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镜像自地址 https://gitee.com/sunhf/gprMax.git 已同步 2025-08-07 04:56:51 +08:00
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Tidy up of logging and initial MPI task farm work.

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Craig Warren
2020-03-06 16:48:21 +00:00
父节点 01d28c204e
当前提交 1e4237c2f5
共有 31 个文件被更改，包括 739 次插入 和 267 次删除
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1
gprMax/__init__.py
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@@ -11,7 +11,6 @@ from ._version import __version__
from .cmds_single_use import Discretisation
from .cmds_single_use import Domain
from .cmds_single_use import TimeWindow
from .cmds_single_use import Messages
from .cmds_single_use import Title
from .cmds_single_use import NumThreads
from .cmds_single_use import TimeStepStabilityFactor

4
gprMax/cmds_geometry/add_grass.py
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@@ -28,7 +28,7 @@ from ..fractals import Grass
from ..materials import Material
from ..utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class AddGrass(UserObjectGeometry):
@@ -193,4 +193,4 @@ class AddGrass(UserObjectGeometry):
volume.fractalsurfaces.append(surface)
log.info(f'{n_blades} blades of grass on surface from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with fractal dimension {surface.dimension:g}, fractal seeding {surface.seed}, and range {limits[0]:g}m to {limits[1]:g}m, added to {surface.operatingonID}.')
logger.info(f'{n_blades} blades of grass on surface from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with fractal dimension {surface.dimension:g}, fractal seeding {surface.seed}, and range {limits[0]:g}m to {limits[1]:g}m, added to {surface.operatingonID}.')

4
gprMax/cmds_geometry/add_surface_roughness.py
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@@ -27,7 +27,7 @@ from ..exceptions import CmdInputError
from ..fractals import FractalSurface
from ..utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class AddSurfaceRoughness(UserObjectGeometry):
@@ -158,4 +158,4 @@ class AddSurfaceRoughness(UserObjectGeometry):
surface.generate_fractal_surface(grid)
volume.fractalsurfaces.append(surface)
log.info(f'Fractal surface from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with fractal dimension {surface.dimension:g}, fractal weightings {surface.weighting[0]:g}, {surface.weighting[1]:g}, fractal seeding {surface.seed}, and range {limits[0]:g}m to {limits[1]:g}m, added to {surface.operatingonID}.')
logger.info(f'Fractal surface from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with fractal dimension {surface.dimension:g}, fractal weightings {surface.weighting[0]:g}, {surface.weighting[1]:g}, fractal seeding {surface.seed}, and range {limits[0]:g}m to {limits[1]:g}m, added to {surface.operatingonID}.')

4
gprMax/cmds_geometry/add_surface_water.py
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@@ -24,7 +24,7 @@ from ..exceptions import CmdInputError
from ..materials import Material
from ..utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class AddSurfaceWater(UserObjectGeometry):
@@ -142,4 +142,4 @@ class AddSurfaceWater(UserObjectGeometry):
if testwater:
raise CmdInputError(self.__str__() + ' requires the time step for the model to be less than the relaxation time required to model water.')
log.info(f'Water on surface from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with depth {filldepth:g}m, added to {surface.operatingonID}.')
logger.info(f'Water on surface from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with depth {filldepth:g}m, added to {surface.operatingonID}.')

4
gprMax/cmds_geometry/box.py
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@@ -26,7 +26,7 @@ from ..cython.geometry_primitives import build_box
from ..exceptions import CmdInputError
from ..materials import Material
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Box(UserObjectGeometry):
@@ -116,4 +116,4 @@ class Box(UserObjectGeometry):
build_box(xs, xf, ys, yf, zs, zf, numID, numIDx, numIDy, numIDz, averaging, grid.solid, grid.rigidE, grid.rigidH, grid.ID)
dielectricsmoothing = 'on' if averaging else 'off'
log.info(f"Box from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
logger.info(f"Box from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")

4
gprMax/cmds_geometry/cmds_geometry.py
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@@ -18,7 +18,7 @@
import logging
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class UserObjectGeometry:
@@ -45,4 +45,4 @@ class UserObjectGeometry:
def create(self, grid, uip):
"""Create the object and add it to the grid."""
log.debug('This method is incomplete')
logger.debug('This method is incomplete')

4
gprMax/cmds_geometry/cylinder.py
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@@ -25,7 +25,7 @@ from ..cython.geometry_primitives import build_cylinder
from ..exceptions import CmdInputError
from ..materials import Material
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Cylinder(UserObjectGeometry):
@@ -121,4 +121,4 @@ class Cylinder(UserObjectGeometry):
build_cylinder(x1, y1, z1, x2, y2, z2, r, grid.dx, grid.dy, grid.dz, numID, numIDx, numIDy, numIDz, averaging, grid.solid, grid.rigidE, grid.rigidH, grid.ID)
dielectricsmoothing = 'on' if averaging else 'off'
log.info(f"Cylinder with face centres {x1:g}m, {y1:g}m, {z1:g}m and {x2:g}m, {y2:g}m, {z2:g}m, with radius {r:g}m, of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
logger.info(f"Cylinder with face centres {x1:g}m, {y1:g}m, {z1:g}m and {x2:g}m, {y2:g}m, {z2:g}m, with radius {r:g}m, of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")

6
gprMax/cmds_geometry/cylindrical_sector.py
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@@ -26,7 +26,7 @@ from ..cython.geometry_primitives import build_cylindrical_sector
from ..exceptions import CmdInputError
from ..materials import Material
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class CylindricalSector(UserObjectGeometry):
@@ -171,6 +171,6 @@ class CylindricalSector(UserObjectGeometry):
if thickness > 0:
dielectricsmoothing = 'on' if averaging else 'off'
log.info(f"Cylindrical sector with centre {ctr1:g}m, {ctr2:g}m, radius {r:g}m, starting angle {(sectorstartangle / (2 * np.pi)) * 360:.1f} degrees, sector angle {(sectorangle / (2 * np.pi)) * 360:.1f} degrees, thickness {thickness:g}m, of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
logger.info(f"Cylindrical sector with centre {ctr1:g}m, {ctr2:g}m, radius {r:g}m, starting angle {(sectorstartangle / (2 * np.pi)) * 360:.1f} degrees, sector angle {(sectorangle / (2 * np.pi)) * 360:.1f} degrees, thickness {thickness:g}m, of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
else:
log.info(f"Cylindrical sector with centre {ctr1:g}m, {ctr2:g}m, radius {r:g}m, starting angle {(sectorstartangle / (2 * np.pi)) * 360:.1f} degrees, sector angle {(sectorangle / (2 * np.pi)) * 360:.1f} degrees, of material(s) {', '.join(materialsrequested)} created.")
logger.info(f"Cylindrical sector with centre {ctr1:g}m, {ctr2:g}m, radius {r:g}m, starting angle {(sectorstartangle / (2 * np.pi)) * 360:.1f} degrees, sector angle {(sectorangle / (2 * np.pi)) * 360:.1f} degrees, of material(s) {', '.join(materialsrequested)} created.")

4
gprMax/cmds_geometry/edge.py
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@@ -25,7 +25,7 @@ from ..cython.geometry_primitives import build_edge_y
from ..cython.geometry_primitives import build_edge_z
from ..exceptions import CmdInputError
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Edge(UserObjectGeometry):
@@ -86,4 +86,4 @@ class Edge(UserObjectGeometry):
for k in range(zs, zf):
build_edge_z(xs, ys, k, material.numID, grid.rigidE, grid.rigidH, grid.ID)
log.info(f'Edge from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m of material {material_id} created.')
logger.info(f'Edge from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m of material {material_id} created.')

4
gprMax/cmds_geometry/fractal_box.py
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@@ -25,7 +25,7 @@ from .cmds_geometry import UserObjectGeometry
from ..exceptions import CmdInputError
from ..fractals import FractalVolume
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class FractalBox(UserObjectGeometry):
@@ -121,6 +121,6 @@ class FractalBox(UserObjectGeometry):
volume.mixingmodel = mixingmodel
dielectricsmoothing = 'on' if volume.averaging else 'off'
log.info(f'Fractal box {volume.ID} from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with {volume.operatingonID}, fractal dimension {volume.dimension:g}, fractal weightings {volume.weighting[0]:g}, {volume.weighting[1]:g}, {volume.weighting[2]:g}, fractal seeding {volume.seed}, with {volume.nbins} material(s) created, dielectric smoothing is {dielectricsmoothing}.')
logger.info(f'Fractal box {volume.ID} from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with {volume.operatingonID}, fractal dimension {volume.dimension:g}, fractal weightings {volume.weighting[0]:g}, {volume.weighting[1]:g}, {volume.weighting[2]:g}, fractal seeding {volume.seed}, with {volume.nbins} material(s) created, dielectric smoothing is {dielectricsmoothing}.')
grid.fractalvolumes.append(volume)

6
gprMax/cmds_geometry/geometry_objects_read.py
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@@ -28,7 +28,7 @@ from ..exceptions import CmdInputError
from ..hash_cmds_file import get_user_objects
from ..utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class GeometryObjectsRead(UserObjectGeometry):
@@ -113,8 +113,8 @@ class GeometryObjectsRead(UserObjectGeometry):
G.rigidE[:, xs:xs + rigidE.shape[1], ys:ys + rigidE.shape[2], zs:zs + rigidE.shape[3]] = rigidE
G.rigidH[:, xs:xs + rigidH.shape[1], ys:ys + rigidH.shape[2], zs:zs + rigidH.shape[3]] = rigidH
G.ID[:, xs:xs + ID.shape[1], ys:ys + ID.shape[2], zs:zs + ID.shape[3]] = ID + numexistmaterials
log.info(f'Geometry objects from file {geofile} inserted at {xs * G.dx:g}m, {ys * G.dy:g}m, {zs * G.dz:g}m, with corresponding materials file {matfile}.')
logger.info(f'Geometry objects from file {geofile} inserted at {xs * G.dx:g}m, {ys * G.dy:g}m, {zs * G.dz:g}m, with corresponding materials file {matfile}.')
except KeyError:
averaging = False
build_voxels_from_array(xs, ys, zs, numexistmaterials, averaging, data, G.solid, G.rigidE, G.rigidH, G.ID)
log.info(f'Geometry objects from file (voxels only){geofile} inserted at {xs * G.dx:g}m, {ys * G.dy:g}m, {zs * G.dz:g}m, with corresponding materials file {matfile}.')
logger.info(f'Geometry objects from file (voxels only){geofile} inserted at {xs * G.dx:g}m, {ys * G.dy:g}m, {zs * G.dz:g}m, with corresponding materials file {matfile}.')

4
gprMax/cmds_geometry/plate.py
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@@ -25,7 +25,7 @@ from ..cython.geometry_primitives import build_face_xz
from ..cython.geometry_primitives import build_face_xy
from ..exceptions import CmdInputError
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Plate(UserObjectGeometry):
@@ -134,4 +134,4 @@ class Plate(UserObjectGeometry):
for j in range(ys, yf):
build_face_xy(i, j, zs, numIDx, numIDy, grid.rigidE, grid.rigidH, grid.ID)
log.info(f"Plate from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m of material(s) {', '.join(materialsrequested)} created.")
logger.info(f"Plate from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m of material(s) {', '.join(materialsrequested)} created.")

4
gprMax/cmds_geometry/sphere.py
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@@ -26,7 +26,7 @@ from ..cython.geometry_primitives import build_sphere
from ..exceptions import CmdInputError
from ..materials import Material
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Sphere(UserObjectGeometry):
@@ -115,4 +115,4 @@ class Sphere(UserObjectGeometry):
build_sphere(xc, yc, zc, r, grid.dx, grid.dy, grid.dz, numID, numIDx, numIDy, numIDz, averaging, grid.solid, grid.rigidE, grid.rigidH, grid.ID)
dielectricsmoothing = 'on' if averaging else 'off'
log.info(f"Sphere with centre {xc * grid.dx:g}m, {yc * grid.dy:g}m, {zc * grid.dz:g}m, radius {r:g}m, of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
logger.info(f"Sphere with centre {xc * grid.dx:g}m, {yc * grid.dy:g}m, {zc * grid.dz:g}m, radius {r:g}m, of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")

6
gprMax/cmds_geometry/triangle.py
查看文件

@@ -26,7 +26,7 @@ from ..cython.geometry_primitives import build_triangle
from ..exceptions import CmdInputError
from ..materials import Material
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Triangle(UserObjectGeometry):
@@ -156,6 +156,6 @@ class Triangle(UserObjectGeometry):
if thickness > 0:
dielectricsmoothing = 'on' if averaging else 'off'
log.info(f"Triangle with coordinates {x1:g}m {y1:g}m {z1:g}m, {x2:g}m {y2:g}m {z2:g}m, {x3:g}m {y3:g}m {z3:g}m and thickness {thickness:g}m of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
logger.info(f"Triangle with coordinates {x1:g}m {y1:g}m {z1:g}m, {x2:g}m {y2:g}m {z2:g}m, {x3:g}m {y3:g}m {z3:g}m and thickness {thickness:g}m of material(s) {', '.join(materialsrequested)} created, dielectric smoothing is {dielectricsmoothing}.")
else:
log.info(f"Triangle with coordinates {x1:g}m {y1:g}m {z1:g}m, {x2:g}m {y2:g}m {z2:g}m, {x3:g}m {y3:g}m {z3:g}m of material(s) {', '.join(materialsrequested)} created.")
logger.info(f"Triangle with coordinates {x1:g}m {y1:g}m {z1:g}m, {x2:g}m {y2:g}m {z2:g}m, {x3:g}m {y3:g}m {z3:g}m of material(s) {', '.join(materialsrequested)} created.")

60
gprMax/cmds_multiple.py
查看文件

@@ -39,7 +39,7 @@ from .subgrids.base import SubGridBase
from .utilities import round_value
from .waveforms import Waveform as WaveformUser
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class UserObjectMulti:
@@ -84,6 +84,7 @@ class Waveform(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 1
self.hash = '#waveform'
def create(self, grid, uip):
@@ -108,7 +109,7 @@ class Waveform(UserObjectMulti):
w.amp = amp
w.freq = freq
log.info(f'Waveform {w.ID} of type {w.type} with maximum amplitude scaling {w.amp:g}, frequency {w.freq:g}Hz created.')
logger.info(f'Waveform {w.ID} of type {w.type} with maximum amplitude scaling {w.amp:g}, frequency {w.freq:g}Hz created.')
grid.waveforms.append(w)
@@ -132,6 +133,7 @@ class VoltageSource(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 2
self.hash = '#voltage_source'
def create(self, grid, uip):
@@ -194,7 +196,7 @@ class VoltageSource(UserObjectMulti):
v.calculate_waveform_values(grid)
log.info(f'Voltage source with polarity {v.polarisation} at {v.xcoord * grid.dx:g}m, {v.ycoord * grid.dy:g}m, {v.zcoord * grid.dz:g}m, resistance {v.resistance:.1f} Ohms,' + startstop + f'using waveform {v.waveformID} created.')
logger.info(f'Voltage source with polarity {v.polarisation} at {v.xcoord * grid.dx:g}m, {v.ycoord * grid.dy:g}m, {v.zcoord * grid.dz:g}m, resistance {v.resistance:.1f} Ohms,' + startstop + f'using waveform {v.waveformID} created.')
grid.voltagesources.append(v)
@@ -217,6 +219,7 @@ class HertzianDipole(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 3
self.hash = '#hertzian_dipole'
def create(self, grid, uip):
@@ -287,9 +290,9 @@ class HertzianDipole(UserObjectMulti):
h.calculate_waveform_values(grid)
if grid.mode == '2D':
log.info(f'Hertzian dipole is a line source in 2D with polarity {h.polarisation} at {h.xcoord * grid.dx:g}m, {h.ycoord * grid.dy:g}m, {h.zcoord * grid.dz:g}m,' + startstop + f'using waveform {h.waveformID} created.')
logger.info(f'Hertzian dipole is a line source in 2D with polarity {h.polarisation} at {h.xcoord * grid.dx:g}m, {h.ycoord * grid.dy:g}m, {h.zcoord * grid.dz:g}m,' + startstop + f'using waveform {h.waveformID} created.')
else:
log.info(f'Hertzian dipole with polarity {h.polarisation} at {h.xcoord * grid.dx:g}m, {h.ycoord * grid.dy:g}m, {h.zcoord * grid.dz:g}m,' + startstop + f'using waveform {h.waveformID} created.')
logger.info(f'Hertzian dipole with polarity {h.polarisation} at {h.xcoord * grid.dx:g}m, {h.ycoord * grid.dy:g}m, {h.zcoord * grid.dz:g}m,' + startstop + f'using waveform {h.waveformID} created.')
grid.hertziandipoles.append(h)
@@ -312,6 +315,7 @@ class MagneticDipole(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 4
self.hash = '#magnetic_dipole'
def create(self, grid, uip):
@@ -372,7 +376,7 @@ class MagneticDipole(UserObjectMulti):
m.calculate_waveform_values(grid)
log.info(f'Magnetic dipole with polarity {m.polarisation} at {m.xcoord * grid.dx:g}m, {m.ycoord * grid.dy:g}m, {m.zcoord * grid.dz:g}m,' + startstop + f'using waveform {m.waveformID} created.')
logger.info(f'Magnetic dipole with polarity {m.polarisation} at {m.xcoord * grid.dx:g}m, {m.ycoord * grid.dy:g}m, {m.zcoord * grid.dz:g}m,' + startstop + f'using waveform {m.waveformID} created.')
grid.magneticdipoles.append(m)
@@ -397,6 +401,7 @@ class TransmissionLine(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 5
self.hash = '#transmission_line'
def create(self, grid, uip):
@@ -464,7 +469,7 @@ class TransmissionLine(UserObjectMulti):
t.calculate_waveform_values(grid)
t.calculate_incident_V_I(grid)
log.info(f'Transmission line with polarity {t.polarisation} at {t.xcoord * grid.dx:g}m, {t.ycoord * grid.dy:g}m, {t.zcoord * grid.dz:g}m, resistance {t.resistance:.1f} Ohms,' + startstop + f'using waveform {t.waveformID} created.')
logger.info(f'Transmission line with polarity {t.polarisation} at {t.xcoord * grid.dx:g}m, {t.ycoord * grid.dy:g}m, {t.zcoord * grid.dz:g}m, resistance {t.resistance:.1f} Ohms,' + startstop + f'using waveform {t.waveformID} created.')
grid.transmissionlines.append(t)
@@ -485,6 +490,7 @@ class Rx(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 6
self.hash = '#rx'
self.constructor = RxUser
@@ -492,7 +498,7 @@ class Rx(UserObjectMulti):
try:
p1 = self.kwargs['p1']
except KeyError:
log.exception(f'KeyError with {self.params_str()}')
logger.exception(f'KeyError with {self.params_str()}')
p = uip.check_src_rx_point(p1, self.params_str())
@@ -519,7 +525,7 @@ class Rx(UserObjectMulti):
else:
raise CmdInputError(f"'{self.params_str()}' contains an output type that is not allowable. Allowable outputs in current context are {allowableoutputs}")
log.info(f"Receiver at {r.xcoord * grid.dx:g}m, {r.ycoord * grid.dy:g}m, {r.zcoord * grid.dz:g}m with output component(s) {', '.join(r.outputs)} created.")
logger.info(f"Receiver at {r.xcoord * grid.dx:g}m, {r.ycoord * grid.dy:g}m, {r.zcoord * grid.dz:g}m with output component(s) {', '.join(r.outputs)} created.")
grid.rxs.append(r)
@@ -539,6 +545,7 @@ class RxArray(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 7
self.hash = '#rx_array'
def create(self, grid, uip):
@@ -573,7 +580,7 @@ class RxArray(UserObjectMulti):
else:
raise CmdInputError(f"'{self.params_str()}' the step size should not be less than the spatial discretisation")
log.info(f'Receiver array {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with steps {dx * grid.dx:g}m, {dy * grid.dy:g}m, {dz * grid.dz:g}m')
logger.info(f'Receiver array {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m with steps {dx * grid.dx:g}m, {dy * grid.dy:g}m, {dz * grid.dz:g}m')
for x in range(xs, xf + 1, dx):
for y in range(ys, yf + 1, dy):
@@ -588,7 +595,7 @@ class RxArray(UserObjectMulti):
r.ID = r.__class__.__name__ + '(' + str(x) + ',' + str(y) + ',' + str(z) + ')'
for key in RxUser.defaultoutputs:
r.outputs[key] = np.zeros(grid.iterations, dtype=config.dtypes['float_or_double'])
log.info(f" Receiver at {r.xcoord * grid.dx:g}m, {r.ycoord * grid.dy:g}m, {r.zcoord * grid.dz:g}m with output component(s) {', '.join(r.outputs)} created.")
logger.info(f" Receiver at {r.xcoord * grid.dx:g}m, {r.ycoord * grid.dy:g}m, {r.zcoord * grid.dz:g}m with output component(s) {', '.join(r.outputs)} created.")
grid.rxs.append(r)
@@ -611,6 +618,7 @@ class Snapshot(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 8
self.hash = '#snapshot'
def create(self, grid, uip):
@@ -657,7 +665,7 @@ class Snapshot(UserObjectMulti):
#else:
s = SnapshotUser(xs, ys, zs, xf, yf, zf, dx, dy, dz, iterations, filename)
log.info(f'Snapshot from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m, discretisation {dx * grid.dx:g}m, {dy * grid.dy:g}m, {dz * grid.dz:g}m, at {s.time * grid.dt:g} secs with filename {s.filename} created.')
logger.info(f'Snapshot from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m, discretisation {dx * grid.dx:g}m, {dy * grid.dy:g}m, {dz * grid.dz:g}m, at {s.time * grid.dt:g} secs with filename {s.filename} created.')
grid.snapshots.append(s)
@@ -677,6 +685,7 @@ class Material(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 9
self.hash = '#material'
def create(self, grid, uip):
@@ -715,7 +724,7 @@ class Material(UserObjectMulti):
if m.se == float('inf'):
m.averagable = False
log.info(f'Material {m.ID} with eps_r={m.er:g}, sigma={m.se:g} S/m; mu_r={m.mr:g}, sigma*={m.sm:g} Ohm/m created.')
logger.info(f'Material {m.ID} with eps_r={m.er:g}, sigma={m.se:g} S/m; mu_r={m.mr:g}, sigma*={m.sm:g} Ohm/m created.')
# Append the new material object to the materials list
grid.materials.append(m)
@@ -736,6 +745,7 @@ class AddDebyeDispersion(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 10
self.hash = '#add_dispersion_debye'
def create(self, grid, uip):
@@ -768,7 +778,7 @@ class AddDebyeDispersion(UserObjectMulti):
disp_material.averagable = False
for i in range(0, poles):
if tau[i] > 0:
log.debug('Not checking if relaxation times are greater than time-step')
logger.debug('Not checking if relaxation times are greater than time-step')
disp_material.deltaer.append(er_delta[i])
disp_material.tau.append(tau[i])
else:
@@ -779,7 +789,7 @@ class AddDebyeDispersion(UserObjectMulti):
# Replace original material with newly created DispersiveMaterial
grid.materials = [disp_material if mat.numID==material.numID else mat for mat in grid.materials]
log.info(f"Debye disperion added to {disp_material.ID} with delta_eps_r={', '.join('%4.2f' % deltaer for deltaer in disp_material.deltaer)}, and tau={', '.join('%4.3e' % tau for tau in disp_material.tau)} secs created.")
logger.info(f"Debye disperion added to {disp_material.ID} with delta_eps_r={', '.join('%4.2f' % deltaer for deltaer in disp_material.deltaer)}, and tau={', '.join('%4.3e' % tau for tau in disp_material.tau)} secs created.")
class AddLorentzDispersion(UserObjectMulti):
@@ -799,6 +809,7 @@ class AddLorentzDispersion(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 11
self.hash = '#add_dispersion_lorentz'
def create(self, grid, uip):
@@ -843,7 +854,7 @@ class AddLorentzDispersion(UserObjectMulti):
# Replace original material with newly created DispersiveMaterial
grid.materials = [disp_material if mat.numID==material.numID else mat for mat in grid.materials]
log.info(f"Lorentz disperion added to {disp_material.ID} with delta_eps_r={', '.join('%4.2f' % deltaer for deltaer in disp_material.deltaer)}, omega={', '.join('%4.3e' % tau for tau in disp_material.tau)} secs, and gamma={', '.join('%4.3e' % alpha for alpha in disp_material.alpha)} created.")
logger.info(f"Lorentz disperion added to {disp_material.ID} with delta_eps_r={', '.join('%4.2f' % deltaer for deltaer in disp_material.deltaer)}, omega={', '.join('%4.3e' % tau for tau in disp_material.tau)} secs, and gamma={', '.join('%4.3e' % alpha for alpha in disp_material.alpha)} created.")
class AddDrudeDispersion(UserObjectMulti):
@@ -861,6 +872,7 @@ class AddDrudeDispersion(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 12
self.hash = '#add_dispersion_drude'
def create(self, grid, uip):
@@ -903,7 +915,7 @@ class AddDrudeDispersion(UserObjectMulti):
# Replace original material with newly created DispersiveMaterial
grid.materials = [disp_material if mat.numID==material.numID else mat for mat in grid.materials]
log.info(f"Drude disperion added to {disp_material.ID} with omega={', '.join('%4.3e' % tau for tau in disp_material.tau)} secs, and gamma={', '.join('%4.3e' % alpha for alpha in disp_material.alpha)} secs created.")
logger.info(f"Drude disperion added to {disp_material.ID} with omega={', '.join('%4.3e' % tau for tau in disp_material.tau)} secs, and gamma={', '.join('%4.3e' % alpha for alpha in disp_material.alpha)} secs created.")
class SoilPeplinski(UserObjectMulti):
@@ -925,6 +937,7 @@ class SoilPeplinski(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 13
self.hash = '#soil_peplinski'
def create(self, grid, uip):
@@ -957,7 +970,7 @@ class SoilPeplinski(UserObjectMulti):
# Create a new instance of the Material class material (start index after pec & free_space)
s = PeplinskiSoilUser(ID, sand_fraction, clay_fraction, bulk_density, sand_density, (water_fraction_lower, water_fraction_upper))
log.info(f'Mixing model (Peplinski) used to create {s.ID} with sand fraction {s.S:g}, clay fraction {s.C:g}, bulk density {s.rb:g}g/cm3, sand particle density {s.rs:g}g/cm3, and water volumetric fraction {s.mu[0]:g} to {s.mu[1]:g} created.')
logger.info(f'Mixing model (Peplinski) used to create {s.ID} with sand fraction {s.S:g}, clay fraction {s.C:g}, bulk density {s.rb:g}g/cm3, sand particle density {s.rs:g}g/cm3, and water volumetric fraction {s.mu[0]:g} to {s.mu[1]:g} created.')
# Append the new material object to the materials list
grid.mixingmodels.append(s)
@@ -981,6 +994,7 @@ class GeometryView(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 14
self.hash = '#geometry_view'
self.multi_grid = False
@@ -1039,7 +1053,7 @@ class GeometryView(UserObjectMulti):
g = GeometryViewUser(xs, ys, zs, xf, yf, zf, dx, dy, dz, filename, fileext, grid)
log.info(f'Geometry view from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m, discretisation {dx * grid.dx:g}m, {dy * grid.dy:g}m, {dz * grid.dz:g}m, multi_grid={self.multi_grid}, grid={grid.name}, with filename base {g.filename} created.')
logger.info(f'Geometry view from {xs * grid.dx:g}m, {ys * grid.dy:g}m, {zs * grid.dz:g}m, to {xf * grid.dx:g}m, {yf * grid.dy:g}m, {zf * grid.dz:g}m, discretisation {dx * grid.dx:g}m, {dy * grid.dy:g}m, {dz * grid.dz:g}m, multi_grid={self.multi_grid}, grid={grid.name}, with filename base {g.filename} created.')
# Append the new GeometryView object to the geometry views list
grid.geometryviews.append(g)
@@ -1059,6 +1073,7 @@ class GeometryObjectsWrite(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 15
self.hash = '#geometry_objects_write'
def create(self, grid, uip):
@@ -1075,7 +1090,7 @@ class GeometryObjectsWrite(UserObjectMulti):
g = GeometryObjectsUser(x0, y0, z0, x1, y1, z1, filename)
log.info(f'Geometry objects in the volume from {p1[0] * grid.dx:g}m, {p1[1] * grid.dy:g}m, {p1[2] * grid.dz:g}m, to {p2[0] * grid.dx:g}m, {p2[1] * grid.dy:g}m, {p2[2] * grid.dz:g}m, will be written to {g.filename}, with materials written to {g.materialsfilename}')
logger.info(f'Geometry objects in the volume from {p1[0] * grid.dx:g}m, {p1[1] * grid.dy:g}m, {p1[2] * grid.dz:g}m, to {p2[0] * grid.dx:g}m, {p2[1] * grid.dy:g}m, {p2[2] * grid.dz:g}m, will be written to {g.filename}, with materials written to {g.materialsfilename}')
# Append the new GeometryView object to the geometry objects to write list
grid.geometryobjectswrite.append(g)
@@ -1114,6 +1129,7 @@ class PMLCFS(UserObjectMulti):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 16
self.hash = '#pml_cfs'
PMLCFS.count += 1
if PMLCFS.count == 2:
@@ -1171,7 +1187,7 @@ class PMLCFS(UserObjectMulti):
cfs.kappa = cfskappa
cfs.sigma = cfssigma
log.info(f'PML CFS parameters: alpha (scaling: {cfsalpha.scalingprofile}, scaling direction: {cfsalpha.scalingdirection}, min: {cfsalpha.min:g}, max: {cfsalpha.max:g}), kappa (scaling: {cfskappa.scalingprofile}, scaling direction: {cfskappa.scalingdirection}, min: {cfskappa.min:g}, max: {cfskappa.max:g}), sigma (scaling: {cfssigma.scalingprofile}, scaling direction: {cfssigma.scalingdirection}, min: {cfssigma.min:g}, max: {cfssigma.max:g}) created.')
logger.info(f'PML CFS parameters: alpha (scaling: {cfsalpha.scalingprofile}, scaling direction: {cfsalpha.scalingdirection}, min: {cfsalpha.min:g}, max: {cfsalpha.max:g}), kappa (scaling: {cfskappa.scalingprofile}, scaling direction: {cfskappa.scalingdirection}, min: {cfskappa.min:g}, max: {cfskappa.max:g}), sigma (scaling: {cfssigma.scalingprofile}, scaling direction: {cfssigma.scalingdirection}, min: {cfssigma.min:g}, max: {cfssigma.max:g}) created.')
grid.cfs.append(cfs)
@@ -1198,4 +1214,4 @@ class SubgridHSG(UserObjectMulti):
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
log.debug('Is this required?')
logger.debug('Is this required?')

50
gprMax/cmds_single_use.py
查看文件

@@ -33,7 +33,7 @@ from .exceptions import CmdInputError
from .waveforms import Waveform
from .utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Properties:
@@ -59,32 +59,6 @@ class UserObjectSingle:
pass
class Messages(UserObjectSingle):
"""Allows you to control the amount of information displayed on screen
when gprMax is run
:param yn: Whether information should be displayed.
:type yn: bool, optional
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.order = 0
def create(self, G, uip):
try:
yn = self.kwargs['yn']
except KeyError:
raise CmdInputError(self.__str__() + ' requires exactly one parameter')
if yn.lower() == 'y':
config.sim_config.general['messages'] = True
elif yn.lower() == 'n':
config.sim_config.general['messages'] = False
else:
raise CmdInputError(self.__str__() + ' requires input values of either y or n')
class Title(UserObjectSingle):
"""Allows you to include a title for your model.
@@ -100,7 +74,7 @@ class Title(UserObjectSingle):
try:
title = self.kwargs['name']
G.title = title
log.info(f'Model title: {G.title}')
logger.info(f'Model title: {G.title}')
except KeyError:
pass
@@ -125,7 +99,7 @@ class Domain(UserObjectSingle):
if G.nx == 0 or G.ny == 0 or G.nz == 0:
raise CmdInputError(f"'{self.params_str()}' requires at least one cell in every dimension")
log.info(f"Domain size: {self.kwargs['p1'][0]:g} x {self.kwargs['p1'][1]:g} x {self.kwargs['p1'][2]:g}m ({G.nx:d} x {G.ny:d} x {G.nz:d} = {(G.nx * G.ny * G.nz):g} cells)")
logger.info(f"Domain size: {self.kwargs['p1'][0]:g} x {self.kwargs['p1'][1]:g} x {self.kwargs['p1'][2]:g}m ({G.nx:d} x {G.ny:d} x {G.nz:d} = {(G.nx * G.ny * G.nz):g} cells)")
# Calculate time step at CFL limit; switch off appropriate PMLs for 2D
if G.nx == 1:
@@ -144,8 +118,8 @@ class Domain(UserObjectSingle):
G.mode = '3D'
G.calculate_dt()
log.info(f'Mode: {G.mode}')
log.info(f'Time step (at CFL limit): {G.dt:g} secs')
logger.info(f'Mode: {G.mode}')
logger.info(f'Time step (at CFL limit): {G.dt:g} secs')
class Discretisation(UserObjectSingle):
@@ -174,7 +148,7 @@ class Discretisation(UserObjectSingle):
if G.dl[2] <= 0:
raise CmdInputError(f"'{self.params_str()}' discretisation requires the z-direction spatial step to be greater than zero")
log.info(f'Spatial discretisation: {G.dl[0]:g} x {G.dl[1]:g} x {G.dl[2]:g}m')
logger.info(f'Spatial discretisation: {G.dl[0]:g} x {G.dl[1]:g} x {G.dl[2]:g}m')
class TimeWindow(UserObjectSingle):
@@ -214,7 +188,7 @@ class TimeWindow(UserObjectSingle):
if not G.timewindow:
raise CmdInputError(f"'{self.params_str()}' specify a time or number of iterations")
log.info(f'Time window: {G.timewindow:g} secs ({G.iterations} iterations)')
logger.info(f'Time window: {G.timewindow:g} secs ({G.iterations} iterations)')
class NumThreads(UserObjectSingle):
@@ -261,7 +235,7 @@ class TimeStepStabilityFactor(UserObjectSingle):
raise CmdInputError(self.__str__() + ' requires the value of the time step stability factor to be between zero and one')
G.dt = G.dt * f
log.info(f'Time step (modified): {G.dt:g} secs')
logger.info(f'Time step (modified): {G.dt:g} secs')
class PMLCells(UserObjectSingle):
@@ -333,7 +307,7 @@ class SrcSteps(UserObjectSingle):
except KeyError:
raise CmdInputError('#src_steps: requires exactly three parameters')
log.info(f'Simple sources will step {G.srcsteps[0] * G.dx:g}m, {G.srcsteps[1] * G.dy:g}m, {G.srcsteps[2] * G.dz:g}m for each model run.')
logger.info(f'Simple sources will step {G.srcsteps[0] * G.dx:g}m, {G.srcsteps[1] * G.dy:g}m, {G.srcsteps[2] * G.dz:g}m for each model run.')
class RxSteps(UserObjectSingle):
@@ -354,7 +328,7 @@ class RxSteps(UserObjectSingle):
except KeyError:
raise CmdInputError('#rx_steps: requires exactly three parameters')
log.info(f'All receivers will step {G.rxsteps[0] * G.dx:g}m, {G.rxsteps[1] * G.dy:g}m, {G.rxsteps[2] * G.dz:g}m for each model run.')
logger.info(f'All receivers will step {G.rxsteps[0] * G.dx:g}m, {G.rxsteps[1] * G.dy:g}m, {G.rxsteps[2] * G.dz:g}m for each model run.')
class ExcitationFile(UserObjectSingle):
@@ -394,7 +368,7 @@ class ExcitationFile(UserObjectSingle):
if not excitationfile.exists():
excitationfile = Path(config.sim_config.input_file_path.parent, excitationfile)
log.info(f'Excitation file: {excitationfile}')
logger.info(f'Excitation file: {excitationfile}')
# Get waveform names
with open(excitationfile, 'r') as f:
@@ -436,7 +410,7 @@ class ExcitationFile(UserObjectSingle):
# Interpolate waveform values
w.userfunc = interpolate.interp1d(waveformtime, singlewaveformvalues, **kwargs)
log.info(f"User waveform {w.ID} created using {timestr} and, if required, interpolation parameters (kind: {kwargs['kind']}, fill value: {kwargs['fill_value']}).")
logger.info(f"User waveform {w.ID} created using {timestr} and, if required, interpolation parameters (kind: {kwargs['kind']}, fill value: {kwargs['fill_value']}).")
G.waveforms.append(w)

48
gprMax/config.py
查看文件

@@ -35,8 +35,7 @@ from .utilities import detect_check_gpus
from .utilities import get_host_info
from .utilities import get_terminal_width
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
# Single instance of SimConfig to hold simulation configuration parameters.
sim_config = None
@@ -185,12 +184,12 @@ class SimulationConfig:
# General settings for the simulation
# inputfilepath: path to inputfile location
# outputfilepath: path to outputfile location
# messages: whether to print all messages as output to stdout or not
# progressbars: whether to show progress bars on stdoout or not
# cpu, cuda, opencl: solver type
# subgrid: whether the simulation uses sub-grids
# precision: data type for electromagnetic field output (single/double)
self.general = {'messages': True,
self.general = {'log_level': logging.WARNING,
'progressbars': True,
'cpu': True,
'cuda': False,
@@ -224,6 +223,10 @@ class SimulationConfig:
if any(isinstance(element, list) for element in self.args.gpu):
self.args.gpu = [val for sublist in self.args.gpu for val in sublist]
# If no deviceID is given default to 0
if not self.args.gpu:
self.args.gpu = [0]
self.cuda['gpus'] = detect_check_gpus(self.args.gpu)
# Subgrid parameter may not exist if user enters via CLI
@@ -243,20 +246,21 @@ class SimulationConfig:
self.scenes = []
# Set more complex parameters
self.set_precision()
self.get_byteorder()
self.set_input_file_path()
self.set_model_start_end()
self.set_single_model()
def is_messages(self):
return self.general['messages']
self._set_precision()
self._get_byteorder()
self._set_input_file_path()
self._set_model_start_end()
self._set_single_model()
def set_model_gpu(self):
"""Specify single GPU object for model."""
return self.cuda['gpus'][0]
"""Specify single GPU object for model.
Uses first GPU deviceID if list of deviceID given."""
def set_precision(self):
for gpu in self.cuda['gpus']:
if gpu.deviceID == self.args.gpu[0]:
return gpu
def _set_precision(self):
"""Data type (precision) for electromagnetic field output.
Solid and ID arrays use 32-bit integers (0 to 4294967295)
@@ -283,19 +287,19 @@ class SimulationConfig:
'C_complex': 'pycuda::complex<double>',
'vtk_float': 'Float64'}
def get_byteorder(self):
def _get_byteorder(self):
"""Check the byte order of system to use for VTK files, i.e. geometry
views and snapshots.
"""
self.vtk_byteorder = 'LittleEndian' if sys.byteorder == 'little' else 'BigEndian'
def set_single_model(self):
def _set_single_model(self):
if self.model_start == 0 and self.model_end == 1:
self.single_model = True
else:
self.single_model = False
def set_model_start_end(self):
def _set_model_start_end(self):
"""Set range for number of models to run (internally 0 index)."""
if self.args.task:
# Job array feeds args.n number of single tasks
@@ -311,7 +315,7 @@ class SimulationConfig:
self.model_start = modelstart
self.model_end = modelend
def set_input_file_path(self):
def _set_input_file_path(self):
"""Set input file path for CLI or API."""
# API
if self.args.inputfile is None:
@@ -329,11 +333,11 @@ class SimulationConfigMPI(SimulationConfig):
def __init__(self, args):
super().__init__(args)
def set_model_start_end(self):
def _set_model_start_end(self):
# Set range for number of models to run
self.model_start = self.args.restart if self.args.restart else 1
self.model_end = self.modelstart + self.args.n
self.model_end = self.model_start + self.args.n
def set_gpus(self):
def set_model_gpu(self):
"""Leave list of GPU object(s) as multi-object list."""
pass

67
gprMax/contexts.py
查看文件

@@ -50,10 +50,33 @@ class Context:
if config.sim_config.general['cuda']:
self.print_gpu_info()
self.tsimstart = timer()
# Clear list of model configs. It can be retained when gprMax is
# called in a loop, and want to avoid this.
config.model_configs = []
self._run()
self.tsimend = timer()
self.print_time_report()
def _run_model(self, i):
"""Process for running a single model."""
config.model_num = i
write_model_config()
# Always create a grid for the first model. The next model to run
# only gets a new grid if the geometry is not re-used.
if i != 0 and config.sim_config.args.geometry_fixed:
config.get_model_config().reuse_geometry = True
else:
G = create_G()
model = ModelBuildRun(G)
model.build()
solver = create_solver(G)
if not config.sim_config.args.geometry_only:
model.solve(solver)
def print_logo_copyright(self):
"""Print gprMax logo, version, and copyright/licencing information."""
logo(__version__ + ' (' + codename + ')')
@@ -82,29 +105,9 @@ class NoMPIContext(Context):
"""
def _run(self):
"""Specialise how the models are farmed out."""
# Clear list of model configs. It can be retained with gprMax is
# called in a loop, and want to avoid this.
config.model_configs = []
"""Specialise how models are run."""
for i in self.model_range:
config.model_num = i
write_model_config()
# Always create a grid for the first model. The next model to run
# only gets a new grid if the geometry is not re-used.
if i != 0 and config.sim_config.args.geometry_fixed:
config.get_model_config().reuse_geometry = True
else:
G = create_G()
model = ModelBuildRun(G)
model.build()
solver = create_solver(G)
if not config.sim_config.args.geometry_only:
model.solve(solver)
self._run_model(i)
class MPIContext(Context):
@@ -116,9 +119,27 @@ class MPIContext(Context):
def __init__(self):
super().__init__()
from mpi4py import MPI
from gprMax.mpi import MPIExecutor
self.comm = MPI.COMM_WORLD
self.rank = self.comm.rank
self.MPIExecutor = MPIExecutor
def _run(self):
pass
"""Specialise how the models are run."""
# compile jobs
jobs = []
for i in range(config.sim_config.args.n):
jobs.append({'i': i})
# Execute jobs
log.info(f'Starting execution of {config.sim_config.args.n} gprMax model runs.')
with self.MPIExecutor(self._run_model, comm=self.comm) as executor:
if executor is not None:
results = executor.submit(jobs)
log.info('Results: %s' % str(results))
log.info('Finished.')
def create_context():

6
gprMax/exceptions.py
查看文件

@@ -22,7 +22,7 @@ from colorama import init
from colorama import Fore
init()
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class GeneralError(ValueError):
@@ -30,7 +30,7 @@ class GeneralError(ValueError):
def __init__(self, message, *args):
self.message = message
super(GeneralError, self).__init__(message, *args)
log.exception(Fore.RED)
logger.exception(Fore.RED)
class CmdInputError(Exception):
@@ -41,4 +41,4 @@ class CmdInputError(Exception):
# def __init__(self, message, *args):
# self.message = message
# super(CmdInputError, self).__init__(message, *args)
# log.exception(Fore.RED)
# logger.exception(Fore.RED)

4
gprMax/fields_outputs.py
查看文件

@@ -24,7 +24,7 @@ import h5py
from ._version import __version__
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
def store_outputs(G):
@@ -126,7 +126,7 @@ def write_hdf5_outputfile(outputfile, G):
write_grid(grp, sg, is_subgrid=True)
if G.rxs or sg_rxs:
log.info(f'Written output file: {outputfile.name}')
logger.info(f'Written output file: {outputfile.name}')
def write_grid(basegrp, G, is_subgrid=False):

10
gprMax/geometry_outputs.py
查看文件

@@ -31,7 +31,7 @@ from .cython.geometry_outputs import define_normal_geometry
from .cython.geometry_outputs import define_fine_geometry
from .utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class GeometryView:
@@ -482,7 +482,7 @@ class GeometryViewFineMultiGrid:
f.write('</Piece>\n</PolyData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
# Write points
log.info('\nWriting points main grid')
logger.info('\nWriting points main grid')
datasize = np.dtype(np.float32).itemsize * self.vtk_numpoints * self.vtk_numpoint_components
f.write(pack('I', datasize))
for i in range(0, G.nx + 1):
@@ -491,7 +491,7 @@ class GeometryViewFineMultiGrid:
f.write(pack('fff', i * G.dx, j * G.dy, k * G.dz))
for sg_v in self.sg_views:
log.info('Writing points subgrid')
logger.info('Writing points subgrid')
sg_v.write_points(f, G)
n_x_lines = self.nx * (self.ny + 1) * (self.nz + 1)
@@ -506,7 +506,7 @@ class GeometryViewFineMultiGrid:
z_lines = np.zeros((n_z_lines, 2), dtype=np.uint32)
z_materials = np.zeros((n_z_lines), dtype=np.uint32)
log.info('Calculate connectivity main grid')
logger.info('Calculate connectivity main grid')
label = 0
counter_x = 0
counter_y = 0
@@ -538,7 +538,7 @@ class GeometryViewFineMultiGrid:
label = label + 1
log.info('Calculate connectivity subgrids')
logger.info('Calculate connectivity subgrids')
for sg_v in self.sg_views:
sg_v.populate_connectivity_and_materials(label)
# use the last subgrids label for the next view

67
gprMax/gprMax.py
查看文件

@@ -21,11 +21,9 @@ import logging
from .config_parser import write_simulation_config
from .contexts import create_context
from .utilities import setup_logging
# Configure logging
log = logging.getLogger(__name__)
# logging.basicConfig(level=logging.DEBUG, format='%(module)s %(lineno)d %(message)s')
logging.basicConfig(level=logging.INFO, format='%(message)s')
logger = logging.getLogger(__name__)
def run(
@@ -36,8 +34,6 @@ def run(
task=None,
restart=None,
mpi=False,
mpi_no_spawn=False,
mpicomm=None,
gpu=None,
subgrid=None,
autotranslate=False,
@@ -45,7 +41,7 @@ def run(
geometry_fixed=False,
write_processed=False,
):
"""This is the main function for gprMax when entering as application
"""This is the main function for gprMax when entering using application
programming interface (API). Run the simulation for the
given list of scenes.
@@ -75,13 +71,13 @@ def run(
from A-scan 45 when creating a B-scan with 60 traces.
:type restart: int, optional
:param mpi: number of Message Passing Interface (MPI) tasks,
i.e. master + workers, for MPI task farm. This option is most
usefully combined with n to allow individual models to be farmed
out using a MPI task farm, e.g. to create a B-scan with 60 traces
and use MPI to farm out each trace1. For further details see the
parallel performance section of the User Guide.
:type mpi: int, optional
:param mpi: flag to use Message Passing Interface (MPI) task farm. This
option is most usefully combined with n to allow individual
models to be farmed out using a MPI task farm, e.g. to create a
B-scan with 60 traces and use MPI to farm out each trace.
For further details see the parallel performance section of the
User Guide.
:type mpi: bool, optional
:param gpu: flag to use NVIDIA GPU or list of NVIDIA GPU device ID(s) for
specific GPU card(s).
@@ -122,7 +118,6 @@ def run(
args.task = task
args.restart = restart
args.mpi = mpi
args.mpicomm = mpicomm
args.gpu = gpu
args.subgrid = subgrid
args.autotranslate = autotranslate
@@ -133,29 +128,47 @@ def run(
try:
run_main(args)
except Exception:
log.exception('Error from main API function', exc_info=True)
logger.exception('Error from main API function', exc_info=True)
def main():
"""Main function for gprMax when entering from the command line interface (CLI)."""
"""Main function for gprMax when entering using the command line interface (CLI)."""
# Parse command line arguments
parser = argparse.ArgumentParser(prog='gprMax', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('inputfile', help='path to, and name of inputfile or file object')
parser.add_argument('-n', default=1, type=int, help='number of times to run the input file, e.g. to create a B-scan')
parser.add_argument('-task', type=int, help='task identifier (model number) for job array on Open Grid Scheduler/Grid Engine (http://gridscheduler.sourceforge.net/index.html)')
parser.add_argument('-restart', type=int, help='model number to restart from, e.g. when creating B-scan')
parser.add_argument('-mpi', type=int, help='number of MPI tasks, i.e. master + workers')
parser.add_argument('-gpu', type=int, action='append', nargs='*', help='flag to use Nvidia GPU or option to give list of device ID(s)')
parser.add_argument('--geometry-only', action='store_true', default=False, help='flag to only build model and produce geometry file(s)')
parser.add_argument('--geometry-fixed', action='store_true', default=False, help='flag to not reprocess model geometry, e.g. for B-scans where the geometry is fixed')
parser.add_argument('--write-processed', action='store_true', default=False, help='flag to write an input file after any Python code and include commands in the original input file have been processed')
parser.add_argument('inputfile',
help='relative or absolute path to inputfile')
parser.add_argument('-n', default=1, type=int,
help='number of times to run the input file, e.g. to create a B-scan')
parser.add_argument('-task', type=int,
help='task identifier (model number) for job array on '
'Open Grid Scheduler/Grid Engine (http://gridscheduler.sourceforge.net/index.html)')
parser.add_argument('-r', '--restart', type=int,
help='model number to restart from, e.g. when creating B-scan')
parser.add_argument('-mpi', action='store_true', default=False,
help='flag to enable MPI task farming')
parser.add_argument('-gpu', type=int, action='append', nargs='*',
help='flag to use Nvidia GPU or option to give list of device ID(s)')
parser.add_argument('--geometry-only', action='store_true', default=False,
help='flag to only build model and produce geometry file(s)')
parser.add_argument('--geometry-fixed', action='store_true', default=False,
help='flag to not reprocess model geometry, e.g. for B-scans where the geometry is fixed')
parser.add_argument('--write-processed', action='store_true', default=False,
help='flag to write an input file after any Python code and include commands '
'in the original input file have been processed')
parser.add_argument('-l', '--logfile', action='store_true', default=False,
help='flag to enable writing to a log file')
parser.add_argument('-v', '--verbose', action='store_true', default=False,
help="flag to increase output")
args = parser.parse_args()
setup_logging()
try:
run_main(args)
except Exception:
log.exception('Error from main CLI function', exc_info=True)
logger.exception('Error from main CLI function', exc_info=True)
def run_main(args):
"""Called by either run (API) or main (CLI).

12
gprMax/hash_cmds_file.py
查看文件

@@ -28,7 +28,7 @@ from .hash_cmds_geometry import process_geometrycmds
from .hash_cmds_multiuse import process_multicmds
from .hash_cmds_singleuse import process_singlecmds
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
def process_python_include_code(inputfile, usernamespace):
@@ -62,7 +62,7 @@ def process_python_include_code(inputfile, usernamespace):
# Process any Python code
if(inputlines[x].startswith('#python:')):
log.warning('#python blocks are deprecated and will be removed in the next release of gprMax. Please convert your model to use our Python API instead.\n')
logger.warning('#python blocks are deprecated and will be removed in the next release of gprMax. Please convert your model to use our Python API instead.\n')
# String to hold Python code to be executed
pythoncode = ''
x += 1
@@ -99,7 +99,7 @@ def process_python_include_code(inputfile, usernamespace):
# Print any generated output that is not commands
if pythonout:
log.info(f'Python messages (from stdout/stderr): {pythonout}\n')
logger.info(f'Python messages (from stdout/stderr): {pythonout}\n')
# Add any other commands to list
elif(inputlines[x].startswith('#')):
@@ -157,7 +157,7 @@ def process_include_files(hashcmds, inputfile):
x += 1
return processedincludecmds
logger
def write_processed_file(processedlines, G):
"""Writes an input file after any Python code and include commands
@@ -176,7 +176,7 @@ def write_processed_file(processedlines, G):
for item in processedlines:
f.write(f'{item}')
log.info(f'Written input commands, after processing any Python code and include commands, to file: {processedfile}\n')
logger.info(f'Written input commands, after processing any Python code and include commands, to file: {processedfile}\n')
def check_cmd_names(processedlines, checkessential=True):
@@ -306,7 +306,7 @@ def parse_hash_commands(scene, G):
for key, value in sorted(usernamespace.items()):
if key != '__builtins__':
uservars += f'{key}: {value}, '
log.info(f'Constants/variables used/available for Python scripting: {{{uservars[:-2]}}}\n')
logger.info(f'Constants/variables used/available for Python scripting: {{{uservars[:-2]}}}\n')
# Write a file containing the input commands after Python or include
# file commands have been processed

12
gprMax/hash_cmds_singleuse.py
查看文件

@@ -16,7 +16,6 @@
# You should have received a copy of the GNU General Public License
# along with gprMax. If not, see <http://www.gnu.org/licenses/>.
from .cmds_single_use import Messages
from .cmds_single_use import Title
from .cmds_single_use import NumThreads
from .cmds_single_use import Discretisation
@@ -46,15 +45,6 @@ def process_singlecmds(singlecmds):
scene_objects = []
# Check validity of command parameters in order needed
cmd = '#messages'
if singlecmds[cmd] is not None:
tmp = singlecmds[cmd].split()
if len(tmp) != 1:
raise CmdInputError(cmd + ' requires exactly one parameter')
messages = Messages(yn=str(tmp[0]))
scene_objects.append(messages)
cmd = '#title'
if singlecmds[cmd] is not None:
title = Title(name=str(singlecmds[cmd]))
@@ -141,7 +131,7 @@ def process_singlecmds(singlecmds):
tmp = singlecmds[cmd].split()
if len(tmp) != 3:
raise CmdInputError(cmd + ' requires exactly three parameters')
p1 = (float(tmp[0]), float(tmp[1]), float(tmp[2]))
src_steps = SrcSteps(p1=p1)
scene_objects.append(src_steps)

48
gprMax/model_build_run.py
查看文件

@@ -50,7 +50,7 @@ from .utilities import human_size
from .utilities import mem_check_all
from .utilities import set_omp_threads
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class ModelBuildRun:
@@ -78,7 +78,7 @@ class ModelBuildRun:
# Normal model reading/building process; bypassed if geometry information to be reused
self.build_geometry() if not config.get_model_config().reuse_geometry else self.reuse_geometry()
log.info(f'\nOutput directory: {config.get_model_config().output_file_path.parent.resolve()}')
logger.info(f'\nOutput directory: {config.get_model_config().output_file_path.parent.resolve()}')
# Adjust position of simple sources and receivers if required
if G.srcsteps[0] != 0 or G.srcsteps[1] != 0 or G.srcsteps[2] != 0:
@@ -110,9 +110,9 @@ class ModelBuildRun:
# Write files for any geometry views and geometry object outputs
if not (G.geometryviews or G.geometryobjectswrite) and config.sim_config.args.geometry_only:
log.warning(Fore.RED + f'\nNo geometry views or geometry objects found.' + Style.RESET_ALL)
logger.warning(Fore.RED + f'\nNo geometry views or geometry objects found.' + Style.RESET_ALL)
for i, geometryview in enumerate(G.geometryviews):
log.info('')
logger.info('')
geometryview.set_filename()
pbar = tqdm(total=geometryview.datawritesize, unit='byte', unit_scale=True,
desc=f'Writing geometry view file {i + 1}/{len(G.geometryviews)}, {geometryview.filename.name}',
@@ -121,7 +121,7 @@ class ModelBuildRun:
geometryview.write_vtk(G, pbar)
pbar.close()
for i, geometryobject in enumerate(G.geometryobjectswrite):
log.info('')
logger.info('')
pbar = tqdm(total=geometryobject.datawritesize, unit='byte', unit_scale=True,
desc=f'Writing geometry object file {i + 1}/{len(G.geometryobjectswrite)}, {geometryobject.filename.name}',
ncols=get_terminal_width() - 1, file=sys.stdout,
@@ -132,13 +132,13 @@ class ModelBuildRun:
def build_geometry(self):
G = self.G
log.info(config.get_model_config().inputfilestr)
logger.info(config.get_model_config().inputfilestr)
scene = self.build_scene()
# Print info on any subgrids
for grid in G.subgrids:
log.info(grid)
logger.info(grid)
# Combine available grids
grids = [G] + G.subgrids
@@ -154,12 +154,12 @@ class ModelBuildRun:
# Check memory requirements
total_mem, mem_strs = mem_check_all(grids)
log.info(f'\nMemory required: {" + ".join(mem_strs)} + ~{human_size(config.get_model_config().mem_overhead)} overhead = {human_size(total_mem)}')
logger.info(f'\nMemory required: {" + ".join(mem_strs)} + ~{human_size(config.get_model_config().mem_overhead)} overhead = {human_size(total_mem)}')
# Build grids
gridbuilders = [GridBuilder(grid) for grid in grids]
for gb in gridbuilders:
log.info(print_pml_info(gb.grid))
logger.info(print_pml_info(gb.grid))
if not all(value == 0 for value in gb.grid.pmlthickness.values()):
gb.build_pmls()
gb.build_components()
@@ -175,21 +175,21 @@ class ModelBuildRun:
# Check to see if numerical dispersion might be a problem
results = dispersion_analysis(gb.grid)
if results['error']:
log.warning(Fore.RED + f"\nNumerical dispersion analysis [{gb.grid.name}] not carried out as {results['error']}" + Style.RESET_ALL)
logger.warning(Fore.RED + f"\nNumerical dispersion analysis [{gb.grid.name}] not carried out as {results['error']}" + Style.RESET_ALL)
elif results['N'] < config.get_model_config().numdispersion['mingridsampling']:
raise GeneralError(f"\nNon-physical wave propagation in [{gb.grid.name}] detected. Material '{results['material'].ID}' has wavelength sampled by {results['N']} cells, less than required minimum for physical wave propagation. Maximum significant frequency estimated as {results['maxfreq']:g}Hz")
elif (results['deltavp'] and np.abs(results['deltavp']) >
config.get_model_config().numdispersion['maxnumericaldisp']):
log.warning(Fore.RED + f"\n[{gb.grid.name}] has potentially significant numerical dispersion. Estimated largest physical phase-velocity error is {results['deltavp']:.2f}% in material '{results['material'].ID}' whose wavelength sampled by {results['N']} cells. Maximum significant frequency estimated as {results['maxfreq']:g}Hz" + Style.RESET_ALL)
logger.warning(Fore.RED + f"\n[{gb.grid.name}] has potentially significant numerical dispersion. Estimated largest physical phase-velocity error is {results['deltavp']:.2f}% in material '{results['material'].ID}' whose wavelength sampled by {results['N']} cells. Maximum significant frequency estimated as {results['maxfreq']:g}Hz" + Style.RESET_ALL)
elif results['deltavp']:
log.info(f"\nNumerical dispersion analysis [{gb.grid.name}]: estimated largest physical phase-velocity error is {results['deltavp']:.2f}% in material '{results['material'].ID}' whose wavelength sampled by {results['N']} cells. Maximum significant frequency estimated as {results['maxfreq']:g}Hz")
logger.info(f"\nNumerical dispersion analysis [{gb.grid.name}]: estimated largest physical phase-velocity error is {results['deltavp']:.2f}% in material '{results['material'].ID}' whose wavelength sampled by {results['N']} cells. Maximum significant frequency estimated as {results['maxfreq']:g}Hz")
def reuse_geometry(self):
# Reset iteration number
self.G.iteration = 0
s = f'\n--- Model {config.get_model_config().appendmodelnumber}/{config.sim_config.model_end}, input file (not re-processed, i.e. geometry fixed): {config.sim_config.input_file_path}'
config.get_model_config().inputfilestr = Fore.GREEN + f"{s} {'-' * (get_terminal_width() - 1 - len(s))}\n" + Style.RESET_ALL
log.info(config.get_model_config().inputfilestr)
logger.info(config.get_model_config().inputfilestr)
for grid in [self.G] + self.G.subgrids:
grid.reset_fields()
@@ -223,7 +223,7 @@ class ModelBuildRun:
snapshotdir = config.get_model_config().snapshot_file_path
snapshotdir.mkdir(exist_ok=True)
log.info('')
logger.info('')
for i, snap in enumerate(self.G.snapshots):
fn = snapshotdir / Path(snap.filename)
snap.filename = fn.with_suffix('.vti')
@@ -231,7 +231,7 @@ class ModelBuildRun:
unit_scale=True, desc=f'Writing snapshot file {i + 1} of {len(self.G.snapshots)}, {snap.filename.name}', ncols=get_terminal_width() - 1, file=sys.stdout, disable=not config.sim_config.general['progressbars'])
snap.write_vtk_imagedata(pbar, self.G)
pbar.close()
log.info('')
logger.info('')
def print_resource_info(self, tsolve, memsolve):
"""Print resource information on runtime and memory usage.
@@ -245,8 +245,8 @@ class ModelBuildRun:
if config.sim_config.general['cuda']:
mem_str = f' host + ~{human_size(memsolve)} GPU'
log.info(f'\nMemory used: ~{human_size(self.p.memory_full_info().uss)}{mem_str}')
log.info(f'Solving time [HH:MM:SS]: {datetime.timedelta(seconds=tsolve)}')
logger.info(f'\nMemory used: ~{human_size(self.p.memory_full_info().uss)}{mem_str}')
logger.info(f'Solving time [HH:MM:SS]: {datetime.timedelta(seconds=tsolve)}')
def solve(self, solver):
"""Solve using FDTD method.
@@ -260,15 +260,15 @@ class ModelBuildRun:
# Check number of OpenMP threads
if config.sim_config.general['cpu']:
log.info(f'CPU (OpenMP) threads for solving: {config.get_model_config().ompthreads}\n')
logger.info(f'CPU (OpenMP) threads for solving: {config.get_model_config().ompthreads}\n')
if config.get_model_config().ompthreads > config.sim_config.hostinfo['physicalcores']:
log.warning(Fore.RED + f"You have specified more threads ({config.get_model_config().ompthreads}) than available physical CPU cores ({config.sim_config.hostinfo['physicalcores']}). This may lead to degraded performance." + Style.RESET_ALL)
logger.warning(Fore.RED + f"You have specified more threads ({config.get_model_config().ompthreads}) than available physical CPU cores ({config.sim_config.hostinfo['physicalcores']}). This may lead to degraded performance." + Style.RESET_ALL)
# Print information about any GPU in use
elif config.sim_config.general['cuda']:
log.info(f"GPU for solving: {config.get_model_config().cuda['gpu'].deviceID} - {config.get_model_config().cuda['gpu'].name}\n")
logger.info(f"GPU for solving: {config.get_model_config().cuda['gpu'].deviceID} - {config.get_model_config().cuda['gpu'].name}\n")
# Prepare iterator
if config.sim_config.is_messages():
if config.sim_config.general['progressbars']:
iterator = tqdm(range(self.G.iterations), desc=f'Running model {config.model_num + 1}/{config.sim_config.model_end}', ncols=get_terminal_width() - 1, file=sys.stdout, disable=not config.sim_config.general['progressbars'])
else:
iterator = range(self.G.iterations)
@@ -303,7 +303,7 @@ class GridBuilder:
def build_components(self):
# Build the model, i.e. set the material properties (ID) for every edge
# of every Yee cell
log.info('')
logger.info('')
pbar = tqdm(total=2, desc=f'Building Yee cells [{self.grid.name}]',
ncols=get_terminal_width() - 1, file=sys.stdout,
disable=not config.sim_config.general['progressbars'])
@@ -335,5 +335,5 @@ class GridBuilder:
materialstable.outer_border = False
materialstable.justify_columns[0] = 'right'
log.info(f'\nMaterials [{self.grid.name}]:')
log.info(materialstable.table)
logger.info(f'\nMaterials [{self.grid.name}]:')
logger.info(materialstable.table)

463
gprMax/mpi.py 普通文件
查看文件

@@ -0,0 +1,463 @@
# Copyright (C) 2015-2020: The University of Edinburgh
# Authors: Tobias Schruff
#
# This file is part of gprMax.
#
# gprMax is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# gprMax is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# 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 gprMax. If not, see <http://www.gnu.org/licenses/>.
from enum import IntEnum
import logging
import time
from mpi4py import MPI
_log = logging.getLogger(__name__)
"""
MPI communication tags.
READY
Send by worker to master to signal that it is ready to receive a new job.
START
Send by master to worker together with a job dict to initiate work.
DONE
Send by worker to master together with the results of the current job.
EXIT
Send by master to worker to initiate worker shutdown and then
send back to master to signal shutdown has completed.
"""
Tags = IntEnum('Tags', 'READY START DONE EXIT')
class MPIExecutor(object):
"""A generic parallel executor based on MPI.
This executor can be used to run generic jobs on multiple
processes based on a master/worker pattern with MPI being used for
communication between the master and the workers.
Examples
--------
A basic example of how to use the `MPIExecutor` to run
`gprMax` models in parallel is given below.
>>> from mpi4py import MPI
>>> from gprMax.mpi import MPIExecutor
>>> from gprMax.model_build_run import run_model
>>> # choose an MPI.Intracomm for communication (MPI.COMM_WORLD by default)
>>> comm = MPI.COMM_WORLD
>>> # choose a target function
>>> func = run_model
>>> # define job parameters
>>> inputfile = 'some_input_file.in'
>>> n_traces = 10
>>> jobs = []
>>> # create jobs
>>> for i in range(n_traces):
>>> jobs.append({
>>> 'inputfile': inputfile,
>>> 'currentmodelrun': i + 1,
>>> 'modelend': n_traces,
>>> 'numbermodelruns': n_traces
>>> })
>>> gpr = MPIExecutor(func, comm=comm)
>>> # send the workers to their work loop
>>> gpr.start()
>>> if gpr.is_master():
>>> results = gpr.submit(jobs)
>>> print('Results:', results)
>>> # make the workers exit their work loop
>>> # and join the main loop again
>>> gpr.join()
A slightly more concise way is to use the context manager
interface of `MPIExecutor` that automatically takes care
of calling `start()` and `join()` at the beginning and end
of the execution, respectively.
>>> with MPIExecutor(func, comm=comm) as executor:
>>> # executor will be None on all ranks except for the master
>>> if executor is not None:
>>> results = executor.submit(jobs)
>>> print('Results:', results)
Limitations
-----------
Because some popular MPI implementations (especially on HPC machines) do not
support concurrent MPI calls from multiple threads yet, the `MPIExecutor` does
not use a separate thread in the master to do the communication between the
master and the workers. Hence, the lowest thread level of MPI_THREAD_SINGLE
(no multi-threading) is enough.
However, this imposes some slight limitations on the usage since it is not
possible to interact with the workers during a call to `submit()` until
`submit()` returns.
In particular, it is not possible to handle exceptions that occur on workers
in the main loop. Instead all exceptions that occur on workers are caught and
logged and the worker returns None instead of the actual result of the worker
function. A second limitation is that it is not possible to terminate workers.
If you need an MPI executor that supports custom exception handling, you should
use a multi-threading implementation such as the `MPICommExecutor` in
`mpi4py.futures`. Below is a brief example of how to use it with the example
given above.
>>> from mpi4py.futures import MPICommExecutor
>>> from concurrent.futures import as_completed
>>> # define comm, func, and jobs like above
>>> with MPICommExecutor(comm, root=0) as executor:
>>> if executor is not None:
>>> futures = [executor.submit(func, **job) for job in jobs]
>>> for future in as_completed(futures):
>>> try:
>>> print(future.result())
>>> except Exception as e:
>>> # custom exception handling for exceptions
>>> # raised in the worker
>>> print(e)
>>> comm.Abort()
"""
def __init__(self, func, master=0, comm=None):
"""Initializes a new executor instance.
Parameters
----------
func: callable
The worker function. Jobs will be passed as keyword arguments,
so `func` must support this. This is usually the case, but
can be a problem when builtin functions are used, e.g. `abs()`.
master: int
The rank of the master. Must be in `comm`. All other
ranks in `comm` will be treated as workers.
comm: MPI.Intracomm
The MPI communicator used for communication between the
master and workers.
"""
if comm is None:
self.comm = MPI.COMM_WORLD
elif not comm.Is_intra():
raise TypeError('MPI.Intracomm expected')
else:
self.comm = comm
self.rank = self.comm.rank
self.size = self.comm.size
if self.size < 2:
raise RuntimeError('MPIExecutor must run with at least 2 processes')
self._up = False
master = int(master)
if master < 0:
raise ValueError('master rank must be non-negative')
elif master >= self.size:
raise ValueError('master not in comm')
else:
self.master = master
# the worker ranks
self.workers = tuple(set(range(self.size)) - {self.master})
# the worker function
if not callable(func):
raise TypeError('func must be a callable')
self.func = func
# holds the state of workers on the master
self.busy = [False] * len(self.workers)
_log.debug(f'MPIExecutor on comm: {self.comm.name}, Master: {self.master}, Workers: {self.workers}')
if self.is_master():
_log.debug('*** MASTER ***')
else:
_log.debug('*** WORKER ***')
def __enter__(self):
"""Context manager enter.
Only the master returns an executor,
all other ranks return None.
"""
self.start()
if self.is_master():
return self
return None
def __exit__(self, exc_type, exc_val, exc_tb):
"""Context manager exit.
"""
if exc_type is not None:
_log.exception(exc_val)
return False
# no exception handling necessary
# since we catch everything in __guarded_work
# exc_type should always be None
self.join()
return True
def is_idle(self):
"""Returns a bool indicating whether the executor is idle.
The executor is considered to be not idle if *any* worker
process is busy with a job. That means, it is idle only
if *all* workers are idle.
Note: This member must not be called on a worker.
"""
assert self.is_master()
return not any(self.busy)
def is_master(self):
"""Returns a bool indicating whether `self` is the master.
"""
return self.rank == self.master
def is_worker(self):
"""Returns a bool indicating whether `self` is a worker.
"""
return not self.is_master()
def start(self):
"""Starts up workers.
A check is performed on the master whether the executor
has already been terminated, in which case a RuntimeError
is raised on the master.
"""
if self.is_master():
if self._up:
raise RuntimeError('start has already been called')
self._up = True
_log.info('Starting up MPIExecutor master/workers')
if self.is_worker():
self.__wait()
def join(self):
"""Joins the workers.
"""
if self.is_master():
_log.debug('Terminating. Sending sentinel to all workers.')
# send sentinel to all workers
for worker in self.workers:
self.comm.send(None, dest=worker, tag=Tags.EXIT)
_log.debug('Waiting for all workers to terminate.')
down = [False] * len(self.workers)
while True:
for i, worker in enumerate(self.workers):
if self.comm.Iprobe(source=worker, tag=Tags.EXIT):
self.comm.recv(source=worker, tag=Tags.EXIT)
down[i] = True
if all(down):
break
self._up = False
_log.debug('All workers terminated.')
def submit(self, jobs, sleep=0.0):
"""Submits a list of jobs to the workers and returns the results.
Parameters
----------
jobs: list
A list of keyword argument dicts. Each dict describes
a job and will be unpacked and supplied to the work function.
sleep: float
The number of seconds the master will sleep for when trying
to find an idle worker. The default value is 0.0, which means
the master will not sleep at all.
Returns
-------
results: list
A list of results, i.e. the return values of the work function,
received from the workers. The order of results is identical to
the order of `jobs`.
"""
if not self._up:
raise RuntimeError('cannot run jobs without a call to start()')
_log.info('Running {:d} jobs.'.format(len(jobs)))
assert self.is_master(), 'run() must not be called on a worker process'
my_jobs = jobs.copy()
num_jobs = len(my_jobs)
results = [None] * num_jobs
while len(my_jobs) or not self.is_idle():
for i, worker in enumerate(self.workers):
if self.comm.Iprobe(source=worker, tag=Tags.DONE):
job_idx, result = self.comm.recv(source=worker, tag=Tags.DONE)
_log.debug(f'Received finished job {job_idx} from worker {worker:d}.')
results[job_idx] = result
self.busy[i] = False
elif self.comm.Iprobe(source=worker, tag=Tags.READY):
if len(my_jobs):
self.comm.recv(source=worker, tag=Tags.READY)
self.busy[i] = True
job_idx = num_jobs - len(my_jobs)
_log.debug(f'Sending job {job_idx} to worker {worker:d}.')
self.comm.send((job_idx, my_jobs.pop(0)), dest=worker, tag=Tags.START)
elif self.comm.Iprobe(source=worker, tag=Tags.EXIT):
_log.debug(f'Worker on rank {worker:d} has terminated.')
self.comm.recv(source=worker, tag=Tags.EXIT)
self.busy[i] = False
time.sleep(sleep)
_log.info('Finished all jobs.')
return results
def __wait(self):
"""The worker main loop.
The worker will enter the loop after `start()` has been called
and stay here until it receives the sentinel, e.g. by calling
`join()` on the master. In the mean time, the worker is
accepting work.
"""
assert self.is_worker()
status = MPI.Status()
_log.debug(f'Starting up worker.')
while True:
self.comm.send(None, dest=self.master, tag=Tags.READY)
_log.debug(f'Worker on rank {self.rank} waiting for job.')
data = self.comm.recv(source=self.master, tag=MPI.ANY_TAG, status=status)
tag = status.tag
if tag == Tags.START:
job_idx, work = data
_log.debug(f'Received job {job_idx} (work={work}).')
result = self.__guarded_work(work)
_log.debug(f'Finished job. Sending results to master.')
self.comm.send((job_idx, result), dest=self.master, tag=Tags.DONE)
elif tag == Tags.EXIT:
_log.debug(f'Received sentinel from master.')
break
_log.debug('Terminating worker.')
self.comm.send(None, dest=self.master, tag=Tags.EXIT)
def __guarded_work(self, work):
"""Executes work safely on the workers.
Parameters
----------
work: dict
Keyword arguments that are unpacked and given to the
work function.
Notes
-----
All exceptions that occur in the work function `func` are caught
and logged. The worker returns `None` to the master in that case
instead of the actual result.
"""
assert self.is_worker()
try:
return self.func(**work)
except Exception as e:
_log.exception(str(e))
return None
# def main(args=None):
# """CLI for gprMax in MPI mode.
# Example Usage:
# mpirun -np 4 python -m mpi -n 10 my_input_file.in
# """
# import argparse
# import os
# from gprMax.constants import c, e0, m0, z0
# from gprMax.model_build_run import run_model
#
# # Parse command line arguments
# parser = argparse.ArgumentParser(prog='gprMax', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# parser.add_argument(
# 'inputfile',
# help='relative or absolute path to inputfile.')
# parser.add_argument(
# '-n', '--num-traces', type=int, default=1,
# help='number of model runs (traces) to create a B-scan')
# parser.add_argument(
# '--geometry-only', action='store_true', default=False,
# help='flag to only build model and produce geometry file(s)')
# parser.add_argument(
# '--geometry-fixed', action='store_true', default=False,
# help='flag to not reprocess model geometry, e.g. for B-scans where the geometry is fixed')
# parser.add_argument(
# '--write-processed', action='store_true', default=False,
# help='flag to write an input file after any Python code and include commands '
# 'in the original input file have been processed')
# parser.add_argument(
# '-r', '--restart', type=int, default=1,
# help='model number to restart from, e.g. when creating B-scan')
# parser.add_argument(
# '-l', '--logfile', action='store_true', default=False,
# help='flag to enable writing to a log file')
# parser.add_argument(
# '-v', '--verbose', action='store_true', default=False,
# help="flag to increase output")
# parser.add_argument(
# '--gpu', type=int, action='append', nargs='*',
# help='flag to use Nvidia GPU or option to give list of device ID(s)')
#
# args = parser.parse_args(args)
#
# comm = MPI.COMM_WORLD
# rank = comm.rank
#
# # set-up logging
# logger = logging.getLogger('gprMax')
# level = logging.DEBUG if args.verbose else logging.INFO
# logger.setLevel(level)
#
# if args.logfile != "":
# mh = logging.FileHandler(f"log_{rank}.txt", mode='w')
# mh.setLevel(level)
# formatter = logging.Formatter('%(asctime)s:%(name)s:%(levelname)s: %(message)s')
# mh.setFormatter(formatter)
# logger.addHandler(mh)
#
# namespace = {
# 'c': c,
# 'e0': e0,
# 'm0': m0,
# 'z0': z0,
# 'number_model_runs': args.num_traces,
# 'inputfile': os.path.abspath(args.inputfile)
# }
#
# model_args = argparse.Namespace(**{
# 'geometry_only': args.geometry_only,
# 'geometry_fixed': args.geometry_fixed,
# 'write_processed': args.write_processed,
# 'task': False,
# 'restart': False,
# 'gpu': args.gpu
# })
#
# # compile jobs
# jobs = []
# for i in range(args.num_traces):
# jobs.append({
# 'args': model_args,
# 'inputfile': args.inputfile,
# 'currentmodelrun': i + 1,
# 'modelend': args.num_traces,
# 'numbermodelruns': args.num_traces,
# 'usernamespace': namespace.copy()
# })
#
# # execute jobs
# logger.info(f'Starting execution of {args.num_traces} gprMax model runs.')
# with MPIExecutor(run_model, comm=comm) as gpr:
# if gpr is not None:
# results = gpr.submit(jobs)
# logger.info('Results: %s' % str(results))
# logger.info('Finished.')
#
#
# if __name__ == '__main__':
# main()

4
gprMax/scene.py
查看文件

@@ -31,7 +31,7 @@ from .subgrids.user_objects import SubGridBase as SubGridUserBase
from .user_inputs import create_user_input_points
from .utilities import human_size
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
class Scene:
@@ -93,7 +93,7 @@ class Scene:
try:
obj.create(grid, uip)
except CmdInputError:
log.exception('Error creating user input object')
logger.exception('Error creating user input object')
return self

2
gprMax/updates.py
查看文件

@@ -38,8 +38,6 @@ from .sources import htod_src_arrays
from .utilities import round32
from .utilities import timer
log = logging.getLogger(__name__)
class CPUUpdates:
"""Defines update functions for CPU-based solver."""

10
gprMax/user_inputs.py
查看文件

@@ -29,7 +29,7 @@ from .exceptions import CmdInputError
from .subgrids.base import SubGridBase
from .utilities import round_value
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
"""Module contains classes to handle points supplied by a user. The
classes implement a common interface such that geometry building objects
@@ -76,7 +76,7 @@ class UserInput:
s = f"'{cmd_str}' the {err.args[0]} {name}-coordinate {i * dl:g} is not within the model domain"
else:
s = f"'{cmd_str}' {err.args[0]}-coordinate {i * dl:g} is not within the model domain"
raise CmdInputError(log.exception(s))
raise CmdInputError(logger.exception(s))
def discretise_point(self, p):
"""Function to get the index of a continuous point with the grid."""
@@ -104,7 +104,7 @@ class MainGridUserInput(UserInput):
p = self.check_point(p, cmd_str, name)
if self.grid.within_pml(p):
log.warning(Fore.RED + f"'{cmd_str}' sources and receivers should not normally be positioned within the PML." + Style.RESET_ALL)
logger.warning(Fore.RED + f"'{cmd_str}' sources and receivers should not normally be positioned within the PML." + Style.RESET_ALL)
return p
@@ -113,7 +113,7 @@ class MainGridUserInput(UserInput):
p2 = self.check_point(p2, cmd_str, name='upper')
if np.greater(p1, p2).any():
raise CmdInputError(log.exception(f"'{cmd_str}' the lower coordinates should be less than the upper coordinates."))
raise CmdInputError(logger.exception(f"'{cmd_str}' the lower coordinates should be less than the upper coordinates."))
return p1, p2
@@ -175,5 +175,5 @@ class SubgridUserInput(MainGridUserInput):
# the OS non-working region.
if (np.less(p_t, self.inner_bound).any() or
np.greater(p_t, self.outer_bound).any()):
log.warning(Fore.RED + f"'{cmd_str}' this object traverses the Outer Surface. This is an advanced feature." + Style.RESET_ALL)
logger.warning(Fore.RED + f"'{cmd_str}' this object traverses the Outer Surface. This is an advanced feature." + Style.RESET_ALL)
return p_t

80
gprMax/utilities.py
查看文件

@@ -44,7 +44,35 @@ import numpy as np
import gprMax.config as config
from .exceptions import GeneralError
log = logging.getLogger(__name__)
logger = logging.getLogger(__name__)
def setup_logging(level=logging.INFO, logfile=False):
"""Setup and configure logging.
Args:
level (logging level): set logging level to stdout.
logfile (bool): additional logging to file.
"""
# Get root logger
logger = logging.getLogger()
logger.setLevel(level)
# Logging to console
mh = logging.StreamHandler()
formatter = logging.Formatter('%(message)s')
mh.setLevel(level)
mh.setFormatter(formatter)
logger.addHandler(mh)
# Logging to file
if logfile:
mh = logging.FileHandler("log_gprMax.txt", mode='w')
formatter = logging.Formatter('%(asctime)s:%(name)s:%(levelname)s: %(message)s')
mh.setLevel(logging.DEBUG)
mh.setFormatter(formatter)
logger.addHandler(mh)
def get_terminal_width():
@@ -83,39 +111,14 @@ def logo(version):
|___/|_|
v""" + version
log.info(f"{description} {'=' * (get_terminal_width() - len(description) - 1)}\n")
log.info(Fore.CYAN + f'{logo}\n')
log.info(Style.RESET_ALL + textwrap.fill(copyright, width=get_terminal_width() - 1, initial_indent=' '))
log.info(textwrap.fill(authors, width=get_terminal_width() - 1, initial_indent=' '))
log.info('')
log.info(textwrap.fill(licenseinfo1, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
log.info(textwrap.fill(licenseinfo2, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
log.info(textwrap.fill(licenseinfo3, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
@contextmanager
def open_path_file(path_or_file):
"""Accepts either a path as a string or a file object and returns a file
object (http://stackoverflow.com/a/6783680).
Args:
path_or_file: path as a string or a file object.
Returns:
f (object): File object.
"""
if isinstance(path_or_file, str):
f = file_to_close = codecs.open(path_or_file, 'r', encoding='utf-8')
else:
f = path_or_file
file_to_close = None
try:
yield f
finally:
if file_to_close:
file_to_close.close()
logger.info(f"{description} {'=' * (get_terminal_width() - len(description) - 1)}\n")
logger.info(Fore.CYAN + f'{logo}\n')
logger.info(Style.RESET_ALL + textwrap.fill(copyright, width=get_terminal_width() - 1, initial_indent=' '))
logger.info(textwrap.fill(authors, width=get_terminal_width() - 1, initial_indent=' '))
logger.info('')
logger.info(textwrap.fill(licenseinfo1, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
logger.info(textwrap.fill(licenseinfo2, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
logger.info(textwrap.fill(licenseinfo3, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
def round_value(value, decimalplaces=0):
@@ -518,10 +521,6 @@ def detect_check_gpus(deviceIDs):
else:
deviceIDsavail = range(drv.Device.count())
# If no device ID is given use default of 0
if not deviceIDs:
deviceIDs = [0]
# Check if requested device ID(s) exist
for ID in deviceIDs:
if ID not in deviceIDsavail:
@@ -532,13 +531,12 @@ def detect_check_gpus(deviceIDs):
for ID in deviceIDsavail:
gpu = GPU(deviceID=ID)
gpu.get_gpu_info(drv)
if ID in deviceIDs:
gpus.append(gpu)
gpus.append(gpu)
return gpus
def timer():
"""Function to return time in fractional seconds."""
log.debug('Review "thread_time" not currently available in macOS and bug (https://bugs.python.org/issue36205) with "process_time"')
logger.debug('"thread_time" not currently available in macOS and bug (https://bugs.python.org/issue36205) with "process_time"')
return timer_fn()

4
gprMax/waveforms.py
查看文件

@@ -16,12 +16,8 @@
# You should have received a copy of the GNU General Public License
# along with gprMax. If not, see <http://www.gnu.org/licenses/>.
import logging
import numpy as np
log = logging.getLogger(__name__)
class Waveform:
"""Definitions of waveform shapes that can be used with sources."""