class tikhonov2(loadclass('postprocess', 'regularize')):
""" Adds regularization options to base class
Available options include 0-, 1-, and 2- order Tikhonov and total
variation regularization. While the underlying theory is classical,
these options are experimental in the sense that their application to
unstructured numerical grids is quite new.
SO FAR, CAN ONLY BE USED FOR 2D WAVEFORM INVERSION.
"""
def check(self):
""" Checks parameters and paths
"""
super(tikhonov2, self).check()
if 'CREEPING' not in PAR:
setattr(PAR, 'CREEPING', False)
if not PAR.LAMBDA:
raise ValueError
def nabla(self, mesh, m, g):
if PAR.CREEPING:
G, grid = mesh2grid(g, mesh)
DG = nabla(G, order=2)
dg = grid2mesh(DG, grid, mesh)
return -dg / np.mean(m)
else:
M, grid = mesh2grid(m, mesh)
DM = nabla(M, order=2)
dm = grid2mesh(DM, grid, mesh)
return dm / np.mean(m)
class total_variation(loadclass('postprocess', 'regularize')):
""" Adds regularization options to base class
Available options include 0-, 1-, and 2- order Tikhonov and total
variation regularization. While the underlying theory is classical,
these options are experimental in the sense that their application to
unstructured numerical grids is quite new.
SO FAR, CAN ONLY BE USED FOR 2D WAVEFORM INVERSION.
"""
def check(self):
""" Checks parameters and paths
"""
super(total_variation, self).check()
if not PAR.LAMBDA:
raise ValueError
if not hasattr(PAR, 'EPSILON'):
setattr(PAR, 'EPSILON', 0.)
def nabla(self, mesh, m, g):
M, grid = mesh2grid(g, mesh)
DM = tv(M, epsilon=PAR.EPSILON)
dm = grid2mesh(DM, grid, mesh)
return dm / np.mean(m)
class tikhonov0(loadclass('postprocess', 'regularize')):
""" Adds regularization options to base class
Available options include 0-, 1-, and 2- order Tikhonov and total
variation regularization. While the underlying theory is classical,
these options are experimental in the sense that their application to
unstructured numerical grids is quite new.
SO FAR, CAN ONLY BE USED FOR 2D WAVEFORM INVERSION.
"""
def check(self):
""" Checks parameters and paths
"""
super(tikhonov0, self).check()
if not PAR.LAMBDA:
raise ValueError
def nabla(self, mesh, m, g):
return m / np.mean(m)
class tiger_lg(loadclass('system', 'slurm_lg')):
""" Specially designed system interface for tiger.princeton.edu
By hiding environment details behind a python interface layer, these
classes provide a consistent command set across different computing
environments.
For more informations, see
http://seisflows.readthedocs.org/en/latest/manual/manual.html#system-interfaces
"""
def check(self):
""" Checks parameters and paths
"""
if 'TITLE' not in PAR:
setattr(PAR, 'TITLE', unix.basename(abspath('.')))
if 'SUBTITLE' not in PAR:
setattr(PAR, 'SUBTITLE', unix.basename(abspath('..')))
if 'GLOBAL' not in PATH:
setattr(
PATH, 'GLOBAL',
join('/scratch/gpfs', unix.whoami(), PAR.SUBTITLE, PAR.TITLE))
if 'LOCAL' not in PATH:
setattr(PATH, 'LOCAL', '')
if 'NPROC_PER_NODE' not in PAR:
setattr(PAR, 'NPROC_PER_NODE', 16)
super(tiger_lg, self).check()
def submit(self, *args, **kwargs):
"""Submits job
"""
unix.ln(PATH.GLOBAL, PATH.SUBMIT + '/' + 'scratch')
super(tiger_lg, self).submit(*args, **kwargs)
def test_load_extension_module(self):
# Get a class from one of seisflow module
cls = tools.loadclass('system', 'tiger_sm')
# Check if we can instanciate the class.
self.assertIsInstance(cls(), cls),
def test_load_base_module(self):
# Get a class from one of seisflow module
cls = tools.loadclass('system', 'serial')
# Check if we can instanciate the class.
self.assertIsInstance(cls(), cls),
def test_noargs(self):
self.assertEqual(tools.Null, tools.loadclass())
import numpy as np
from seisflows.tools import unix
from seisflows.tools.array import loadnpy, savenpy
from seisflows.tools.code import exists
from seisflows.tools.config import SeisflowsParameters, SeisflowsPaths, \
loadclass, ParameterError
PAR = SeisflowsParameters()
PATH = SeisflowsPaths()
import solver
import postprocess
migration = loadclass('workflow','migration')()
class test_postprocess(object):
""" Postprocessing class
"""
def check(self):
""" Checks parameters and paths
"""
migration.check()
if 'INPUT' not in PATH:
setattr(PATH, 'INPUT', None)
class specfem2d(loadclass('solver', 'base')):
""" Python interface for SPECFEM2D
See base class for method descriptions
"""
if PAR.MATERIALS == 'LegacyAcoustic':
parameters = []
parameters += ['vs']
def check(self):
""" Checks parameters and paths
"""
super(specfem2d, self).check()
# check time stepping parameters
if 'NT' not in PAR:
raise Exception
if 'DT' not in PAR:
raise Exception
if 'F0' not in PAR:
raise Exception
def check_solver_parameter_files(self):
""" Checks solver parameters
"""
nt = getpar('nt', cast=int)
dt = getpar('deltat', cast=float)
f0 = getpar('f0', file='DATA/SOURCE', cast=float)
if nt != PAR.NT:
if self.getnode == 0: print "WARNING: nt != PAR.NT"
setpar('nt', PAR.NT)
if dt != PAR.DT:
if self.getnode == 0: print "WARNING: dt != PAR.DT"
setpar('deltat', PAR.DT)
if f0 != PAR.F0:
if self.getnode == 0: print "WARNING: f0 != PAR.F0"
setpar('f0', PAR.F0, file='DATA/SOURCE')
if self.mesh.nproc != PAR.NPROC:
if self.getnode == 0:
print 'Warning: mesh.nproc != PAR.NPROC'
if 'MULTIPLES' in PAR:
if PAR.MULTIPLES:
setpar('absorbtop', '.false.')
else:
setpar('absorbtop', '.true.')
def generate_data(self, **model_kwargs):
""" Generates data
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.getpath)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
self.mpirun('bin/xmeshfem2D')
self.mpirun('bin/xspecfem2D', output='log.solver')
unix.mv(self.data_wildcard, 'traces/obs')
self.export_traces(PATH.OUTPUT, 'traces/obs')
def generate_mesh(self,
model_path=None,
model_name=None,
model_type='gll'):
""" Performs meshing and database generation
"""
assert (model_name)
assert (model_type)
self.initialize_solver_directories()
unix.cd(self.getpath)
assert (exists(model_path))
self.check_mesh_properties(model_path)
src = glob(join(model_path, '*'))
dst = join(self.getpath, 'DATA')
unix.cp(src, dst)
self.export_model(PATH.OUTPUT + '/' + model_name)
### low-level solver interface
def forward(self):
""" Calls SPECFEM2D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
self.mpirun('bin/xmeshfem2D')
self.mpirun('bin/xspecfem2D')
def adjoint(self):
""" Calls SPECFEM2D adjoint solver
"""
setpar('SIMULATION_TYPE', '3')
setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
self.mpirun('bin/xmeshfem2D')
self.mpirun('bin/xspecfem2D')
### postprocessing utilities
def smooth(self, path='', parameters='dummy', span=0.):
""" Smooths SPECFEM2D kernels by convolving them with a Gaussian
"""
from seisflows.tools.array import meshsmooth, stack
#assert parameters == self.parameters
# implementing nproc > 1 would be straightforward, but a bit tedious
#assert self.mesh.nproc == 1
kernels = self.load(path, suffix='_kernel')
if not span:
return kernels
# set up grid
_, x = loadbypar(PATH.MODEL_INIT, ['x'], 0)
_, z = loadbypar(PATH.MODEL_INIT, ['z'], 0)
mesh = stack(x[0], z[0])
for key in self.parameters:
kernels[key] = [meshsmooth(kernels[key][0], mesh, span)]
unix.rm(path + '_nosmooth')
unix.mv(path, path + '_nosmooth')
self.save(path, kernels, suffix='_kernel')
### file transfer utilities
def import_model(self, path):
src = glob(path + '/' + 'model/*')
dst = join(self.getpath, 'DATA/')
unix.cp(src, dst)
def export_model(self, path):
if self.getnode == 0:
unix.mkdir(path)
src = glob(join(self.getpath, 'DATA/*.bin'))
dst = path
unix.cp(src, dst)
### input file writers
def write_parameters(self):
unix.cd(self.getpath)
solvertools.write_parameters(vars(PAR))
def write_receivers(self):
unix.cd(self.getpath)
key = 'use_existing_STATIONS'
val = '.true.'
setpar(key, val)
_, h = preprocess.load('traces/obs')
solvertools.write_receivers(h.nr, h.rx, h.rz)
def write_sources(self):
unix.cd(self.getpath)
_, h = preprocess.load(dir='traces/obs')
solvertools.write_sources(vars(PAR), h)
### utility functions
def mpirun(self, script, output='/dev/null'):
""" Wrapper for mpirun
"""
with open(output, 'w') as f:
subprocess.call(script, shell=True, stdout=f)
### miscellaneous
@property
def data_wildcard(self):
return glob('OUTPUT_FILES/U?_file_single.su')
#return glob('OUTPUT_FILES/*semd')
@property
def model_databases(self):
return join(self.getpath, 'DATA')
@property
def kernel_databases(self):
return join(self.getpath, 'OUTPUT_FILES')
@property
def source_prefix(self):
return 'SOURCE'
def combine(self, path='', parameters=[]):
""" Sums individual source contributions. Wrapper over xcombine_sem
utility.
"""
unix.cd(self.getpath)
names = self.check_source_names()
with open('kernel_paths', 'w') as f:
f.writelines([join(path, dir) + '\n' for dir in names])
unix.mkdir(path + '/' + 'sum')
for name in parameters:
self.mpirun(PATH.SPECFEM_BIN + '/' + 'xcombine_sem ' + name +
'_kernel' + ' ' + 'kernel_paths' + ' ' + path + '/' +
'sum')
class slurm_lg(loadclass('system', 'base')):
""" An interface through which to submit workflows, run tasks in serial or
parallel, and perform other system functions.
By hiding environment details behind a python interface layer, these
classes provide a consistent command set across different computing
environments.
For more informations, see
http://seisflows.readthedocs.org/en/latest/manual/manual.html#system-interfaces
"""
def check(self):
""" Checks parameters and paths
"""
if 'TITLE' not in PAR:
setattr(PAR, 'TITLE', unix.basename(abspath('..')))
if 'SUBTITLE' not in PAR:
setattr(PAR, 'SUBTITLE', unix.basename(abspath('.')))
# check parameters
if 'WALLTIME' not in PAR:
setattr(PAR, 'WALLTIME', 30.)
if 'STEPTIME' not in PAR:
setattr(PAR, 'STEPTIME', 30.)
if 'SLEEPTIME' not in PAR:
setattr(PAR, 'SLEEPTIME', 1.)
if 'VERBOSE' not in PAR:
setattr(PAR, 'VERBOSE', 1)
if 'NTASK' not in PAR:
raise ParameterError(PAR, 'NTASK')
if 'NPROC' not in PAR:
raise ParameterError(PAR, 'NPROC')
if 'NODESIZE' not in PAR:
raise ParameterError(PAR, 'NODESIZE')
# check paths
if 'GLOBAL' not in PATH:
setattr(PATH, 'GLOBAL', join(abspath('.'), 'scratch'))
if 'LOCAL' not in PATH:
setattr(PATH, 'LOCAL', None)
if 'SUBMIT' not in PATH:
setattr(PATH, 'SUBMIT', unix.pwd())
if 'OUTPUT' not in PATH:
setattr(PATH, 'OUTPUT', join(PATH.SUBMIT, 'output'))
if 'SYSTEM' not in PATH:
setattr(PATH, 'SYSTEM', join(PATH.GLOBAL, 'system'))
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
unix.mkdir(PATH.SUBMIT + '/' + 'output.slurm')
self.checkpoint()
# prepare sbatch arguments
unix.run('sbatch ' + '--job-name=%s ' % PAR.SUBTITLE + '--output %s ' %
(PATH.SUBMIT + '/' + 'output.log') +
'--ntasks-per-node=%d ' % PAR.NODESIZE + '--nodes=%d ' % 1 +
'--time=%d ' % PAR.WALLTIME + findpath('system') + '/' +
'slurm/wrapper_sbatch ' + PATH.OUTPUT)
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts.
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
jobs = self._launch(classname, funcname, hosts)
while 1:
time.sleep(60. * PAR.SLEEPTIME)
self._timestamp()
isdone, jobs = self._status(classname, funcname, jobs)
if isdone:
return
def mpiargs(self):
return 'srun '
def getnode(self):
""" Gets number of running task
"""
try:
return int(os.getenv('SEISFLOWS_TASK_ID'))
except:
try:
return int(os.getenv('SLURM_ARRAY_TASK_ID'))
except:
raise Exception("TASK_ID environment variable not defined.")
### private methods
def _launch(self, classname, funcname, hosts='all'):
unix.mkdir(PATH.SYSTEM)
# prepare sbatch arguments
if hosts == 'all':
args = ('--array=%d-%d ' % (0, PAR.NTASK - 1) + '--output %s ' %
(PATH.SUBMIT + '/' + 'output.slurm/' + '%A_%a'))
elif hosts == 'head':
args = ('--array=%d-%d ' % (0, 0) + '--output=%s ' %
(PATH.SUBMIT + '/' + 'output.slurm/' + '%j'))
#+('--export=SEISFLOWS_TASK_ID=%s ' % 0
# submit job
with open(PATH.SYSTEM + '/' + 'job_id', 'w') as f:
subprocess.call(
'sbatch ' + '--job-name=%s ' % PAR.TITLE +
'--nodes=%d ' % math.ceil(PAR.NPROC / float(PAR.NODESIZE)) +
'--ntasks-per-node=%d ' % PAR.NODESIZE +
'--time=%d ' % PAR.STEPTIME + args + findpath('system') + '/' +
'slurm/wrapper_srun ' + PATH.OUTPUT + ' ' + classname + ' ' +
funcname + ' ',
shell=1,
stdout=f)
# retrieve job ids
with open(PATH.SYSTEM + '/' + 'job_id', 'r') as f:
line = f.readline()
job = line.split()[-1].strip()
if hosts == 'all' and PAR.NTASK > 1:
nn = range(PAR.NTASK)
return [job + '_' + str(ii) for ii in nn]
else:
return [job]
def _status(self, classname, funcname, jobs):
""" Determines completion status of one or more jobs
"""
for job in jobs:
state = self._query(job)
states = []
if state in ['COMPLETED']:
states += [1]
else:
states += [0]
if state in ['FAILED', 'NODE_FAIL', 'TIMEOUT']:
print msg.TaskError_SLURM % (classname, funcname, job)
sys.exit(-1)
isdone = all(states)
return isdone, jobs
def _query(self, jobid):
""" Queries job state from SLURM database
"""
with open(PATH.SYSTEM + '/' + 'job_status', 'w') as f:
subprocess.call('sacct -n -o state -j ' + jobid,
shell=True,
stdout=f)
with open(PATH.SYSTEM + '/' + 'job_status', 'r') as f:
line = f.readline()
state = line.strip()
return state
### utility function
def _timestamp(self):
with open(PATH.SYSTEM + '/' + 'timestamps', 'a') as f:
line = time.strftime('%H:%M:%S') + '\n'
f.write(line)
def save_kwargs(self, classname, funcname, kwargs):
kwargspath = join(PATH.OUTPUT, 'SeisflowsObjects',
classname + '_kwargs')
kwargsfile = join(kwargspath, funcname + '.p')
unix.mkdir(kwargspath)
saveobj(kwargsfile, kwargs)
from seisflows.tools.config import loadclass, loadvars, ConfigObj, ParameterObj, Null
OBJ = ConfigObj('SeisflowsObjects')
PAR = ParameterObj('SeisflowsParameters')
PATH = ParameterObj('SeisflowsPaths')
# run test
if __name__ == '__main__':
PAR.update(loadvars('parameters', '.'))
PATH.update(loadvars('paths', '.'))
register = OBJ.register
system = loadclass('system', PAR.SYSTEM)()
register('system', system)
preprocess = Null()
register('preprocess', preprocess)
solver = Null()
register('solver', solver)
postprocess = Null()
register('postprocess', postprocess)
optimize = Null()
register('optimize', optimize)
workflow = loadclass('workflow', 'test_system')()
class specfem3d_globe(loadclass('solver', 'base')):
""" Python interface for SPECFEM3D_GLOBE
See base class for method descriptions
"""
if PAR.MATERIALS in ['Isotropic']:
parameters = []
parameters += ['vp']
parameters += ['vs']
else:
parameters = []
parameters += ['vpv']
parameters += ['vph']
parameters += ['vsv']
parameters += ['vsh']
parameters += ['eta']
def check(self):
""" Checks parameters and paths
"""
super(specfem3d_globe, self).check()
def generate_data(self, **model_kwargs):
""" Generates data
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.getpath)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
self.mpirun('bin/xspecfem3D')
unix.mv(self.data_wildcard, 'traces/obs')
self.export_traces(PATH.OUTPUT, 'traces/obs')
def generate_mesh(self,
model_path=None,
model_name=None,
model_type='gll'):
""" Performs meshing and database generation
"""
assert (model_name)
assert (model_type)
self.initialize_solver_directories()
unix.cd(self.getpath)
if model_type == 'gll':
assert (exists(model_path))
self.check_mesh_properties(model_path)
unix.cp(glob(model_path + '/' + '*'), self.model_databases)
self.mpirun('bin/xmeshfem3D')
self.export_model(PATH.OUTPUT + '/' + model_name)
else:
raise NotImplementedError
### model input/output
def load(self, path, prefix='reg1_', suffix='', verbose=False):
""" reads SPECFEM model or kernel
Models are stored in Fortran binary format and separated into multiple
files according to material parameter and processor rank.
"""
model = Model(self.parameters)
minmax = Minmax(self.parameters)
for iproc in range(self.mesh.nproc):
# read database files
keys, vals = loadbypar(path, self.parameters, iproc, prefix,
suffix)
for key, val in zip(keys, vals):
model[key] += [val]
minmax.update(keys, vals)
if verbose:
minmax.write(path, logpath=PATH.SUBMIT)
return model
def save(self, path, model, prefix='reg1_', suffix=''):
""" writes SPECFEM3D_GLOBE transerverly isotropic model
"""
unix.mkdir(path)
for iproc in range(self.mesh.nproc):
for key in ['vpv', 'vph', 'vsv', 'vsh', 'eta']:
if key in self.parameters:
savebin(model[key][iproc], path, iproc,
prefix + key + suffix)
elif 'kernel' in suffix:
pass
else:
src = PATH.OUTPUT + '/' + 'model_init'
dst = path
copybin(src, dst, iproc, prefix + key + suffix)
if 'rho' in self.parameters:
savebin(model['rho'][iproc], path, iproc,
prefix + 'rho' + suffix)
elif 'kernel' in suffix:
pass
else:
src = PATH.OUTPUT + '/' + 'model_init'
dst = path
copybin(src, dst, iproc, prefix + 'rho' + suffix)
### low-level solver interface
def forward(self):
""" Calls SPECFEM3D_GLOBE forward solver
"""
solvertools.setpar('SIMULATION_TYPE', '1')
solvertools.setpar('SAVE_FORWARD', '.true.')
self.mpirun('bin/xspecfem3D')
unix.mv(self.data_wildcard, 'traces/syn')
def adjoint(self):
""" Calls SPECFEM3D_GLOBE adjoint solver
"""
solvertools.setpar('SIMULATION_TYPE', '3')
solvertools.setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
self.mpirun('bin/xspecfem3D')
### utility functions
@property
def data_wildcard(self):
return glob('OUTPUT_FILES/*.sem.ascii')
@property
def kernel_databases(self):
return join(self.getpath, 'OUTPUT_FILES/DATABASES_MPI')
@property
def model_databases(self):
return join(self.getpath, 'OUTPUT_FILES/DATABASES_MPI')
@property
def source_prefix(self):
return 'CMTSOLUTION'
class slurm_sm(loadclass('system', 'base')):
""" An interface through which to submit workflows, run tasks in serial or
parallel, and perform other system functions.
By hiding environment details behind a python interface layer, these
classes provide a consistent command set across different computing
environments.
For more informations, see
http://seisflows.readthedocs.org/en/latest/manual/manual.html#system-interfaces
"""
def check(self):
""" Checks parameters and paths
"""
if 'TITLE' not in PAR:
setattr(PAR, 'TITLE', unix.basename(abspath('..')))
if 'SUBTITLE' not in PAR:
setattr(PAR, 'SUBTITLE', unix.basename(abspath('.')))
# check parameters
if 'WALLTIME' not in PAR:
setattr(PAR, 'WALLTIME', 30.)
if 'VERBOSE' not in PAR:
setattr(PAR, 'VERBOSE', 1)
if 'NPROC' not in PAR:
raise ParameterError(PAR, 'NPROC')
if 'NTASK' not in PAR:
raise ParameterError(PAR, 'NTASK')
# check paths
if 'GLOBAL' not in PATH:
setattr(PATH, 'GLOBAL', join(abspath('.'), 'scratch'))
if 'LOCAL' not in PATH:
setattr(PATH, 'LOCAL', None)
if 'SUBMIT' not in PATH:
setattr(PATH, 'SUBMIT', unix.pwd())
if 'OUTPUT' not in PATH:
setattr(PATH, 'OUTPUT', join(PATH.SUBMIT, 'output'))
def submit(self, workflow):
""" Submits workflow
"""
unix.mkdir(PATH.OUTPUT)
unix.cd(PATH.OUTPUT)
self.checkpoint()
# submit workflow
unix.run('sbatch ' + '--job-name=%s ' % PAR.SUBTITLE + '--output=%s ' %
(PATH.SUBMIT + '/' + 'output.log') +
'--cpus-per-task=%d ' % PAR.NPROC +
'--ntasks=%d ' % PAR.NTASK + '--time=%d ' % PAR.WALLTIME +
findpath('system') + '/' + 'slurm/wrapper_sbatch ' +
PATH.OUTPUT)
def run(self, classname, funcname, hosts='all', **kwargs):
""" Runs tasks in serial or parallel on specified hosts
"""
self.checkpoint()
self.save_kwargs(classname, funcname, kwargs)
if hosts == 'all':
# run on all available nodes
unix.run('srun ' + '--wait=0 ' +
join(findpath('system'), 'slurm/wrapper_srun ') +
PATH.OUTPUT + ' ' + classname + ' ' + funcname)
elif hosts == 'head':
# run on head node
unix.run('srun ' + '--wait=0 ' +
join(findpath('system'), 'slurm/wrapper_srun_head ') +
PATH.OUTPUT + ' ' + classname + ' ' + funcname)
def getnode(self):
""" Gets number of running task
"""
gid = os.getenv('SLURM_GTIDS').split(',')
lid = int(os.getenv('SLURM_LOCALID'))
return int(gid[lid])
def mpiargs(self):
return 'mpirun -np %d ' % PAR.NPROC
def save_kwargs(self, classname, funcname, kwargs):
kwargspath = join(PATH.OUTPUT, 'SeisflowsObjects',
classname + '_kwargs')
kwargsfile = join(kwargspath, funcname + '.p')
unix.mkdir(kwargspath)
saveobj(kwargsfile, kwargs)
class regularize(loadclass('postprocess', 'base')):
""" Adds regularization options to base class
Available options include 0-, 1-, and 2- order Tikhonov and total
variation regularization. While the underlying theory is classical,
these options are experimental in the sense that their application to
unstructured numerical grids is quite new.
SO FAR, CAN ONLY BE USED FOR 2D WAVEFORM INVERSION.
Prior to regularizing gradient, near field artifacts must be corrected.
The "FIXRADIUS" parameter specifies the radius, in number of GLL points,
within which the correction is applied.
"""
def check(self):
""" Checks parameters and paths
"""
super(regularize, self).check()
if 'FIXRADIUS' not in PAR:
setattr(PAR, 'FIXRADIUS', 7.5)
if 'LAMBDA' not in PAR:
setattr(PAR, 'LAMBDA', 0.)
def write_gradient(self, path):
super(regularize, self).write_gradient(path)
g = self.regularize(path)
self.save(path, g, backup='noregularize')
def process_kernels(self, path, parameters):
""" Processes kernels in accordance with parameter settings
"""
fullpath = path + '/' + 'kernels'
assert exists(path)
if exists(fullpath + '/' + 'sum'):
unix.mv(fullpath + '/' + 'sum', fullpath + '/' + 'sum_nofix')
# mask sources and receivers
system.run('postprocess', 'fix_near_field', hosts='all', path=fullpath)
system.run('solver',
'combine',
hosts='head',
path=fullpath,
parameters=parameters)
def fix_near_field(self, path=''):
"""
"""
import preprocess
preprocess.setup()
name = solver.check_source_names()[solver.getnode]
fullpath = path + '/' + name
g = solver.load(fullpath, suffix='_kernel')
if not PAR.FIXRADIUS:
return
mesh = self.getmesh()
x, z = self.getxz()
lx = x.max() - x.min()
lz = z.max() - z.min()
nn = x.size
nx = np.around(np.sqrt(nn * lx / lz))
nz = np.around(np.sqrt(nn * lz / lx))
dx = lx / nx
dz = lz / nz
sigma = 0.5 * PAR.FIXRADIUS * (dx + dz)
_, h = preprocess.load(solver.getpath + '/' + 'traces/obs')
# mask sources
mask = np.exp(-0.5 * ((x - h.sx[0])**2. + (z - h.sy[0])**2.) /
sigma**2.)
for key in solver.parameters:
weight = np.sum(mask * g[key][0]) / np.sum(mask)
g[key][0] *= 1. - mask
g[key][0] += mask * weight
# mask receivers
for ir in range(h.nr):
mask = np.exp(-0.5 * ((x - h.rx[ir])**2. + (z - h.ry[ir])**2.) /
sigma**2.)
for key in solver.parameters:
weight = np.sum(mask * g[key][0]) / np.sum(mask)
g[key][0] *= 1. - mask
g[key][0] += mask * weight
solver.save(fullpath, g, suffix='_kernel')
def regularize(self, path):
assert (exists(path))
g = solver.load(path + '/' + 'gradient', suffix='_kernel')
if not PAR.LAMBDA:
return solver.merge(g)
m = solver.load(path + '/' + 'model')
mesh = self.getmesh()
for key in solver.parameters:
for iproc in range(PAR.NPROC):
g[key][iproc] += PAR.LAMBDA *\
self.nabla(mesh, m[key][iproc], g[key][iproc])
#self.nabla(m[key][iproc], g[key][iproc] , mesh, h)
return solver.merge(g)
def nabla(self, mesh, m, g):
raise NotImplementedError("Must be implemented by subclass.")
def getmesh(self):
model_path = PATH.OUTPUT + '/' + 'model_init'
try:
m = solver.load(model_path)
x = m['x'][0]
z = m['z'][0]
mesh = stack(x, z)
except:
from seisflows.seistools.io import loadbin
x = loadbin(model_path, 0, 'x')
z = loadbin(model_path, 0, 'z')
mesh = stack(x, z)
return mesh
def getxz(self):
model_path = PATH.OUTPUT + '/' + 'model_init'
try:
m = solver.load(model_path)
x = m['x'][0]
z = m['z'][0]
except:
from seisflows.seistools.io import loadbin
x = loadbin(model_path, 0, 'x')
z = loadbin(model_path, 0, 'z')
return x, z
from seisflows.tools.config import ConfigObj, ParameterObj, loadclass
OBJ = ConfigObj('SeisflowsObjects')
PAR = ParameterObj('SeisflowsParameters')
PATH = ParameterObj('SeisflowsPaths')
# ensure number of processers per source is defined
if 'NPROC' not in PAR:
raise Exception
# there are 16 processers per node on tiger
if 'NPROC_PER_NODE' in PAR:
assert (PAR.NPROC_PER_NODE == 16)
else:
PAR.NPROC_PER_NODE = 16
# if nproc per source exceeds nproc per node, use tiger_lg
# otherwise, use tiger_sm
if PAR.NPROC > PAR.NPROC_PER_NODE:
tiger = loadclass('system', 'tiger_lg')
else:
tiger = loadclass('system', 'tiger_sm')
class specfem3d(loadclass('solver', 'base')):
""" Python interface for SPECFEM3D
See base class for method descriptions
"""
def check(self):
""" Checks parameters and paths
"""
super(specfem3d, self).check()
# check time stepping parameters
if 'NT' not in PAR:
raise Exception
if 'DT' not in PAR:
raise Exception
if 'F0' not in PAR:
raise Exception
def generate_data(self, **model_kwargs):
""" Generates data
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.getpath)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
self.mpirun('bin/xspecfem3D')
unix.mv(self.data_wildcard, 'traces/obs')
self.export_traces(PATH.OUTPUT, 'traces/obs')
def generate_mesh(self, model_path=None, model_name=None, model_type='gll'):
""" Performs meshing and database generation
"""
assert(model_name)
assert(model_type)
self.initialize_solver_directories()
unix.cd(self.getpath)
if model_type in ['gll']:
par = getpar('MODEL').strip()
if par != 'gll':
if self.getnode == 0:
print 'WARNING: Unexpected Par_file setting:'
print 'MODEL =', par
assert(exists(model_path))
self.check_mesh_properties(model_path)
src = glob(model_path +'/'+ '*')
dst = self.model_databases
unix.cp(src, dst)
self.mpirun('bin/xmeshfem3D')
self.mpirun('bin/xgenerate_databases')
self.export_model(PATH.OUTPUT +'/'+ model_name)
else:
raise NotImplementedError
### low-level solver interface
def forward(self):
""" Calls SPECFEM3D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
self.mpirun('bin/xgenerate_databases')
self.mpirun('bin/xspecfem3D')
def adjoint(self):
""" Calls SPECFEM3D adjoint solver
"""
setpar('SIMULATION_TYPE', '3')
setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
self.mpirun('bin/xspecfem3D')
### input file writers
def check_solver_parameter_files(self):
""" Checks solver parameters
"""
nt = getpar('NSTEP', cast=int)
dt = getpar('DT', cast=float)
if nt != PAR.NT:
if self.getnode == 0: print "WARNING: nt != PAR.NT"
setpar('NSTEP', PAR.NT)
if dt != PAR.DT:
if self.getnode == 0: print "WARNING: dt != PAR.DT"
setpar('DT', PAR.DT)
if self.mesh.nproc != PAR.NPROC:
if self.getnode == 0:
print 'Warning: mesh.nproc != PAR.NPROC'
if 'MULTIPLES' in PAR:
raise NotImplementedError
def write_parameters(self):
unix.cd(self.getpath)
solvertools.write_parameters(vars(PAR))
def write_receivers(self):
unix.cd(self.getpath)
key = 'use_existing_STATIONS'
val = '.true.'
setpar(key, val)
_, h = preprocess.load('traces/obs')
solvertools.write_receivers(h.nr, h.rx, h.rz)
def write_sources(self):
unix.cd(self.getpath)
_, h = preprocess.load(dir='traces/obs')
solvertools.write_sources(vars(PAR), h)
### miscellaneous
@property
def data_wildcard(self):
return glob('OUTPUT_FILES/*SU')
@property
def kernel_databases(self):
return join(self.getpath, 'OUTPUT_FILES/DATABASES_MPI')
@property
def model_databases(self):
return join(self.getpath, 'OUTPUT_FILES/DATABASES_MPI')
@property
def source_prefix(self):
return 'FORCESOLUTION'
from seisflows.tools.config import loadclass, loadvars, ConfigObj, ParameterObj, Null
OBJ = ConfigObj('SeisflowsObjects')
PAR = ParameterObj('SeisflowsParameters')
PATH = ParameterObj('SeisflowsPaths')
# run test
if __name__ == '__main__':
PAR.update(loadvars('parameters', '.'))
PATH.update(loadvars('paths', '.'))
register = OBJ.register
system = loadclass('system', PAR.SYSTEM)()
register('system', system)
preprocess = Null()
register('preprocess', preprocess)
solver = Null()
register('solver', solver)
postprocess = Null()
register('postprocess', postprocess)
optimize = loadclass('optimize', PAR.OPTIMIZE)()
register('optimize', optimize)
workflow = loadclass('workflow', 'test_optimize')()
import numpy as np
from seisflows.tools import unix
from seisflows.tools.array import loadnpy, savenpy
from seisflows.tools.code import exists
from seisflows.tools.config import SeisflowsParameters, SeisflowsPaths, \
loadclass, ParameterError
PAR = SeisflowsParameters()
PATH = SeisflowsPaths()
import solver
import postprocess
migration = loadclass('workflow', 'migration')()
class test_postprocess(object):
""" Postprocessing class
"""
def check(self):
""" Checks parameters and paths
"""
migration.check()
if 'INPUT' not in PATH:
setattr(PATH, 'INPUT', None)
def main(self):
""" Writes gradient of objective function
"""
from seisflows.tools.config import loadclass
from seisflows.tools.config import ParameterError, SeisflowsParameters, SeisflowsPaths
PAR = SeisflowsParameters()
PATH = SeisflowsPaths()
# ensure number of processers per source is defined
if "NPROC" not in PAR:
raise Exception
# there are 16 processers per node on tiger
if "NODESIZE" in PAR:
assert PAR.NODESIZE == 16
else:
PAR.NODESIZE = 16
# if nproc per source exceeds nproc per node, use tiger_lg
# otherwise, use tiger_sm
if PAR.NPROC > PAR.NODESIZE:
tiger = loadclass("system", "tiger_lg")
else:
tiger = loadclass("system", "tiger_sm")