def run(self, rank, stdout=sys.stdout, stderr=sys.stderr):
""" Runs the program. All command-line arguments must be set before
calling this method. Command-line arguments should be set in setup()
"""
from subprocess import Popen, PIPE
# If this has not been set up yet
# then raise a stink
if not self.calc_setup:
raise CalcError('Cannot run a calculation without calling its' +
' its setup() function!')
# Make sure the inptraj and output are rank-substituted
instring = self._get_instring(rank)
process = Popen([self.program, self.prmtop],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
out, err = process.communicate(instring.encode())
calc_failed = bool(process.wait())
if calc_failed:
raise CalcError('%s failed with prmtop %s!' %
(self.program, self.prmtop))
def run(self, rank, stdout=sys.stdout, stderr=sys.stderr):
""" Runs the program. All command-line arguments must be set before
calling this method. Command-line arguments should be set in setup()
"""
from subprocess import Popen
# If this has not been set up yet
# then raise a stink
if not self.calc_setup:
raise CalcError('Cannot run a calculation without calling its' +
' its setup() function!')
# Here, make sure that we could pass a file *OR* a string as stdout/stderr.
# If they are strings, then open files up with that name, and make sure to
# close them afterwards. The setup() method should make sure that they are
# either a file or a string!
own_handleo = own_handlee = False
try:
process_stdout = open(stdout, 'w')
own_handleo = True
except TypeError:
process_stdout = stdout
try:
process_stderr = open(stderr, 'w')
own_handlee = True
except TypeError:
process_stderr = stderr
# The setup() method sets the command-line arguments and makes sure that
# all of the CL arguments are set. Now all we have to do is start the
# process and monitor it for success.
# Popen can only take strings as command-line arguments, so convert
# everything to a string here. And if it appears to need the rank
# substituted into the file name, substitute that in here
try:
for i in range(len(self.command_args)):
self.command_args[i] = str(self.command_args[i])
if '%d' in self.command_args[i]:
self.command_args[i] = self.command_args[i] % rank
process = Popen(self.command_args,
stdin=None,
stdout=process_stdout,
stderr=process_stderr)
calc_failed = bool(process.wait())
if calc_failed:
raise CalcError('%s failed with prmtop %s!' %
(self.program, self.prmtop))
finally:
if own_handleo: process_stdout.close()
if own_handlee: process_stdout.close()
def run(self, rank, stdout=sys.stdout, stderr=sys.stderr):
"""
Runs the program. All command-line arguments must be set before calling
this method. Command-line arguments should be set in setup()
stdout is ignored here because we need to parse it for errors
"""
import re
from subprocess import Popen, PIPE
# If this has not been set up yet
# then raise a stink
if not self.calc_setup:
raise CalcError('Cannot run a calculation without calling its' +
' its setup() function!')
errorre = re.compile('(pb (?:bomb)|(?:warning))', re.I)
# Here, make sure that we could pass a file *OR* a string as stderr.
own_handle = False
try:
process_stderr = open(stderr, 'w')
own_handle = True
except TypeError:
process_stderr = stderr
# The setup() method sets the command-line arguments and makes sure that
# all of the CL arguments are set. Now all we have to do is start the
# process and monitor it for success.
# Popen can only take strings as command-line arguments, so convert
# everything to a string here. If rank needs to be substituted in, do that
# here
try:
for i in range(len(self.command_args)):
self.command_args[i] = str(self.command_args[i])
if '%d' in self.command_args[i]:
self.command_args[i] = self.command_args[i] % rank
process = Popen(self.command_args, stdin=None, stdout=PIPE,
stderr=process_stderr)
out, err = process.communicate(b'')
calc_failed = bool(process.wait())
if calc_failed:
error_list = [s.strip() for s in out.split('\n')
if errorre.match(s.strip())]
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
self.prmtop) + '\n\t'.join(error_list) + '\n')
finally:
if own_handle: process_stderr.close()
def setup(self):
""" Sets up a Quasi-harmonic calculation """
from subprocess import Popen, PIPE
# Determine the prefix from our input file... hack way to do this
if self.input_file.startswith(self.fnpre + 'mutant_'):
prefix = self.fnpre + 'mutant_'
else:
prefix = self.fnpre
# Make sure masks are a list, and that there are enough masks
# First thing we need is the average PDB as a reference
ptraj_str = 'trajin %s\naverage %savgcomplex.pdb pdb chainid " "\ngo' % (
self.inptraj, prefix)
outfile = open(self.fnpre + 'create_average.out', 'w')
process = Popen([self.program, self.prmtop],
stdin=PIPE,
stdout=outfile)
out, err = process.communicate(ptraj_str.encode())
if process.wait():
raise CalcError('Failed creating average PDB')
outfile.close()
# Now that we have the PDB file
self.command_args.extend((self.prmtop, self.input_file))
self.calc_setup = True