def open_std_fd(fdname):
# fdname is 'stdout' or 'stderr'
stdfspec = kwargs.get(fdname) # spec is str name or tuple (name, mode)
if stdfspec is None:
return None
elif isinstance(stdfspec, str):
fname = stdfspec
mode = 'a+'
elif isinstance(stdfspec, tuple):
if len(stdfspec) != 2:
raise pe.BadStdStreamFile(
"std descriptor %s has incorrect tuple length %s" %
(fdname, len(stdfspec)), TypeError('Bad Tuple Length'))
fname, mode = stdfspec
else:
raise pe.BadStdStreamFile(
"std descriptor %s has unexpected type %s" %
(fdname, str(type(stdfspec))), TypeError('Bad Tuple Type'))
try:
if os.path.dirname(fname):
os.makedirs(os.path.dirname(fname), exist_ok=True)
fd = open(fname, mode)
except Exception as e:
raise pe.BadStdStreamFile(fname, e)
return fd
def get_std_fname_mode(fdname: str, stdfspec: Union[str, Tuple[str, str]]) -> Tuple[str, str]:
import parsl.app.errors as pe
if stdfspec is None:
return None, None
elif isinstance(stdfspec, str):
fname = stdfspec
mode = 'a+'
elif isinstance(stdfspec, tuple):
if len(stdfspec) != 2:
raise pe.BadStdStreamFile("std descriptor %s has incorrect tuple length %s" % (fdname, len(stdfspec)), TypeError('Bad Tuple Length'))
fname, mode = stdfspec
if not isinstance(fname, str) or not isinstance(mode, str):
raise pe.BadStdStreamFile("std descriptor %s has unexpected type %s" % (fdname, str(type(stdfspec))), TypeError('Bad Tuple Type'))
else:
raise pe.BadStdStreamFile("std descriptor %s has unexpected type %s" % (fdname, str(type(stdfspec))), TypeError('Bad Tuple Type'))
return fname, mode
def open_std_fd(fdname):
# fdname is 'stdout' or 'stderr'
stdfspec = kwargs.get(fdname) # spec is str name or tuple (name, mode)
if stdfspec is None:
return None
fname, mode = get_std_fname_mode(fdname, stdfspec)
try:
if os.path.dirname(fname):
os.makedirs(os.path.dirname(fname), exist_ok=True)
fd = open(fname, mode)
except Exception as e:
raise pe.BadStdStreamFile(fname, e)
return fd
def remote_side_bash_executor(func, *args, **kwargs):
''' The callable fn for external apps.
This is the function that executes the bash app type function that returns
the commandline string. This string is reformatted with the *args, and **kwargs
from call time.
'''
import os
import time
import subprocess
import logging
import parsl.app.errors as pe
logging.basicConfig(filename='/tmp/bashexec.{0}.log'.format(time.time()), level=logging.DEBUG)
start_t = time.time()
func_name = func.__name__
# Try to run the func to compose the commandline
try:
# Execute the func to get the commandline
partial_cmdline = func(*args, **kwargs)
# Reformat the commandline with current args and kwargs
executable = partial_cmdline.format(*args, **kwargs)
except AttributeError as e:
if partial_cmdline :
raise pe.AppBadFormatting("[{}] AppFormatting failed during cmd_line resolution {}".format(func_name,
e), None)
else:
raise pe.BashAppNoReturn("[{}] Bash App returned NoneType, must return str object".format(func_name), None)
except IndexError as e:
raise pe.AppBadFormatting("[{}] AppFormatting failed during cmd_line resolution {}".format(func_name,
e), None)
except Exception as e:
logging.error("[{}] Caught exception during cmd_line resolution : {}".format(func_name,
e))
raise e
# Updating stdout, stderr if values passed at call time.
stdout = kwargs.get('stdout', None)
stderr = kwargs.get('stderr', None)
timeout = kwargs.get('walltime', None)
logging.debug("Stdout : %s", stdout)
logging.debug("Stderr : %s", stderr)
try :
std_out = open(stdout, 'w') if stdout else None
std_err = open(stderr, 'w') if stderr else None
except Exception as e:
raise pe.BadStdStreamFile([stdout, stderr], e)
start_time = time.time()
returncode = None
try :
proc = subprocess.Popen(executable, stdout=std_out, stderr=std_err, shell=True, executable='/bin/bash')
proc.wait(timeout=timeout)
returncode = proc.returncode
except subprocess.TimeoutExpired as e:
print("Timeout")
status = 'failed'
raise pe.AppTimeout("[{}] App exceeded walltime: {}".format(func_name, timeout), e)
except Exception as e:
print ("Caught exception : ", e)
error = e
status = 'failed'
raise pe.AppException("[{}] App caught exception : {}".format(func_name, proc.returncode), e)
if returncode != 0:
raise pe.AppFailure("[{}] App Failed exit code: {}".format(func_name, proc.returncode), proc.returncode)
# TODO : Add support for globs here
missing = []
for outputfile in kwargs.get('outputs', []):
fpath = outputfile
if type(outputfile) != str:
fpath = outputfile.filepath
if not os.path.exists(fpath):
missing.extend([outputfile])
if missing:
raise pe.MissingOutputs("[{}] Missing outputs".format(func_name), missing)
exec_duration = time.time() - start_t
return returncode
def remote_side_bash_executor(func, *args, **kwargs):
"""Execute the bash app type function and return the command line string.
This string is reformatted with the *args, and **kwargs
from call time.
"""
import os
import time
import subprocess
import logging
import parsl.app.errors as pe
logging.basicConfig(filename='/tmp/bashexec.{0}.log'.format(time.time()),
level=logging.DEBUG)
# start_t = time.time()
func_name = func.__name__
partial_cmdline = None
# Try to run the func to compose the commandline
try:
# Execute the func to get the commandline
partial_cmdline = func(*args, **kwargs)
# Reformat the commandline with current args and kwargs
executable = partial_cmdline.format(*args, **kwargs)
except AttributeError as e:
if partial_cmdline is not None:
raise pe.AppBadFormatting(
"App formatting failed for app '{}' with AttributeError: {}".
format(func_name, e))
else:
raise pe.BashAppNoReturn(
"Bash app '{}' did not return a value, or returned none - with this exception: {}"
.format(func_name, e), None)
except IndexError as e:
raise pe.AppBadFormatting(
"App formatting failed for app '{}' with IndexError: {}".format(
func_name, e))
except Exception as e:
logging.error(
"Caught exception during formatting of app '{}': {}".format(
func_name, e))
raise e
logging.debug("Executable: %s", executable)
# Updating stdout, stderr if values passed at call time.
stdout = kwargs.get('stdout')
stderr = kwargs.get('stderr')
timeout = kwargs.get('walltime')
logging.debug("Stdout: %s", stdout)
logging.debug("Stderr: %s", stderr)
try:
std_out = open(stdout, 'a+') if stdout else None
except Exception as e:
raise pe.BadStdStreamFile(stdout, e)
try:
std_err = open(stderr, 'a+') if stderr else None
except Exception as e:
raise pe.BadStdStreamFile(stderr, e)
returncode = None
try:
proc = subprocess.Popen(executable,
stdout=std_out,
stderr=std_err,
shell=True,
executable='/bin/bash')
proc.wait(timeout=timeout)
returncode = proc.returncode
except subprocess.TimeoutExpired:
# print("Timeout")
raise pe.AppTimeout("[{}] App exceeded walltime: {}".format(
func_name, timeout))
except Exception as e:
# print("Caught exception: ", e)
raise pe.AppException(
"[{}] App caught exception: {}".format(func_name, proc.returncode),
e)
if returncode != 0:
raise pe.AppFailure(
"[{}] App failed with exit code: {}".format(
func_name, proc.returncode), proc.returncode)
# TODO : Add support for globs here
missing = []
for outputfile in kwargs.get('outputs', []):
fpath = outputfile
if type(outputfile) != str:
fpath = outputfile.filepath
if not os.path.exists(fpath):
missing.extend([outputfile])
if missing:
raise pe.MissingOutputs("[{}] Missing outputs".format(func_name),
missing)
# exec_duration = time.time() - start_t
return returncode
