def file(self, f):
"""
Return a file location to a file inside the trajectory folder
Parameters
----------
f : str or `OutputTypeDescription`
the filename to be appended to the trajectories directory
Returns
-------
`File`
the object containing the location
"""
if isinstance(f, six.string_types):
return File(os.path.join(self.location, f))
elif isinstance(f, OutputTypeDescription):
return self.file(f.filename)
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
from __future__ import absolute_import
import os
import ujson
# from adaptivemd.task import PythonTask
from adaptivemd.file import Location, File
from adaptivemd.engine import (Engine, Frame, Trajectory,
TrajectoryGenerationTask,
TrajectoryExtensionTask)
exec_file = File(
'file://' +
os.path.join(os.path.dirname(__file__), 'openmmrun.py')).load()
class OpenMMEngine(Engine):
"""
OpenMM Engine to be used by Adaptive MD
Attributes
----------
system_file : `File`
the system.xml file for OpenMM
integrator_file : `File`
the integrator.xml file for OpenMM
pdb_file : `File`
the .pdb file for the topology
def run(self,
target,
resource_name=None,
export_path=None,
cpu_threads=1,
gpu_contexts=0,
mpi_rank=0):
t = TrajectoryGenerationTask(self,
target,
cpu_threads=cpu_threads,
gpu_contexts=gpu_contexts,
mpi_rank=mpi_rank)
if resource_name is None:
resource_name = list()
elif isinstance(resource_name, str):
resource_name = [resource_name]
assert isinstance(resource_name, list)
t.resource_name = resource_name
if export_path:
t.append(export_path)
initial_pdb = t.pre_link(self['pdb_file_stage'],
Location('initial.pdb'))
t.pre_link(self['system_file_stage'])
t.pre_link(self['integrator_file_stage'])
t.pre_link(self['_executable_file_stage'], hard=True)
if target.frame in [self['pdb_file'], self['pdb_file_stage']]:
input_pdb = initial_pdb
elif isinstance(target.frame, File):
loc = Location('coordinates.%s' % target.frame.extension)
input_pdb = t.get(target.frame, loc)
elif isinstance(target.frame, Frame):
input_traj = t.pre_link(target.frame.trajectory, 'source/')
input_pdb = File('input.pdb')
# frame index is in canonical stride = 1
# we need to figure out which frame in the traj this actually is
# also, we need a traj with full coordinates / selection = None
ty, idx = target.frame.index_in_outputs
if ty is None:
# cannot use a trajectory where we do not have full coordinates
return
cmd = (
'mdconvert -o {target} -i {index} -t {pdb} {source}'.format(
target=input_pdb, # input.pdb is used as starting structure
index=idx, # the index from the source trajectory
pdb=initial_pdb, # use the main pdb
source=input_traj.outputs(ty))) # we pick output ty
t.pre.append(cmd)
else:
# for now we assume that if the initial frame is None or
# not specific use the engines internal. That should be changed
# todo: Raise exception here
return
# this represents our output trajectory
output = Trajectory('traj/',
target.frame,
length=target.length,
engine=self)
# create the directory
t.touch(output)
# TODO option for retry
# - use filenames from engine
cmd = 'python openmmrun.py {args} {types} -s {system} -i {integrator} -t {pdb} --length {length} {output}'.format(
pdb=input_pdb,
types=self._create_output_str(),
length=target.length,
system=self['system_file'].basename,
integrator=self['integrator_file'].basename,
output=output,
args=self.args,
)
# TODO option for retry
# TODO use filenames from engine
retry = '\nj=0\ntries=3\n'
retry += '\ntrajfile=traj/protein.dcd\n\n'
"\n\n"
retry += (
'function timestamp {{\n'
' date +\'%Y-%m-%d %H:%M:%S.%3N\'\n'
'}}\n'
'while [ ! -f "$trajfile" ] && [ $j -le "$tries" ]\n'
'do\n'
' {0} & last="$!"\n'
' sleep 20\n'
'\n'
' echo "$(timestamp) running.sh - checking for trajectory output"\n'
' echo "$(timestamp) openmmrun - PID: $last"\n'
' echo "$(ps faux | grep $last | grep -v grep)"\n'
' echo "$(timestamp) trajectory output"\n'
' echo "$(ls -gt traj)"\n'
'\n'
' if [ ! -f $trajfile ]\n'
' then\n'
' j=$((j+1))\n'
' echo "$(timestamp) output not found"\n'
'\n'
' if [ "$(ps faux | grep $last | grep -v grep)" ]\n'
' then\n'
' kill "$last" || echo "kill missed"\n'
'\n'
' echo "$(timestamp) found and kill last=$last"\n'
' echo "$(timestamp) waiting to check on kill"\n'
' sleep 5\n'
'\n'
' if [ "$(ps faux | grep $last | grep -v grep)" ]\n'
' then\n'
' echo "$(timestamp) superkilling last=$last"\n'
' kill -9 "$last" || echo "superkill missed"\n'
'\n'
' fi\n'
' fi\n'
'\n'
' echo "$(timestamp) kill is done"\n'
'\n'
' else\n'
' echo "$(timestamp) seems like the trajectory is rolling out"\n'
' j=$((tries+1))\n'
'\n'
' fi\n'
' echo "$(timestamp) Done $j retry iter of main task loop"\n'
'\n'
'done\n'
'\n'
'wait "$last"\n'
'echo "$(timestamp) Done with main task loop"\n')
cmd = 'python openmmrun.py {args} {types} -s {system} -i {integrator} -t {pdb} --length {length} {output}'.format(
pdb=input_pdb,
types=self._create_output_str(),
length=target.length,
system=self['system_file'].basename,
integrator=self['integrator_file'].basename,
output=output,
args=self.args,
)
cmd = retry.format(cmd)
t.append(cmd)
t.put(output, target)
return t
def run(self,
target,
resource_name=None,
export_path=None,
cpu_threads=1,
gpu_contexts=0,
mpi_rank=0):
t = TrajectoryGenerationTask(self,
target,
cpu_threads=cpu_threads,
gpu_contexts=gpu_contexts,
mpi_rank=mpi_rank)
if resource_name is None:
resource_name = list()
elif isinstance(resource_name, str):
resource_name = [resource_name]
assert isinstance(resource_name, list)
t.resource_name = resource_name
if export_path:
t.append(export_path)
initial_pdb = t.pre_link(self['pdb_file_stage'],
Location('initial.pdb'))
t.pre_link(self['system_file_stage'])
t.pre_link(self['integrator_file_stage'])
t.pre_link(self['_executable_file_stage'])
if target.frame in [self['pdb_file'], self['pdb_file_stage']]:
input_pdb = initial_pdb
elif isinstance(target.frame, File):
loc = Location('coordinates.%s' % target.frame.extension)
input_pdb = t.get(target.frame, loc)
elif isinstance(target.frame, Frame):
input_traj = t.pre_link(target.frame.trajectory, 'source/')
input_pdb = File('input.pdb')
# frame index is in canonical stride = 1
# we need to figure out which frame in the traj this actually is
# also, we need a traj with full coordinates / selection = None
ty, idx = target.frame.index_in_outputs
if ty is None:
# cannot use a trajectory where we do not have full coordinates
return
cmd = (
'mdconvert -o {target} -i {index} -t {pdb} {source}'.format(
target=input_pdb, # input.pdb is used as starting structure
index=idx, # the index from the source trajectory
pdb=initial_pdb, # use the main pdb
source=input_traj.outputs(ty))) # we pick output ty
t.pre.append(cmd)
else:
# for now we assume that if the initial frame is None or
# not specific use the engines internal. That should be changed
# todo: Raise exception here
return
# this represents our output trajectory
output = Trajectory('traj/',
target.frame,
length=target.length,
engine=self)
# create the directory
t.touch(output)
# TODO option for retry
# - use filenames from engine
cmd = 'python openmmrun.py {args} {types} -s {system} -i {integrator} -t {pdb} --length {length} {output}'.format(
pdb=input_pdb,
types=self._create_output_str(),
length=target.length,
system=self['system_file'].basename,
integrator=self['integrator_file'].basename,
output=output,
args=self.args,
)
t.append(cmd)
t.put(output, target)
return t