def setUpClass(cls):
# init project and resource
import tempfile
cls.shared_path = tempfile.mkdtemp(prefix="adaptivemd")
Project.delete('example-simple-1')
cls.project = Project('example-simple-1')
# ----------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# ----------------------------------------------------------------------
cls.project.initialize({'shared_path': cls.shared_path})
if os.getenv('CONDA_BUILD', False):
# activate the conda build test environment for workers
cls.f_base = 'examples/files/alanine/'
prefix = os.getenv('PREFIX')
assert os.path.exists(prefix)
cls.project.configuration.wrapper.pre.insert(
0, 'source activate {prefix}'.format(prefix=prefix))
# TODO why does test_simple_wrapper not
# have a chdir to ci test environment?
test_tmp = prefix + '/../test_tmp/'
if os.getcwd() is not test_tmp:
os.chdir(test_tmp)
else:
# set the path for the workers to the path of the test interpreter.
import sys
cls.f_base = '../../examples/files/alanine/'
cls.project.configuration.wrapper.pre.insert(
0, 'PATH={python_path}:$PATH'.format(
python_path=os.path.dirname(sys.executable)))
return cls
def setUpClass(cls):
'''
Operations that configure the test environment
----------------------------------------------
env :
determine if local or in integration environment
pkg :
object imports and coordination
cfg :
object instantiation and building
one-time operations that set up for test
'''
# init project and resource
import tempfile
cls.shared_path = tempfile.mkdtemp(prefix="adaptivemd")
Project.delete('test-skeleton')
cls.project = Project('test-skeleton')
cls.project.initialize({'shared_path': cls.shared_path})
# ----------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# ----------------------------------------------------------------------
if os.getenv('CONDA_BUILD', False):
# activate the conda build test environment
cls.f_base = 'examples/files/alanine/'
prefix = os.getenv('PREFIX')
assert os.path.exists(prefix)
cls.project.configuration.wrapper.pre.insert(
0, 'source activate {prefix}'.format(prefix=prefix))
# TODO why does test_simple_wrapped not
# have a chdir to ci test environment?
# TODO this is dealing in relative paths
# --> should check cwd based on absolute path
test_tmp = prefix + '/../test_tmp/'
if os.getcwd() is not test_tmp:
os.chdir(test_tmp)
else:
# set the path for the workers to the path of the test interpreter.
import sys
cls.f_base = '../../examples/files/alanine/'
cls.project.configuration.wrapper.pre.insert(
0, 'PATH={python_path}:$PATH'.format(
python_path=os.path.dirname(sys.executable)))
return cls
os.environ['RADICAL_PILOT_DBURL'] = path_to_db
# import adaptive components
from adaptivemd import Project
from adaptivemd import LocalResource
from adaptivemd import OpenMMEngine
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
project.initialize(LocalResource('$HOME/miniconda2/bin'))
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named('initial_pdb')
engine = OpenMMEngine(
# import adaptive components
import time
from adaptivemd import Project, ExecutionPlan
from adaptivemd import AllegroCluster
from adaptivemd import ExecutionPlan
from adaptivemd.engine.openmm import OpenMMEngine
from adaptivemd.analysis.pyemma import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcaseallegro')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
# resource_id = 'fub.allegro'
project.initialize(AllegroCluster())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named(
'initial_pdb').load()
def init_project(p_name,
sys_name=None,
m_freq=None,
p_freq=None,
platform=None,
reinitialize=False): #, dblocation=None):
#def init_project(p_name, **freq):
from adaptivemd import Project
#if p_name in Project.list():
# print("Deleting existing version of this test project")
# Project.delete(p_name)
dburl = os.environ.get("ADMD_DBURL", 0)
if dburl:
logger.info("Set ADMD_DBURL to: " + dburl)
Project.set_dburl(dburl)
# if dblocation is not None:
# Project.set_dblocation(dblocation)
if reinitialize:
logger.info(
"Project {0} exists, deleting it from database to reinialize".
format(p_name))
Project.delete(p_name)
if p_name in Project.list():
logger.info(
"Project {0} exists, reading it from database".format(p_name))
project = Project(p_name)
elif not all([sys_name, m_freq, p_freq, platform]):
raise ValueError(
"Must define all parameters [{0}] to initialize new project\nHave: {1}"
.format("sys_name,m_freq,p_freq,platform",
[sys_name, m_freq, p_freq, platform].__repr__()))
else:
project = Project(p_name)
from adaptivemd import File, OpenMMEngine
from adaptivemd.analysis.pyemma import PyEMMAAnalysis
# Initialize w/ config file: 1 of multiple options
# TODO add config filename argument
configuration_file = 'configuration.cfg'
project.initialize(configuration_file)
f_name = '{0}.pdb'.format(sys_name)
# FIXME add system specifications to configuration file
f_base = 'file:///$ADMD_FILES/{0}/'.format(sys_name)
f_structure = File(f_base + f_name).load()
f_system_2 = File(f_base + 'system-2.xml').load()
f_integrator_2 = File(f_base + 'integrator-2.xml').load()
f_system_5 = File(f_base + 'system-5.xml').load()
f_integrator_5 = File(f_base + 'integrator-5.xml').load()
sim_args = '-r -p {0}'.format(platform)
engine_2 = OpenMMEngine(f_system_2, f_integrator_2, f_structure,
sim_args).named('openmm-2')
engine_5 = OpenMMEngine(f_system_5, f_integrator_5, f_structure,
sim_args).named('openmm-5')
# FIXME this is dumb and hard for user to deal with
# TODO engine selection by name
m_freq_2 = m_freq
p_freq_2 = p_freq
m_freq_5 = m_freq * 2 / 5
p_freq_5 = p_freq * 2 / 5
engine_2.add_output_type('master', 'allatoms.dcd', stride=m_freq_2)
engine_2.add_output_type('protein',
'protein.dcd',
stride=p_freq_2,
selection='protein')
engine_5.add_output_type('master', 'allatoms.dcd', stride=m_freq_5)
engine_5.add_output_type('protein',
'protein.dcd',
stride=p_freq_5,
selection='protein')
ca_features = {'add_distances_ca': None}
#features = {'add_inverse_distances': {'select_Backbone': None}}
ca_modeller_2 = PyEMMAAnalysis(engine_2, 'protein',
ca_features).named('pyemma-ca-2')
ca_modeller_5 = PyEMMAAnalysis(engine_5, 'protein',
ca_features).named('pyemma-ca-5')
pos = [
'(rescode K and mass > 13) ' + 'or (rescode R and mass > 13) ' +
'or (rescode H and mass > 13)'
]
neg = ['(rescode D and mass > 13) ' + 'or (rescode E and mass > 13)']
ionic_features = {
'add_distances': {
'select': pos
},
'kwargs': {
'indices2': {
'select': neg
}
}
}
all_features = [ca_features, ionic_features]
inv_ca_features = {'add_inverse_distances': {'select_Ca': None}}
#ok#ionic_modeller = {'add_distances': {'select':
#ok# ['rescode K or rescode R or rescode H']},
#ok# 'kwargs': {'indices2': {'select':
#ok# 'rescode D or rescode E']}}}
#contact_features = [ {'add_inverse_distances':
# {'select_Backbone': None}},
# {'add_residue_mindist': None,
# 'kwargs': {'threshold': 0.6}}
# ]
all_modeller_2 = PyEMMAAnalysis(engine_2, 'protein',
all_features).named('pyemma-ionic-2')
all_modeller_5 = PyEMMAAnalysis(engine_5, 'protein',
all_features).named('pyemma-ionic-5')
inv_modeller_2 = PyEMMAAnalysis(
engine_2, 'protein', inv_ca_features).named('pyemma-invca-2')
inv_modeller_5 = PyEMMAAnalysis(
engine_5, 'protein', inv_ca_features).named('pyemma-invca-5')
project.generators.add(ca_modeller_2)
project.generators.add(all_modeller_2)
project.generators.add(inv_modeller_2)
project.generators.add(ca_modeller_5)
project.generators.add(all_modeller_5)
project.generators.add(inv_modeller_5)
project.generators.add(engine_2)
project.generators.add(engine_5)
#[print(g) for g in project.generators]
return project
import os
from adaptivemd import Project
from adaptivemd import OpenMMEngine
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
from adaptivemd import WorkerScheduler
import mdtraj as md
if __name__ == '__main__':
Project.delete('example-simple-1')
project = Project('example-simple-1')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
project.initialize({'shared_path': '$HOME'})
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../../examples/files/alanine/alanine.pdb').named(
#
# os.environ['RADICAL_PILOT_DBURL'] = path_to_db
# import adaptive components
from adaptivemd import Project
from adaptivemd import LocalResource, AllegroCluster
from adaptivemd import OpenMMEngine4CUDA
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource_id = 'fub.allegro'
if len(sys.argv) > 2:
exit()
elif len(sys.argv) == 2:
resource_id = sys.argv[1]
if resource_id == 'local.jhp':
project.initialize(LocalResource())
# os.environ['RADICAL_PILOT_DBURL'] = path_to_db
# import adaptive components
from adaptivemd import Project
from adaptivemd import LocalResource AllegroCluster
from adaptivemd import OpenMMEngine
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File, Directory
if __name__ == '__main__':
project = Project('testcase')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource_id = 'local.jhp'
if len(sys.argv) > 2:
exit()
elif len(sys.argv) == 2:
resource_id = sys.argv[1]
if resource_id == 'local.jhp':
project.initialize(LocalJHP())
#!/usr/bin/env python
import sys
# import adaptive components
from adaptivemd import Project
from adaptivemd import AllegroCluster
from adaptivemd import OpenMMEngine
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource = AllegroCluster()
project.initialize(resource)
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named('initial_pdb')
'to get less traffic on the DB')
args = parser.parse_args()
if args.allegro:
db_path = "mongodb://ensembletk.imp.fu-berlin.de:27017/"
elif args.sheep:
db_path = "mongodb://sheep:27017/"
elif args.local:
db_path = "mongodb://localhost:27017/"
else:
db_path = args.mongo_db_path
MongoDBStorage._db_url = db_path
project = Project(args.project)
print project.resource
print project.trajectories
# --------------------------------------------------------------------------
# CREATE THE WORKER
# the instance that knows about the current state
# --------------------------------------------------------------------------
worker = Worker(
walltime=args.walltime,
generators=args.generators,
sleep=args.sleep,
heartbeat=10.0
#
# os.environ['RADICAL_PILOT_DBURL'] = path_to_db
# import adaptive components
from adaptivemd import Project
from adaptivemd import AllegroCluster
from adaptivemd import OpenMMEngine4CUDA
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource_id = 'fub.allegro'
project.initialize(AllegroCluster())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named('initial_pdb')
# import adaptive components
import time
from adaptivemd import Project, ExecutionPlan
from adaptivemd import AllegroCluster
from adaptivemd import ExecutionPlan
from adaptivemd import OpenMMEngine
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase-4')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource_id = 'fub.allegro'
project.initialize(AllegroCluster())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named('initial_pdb')
if __name__ == '__main__':
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
# use the resource specified as argument, fall back to localhost
resource_id = 'local.jhp'
if len(sys.argv) > 3:
exit()
project_id = sys.argv[1]
project = Project(project_id)
if len(sys.argv) == 3:
resource_id = sys.argv[2]
if resource_id == 'local.jhp':
project.initialize(LocalJHP)
elif resource_id == 'local.sheep':
project.initialize(LocalSheep)
elif resource_id == 'fub.allegro':
project.initialize(AllegroCluster)
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
import os
from adaptivemd import Project
from adaptivemd import LocalResource
from adaptivemd import OpenMMEngine
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
from adaptivemd import WorkerScheduler
import mdtraj as md
if __name__ == '__main__':
Project.delete('example-simple-1')
project = Project('example-simple-1')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
project.initialize(LocalResource())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../../examples/files/alanine/alanine.pdb').named(
os.environ['RADICAL_PILOT_DBURL'] = path_to_db
# import adaptive components
from adaptivemd import Project, ExecutionPlan
from adaptivemd import LocalJHP
from adaptivemd import ExecutionPlan
from adaptivemd import OpenMMEngine
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase-worker')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
# resource_id = 'fub.allegro'
project.initialize(LocalJHP())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named(
'initial_pdb').load()
if __name__ == '__main__':
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
# use the resource specified as argument, fall back to localhost
resource_id = 'local.jhp'
if len(sys.argv) > 3 or len(sys.argv) < 2:
exit()
project_name = sys.argv[1]
project = Project(project_name)
if len(sys.argv) == 3:
if resource_id == 'local.jhp':
project.initialize(LocalJHP)
elif resource_id == 'local.sheep':
project.initialize(LocalSheep)
elif resource_id == 'fub.allegro':
project.initialize(AllegroCluster)
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://files/input.pdb')
def init_project(p_name,
sys_name=None,
m_freq=None,
p_freq=None,
platform=None,
dbhost=None,
w_threads=None):
#def init_project(p_name, **freq):
from adaptivemd import Project
#if p_name in Project.list():
# print(project.name, "Deleting existing version of this test project")
# Project.delete(p_name)
if dbhost is not None:
Project.set_dbhost(dbhost)
project = Project(p_name)
if project.name in Project.list():
print(
project.name,
"Project {0} exists, reading it from database".format(
project.name))
else:
from adaptivemd import File, OpenMMEngine
from adaptivemd.analysis.pyemma import PyEMMAAnalysis
#####################################
# NEW initialize sequence
configuration_file = 'configuration.cfg'
project.initialize(configuration_file)
#
# OLD initialize sequence
#from adaptivemd import LocalResource
#resource = LocalResource('/lustre/atlas/scratch/jrossyra/bip149/admd/')
#project.initialize(resource)
#####################################
f_name = '{0}.pdb'.format(sys_name)
# only works if filestructure is preserved as described in 'jro_ntl9.ipynb'
# and something akin to job script in 'admd_workers.pbs' is used
f_base = 'file:///$ADAPTIVEMD/examples/files/{0}/'.format(sys_name)
f_structure = File(f_base + f_name).load()
f_system_2 = File(f_base + 'system-2.xml').load()
f_integrator_2 = File(f_base + 'integrator-2.xml').load()
f_system_5 = File(f_base + 'system-5.xml').load()
f_integrator_5 = File(f_base + 'integrator-5.xml').load()
sim_args = '-r -p {0}'.format(platform)
if platform == 'CPU':
print(
project.name,
"Using CPU simulation platform with {0} threads per worker".
format(w_threads))
sim_args += ' --cpu-cpu-threads {0}'.format(w_threads)
engine_2 = OpenMMEngine(f_system_2, f_integrator_2, f_structure,
sim_args).named('openmm-2')
engine_5 = OpenMMEngine(f_system_5, f_integrator_5, f_structure,
sim_args).named('openmm-5')
m_freq_2 = m_freq
p_freq_2 = p_freq
m_freq_5 = m_freq * 2 / 5
p_freq_5 = p_freq * 2 / 5
engine_2.add_output_type('master', 'allatoms.dcd', stride=m_freq_2)
engine_2.add_output_type('protein',
'protein.dcd',
stride=p_freq_2,
selection='protein')
engine_5.add_output_type('master', 'allatoms.dcd', stride=m_freq_5)
engine_5.add_output_type('protein',
'protein.dcd',
stride=p_freq_5,
selection='protein')
ca_features = {'add_distances_ca': None}
#features = {'add_inverse_distances': {'select_Backbone': None}}
ca_modeller_2 = PyEMMAAnalysis(engine_2, 'protein',
ca_features).named('pyemma-ca-2')
ca_modeller_5 = PyEMMAAnalysis(engine_5, 'protein',
ca_features).named('pyemma-ca-5')
pos = [
'(rescode K and mass > 13) ' + 'or (rescode R and mass > 13) ' +
'or (rescode H and mass > 13)'
]
neg = ['(rescode D and mass > 13) ' + 'or (rescode E and mass > 13)']
ionic_features = {
'add_distances': {
'select': pos
},
'kwargs': {
'indices2': {
'select': neg
}
}
}
all_features = [ca_features, ionic_features]
#ok#ionic_modeller = {'add_distances': {'select':
#ok# ['rescode K or rescode R or rescode H']},
#ok# 'kwargs': {'indices2': {'select':
#ok# 'rescode D or rescode E']}}}
#contact_features = [ {'add_inverse_distances':
# {'select_Backbone': None}},
# {'add_residue_mindist': None,
# 'kwargs': {'threshold': 0.6}}
# ]
all_modeller_2 = PyEMMAAnalysis(engine_2, 'protein',
all_features).named('pyemma-ionic-2')
all_modeller_5 = PyEMMAAnalysis(engine_5, 'protein',
all_features).named('pyemma-ionic-5')
project.generators.add(ca_modeller_2)
project.generators.add(all_modeller_2)
project.generators.add(ca_modeller_5)
project.generators.add(all_modeller_5)
project.generators.add(engine_2)
project.generators.add(engine_5)
[print(g) for g in project.generators]
return project
# import adaptive components
import time
from adaptivemd import Project, ExecutionPlan
from adaptivemd import AllegroCluster
from adaptivemd import ExecutionPlan
from adaptivemd import OpenMMEngine4CUDA
from adaptivemd import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase-5')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource_id = 'fub.allegro'
project.initialize(AllegroCluster())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named('initial_pdb')