def _checkInput(self):
async_re_job._checkInput(self)
try:
engine = str(self.keywords.get('ENGINE')).upper()
engine = SUPPORTED_AMBER_ENGINES[engine]
except KeyError:
_exit('Requested ENGINE (%s) is either invalid or not '
'currently supported.'%self.keywords.get('ENGINE'))
if int(self.keywords.get('SUBJOB_CORES')) > 1:
self.spmd = 'mpi'
engine = '%s.MPI'%engine
if ((engine == 'sander.MPI' and not at.SANDER_MPI_EXE)
or engine == 'pmemd.MPI' and not at.PMEMD_MPI_EXE):
no_exe = True
else:
no_exe = False
else:
self.spmd = 'single'
if ((engine == 'sander' and not at.SANDER_SERIAL_EXE)
or engine == 'pmemd' and not at.PMEMD_SERIAL_EXE):
no_exe = True
else:
no_exe = False
if no_exe:
_exit('Cannot find %s executable. Is it compiled and in '
'AMBERHOME/bin?'%engine)
self.exe = os.path.join(at.AMBERHOME,'bin',engine)
self.states = amber_states_from_configobj(self.keywords,self.verbose)
self.nreplicas = len(self.states)
def amber_states_from_configobj(keywords, verbose=False):
"""Return an AmberRunCollection from an ASyncRE command file."""
# keywords = ConfigObj(command_file)
try:
engine = keywords.get('ENGINE').upper()
engine = SUPPORTED_AMBER_ENGINES[engine]
except KeyError:
_exit('Requested ENGINE (%s) is either invalid or not currently '
'supported.'%keywords.get('ENGINE'))
# Set up the general state/replica information - 2 methods
#
# (1) If present, read the AMBER groupfile and define the states,
if keywords.get('AMBER_GROUPFILE') is not None:
groupfile = keywords.get('AMBER_GROUPFILE')
states = read_amber_groupfile(groupfile,engine)
if verbose:
print ('Created %d replicas from AMBER groupfile: %s'
%(len(states),groupfile))
# (2) otherwise assume that the states can be inferred from the extfiles
# and input from a specific application (e.g. umbrella sampling).
else:
basename = keywords.get('ENGINE_INPUT_BASENAME')
extfiles = keywords.get('ENGINE_INPUT_EXTFILES')
if extfiles is not None and extfiles != '':
extfiles = extfiles.split(',')
else:
extfiles = None
nreplicas = int(keywords.get('NREPLICAS'))
if nreplicas is None:
_exit('Could not determine the replica count from the input '
'provided (set NREPLICAS directly or provide an AMBER '
'groupfile)')
try:
states = amberrun_from_files(basename,extfiles,nreplicas,'-O',
engine)
except IOError:
_exit('Problem creating replicas, not enough information?')
if verbose:
print ('Created %d replicas using the provided '
'ENGINE_INPUT_EXTFILES and ENGINE_INPUT_BASENAME'
%nreplicas)
return states
def _checkInput(self):
async_re_job._checkInput(self)
try:
engine = self.keywords.get('ENGINE').upper()
engine = SUPPORTED_AMBER_ENGINES[engine]
except KeyError:
_exit('Requested ENGINE (%s) is either invalid or not '
'currently supported.'%self.keywords.get('ENGINE'))
if int(self.keywords.get('SUBJOB_CORES')) > 1:
self.spmd = 'mpi'
engine = '%s.MPI'%engine
if not at.AMBER_MPI_EXES:
_exit('Cannot find AMBER MPI executables. Are these compiled '
'and in AMBERHOME/bin?')
else:
self.spmd = 'single'
if not at.AMBER_SERIAL_EXES:
_exit('Cannot find AMBER serial executables. Are these '
'compiled and in AMBERHOME/bin?')
self.exe = os.path.join(at.AMBERHOME,'bin',engine)
self.states = amber_states_from_configobj(self.keywords,self.verbose)
self.nreplicas = len(self.states)