class ExternalCode(Component):
"""
Run an external code as a component
Default stdin is the 'null' device, default stdout is the console, and
default stderr is ``error.out``.
Options
-------
fd_options['force_fd'] : bool(False)
Set to True to finite difference this system.
fd_options['form'] : str('forward')
Finite difference mode. (forward, backward, central) You can also set
to 'complex_step' to peform the complex step method if your components
support it.
fd_options['step_size'] : float(1e-06)
Default finite difference stepsize
fd_options['step_type'] : str('absolute')
Set to absolute, relative
fd_options['extra_check_partials_form'] : None or str
Finite difference mode: ("forward", "backward", "central", "complex_step")
During check_partial_derivatives, you can optionally do a
second finite difference with a different mode.
fd_options['linearize'] : bool(False)
Set to True if you want linearize to be called even though you are using FD.
options['command'] : list([])
Command to be executed. Command must be a list of command line args.
options['env_vars'] : dict({})
Environment variables required by the command
options['external_input_files'] : list([])
(optional) list of input file names to check the existence of before solve_nonlinear
options['external_output_files'] : list([])
(optional) list of input file names to check the existence of after solve_nonlinear
options['poll_delay'] : float(0.0)
Delay between polling for command completion. A value of zero will use
an internally computed default.
options['timeout'] : float(0.0)
Maximum time in seconds to wait for command completion. A value of zero
implies an infinite wait. If the timeout interval is exceeded, an
AnalysisError will be raised.
options['fail_hard'] : bool(True)
Behavior on error returned from code, either raise a 'hard' error (RuntimeError) if True
or a 'soft' error (AnalysisError) if False.
"""
def __init__(self):
super(ExternalCode, self).__init__()
self.STDOUT = STDOUT
self.DEV_NULL = DEV_NULL
# Input options for this Component
self.options = OptionsDictionary()
self.options.add_option('command', [], desc='command to be executed')
self.options.add_option(
'env_vars', {},
desc='Environment variables required by the command')
self.options.add_option(
'poll_delay',
0.0,
lower=0.0,
desc=
'Delay between polling for command completion. A value of zero will use an internally computed default'
)
self.options.add_option(
'timeout',
0.0,
lower=0.0,
desc=
'Maximum time to wait for command completion. A value of zero implies an infinite wait'
)
self.options.add_option(
'external_input_files', [],
desc=
'(optional) list of input file names to check the existence of before solve_nonlinear'
)
self.options.add_option(
'external_output_files', [],
desc=
'(optional) list of input file names to check the existence of after solve_nonlinear'
)
self.options.add_option(
'fail_hard',
True,
desc=
"If True, external code errors raise a 'hard' exception (RuntimeError). Otherwise raise a 'soft' exception (AnalysisError)."
)
# Outputs of the run of the component or items that will not work with the OptionsDictionary
self.return_code = 0 # Return code from the command
self.stdin = self.DEV_NULL
self.stdout = None
self.stderr = "error.out"
def check_setup(self, out_stream=sys.stdout):
"""Write a report to the given stream indicating any potential problems found
with the current configuration of this ``Problem``.
Args
----
out_stream : a file-like object, optional
"""
# check for the command
cmd = [c for c in self.options['command'] if c.strip()]
if not cmd:
out_stream.write("The command cannot be empty")
else:
program_to_execute = self.options['command'][0]
command_full_path = find_executable(program_to_execute)
if not command_full_path:
out_stream.write("The command to be executed, '%s', "
"cannot be found" % program_to_execute)
# Check for missing input files
missing = self._check_for_files(self.options['external_input_files'])
if missing:
out_stream.write("The following input files are missing at setup "
" time: %s" % missing)
def solve_nonlinear(self, params, unknowns, resids):
"""Runs the component
"""
self.return_code = -12345678
if not self.options['command']:
raise ValueError('Empty command list')
if self.options['fail_hard']:
err_class = RuntimeError
else:
err_class = AnalysisError
return_code = None
try:
missing = self._check_for_files(
self.options['external_input_files'])
if missing:
raise err_class("The following input files are missing: %s" %
sorted(missing))
return_code, error_msg = self._execute_local()
if return_code is None:
raise AnalysisError('Timed out after %s sec.' %
self.options['timeout'])
elif return_code:
if isinstance(self.stderr, str):
if os.path.exists(self.stderr):
stderrfile = open(self.stderr, 'r')
error_desc = stderrfile.read()
stderrfile.close()
err_fragment = "\nError Output:\n%s" % error_desc
else:
err_fragment = "\n[stderr %r missing]" % self.stderr
else:
err_fragment = error_msg
raise err_class('return_code = %d%s' %
(return_code, err_fragment))
missing = self._check_for_files(
self.options['external_output_files'])
if missing:
raise err_class("The following output files are missing: %s" %
sorted(missing))
finally:
self.return_code = -999999 if return_code is None else return_code
def _check_for_files(self, files):
""" Check that specified files exist. """
return [path for path in files if not os.path.exists(path)]
def _execute_local(self):
""" Run command. """
# check to make sure command exists
if isinstance(self.options['command'], str):
program_to_execute = self.options['command']
else:
program_to_execute = self.options['command'][0]
# suppress message from find_executable function, we'll handle it
numpy.distutils.log.set_verbosity(-1)
command_full_path = find_executable(program_to_execute)
if not command_full_path:
raise ValueError(
"The command to be executed, '%s', cannot be found" %
program_to_execute)
command_for_shell_proc = self.options['command']
if sys.platform == 'win32':
command_for_shell_proc = ['cmd.exe', '/c'] + command_for_shell_proc
self._process = \
ShellProc(command_for_shell_proc, self.stdin,
self.stdout, self.stderr, self.options['env_vars'])
try:
return_code, error_msg = \
self._process.wait(self.options['poll_delay'], self.options['timeout'])
finally:
self._process.close_files()
self._process = None
return (return_code, error_msg)
class ExternalCode(Component):
"""
Run an external code as a component
Default stdin is the 'null' device, default stdout is the console, and
default stderr is ``error.out``.
Options
-------
fd_options['force_fd'] : bool(False)
Set to True to finite difference this system.
fd_options['form'] : str('forward')
Finite difference mode. (forward, backward, central) You can also set to 'complex_step' to peform the complex step method if your components support it.
fd_options['step_size'] : float(1e-06)
Default finite difference stepsize
fd_options['step_type'] : str('absolute')
Set to absolute, relative
options['check_external_outputs'] : bool(True)
Check that all input or output external files exist
options['command'] : list([])
command to be executed
options['env_vars'] : dict({})
Environment variables required by the command
options['external_input_files'] : list([])
(optional) list of input file names to check the pressence of before solve_nonlinear
options['external_output_files'] : list([])
(optional) list of input file names to check the pressence of after solve_nonlinear
options['poll_delay'] : float(0.0)
Delay between polling for command completion. A value of zero will use an internally computed default
options['timeout'] : float(0.0)
Maximum time to wait for command completion. A value of zero implies an infinite wait
"""
def __init__(self):
super(ExternalCode, self).__init__()
self.STDOUT = STDOUT
self.DEV_NULL = DEV_NULL
# Input options for this Component
self.options = OptionsDictionary()
self.options.add_option('command', [], desc='command to be executed')
self.options.add_option('env_vars', {}, desc='Environment variables required by the command')
self.options.add_option('poll_delay', 0.0, lower=0.0,
desc='Delay between polling for command completion. A value of zero will use an internally computed default')
self.options.add_option('timeout', 0.0, lower=0.0,
desc='Maximum time to wait for command completion. A value of zero implies an infinite wait')
self.options.add_option('check_external_outputs', True,
desc='Check that all input or output external files exist')
self.options.add_option( 'external_input_files', [],
desc='(optional) list of input file names to check the pressence of before solve_nonlinear')
self.options.add_option( 'external_output_files', [],
desc='(optional) list of input file names to check the pressence of after solve_nonlinear')
# Outputs of the run of the component or items that will not work with the OptionsDictionary
self.return_code = 0 # Return code from the command
self.timed_out = False # True if the command timed-out
self.stdin = self.DEV_NULL
self.stdout = None
self.stderr = "error.out"
def check_setup(self, out_stream=sys.stdout):
"""Write a report to the given stream indicating any potential problems found
with the current configuration of this ``Problem``.
Args
----
out_stream : a file-like object, optional
"""
# check for the command
if not self.options['command']:
out_stream.write( "The command cannot be empty")
else:
if isinstance(self.options['command'], str):
program_to_execute = self.options['command']
else:
program_to_execute = self.options['command'][0]
command_full_path = find_executable( program_to_execute )
if not command_full_path:
msg = "The command to be executed, '%s', cannot be found" % program_to_execute
out_stream.write(msg)
# Check for missing input files
missing_files = self._check_for_files(input=True)
for iotype, path in missing_files:
msg = "The %s file %s is missing" % ( iotype, path )
out_stream.write(msg)
def solve_nonlinear(self, params, unknowns, resids):
"""Runs the component
"""
self.return_code = -12345678
self.timed_out = False
if not self.options['command']:
raise ValueError('Empty command list')
# self.check_files(inputs=True)
return_code = None
error_msg = ''
try:
return_code, error_msg = self._execute_local()
if return_code is None:
# if self._stop:
# raise RuntimeError('Run stopped')
# else:
self.timed_out = True
raise RuntimeError('Timed out')
elif return_code:
if isinstance(self.stderr, str):
if os.path.exists(self.stderr):
stderrfile = open(self.stderr, 'r')
error_desc = stderrfile.read()
stderrfile.close()
err_fragment = "\nError Output:\n%s" % error_desc
else:
err_fragment = "\n[stderr %r missing]" % self.stderr
else:
err_fragment = error_msg
raise RuntimeError('return_code = %d%s' % (return_code, err_fragment))
if self.options['check_external_outputs']:
missing_files = self._check_for_files(input=False)
msg = ""
for iotype, path in missing_files:
msg += "%s file %s is missing\n" % (iotype, path)
if msg:
raise RuntimeError( "Missing files: %s" % msg )
# self.check_files(inputs=False)
finally:
self.return_code = -999999 if return_code is None else return_code
def _check_for_files(self, input=True):
"""
Check that all 'specific' input external files exist.
input: bool
If True, check inputs. Else check outputs
"""
missing_files = []
if input:
files = self.options['external_input_files']
else:
files = self.options['external_output_files']
for path in files:
if not os.path.exists(path):
missing_files.append(('input', path))
return missing_files
def _execute_local(self):
""" Run command. """
#self._logger.info('executing %s...', self.options['command'])
# start_time = time.time()
# check to make sure command exists
if isinstance(self.options['command'], str):
program_to_execute = self.options['command']
else:
program_to_execute = self.options['command'][0]
# suppress message from find_executable function, we'll handle it
numpy.distutils.log.set_verbosity(-1)
command_full_path = find_executable( program_to_execute )
if not command_full_path:
raise ValueError("The command to be executed, '%s', cannot be found" % program_to_execute)
command_for_shell_proc = self.options['command']
if sys.platform == 'win32':
command_for_shell_proc = ['cmd.exe', '/c' ] + command_for_shell_proc
self._process = \
ShellProc(command_for_shell_proc, self.stdin,
self.stdout, self.stderr, self.options['env_vars'])
#self._logger.debug('PID = %d', self._process.pid)
try:
return_code, error_msg = \
self._process.wait(self.options['poll_delay'], self.options['timeout'])
finally:
self._process.close_files()
self._process = None
# et = time.time() - start_time
#if et >= 60: #pragma no cover
#self._logger.info('elapsed time: %.1f sec.', et)
return (return_code, error_msg)
class ExternalCode(Component):
"""
Run an external code as a component
Default stdin is the 'null' device, default stdout is the console, and
default stderr is ``error.out``.
Options
-------
deriv_options['type'] : str('user')
Derivative calculation type ('user', 'fd', 'cs')
Default is 'user', where derivative is calculated from
user-supplied derivatives. Set to 'fd' to finite difference
this system. Set to 'cs' to perform the complex step
if your components support it.
deriv_options['form'] : str('forward')
Finite difference mode. (forward, backward, central)
deriv_options['step_size'] : float(1e-06)
Default finite difference stepsize
deriv_options['step_calc'] : str('absolute')
Set to absolute, relative
deriv_options['check_type'] : str('fd')
Type of derivative check for check_partial_derivatives. Set
to 'fd' to finite difference this system. Set to
'cs' to perform the complex step method if
your components support it.
deriv_options['check_form'] : str('forward')
Finite difference mode: ("forward", "backward", "central")
During check_partial_derivatives, the difference form that is used
for the check.
deriv_options['check_step_calc'] : str('absolute',)
Set to 'absolute' or 'relative'. Default finite difference
step calculation for the finite difference check in check_partial_derivatives.
deriv_options['check_step_size'] : float(1e-06)
Default finite difference stepsize for the finite difference check
in check_partial_derivatives"
deriv_options['linearize'] : bool(False)
Set to True if you want linearize to be called even though you are using FD.
options['command'] : list([])
Command to be executed. Command must be a list of command line args.
options['env_vars'] : dict({})
Environment variables required by the command
options['external_input_files'] : list([])
(optional) list of input file names to check the existence of before solve_nonlinear
options['external_output_files'] : list([])
(optional) list of input file names to check the existence of after solve_nonlinear
options['poll_delay'] : float(0.0)
Delay between polling for command completion. A value of zero will use
an internally computed default.
options['timeout'] : float(0.0)
Maximum time in seconds to wait for command completion. A value of zero
implies an infinite wait. If the timeout interval is exceeded, an
AnalysisError will be raised.
options['fail_hard'] : bool(True)
Behavior on error returned from code, either raise a 'hard' error (RuntimeError) if True
or a 'soft' error (AnalysisError) if False.
"""
def __init__(self):
super(ExternalCode, self).__init__()
self.STDOUT = STDOUT
self.DEV_NULL = DEV_NULL
# Input options for this Component
self.options = OptionsDictionary()
self.options.add_option('command', [], desc='command to be executed')
self.options.add_option('env_vars', {},
desc='Environment variables required by the command')
self.options.add_option('poll_delay', 0.0, lower=0.0,
desc='Delay between polling for command completion. A value of zero will use an internally computed default')
self.options.add_option('timeout', 0.0, lower=0.0,
desc='Maximum time to wait for command completion. A value of zero implies an infinite wait')
self.options.add_option( 'external_input_files', [],
desc='(optional) list of input file names to check the existence of before solve_nonlinear')
self.options.add_option( 'external_output_files', [],
desc='(optional) list of input file names to check the existence of after solve_nonlinear')
self.options.add_option('fail_hard', True,
desc="If True, external code errors raise a 'hard' exception (RuntimeError). Otherwise raise a 'soft' exception (AnalysisError).")
# Outputs of the run of the component or items that will not work with the OptionsDictionary
self.return_code = 0 # Return code from the command
self.stdin = self.DEV_NULL
self.stdout = None
self.stderr = "error.out"
def check_setup(self, out_stream=sys.stdout):
"""Write a report to the given stream indicating any potential problems found
with the current configuration of this ``Problem``.
Args
----
out_stream : a file-like object, optional
"""
# check for the command
cmd = [c for c in self.options['command'] if c.strip()]
if not cmd:
out_stream.write( "The command cannot be empty")
else:
program_to_execute = self.options['command'][0]
command_full_path = find_executable( program_to_execute )
if not command_full_path:
out_stream.write("The command to be executed, '%s', "
"cannot be found" % program_to_execute)
# Check for missing input files
missing = self._check_for_files(self.options['external_input_files'])
if missing:
out_stream.write("The following input files are missing at setup "
" time: %s" % missing)
def solve_nonlinear(self, params, unknowns, resids):
"""Runs the component
"""
self.return_code = -12345678
if not self.options['command']:
raise ValueError('Empty command list')
if self.options['fail_hard']:
err_class = RuntimeError
else:
err_class = AnalysisError
return_code = None
try:
missing = self._check_for_files(self.options['external_input_files'])
if missing:
raise err_class("The following input files are missing: %s"
% sorted(missing))
return_code, error_msg = self._execute_local()
if return_code is None:
raise AnalysisError('Timed out after %s sec.' %
self.options['timeout'])
elif return_code:
if isinstance(self.stderr, str):
if os.path.exists(self.stderr):
stderrfile = open(self.stderr, 'r')
error_desc = stderrfile.read()
stderrfile.close()
err_fragment = "\nError Output:\n%s" % error_desc
else:
err_fragment = "\n[stderr %r missing]" % self.stderr
else:
err_fragment = error_msg
raise err_class('return_code = %d%s' % (return_code,
err_fragment))
missing = self._check_for_files(self.options['external_output_files'])
if missing:
raise err_class("The following output files are missing: %s"
% sorted(missing))
finally:
self.return_code = -999999 if return_code is None else return_code
def _check_for_files(self, files):
""" Check that specified files exist. """
return [path for path in files if not os.path.exists(path)]
def _execute_local(self):
""" Run command. """
# check to make sure command exists
if isinstance(self.options['command'], str):
program_to_execute = self.options['command']
else:
program_to_execute = self.options['command'][0]
# suppress message from find_executable function, we'll handle it
numpy.distutils.log.set_verbosity(-1)
command_full_path = find_executable( program_to_execute )
if not command_full_path:
raise ValueError("The command to be executed, '%s', cannot be found" % program_to_execute)
command_for_shell_proc = self.options['command']
if sys.platform == 'win32':
command_for_shell_proc = ['cmd.exe', '/c' ] + command_for_shell_proc
self._process = \
ShellProc(command_for_shell_proc, self.stdin,
self.stdout, self.stderr, self.options['env_vars'])
try:
return_code, error_msg = \
self._process.wait(self.options['poll_delay'], self.options['timeout'])
finally:
self._process.close_files()
self._process = None
return (return_code, error_msg)
