes,
self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
memreq += numpy.prod(interim_stock_shape) * bits_64
#available_memory = 25769803776 #TODO: (this is for my machine)
if psutil and memreq > psutil.virtual_memory().total:
LOG.error("This is gonna get ugly...")
self._memory_requirement_guess = magic_number * memreq
#import pdb; pdb.set_trace()
msg = "Memory requirement guesstimate: simulation will need about %.1f MB"
LOG.info(msg % (self._memory_requirement_guess / 1048576.0))
def _guesstimate_memory_requirement(self):
"""
guesstimate the memory required for this simulator.
Guesstimate is based on the shape of the dominant arrays, and as such
can operate before configuration.
NOTE: Assumes returned/yeilded data is in some sense "taken care of" in
the world outside the simulator, and so doesn't consider it, making
the simulator's history, and surface if present, the dominant
memory pigs...
"""
if self.surface:
number_of_nodes = self.surface.number_of_vertices
else:
number_of_nodes = self.connectivity.number_of_regions
number_of_regions = self.connectivity.number_of_regions
magic_number = 2.42 # Current guesstimate is low by about a factor of 2, seems safer to over estimate...
bits_64 = 8.0 # Bytes
bits_32 = 4.0 # Bytes
#NOTE: The speed hack for getting the first element of hist shape should
# partially resolves calling of this method with a non-configured
# connectivity, there remains the less common issue if no tract_lengths...
hist_shape = (
self.connectivity.tract_lengths.max() /
(self.conduction_speed or self.connectivity.speed or 3.0) /
self.integrator.dt, self.model.nvar, number_of_nodes,
self.model.number_of_modes)
memreq = numpy.prod(hist_shape) * bits_64
if self.surface:
memreq += self.surface.number_of_triangles * 3 * bits_32 * 2 # normals
memreq += self.surface.number_of_vertices * 3 * bits_64 * 2 # normals
memreq += number_of_nodes * number_of_regions * bits_64 * 4 # vertex_mapping, region_average, region_sum
#???memreq += self.surface.local_connectivity.matrix.nnz * 8
if not isinstance(self.monitors, (list, tuple)):
monitors = [self.monitors]
else:
monitors = self.monitors
for monitor in monitors:
if not isinstance(monitor, monitors_module.Bold):
stock_shape = (monitor.period / self.integrator.dt,
self.model.variables_of_interest.shape[0],
number_of_nodes, self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
if hasattr(monitor, "sensors"):
try:
memreq += number_of_nodes * monitor.sensors.number_of_sensors * bits_64 # projection_matrix
except AttributeError:
LOG.debug(
"No sensors specified, guessing memory based on default EEG."
)
memreq += number_of_nodes * 62.0 * bits_64
else:
stock_shape = (monitor.hrf_length * monitor._stock_sample_rate,
self.model.variables_of_interest.shape[0],
number_of_nodes, self.model.number_of_modes)
interim_stock_shape = (
1.0 / (2.0**-2 * self.integrator.dt),
self.model.variables_of_interest.shape[0], number_of_nodes,
self.model.number_of_modes)
memreq += numpy.prod(stock_shape) * bits_64
memreq += numpy.prod(interim_stock_shape) * bits_64
if psutil and memreq > psutil.virtual_memory().total:
LOG.error("This is gonna get ugly...")
self._memory_requirement_guess = magic_number * memreq
msg = "Memory requirement guesstimate: simulation will need about %.1f MB"
LOG.info(msg % (self._memory_requirement_guess / 1048576.0))