def export_kernels(self, path):
unix.cd(self.kernel_databases)
# work around conflicting name conventions
files = []
files += glob('*proc??????_alpha_kernel.bin')
files += glob('*proc??????_alpha[hv]_kernel.bin')
files += glob('*proc??????_reg1_alpha_kernel.bin')
files += glob('*proc??????_reg1_alpha[hv]_kernel.bin')
unix.rename('alpha', 'vp', files)
files = []
files += glob('*proc??????_beta_kernel.bin')
files += glob('*proc??????_beta[hv]_kernel.bin')
files += glob('*proc??????_reg1_beta_kernel.bin')
files += glob('*proc??????_reg1_beta[hv]_kernel.bin')
unix.rename('beta', 'vs', files)
# hack to deal with problems on parallel filesystem
unix.mkdir(join(path, 'kernels'), noexit=True)
unix.mkdir(join(path, 'kernels', basename(self.getpath)))
src = join(glob('*_kernel.bin'))
dst = join(path, 'kernels', basename(self.getpath))
unix.mv(src, dst)
def clip(self, path='', parameters=[], minval=-np.inf, maxval=np.inf):
""" Clips kernels by convolving them with a Gaussian. Wrapper over
xclip_sem utility.
"""
assert exists(path)
assert len(parameters) > 0
unix.cd(self.getpath)
for name in self.parameters:
self.mpirun(
PATH.SPECFEM_BIN +'/'+ 'xclip_sem '
+ str(minval) + ' '
+ str(maxval) + ' '
+ name + '_kernel' + ' '
+ path + '/ '
+ path + '/ ')
# move input files
src = path
dst = path + '_noclip'
unix.mkdir(dst)
for name in self.parameters:
unix.mv(glob(src+'/*'+name+'.bin'), dst)
# rename output files
unix.rename('_clip', '', glob(src+'/*'))
def generate_data(self, **model_kwargs):
""" Generates data (perform meshing and database generation first)
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.cwd)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.false.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D', output='mesher.log')
call_solver(system.mpiexec(), 'bin/xspecfem2D', output='solver.log')
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*.su')
# work around SPECFEM2D's different file names (depending on the
# version used :
# ?? junliu
# _d?
unix.rename('single_d.su', 'single.su', src)
src = glob('OUTPUT_FILES/*.su')
dst = 'traces/obs'
unix.mv(src, dst)
if PAR.SAVETRACES:
self.export_traces(PATH.OUTPUT + '/' + 'traces/obs')
def export_kernels(self, path):
unix.cd(self.kernel_databases)
# work around conflicting name conventions
files = []
files += glob('*proc??????_alpha_kernel.bin')
files += glob('*proc??????_alpha[hv]_kernel.bin')
files += glob('*proc??????_reg1_alpha_kernel.bin')
files += glob('*proc??????_reg1_alpha[hv]_kernel.bin')
unix.rename('alpha', 'vp', files)
files = []
files += glob('*proc??????_beta_kernel.bin')
files += glob('*proc??????_beta[hv]_kernel.bin')
files += glob('*proc??????_reg1_beta_kernel.bin')
files += glob('*proc??????_reg1_beta[hv]_kernel.bin')
unix.rename('beta', 'vs', files)
# hack to deal with problems on parallel filesystem
unix.mkdir(join(path, 'kernels'), noexit=True)
unix.mkdir(join(path, 'kernels', basename(self.getpath)))
src = join(glob('*_kernel.bin'))
dst = join(path, 'kernels', basename(self.getpath))
unix.mv(src, dst)
def smooth(self, path='', tag='gradient', span=0.):
""" smooths SPECFEM3D kernels
"""
unix.cd(self.getpath)
# list kernels
kernels = []
for name in self.model_parameters:
if name in self.inversion_parameters:
flag = True
else:
flag = False
kernels = kernels + [[name, flag]]
# smooth kernels
for name, flag in kernels:
if flag:
print ' smoothing', name
self.mpirun(PATH.SOLVER_BINARIES + '/' + 'xsmooth_sem ' +
str(span) + ' ' + str(span) + ' ' + name + ' ' +
path + '/' + tag + '/ ' + path + '/' + tag + '/ ')
# move kernels
src = path + '/' + tag
dst = path + '/' + tag + '_nosmooth'
unix.mkdir(dst)
for name, flag in kernels:
if flag:
unix.mv(glob(src + '/*' + name + '.bin'), dst)
else:
unix.cp(glob(src + '/*' + name + '.bin'), dst)
unix.rename('_smooth', '', glob(src + '/*'))
print ''
unix.cd(path)
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(system.mpiexec(),
PATH.SPECFEM_BIN + '/' + 'xsmooth_sem ' + str(span) +
' ' + str(span) + ' ' + name + '_kernel' + ' ' +
input_path + '/ ' + output_path + '/ ',
output='/dev/null')
print ''
# rename output files
files = glob(output_path + '/*')
unix.rename('_smooth', '', files)
def smooth(self, path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
assert exists(path)
assert len(parameters) > 0
# apply smoothing operator
unix.cd(self.getpath)
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xsmooth_sem '
+ str(span) + ' '
+ str(span) + ' '
+ name + '_kernel' + ' '
+ path + '/ '
+ path + '/ ',
output=self.getpath+'/'+'OUTPUT_FILES/output_smooth_sem.txt')
print ''
# move input files
src = path
dst = path + '_nosmooth'
unix.mkdir(dst)
for name in parameters or self.parameters:
unix.mv(glob(src+'/*'+name+'_kernel.bin'), dst)
# rename output files
unix.rename('_smooth', '', glob(src+'/*'))
def clip(self, path='', parameters=[], minval=-np.inf, maxval=np.inf):
""" Clips kernels by convolving them with a Gaussian. Wrapper over
xclip_sem utility.
"""
assert exists(path)
assert len(parameters) > 0
unix.cd(self.getpath)
for name in parameters or self.parameters:
call_solver(
system.mpiexec,
PATH.SPECFEM_BIN +'/'+ 'xclip_sem '
+ str(minval) + ' '
+ str(maxval) + ' '
+ name + '_kernel' + ' '
+ path + '/ '
+ path + '/ ')
# move input files
src = path
dst = path + '_noclip'
unix.mkdir(dst)
for name in parameters or self.parameters:
unix.mv(glob(src+'/*'+name+'.bin'), dst)
# rename output files
unix.rename('_clip', '', glob(src+'/*'))
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xsmooth_sem '
+ str(span) + ' '
+ str(span) + ' '
+ name + '_kernel' + ' '
+ input_path + '/ '
+ output_path + '/ ',
output='/dev/null')
print ''
# rename output files
files = glob(output_path+'/*')
unix.rename('_smooth', '', files)
def smooth(self, path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
assert exists(path)
assert len(parameters) > 0
# apply smoothing operator
unix.cd(self.getpath)
for name in parameters:
print ' smoothing', name
self.mpirun(
PATH.SPECFEM_BIN +'/'+ 'xsmooth_sem '
+ str(span) + ' '
+ str(span) + ' '
+ name + '_kernel' + ' '
+ path + '/ '
+ path + '/ ',
output=self.getpath+'/'+'OUTPUT_FILES/output_smooth_sem.txt')
print ''
# move input files
src = path
dst = path + '_nosmooth'
unix.mkdir(dst)
for name in self.parameters:
unix.mv(glob(src+'/*'+name+'.bin'), dst)
# rename output files
unix.rename('_smooth', '', glob(src+'/*'))
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
files = []
files += glob(PATH.MODEL_INIT + '/proc??????_x.bin')
files += glob(PATH.MODEL_INIT + '/proc??????_z.bin')
files += glob(PATH.MODEL_INIT + '/proc??????_NSPEC_ibool.bin')
files += glob(PATH.MODEL_INIT + '/proc??????_jacobian.bin')
for file in files:
unix.cp(file, input_path)
for name in parameters or self.parameters:
print(' smoothing', name)
call_solver(system.mpiexec(),
PATH.SPECFEM_BIN + '/' + 'xsmooth_sem ' + str(span) +
' ' + str(span) + ' ' + name + '_kernel' + ' ' +
input_path + '/ ' + output_path + '/ F',
output=output_path + '/smooth_' + name + '.log')
print('')
# rename output files
files = glob(output_path + '/*')
unix.rename('_smooth', '', files)
def initialize_adjoint_traces(self):
super(specfem3d_globe, self).initialize_adjoint_traces()
# workaround for SPECFEM2D's use of different name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['ASCII', 'ascii']:
files = glob(self.cwd +'/'+ 'traces/adj/*sem.ascii')
unix.rename('sem.ascii', 'adj', files)
def initialize_adjoint_traces(self):
super(specfem3d_globe, self).initialize_adjoint_traces()
# workaround for SPECFEM2D's use of different name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['ASCII', 'ascii']:
files = glob(self.cwd + '/' + 'traces/adj/*sem.ascii')
unix.rename('sem.ascii', 'adj', files)
def export_att_kernel(self, path):
unix.cd(self.kernel_databases)
# work around conflicting name conventions
files = []
files += glob('*proc??????_c_acoustic_kernel.bin')
unix.rename('c_acoustic', 'Qkappa', files)
src = glob('*Qkappa_kernel.bin')
dst = join(path, 'kernels', self.source_name)
unix.mkdir(dst)
unix.mv(src, dst)
def adjoint_att(self):
""" Calls SPECFEM2D adjoint solver
"""
unix.rm('SEM')
unix.ln('traces/adj_att', 'SEM')
# hack to deal with different SPECFEM2D name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj_att/*.su')
unix.rename('.su', '.su.adj', files)
call_solver(system.mpiexec(), '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')
# hack to deal with different SPECFEM2D name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj/*.su')
unix.rename('.su', '.su.adj', files)
call_solver(system.mpiexec(), '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')
# hack to deal with different SPECFEM2D name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj/*.su')
unix.rename('.su', '.su.adj', files)
call_solver(system.mpiexec(), 'bin/xmeshfem2D')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
def rename_kernels(self):
""" Works around conflicting kernel filename conventions
"""
files = []
files += glob('*proc??????_alpha_kernel.bin')
files += glob('*proc??????_alpha[hv]_kernel.bin')
files += glob('*proc??????_reg1_alpha_kernel.bin')
files += glob('*proc??????_reg1_alpha[hv]_kernel.bin')
unix.rename('alpha', 'vp', files)
files = []
files += glob('*proc??????_beta_kernel.bin')
files += glob('*proc??????_beta[hv]_kernel.bin')
files += glob('*proc??????_reg1_beta_kernel.bin')
files += glob('*proc??????_reg1_beta[hv]_kernel.bin')
unix.rename('beta', 'vs', files)
def forward(self, path='traces/syn'):
""" Calls SPECFEM2D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
if PAR.FORMAT in ['SU', 'su']:
filenames = glob('OUTPUT_FILES/*.su')
# work around SPECFEM2D's different file names (depending on the
# version used :
unix.rename('single_p.su', 'single.su', filenames)
filenames = glob('OUTPUT_FILES/*.su')
unix.mv(filenames, path)
def rename_kernels(self):
""" Works around conflicting kernel filename conventions
"""
files = []
files += glob('*proc??????_alpha_kernel.bin')
files += glob('*proc??????_alpha[hv]_kernel.bin')
files += glob('*proc??????_reg1_alpha_kernel.bin')
files += glob('*proc??????_reg1_alpha[hv]_kernel.bin')
unix.rename('alpha', 'vp', files)
files = []
files += glob('*proc??????_beta_kernel.bin')
files += glob('*proc??????_beta[hv]_kernel.bin')
files += glob('*proc??????_reg1_beta_kernel.bin')
files += glob('*proc??????_reg1_beta[hv]_kernel.bin')
unix.rename('beta', 'vs', files)
def initialize_adjoint_traces(self):
super(specfem3d, self).initialize_adjoint_traces()
# workaround for SPECFEM2D's use of different name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob(self.cwd +'/'+ 'traces/adj/*SU')
unix.rename('_SU', '_SU.adj', files)
# workaround for SPECFEM3D's requirement that all components exist,
# even ones not in use
unix.cd(self.cwd +'/'+ 'traces/adj')
for iproc in range(PAR.NPROC):
for channel in ['x', 'y', 'z']:
src = '%d_d%s_SU.adj' % (iproc, PAR.CHANNELS[0])
dst = '%d_d%s_SU.adj' % (iproc, channel)
if not exists(dst):
unix.cp(src, dst)
def initialize_adjoint_traces(self):
super(specfem2d, self).initialize_adjoint_traces()
# work around SPECFEM2D's use of different name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj/*.su')
unix.rename('.su', '.su.adj', files)
# work around SPECFEM2D's requirement that all components exist,
# even ones not in use
if PAR.FORMAT in ['SU', 'su']:
unix.cd(self.cwd +'/'+ 'traces/adj')
for channel in ['x', 'y', 'z', 'p']:
src = 'U%s_file_single.su.adj' % PAR.CHANNELS[0]
dst = 'U%s_file_single.su.adj' % channel
if not exists(dst):
unix.cp(src, dst)
def initialize_adjoint_traces(self):
super(specfem3d_nz, self).initialize_adjoint_traces()
# workaround for SPECFEM2D's use of different name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob(self.cwd + '/' + 'traces/adj/*SU')
unix.rename('_SU', '_SU.adj', files)
# workaround for SPECFEM3D's requirement that all components exist,
# even ones not in use
unix.cd(self.cwd + '/' + 'traces/adj')
for iproc in range(PAR.NPROC):
for channel in ['x', 'y', 'z']:
src = '%d_d%s_SU.adj' % (iproc, PAR.CHANNELS[0])
dst = '%d_d%s_SU.adj' % (iproc, channel)
if not exists(dst):
unix.cp(src, dst)
def initialize_adjoint_traces(self):
super(specfem2d, self).initialize_adjoint_traces()
# work around SPECFEM2D's use of different name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj/*.su')
unix.rename('.su', '.su.adj', files)
# work around SPECFEM2D's requirement that all components exist,
# even ones not in use
if PAR.FORMAT in ['SU', 'su']:
unix.cd(self.getpath + '/' + 'traces/adj')
for channel in ['x', 'y', 'z', 'p']:
src = 'U%s_file_single.su.adj' % PAR.CHANNELS[0]
dst = 'U%s_file_single.su.adj' % channel
if not exists(dst):
unix.cp(src, dst)
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_x.bin'
dst = '/scratch/gpfs/etienneb/2D_inversion_80_elem/scratch/evalgrad/kernels/sum_nosmooth'
unix.cp(src, dst)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_z.bin'
unix.cp(src, dst)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_NSPEC_ibool.bin'
unix.cp(src, dst)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_jacobian.bin'
unix.cp(src, dst)
print input_path
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xsmooth_sem '
+ str(span) + ' '
+ str(span) + ' '
+ name + '_kernel' + ' '
+ input_path + '/ '
+ output_path + '/ T',
output='/scratch/gpfs/etienneb/2D_inversion_80_elem/smooth_output.log')
print ''
# rename output files
files = glob(output_path+'/*')
unix.rename('_smooth', '', files)
def smooth(self,
input_path='',
output_path='',
parameters=[],
span_h=0.,
span_v=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
smooth() in base.py has the incorrect command line call, specfem
requires that NPROC be specified
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
print 'smoothing parameters ', self.parameters
for name in parameters or self.parameters:
print 'smoothing', name
solver_call = " ".join([
PATH.SPECFEM_BIN + '/' + 'xsmooth_sem', # ./bin/xsmooth_sem
str(span_h), # SIGMA_H
str(span_v), # SIGMA_V
name + '_kernel', # KERNEL_NAME
input_path + '/', # INPUT_DIR
output_path + '/', # OUTPUT_DIR
'.false' # USE_GPU
])
call_solver(system.mpiexec(), solver_call)
print ''
# rename output files
files = glob(output_path + '/*')
unix.rename('_smooth', '', files)
def rename_kernels(self):
""" Works around conflicting kernel filename conventions
"""
#files = []
#files += glob('*proc??????_alpha_acoustic_kernel.bin')
#unix.rename('alpha_acoustic', 'vp', files)
files = []
files += glob('*proc??????_alpha_kernel.bin')
unix.rename('alpha', 'vp', files)
files = []
files += glob('*proc??????_c_acoustic_kernel.bin')
unix.rename('c_acoustic', 'vp', files)
# unix.rename('c_acoustic', 'Qkappa', files)
files = []
files += glob('*proc??????_rhop_acoustic_kernel.bin')
unix.rename('rhop_acoustic', 'rho', files)
files = []
files += glob('*proc??????_beta_kernel.bin')
unix.rename('beta', 'vs', files)
def rename_kernels(self):
""" Works around conflicting kernel filename conventions
"""
files = []
files += glob('*proc??????_c_acoustic_kernel.bin')
files += glob('*proc??????_alpha_kernel.bin')
files += glob('*proc??????_alpha[hv]_kernel.bin')
files += glob('*proc??????_reg1_alpha_kernel.bin')
files += glob('*proc??????_reg1_alpha[hv]_kernel.bin')
# Replace 'alpha' by 'vp' is all files names :
unix.rename('alpha', 'vp', files)
# Replace 'c_acoustic' by 'vp' is all files names :
unix.rename('c_acoustic', 'vp', files)
files = []
files += glob('*proc??????_beta_kernel.bin')
files += glob('*proc??????_beta[hv]_kernel.bin')
files += glob('*proc??????_reg1_beta_kernel.bin')
files += glob('*proc??????_reg1_beta[hv]_kernel.bin')
# Replace 'beta' by 'vs' is all files names :
unix.rename('beta', 'vs', files)
def rename_data(self):
""" Works around conflicting data filename conventions
"""
files = glob(self.cwd +'/'+ 'traces/adj/*sem.ascii')
unix.rename('sem.ascii', 'sem.ascii.adj', files)
def rename_data(self):
""" Works around conflicting data filename conventions
"""
files = glob(self.cwd + '/' + 'traces/adj/*sem.ascii')
unix.rename('sem.ascii', 'sem.ascii.adj', files)
def rename_data(self):
""" Works around conflicting data filename conventions
"""
if PAR.FORMAT in ['SU', 'su']:
files = glob(self.cwd + '/' + 'traces/adj/*SU')
unix.rename('_SU', '_SU.adj', files)
def rename_data(self):
""" Works around conflicting data filename conventions
"""
if PAR.FORMAT in ['SU', 'su']:
files = glob(self.cwd +'/'+ 'traces/adj/*SU')
unix.rename('_SU', '_SU.adj', files)