def __init__(self, r_cut, nlist):
hoomd.util.print_status_line();
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData().getDomainDecomposition():
hoomd.context.msg.error("pair.cgcmm is not supported in multi-processor simulations.\n\n")
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
hoomd.md.force._force.__init__(self);
# this class extends force, so we need to store the r_cut explicitly as a member
# to be used in get_rcut
# the authors of this potential also did not incorporate pairwise cutoffs, so we just use
# the same number for everything
self.r_cut = r_cut
# setup the coefficient matrix
self.pair_coeff = hoomd.md.pair.coeff();
self.nlist = nlist
self.nlist.subscribe(lambda:self.get_rcut())
self.nlist.update_rcut()
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _cgcmm.CGCMMForceCompute(hoomd.context.current.system_definition, self.nlist.cpp_nlist, r_cut);
else:
self.nlist.cpp_nlist.setStorageMode(_md.NeighborList.storageMode.full);
self.cpp_force = _cgcmm.CGCMMForceComputeGPU(hoomd.context.current.system_definition, self.nlist.cpp_nlist, r_cut);
self.cpp_force.setBlockSize(128);
hoomd.context.current.system.addCompute(self.cpp_force, self.force_name);
def _perform_common_init_tasks():
# create the sorter
hoomd.context.current.sorter = hoomd.update.sort()
# create the default compute.thermo on the all group
hoomd.util.quiet_status()
all = hoomd.group.all()
hoomd.compute._get_unique_thermo(group=all)
hoomd.util.unquiet_status()
# set up Communicator, and register it with the System
if _hoomd.is_MPI_available():
cpp_decomposition = hoomd.context.current.system_definition.getParticleData(
).getDomainDecomposition()
if cpp_decomposition is not None:
# create the c++ Communicator
if not hoomd.context.exec_conf.isCUDAEnabled():
cpp_communicator = _hoomd.Communicator(
hoomd.context.current.system_definition, cpp_decomposition)
else:
cpp_communicator = _hoomd.CommunicatorGPU(
hoomd.context.current.system_definition, cpp_decomposition)
# set Communicator in C++ System
hoomd.context.current.system.setCommunicator(cpp_communicator)
def __init__(self, x=True, y=True, z=True, tolerance=1.02, maxiter=1, period=1000, phase=0):
hoomd.util.print_status_line();
# initialize base class
_updater.__init__(self);
# balancing cannot be done without mpi
if not _hoomd.is_MPI_available() or hoomd.context.current.decomposition is None:
hoomd.context.msg.warning("Ignoring balance command, not supported in current configuration.\n")
return
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_updater = _hoomd.LoadBalancer(hoomd.context.current.system_definition, hoomd.context.current.decomposition.cpp_dd);
else:
self.cpp_updater = _hoomd.LoadBalancerGPU(hoomd.context.current.system_definition, hoomd.context.current.decomposition.cpp_dd);
self.setupUpdater(period,phase)
# stash arguments to metadata
self.metadata_fields = ['tolerance','maxiter','period','phase']
self.period = period
self.phase = phase
# configure the parameters
hoomd.util.quiet_status()
self.set_params(x,y,z,tolerance, maxiter)
hoomd.util.unquiet_status()
def __init__(self, x=True, y=True, z=True, tolerance=1.02, maxiter=1, period=1000, phase=0):
hoomd.util.print_status_line();
# initialize base class
_updater.__init__(self);
# balancing cannot be done without mpi
if not _hoomd.is_MPI_available() or hoomd.context.current.decomposition is None:
hoomd.context.msg.warning("Ignoring balance command, not supported in current configuration.\n")
return
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_updater = _hoomd.LoadBalancer(hoomd.context.current.system_definition, hoomd.context.current.decomposition.cpp_dd);
else:
self.cpp_updater = _hoomd.LoadBalancerGPU(hoomd.context.current.system_definition, hoomd.context.current.decomposition.cpp_dd);
self.setupUpdater(period,phase)
# stash arguments to metadata
self.metadata_fields = ['tolerance','maxiter','period','phase']
self.period = period
self.phase = phase
# configure the parameters
hoomd.util.quiet_status()
self.set_params(x,y,z,tolerance, maxiter)
hoomd.util.unquiet_status()
def __init__(self, communicator, notice_level, msg_file, shared_msg_file):
# metadata stuff
hoomd.meta._metadata.__init__(self)
self.metadata_fields = ['gpu_ids', 'mode', 'num_ranks']
if _hoomd.is_TBB_available():
self.metadata_fields.append('num_threads')
# check shared_msg_file
if shared_msg_file is not None:
if not _hoomd.is_MPI_available():
raise RuntimeError(
"Shared log files are only available in MPI builds.\n")
# MPI communicator
if communicator is None:
self._comm = hoomd.comm.Communicator()
else:
self._comm = communicator
# c++ messenger object
self.cpp_msg = _create_messenger(self.comm.cpp_mpi_conf, notice_level,
msg_file, shared_msg_file)
# output the version info on initialization
self.cpp_msg.notice(1, _hoomd.output_version_info())
# c++ execution configuration mirror class
self.cpp_exec_conf = None
# name of the message file
self._msg_file = msg_file
def __init__(self, r_cut, nlist):
hoomd.util.print_status_line();
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData().getDomainDecomposition():
hoomd.context.msg.error("pair.cgcmm is not supported in multi-processor simulations.\n\n")
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
hoomd.md.force._force.__init__(self);
# this class extends force, so we need to store the r_cut explicitly as a member
# to be used in get_rcut
# the authors of this potential also did not incorporate pairwise cutoffs, so we just use
# the same number for everything
self.r_cut = r_cut
# setup the coefficent matrix
self.pair_coeff = hoomd.md.pair.coeff();
self.nlist = nlist
self.nlist.subscribe(lambda:self.get_rcut())
self.nlist.update_rcut()
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _cgcmm.CGCMMForceCompute(hoomd.context.current.system_definition, self.nlist.cpp_nlist, r_cut);
else:
self.nlist.cpp_nlist.setStorageMode(_md.NeighborList.storageMode.full);
self.cpp_force = _cgcmm.CGCMMForceComputeGPU(hoomd.context.current.system_definition, self.nlist.cpp_nlist, r_cut);
self.cpp_force.setBlockSize(128);
hoomd.context.current.system.addCompute(self.cpp_force, self.force_name);
def _create_messenger(mpi_config, options):
global msg
# use a cached messenger if available
if msg is not None:
return msg
msg = _hoomd.Messenger(mpi_config)
# try to detect if we're running inside an MPI job
inside_mpi_job = mpi_config.getNRanksGlobal() > 1
if ('OMPI_COMM_WORLD_RANK' in os.environ or
'MV2_COMM_WORLD_LOCAL_RANK' in os.environ or
'PMI_RANK' in os.environ or
'ALPS_APP_PE' in os.environ):
inside_mpi_job = True
# only open python stdout/stderr in non-MPI runs
if not inside_mpi_job:
msg.openPython();
if options.notice_level is not None:
msg.setNoticeLevel(options.notice_level);
if options.msg_file is not None:
msg.openFile(options.msg_file);
if options.shared_msg_file is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error("Shared log files are only available in MPI builds.\n");
raise RuntimeError('Error setting option');
msg.setSharedFile(options.shared_msg_file);
return msg
def __init__(self, file, type, nlist):
c = hoomd.cite.article(
cite_key='lin2017',
author=['L Yang', 'F Zhang', 'K M Ho', 'C Z Wang', 'A Travesset'],
title='Implementation of EAM and FS potentials in HOOMD-blue',
journal='Computer Physics Communications',
volume=0,
number=0,
pages='0--0',
year='2017',
doi='0',
feature='EAM')
hoomd.cite._ensure_global_bib().add(c)
hoomd.util.print_status_line()
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData(
).getDomainDecomposition():
hoomd.context.msg.error(
"pair.eam is not supported in multi-processor simulations.\n\n"
)
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
force._force.__init__(self)
# Translate type
if (type == 'Alloy'): type_of_file = 0
elif (type == 'FS'): type_of_file = 1
else: raise RuntimeError('Unknown EAM input file type')
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metal.EAMForceCompute(
hoomd.context.current.system_definition, file, type_of_file)
else:
self.cpp_force = _metal.EAMForceComputeGPU(
hoomd.context.current.system_definition, file, type_of_file)
#After load EAMForceCompute we know r_cut from EAM potential`s file. We need update neighbor list.
self.r_cut_new = self.cpp_force.get_r_cut()
self.nlist = nlist
self.nlist.subscribe(lambda: self.get_rcut())
self.nlist.update_rcut()
#Load neighbor list to compute.
self.cpp_force.set_neighbor_list(self.nlist.cpp_nlist)
if hoomd.context.exec_conf.isCUDAEnabled():
self.nlist.cpp_nlist.setStorageMode(
_md.NeighborList.storageMode.full)
hoomd.context.msg.notice(
2, "Set r_cut = " + str(self.r_cut_new) +
" from potential`s file '" + str(file) + "'.\n")
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
self.pair_coeff = hoomd.md.pair.coeff()
def __init__(self, mpi_comm=None, nrank=None):
# check nrank
if nrank is not None:
if not _hoomd.is_MPI_available():
raise RuntimeError("The nrank option is only available in MPI builds.\n")
mpi_available = _hoomd.is_MPI_available();
self.cpp_mpi_conf = None
# create the specified configuration
if mpi_comm is None:
self.cpp_mpi_conf = _hoomd.MPIConfiguration();
else:
if not mpi_available:
raise RuntimeError("mpi_comm is not supported in serial builds");
handled = False;
# pass in pointer to MPI_Comm object provided by mpi4py
try:
import mpi4py
if isinstance(mpi_comm, mpi4py.MPI.Comm):
addr = mpi4py.MPI._addressof(mpi_comm);
self.cpp_mpi_conf = _hoomd.MPIConfiguration._make_mpi_conf_mpi_comm(addr);
handled = True
except ImportError:
# silently ignore when mpi4py is missing
pass
# undocumented case: handle plain integers as pointers to MPI_Comm objects
if not handled and isinstance(mpi_comm, int):
self.cpp_mpi_conf = _hoomd.MPIConfiguration._make_mpi_conf_mpi_comm(mpi_comm);
handled = True
if not handled:
raise RuntimeError("Invalid mpi_comm object: {}".format(mpi_comm));
if nrank is not None:
# check validity
if (self.cpp_mpi_conf.getNRanksGlobal() % nrank):
raise RuntimeError('Total number of ranks is not a multiple of --nrank');
# split the communicator into partitions
self.cpp_mpi_conf.splitPartitions(nrank)
def barrier_all():
""" Perform a MPI barrier synchronization across the whole MPI run.
Note:
Does nothing in in non-MPI builds.
"""
if _hoomd.is_MPI_available():
_hoomd.mpi_barrier_world()
def barrier_all():
""" Perform a MPI barrier synchronization across the whole MPI run.
Note:
Does nothing in in non-MPI builds.
"""
if _hoomd.is_MPI_available():
_hoomd.mpi_barrier_world();
def __init__(self, x=None, y=None, z=None, nx=None, ny=None, nz=None, linear=False, onelevel=False):
# check that the context has been initialized though
if hoomd.context.current is None:
raise RuntimeError("Cannot initialize decomposition without context.initialize() first")
# check that system is not initialized
if hoomd.context.current.system is not None:
hoomd.context.current.device.cpp_msg.error("comm.decomposition: cannot modify decomposition after system is initialized. Call before init.*\n")
raise RuntimeError("Cannot create decomposition after system is initialized. Call before init.*")
# make sure MPI is enabled if any arguments are not None
if (x or y or z or nx or ny or nz) and (not _hoomd.is_MPI_available()):
raise RuntimeError("the x, y, z, nx, ny, nz options are only available in MPI builds")
self._onelevel = onelevel # cache this for later when we can make the cpp object
# check that there are ranks available for decomposition
if hoomd.context.current.device.comm.cpp_mpi_conf == 1:
hoomd.context.current.device.cpp_msg.warning("Only 1 rank in system, ignoring decomposition to use optimized code pathways.\n")
return
else:
self.x = []
self.y = []
self.z = []
self.nx = 0
self.ny = 0
self.nz = 0
self.uniform_x = True
self.uniform_y = True
self.uniform_z = True
self.set_params(x,y,z,nx,ny,nz)
"""
# do a one time update of the cuts to the global values if a global is set
if not self.x and self.nx == 0 and hoomd.context.options.nx is not None:
self.nx = hoomd.context.options.nx
self.uniform_x = True
if not self.y and self.ny == 0 and hoomd.context.options.ny is not None:
self.ny = hoomd.context.options.ny
self.uniform_y = True
if not self.z and self.nz == 0:
if linear:
self.nz = hoomd.context.current.device.cpp_mpi_conf.getNRanks()
self.uniform_z = True
elif hoomd.context.options.nz is not None:
self.nz = hoomd.context.options.nz
self.uniform_z = True
"""
# set the global decomposition to this class
if hoomd.context.current.decomposition is not None:
hoomd.context.current.device.cpp_msg.warning("comm.decomposition: overriding currently defined domain decomposition\n")
hoomd.context.current.decomposition = self
def barrier():
""" Perform a MPI barrier synchronization across all ranks in the partition.
Note:
Does nothing in in non-MPI builds.
"""
hoomd.context._verify_init()
if _hoomd.is_MPI_available():
hoomd.context.exec_conf.barrier()
def barrier():
""" Perform a MPI barrier synchronization across all ranks in the partition.
Note:
Does nothing in in non-MPI builds.
"""
hoomd.context._verify_init();
if _hoomd.is_MPI_available():
hoomd.context.exec_conf.barrier()
def _create_exec_conf():
global exec_conf, options, msg
# use a cached execution configuration if available
if exec_conf is not None:
return exec_conf
mpi_available = _hoomd.is_MPI_available()
# error out on nyx/flux if the auto mode is set
if options.mode == 'auto':
host = _get_proc_name()
if "flux" in host or "nyx" in host:
msg.error(
"--mode=gpu or --mode=cpu must be specified on nyx/flux\n")
raise RuntimeError("Error initializing")
exec_mode = _hoomd.ExecutionConfiguration.executionMode.AUTO
elif options.mode == "cpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.CPU
elif options.mode == "gpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.GPU
else:
raise RuntimeError("Invalid mode")
# convert None options to defaults
if options.gpu is None:
gpu_id = -1
else:
gpu_id = int(options.gpu)
if options.nrank is None:
nrank = 0
else:
nrank = int(options.nrank)
# create the specified configuration
exec_conf = _hoomd.ExecutionConfiguration(exec_mode, gpu_id,
options.min_cpu,
options.ignore_display, msg,
nrank)
# if gpu_error_checking is set, enable it on the GPU
if options.gpu_error_checking:
exec_conf.setCUDAErrorChecking(True)
if _hoomd.is_TBB_available():
# set the number of TBB threads as necessary
if options.nthreads != None:
exec_conf.setNumThreads(options.nthreads)
exec_conf = exec_conf
return exec_conf
def __init__(self, file, type, nlist):
c = hoomd.cite.article(cite_key = 'lin2017',
author=['L Yang', 'F Zhang', 'K M Ho', 'C Z Wang','A Travesset'],
title = 'Implementation of EAM and FS potentials in HOOMD-blue',
journal = 'Computer Physics Communications',
volume = 0,
number = 0,
pages = '0--0',
year = '2017',
doi = '0',
feature = 'EAM')
hoomd.cite._ensure_global_bib().add(c)
hoomd.util.print_status_line();
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData().getDomainDecomposition():
hoomd.context.msg.error("pair.eam is not supported in multi-processor simulations.\n\n")
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
force._force.__init__(self);
# Translate type
if(type == 'Alloy'): type_of_file = 0;
elif(type == 'FS'): type_of_file = 1;
else: raise RuntimeError('Unknown EAM input file type');
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metal.EAMForceCompute(hoomd.context.current.system_definition, file, type_of_file);
else:
self.cpp_force = _metal.EAMForceComputeGPU(hoomd.context.current.system_definition, file, type_of_file);
#After load EAMForceCompute we know r_cut from EAM potential`s file. We need update neighbor list.
self.r_cut_new = self.cpp_force.get_r_cut();
self.nlist = nlist
self.nlist.subscribe(lambda : self.get_rcut())
self.nlist.update_rcut()
#Load neighbor list to compute.
self.cpp_force.set_neighbor_list(self.nlist.cpp_nlist);
if hoomd.context.exec_conf.isCUDAEnabled():
self.nlist.cpp_nlist.setStorageMode(_md.NeighborList.storageMode.full);
hoomd.context.msg.notice(2, "Set r_cut = " + str(self.r_cut_new) + " from potential`s file '" + str(file) + "'.\n");
hoomd.context.current.system.addCompute(self.cpp_force, self.force_name);
self.pair_coeff = hoomd.md.pair.coeff();
def _create_domain_decomposition(box):
if not _hoomd.is_MPI_available():
return None
# if we are only running on one processor, we use optimized code paths
# for single-GPU execution
if hoomd.context.current.device.cpp_exec_conf.getNRanks() == 1:
return None
# okay, we want a decomposition but one isn't set, so make a default one
if hoomd.context.current.decomposition is None:
# this is happening transparently to the user, so hush this up
hoomd.context.current.decomposition = hoomd.comm.decomposition()
return hoomd.context.current.decomposition._make_cpp_decomposition(box)
def get_num_ranks():
""" Get the number of ranks in this partition.
Returns:
The number of MPI ranks in this partition.
Note:
Returns 1 in non-mpi builds.
"""
hoomd.context._verify_init()
if _hoomd.is_MPI_available():
return hoomd.context.exec_conf.getNRanks()
else:
return 1
def num_ranks(self):
""" Get the number of ranks in this partition.
Returns:
The number of MPI ranks in this partition.
Note:
Returns 1 in non-mpi builds.
"""
hoomd.context._verify_init();
if _hoomd.is_MPI_available():
return self.cpp_mpi_conf.getNRanks();
else:
return 1;
def get_partition():
""" Get the current partition index.
Returns:
Index of the current partition.
Note:
Always returns 0 in non-mpi builds.
"""
hoomd.context._verify_init();
if _hoomd.is_MPI_available():
return hoomd.context.exec_conf.getPartition()
else:
return 0;
def get_partition():
""" Get the current partition index.
Returns:
Index of the current partition.
Note:
Always returns 0 in non-mpi builds.
"""
hoomd.context._verify_init()
if _hoomd.is_MPI_available():
return hoomd.context.exec_conf.getPartition()
else:
return 0
def get_num_ranks():
""" Get the number of ranks in this partition.
Returns:
The number of MPI ranks in this partition.
Note:
Returns 1 in non-mpi builds.
"""
hoomd.context._verify_init();
if _hoomd.is_MPI_available():
return hoomd.context.exec_conf.getNRanks();
else:
return 1;
def get_rank():
""" Get the current rank.
Returns:
Index of the current rank in this partition.
Note:
Always returns 0 in non-mpi builds.
"""
hoomd.context._verify_init()
if _hoomd.is_MPI_available():
return hoomd.context.mpi_conf.getRank()
else:
return 0
def _create_mpi_conf(mpi_comm, options):
global mpi_conf
# use a cached MPI configuration if available
if mpi_conf is not None:
return mpi_conf
mpi_available = _hoomd.is_MPI_available();
# create the specified configuration
if mpi_comm is None:
mpi_conf = _hoomd.MPIConfiguration();
else:
if not mpi_available:
raise RuntimeError("mpi_comm is not supported in serial builds");
handled = False;
# pass in pointer to MPI_Comm object provided by mpi4py
try:
import mpi4py
if isinstance(mpi_comm, mpi4py.MPI.Comm):
addr = mpi4py.MPI._addressof(mpi_comm);
mpi_conf = _hoomd.MPIConfiguration._make_mpi_conf_mpi_comm(addr);
handled = True
except ImportError:
# silently ignore when mpi4py is missing
pass
# undocumented case: handle plain integers as pointers to MPI_Comm objects
if not handled and isinstance(mpi_comm, int):
mpi_conf = _hoomd.MPIConfiguration._make_mpi_conf_mpi_comm(mpi_comm);
handled = True
if not handled:
raise RuntimeError("Invalid mpi_comm object: {}".format(mpi_comm));
if options.nrank is not None:
# check validity
nrank = options.nrank
if (mpi_conf.getNRanksGlobal() % nrank):
raise RuntimeError('Total number of ranks is not a multiple of --nrank');
# split the communicator into partitions
mpi_conf.splitPartitions(nrank)
return mpi_conf
def _create_domain_decomposition(box):
if not _hoomd.is_MPI_available():
return None
# if we are only running on one processor, we use optimized code paths
# for single-GPU execution
if hoomd.context.exec_conf.getNRanks() == 1:
return None
# okay, we want a decomposition but one isn't set, so make a default one
if hoomd.context.current.decomposition is None:
# this is happening transparently to the user, so hush this up
hoomd.util.quiet_status()
hoomd.context.current.decomposition = hoomd.comm.decomposition()
hoomd.util.unquiet_status()
return hoomd.context.current.decomposition._make_cpp_decomposition(box)
def __init__(self, group, r=None, rx=None, ry=None, rz=None, P=(0, 0, 0)):
hoomd.util.print_status_line()
period = 1
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if context.current.system_definition.getParticleData(
).getDomainDecomposition():
context.msg.error(
"constrain.ellipsoid is not supported in multi-processor simulations.\n\n"
)
raise RuntimeError("Error initializing updater.")
# Error out if no radii are set
if (r is None and rx is None and ry is None and rz is None):
context.msg.error(
"no radii were defined in update.constraint_ellipsoid.\n\n")
raise RuntimeError("Error initializing updater.")
# initialize the base class
_updater.__init__(self)
# Set parameters
P = _hoomd.make_scalar3(P[0], P[1], P[2])
if (r is not None): rx = ry = rz = r
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_updater = _md.ConstraintEllipsoid(
hoomd.context.current.system_definition, group.cpp_group, P,
rx, ry, rz)
else:
self.cpp_updater = _md.ConstraintEllipsoidGPU(
hoomd.context.current.system_definition, group.cpp_group, P,
rx, ry, rz)
self.setupUpdater(period)
# store metadata
self.group = group
self.P = P
self.rx = rx
self.ry = ry
self.rz = rz
self.metadata_fields = ['group', 'P', 'rx', 'ry', 'rz']
def _create_exec_conf():
global exec_conf, options, msg
# use a cached execution configuration if available
if exec_conf is not None:
return exec_conf
mpi_available = _hoomd.is_MPI_available();
# error out on nyx/flux if the auto mode is set
if options.mode == 'auto':
host = _get_proc_name()
if "flux" in host or "nyx" in host:
msg.error("--mode=gpu or --mode=cpu must be specified on nyx/flux\n");
raise RuntimeError("Error initializing");
exec_mode = _hoomd.ExecutionConfiguration.executionMode.AUTO;
elif options.mode == "cpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.CPU;
elif options.mode == "gpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.GPU;
else:
raise RuntimeError("Invalid mode");
# convert None options to defaults
if options.gpu is None:
gpu_id = -1;
else:
gpu_id = int(options.gpu);
if options.nrank is None:
nrank = 0;
else:
nrank = int(options.nrank);
# create the specified configuration
exec_conf = _hoomd.ExecutionConfiguration(exec_mode, gpu_id, options.min_cpu, options.ignore_display, msg, nrank);
# if gpu_error_checking is set, enable it on the GPU
if options.gpu_error_checking:
exec_conf.setCUDAErrorChecking(True);
exec_conf = exec_conf;
return exec_conf;
def _perform_common_init_tasks():
# create the sorter
hoomd.context.current.sorter = hoomd.update.sort();
# create the default compute.thermo on the all group
hoomd.util.quiet_status();
all = hoomd.group.all();
hoomd.compute._get_unique_thermo(group=all);
hoomd.util.unquiet_status();
# set up Communicator, and register it with the System
if _hoomd.is_MPI_available():
cpp_decomposition = hoomd.context.current.system_definition.getParticleData().getDomainDecomposition();
if cpp_decomposition is not None:
# create the c++ Communicator
if not hoomd.context.exec_conf.isCUDAEnabled():
cpp_communicator = _hoomd.Communicator(hoomd.context.current.system_definition, cpp_decomposition)
else:
cpp_communicator = _hoomd.CommunicatorGPU(hoomd.context.current.system_definition, cpp_decomposition)
# set Communicator in C++ System
hoomd.context.current.system.setCommunicator(cpp_communicator)
def __init__(self, group, r=None, rx=None, ry=None, rz=None, P=(0,0,0)):
hoomd.util.print_status_line();
period = 1;
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if context.current.system_definition.getParticleData().getDomainDecomposition():
context.msg.error("constrain.ellipsoid is not supported in multi-processor simulations.\n\n")
raise RuntimeError("Error initializing updater.")
# Error out if no radii are set
if (r is None and rx is None and ry is None and rz is None):
context.msg.error("no radii were defined in update.constraint_ellipsoid.\n\n")
raise RuntimeError("Error initializing updater.")
# initialize the base class
_updater.__init__(self);
# Set parameters
P = _hoomd.make_scalar3(P[0], P[1], P[2]);
if (r is not None): rx = ry = rz = r
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_updater = _md.ConstraintEllipsoid(hoomd.context.current.system_definition, group.cpp_group, P, rx, ry, rz);
else:
self.cpp_updater = _md.ConstraintEllipsoidGPU(hoomd.context.current.system_definition, group.cpp_group, P, rx, ry, rz);
self.setupUpdater(period);
# store metadata
self.group = group
self.P = P
self.rx = rx
self.ry = ry
self.rz = rz
self.metadata_fields = ['group','P', 'rx', 'ry', 'rz']
util.unquiet_status();
def get_step():
""" Get the current simulation time step.
Returns:
The current simulation time step.
Example::
print(hoomd.get_step())
"""
# check if initialization has occurred
if not init.is_initialized():
context.msg.error("Cannot get step before initialization\n");
raise RuntimeError('Error getting step');
return context.current.system.getCurrentTimeStep();
# Check to see if we are built without MPI support and the user used mpirun
if (not _hoomd.is_MPI_available()
and ( 'OMPI_COMM_WORLD_RANK' in os.environ
or 'MV2_COMM_WORLD_LOCAL_RANK' in os.environ
or 'PMI_RANK' in os.environ
or 'ALPS_APP_PE' in os.environ)
):
print('HOOMD-blue is built without MPI support, but seems to have been launched with mpirun');
print('exiting now to prevent many sequential jobs from starting');
raise RuntimeError('Error launching hoomd')
def initialize(args=None, memory_traceback=False, mpi_comm=None):
R""" Initialize the execution context
Args:
args (str): Arguments to parse. When *None*, parse the arguments passed on the command line.
memory_traceback (bool): If true, enable memory allocation tracking (*only for debugging/profiling purposes*)
mpi_comm: Accepts an mpi4py communicator. Use this argument to perform many independent hoomd simulations
where you communicate between those simulations using your own mpi4py code.
:py:func:`hoomd.context.initialize()` parses the command line arguments given, sets the options and initializes MPI and GPU execution
(if any). By default, :py:func:`hoomd.context.initialize()` reads arguments given on the command line. Provide a string to :py:func:`hoomd.context.initialize()`
to set the launch configuration within the job script.
:py:func:`hoomd.context.initialize()` can be called more than once in a script. However, the execution parameters are fixed on the first call
and *args* is ignored. Subsequent calls to :py:func:`hoomd.context.initialize()` create a new :py:class:`SimulationContext` and set it current. This
behavior is primarily to support use of hoomd in jupyter notebooks, so that a new clean simulation context is
set when rerunning the notebook within an existing kernel.
Example::
from hoomd import *
context.initialize();
context.initialize("--mode=gpu --nrank=64");
context.initialize("--mode=cpu --nthreads=64");
world = MPI.COMM_WORLD
comm = world.Split(world.Get_rank(), 0)
hoomd.context.initialize(mpi_comm=comm)
"""
global mpi_conf, exec_conf, msg, options, current, _prev_args
if mpi_conf is not None or exec_conf is not None:
if args != _prev_args:
msg.warning("Ignoring new options, cannot change execution mode after initialization.\n");
current = SimulationContext();
return current
_prev_args = args;
options = hoomd.option.options();
hoomd.option._parse_command_line(args);
# Check to see if we are built without MPI support and the user used mpirun
if (not _hoomd.is_MPI_available() and not options.single_mpi
and ( 'OMPI_COMM_WORLD_RANK' in os.environ
or 'MV2_COMM_WORLD_LOCAL_RANK' in os.environ
or 'PMI_RANK' in os.environ
or 'ALPS_APP_PE' in os.environ)
):
print('HOOMD-blue is built without MPI support, but seems to have been launched with mpirun');
print('exiting now to prevent many sequential jobs from starting');
raise RuntimeError('Error launching hoomd')
# create the MPI configuration
mpi_conf = _create_mpi_conf(mpi_comm, options)
# set options on messenger object
msg = _create_messenger(mpi_conf, options)
# output the version info on initialization
msg.notice(1, _hoomd.output_version_info())
# ensure creation of global bibliography to print HOOMD base citations
cite._ensure_global_bib()
# create the parallel execution configuration
exec_conf = _create_exec_conf(mpi_conf, msg, options);
# set memory tracing option
exec_conf.setMemoryTracing(memory_traceback)
current = SimulationContext();
return current
def __init__(self, file, type, nlist):
c = hoomd.cite.article(
cite_key='morozov2011',
author=[
'I V Morozov', 'A M Kazennova', 'R G Bystryia', 'G E Normana',
'V V Pisareva', 'V V Stegailova'
],
title=
'Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs',
journal='Computer Physics Communications',
volume=182,
number=9,
pages='1974--1978',
year='2011',
doi='10.1016/j.cpc.2010.12.026',
feature='EAM')
hoomd.cite._ensure_global_bib().add(c)
hoomd.util.print_status_line()
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData(
).getDomainDecomposition():
hoomd.context.msg.error(
"pair.eam is not supported in multi-processor simulations.\n\n"
)
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
force._force.__init__(self)
# Translate type
if (type == 'Alloy'): type_of_file = 0
elif (type == 'FS'): type_of_file = 1
else: raise RuntimeError('Unknown EAM input file type')
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metal.EAMForceCompute(
hoomd.context.current.system_definition, file, type_of_file)
else:
self.cpp_force = _metal.EAMForceComputeGPU(
hoomd.context.current.system_definition, file, type_of_file)
#After load EAMForceCompute we know r_cut from EAM potential`s file. We need update neighbor list.
r_cut_new = self.cpp_force.get_r_cut()
self.nlist = nlist
self.nlist.subscribe(lambda: r_cut_new)
self.nlist.update_rcut()
#Load neighbor list to compute.
self.cpp_force.set_neighbor_list(self.nlist)
if hoomd.context.exec_conf.isCUDAEnabled():
self.nlist.setStorageMode(_md.NeighborList.storageMode.full)
hoomd.context.msg.notice(
2, "Set r_cut = " + str(r_cut_new) + " from potential`s file '" +
str(file) + "'.\n")
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
self.pair_coeff = coeff()
def _parse_command_line(arg_string=None):
parser = OptionParser()
parser.add_option("--mode",
dest="mode",
help="Execution mode (cpu or gpu)",
default='auto')
parser.add_option("--gpu", dest="gpu", help="GPU on which to execute")
parser.add_option("--gpu_error_checking",
dest="gpu_error_checking",
action="store_true",
default=False,
help="Enable error checking on the GPU")
parser.add_option(
"--minimize-cpu-usage",
dest="min_cpu",
action="store_true",
default=False,
help=
"Enable to keep the CPU usage of HOOMD to a bare minimum (will degrade overall performance somewhat)"
)
parser.add_option("--ignore-display-gpu",
dest="ignore_display",
action="store_true",
default=False,
help="Attempt to avoid running on the display GPU")
parser.add_option("--notice-level",
dest="notice_level",
help="Minimum level of notice messages to print")
parser.add_option("--msg-file",
dest="msg_file",
help="Name of file to write messages to")
parser.add_option(
"--shared-msg-file",
dest="shared_msg_file",
help=
"(MPI only) Name of shared file to write message to (append partition #)"
)
parser.add_option("--nrank",
dest="nrank",
help="(MPI) Number of ranks to include in a partition")
parser.add_option("--nx",
dest="nx",
help="(MPI) Number of domains along the x-direction")
parser.add_option("--ny",
dest="ny",
help="(MPI) Number of domains along the y-direction")
parser.add_option("--nz",
dest="nz",
help="(MPI) Number of domains along the z-direction")
parser.add_option(
"--linear",
dest="linear",
action="store_true",
default=False,
help="(MPI only) Force a slab (1D) decomposition along the z-direction"
)
parser.add_option(
"--onelevel",
dest="onelevel",
action="store_true",
default=False,
help="(MPI only) Disable two-level (node-local) decomposition")
parser.add_option("--single-mpi",
dest="single_mpi",
action="store_true",
help="Allow single-threaded HOOMD builds in MPI jobs")
parser.add_option("--user", dest="user", help="User options")
parser.add_option("--nthreads",
dest="nthreads",
help="Number of TBB threads")
input_args = None
if arg_string is not None:
input_args = shlex.split(arg_string)
(cmd_options, args) = parser.parse_args(args=input_args)
# chedk for valid mode setting
if cmd_options.mode is not None:
if not (cmd_options.mode == "cpu" or cmd_options.mode == "gpu"
or cmd_options.mode == "auto"):
parser.error("--mode must be either cpu, gpu, or auto")
# check for sane options
if cmd_options.mode == "cpu" and (cmd_options.gpu is not None):
parser.error("--mode=cpu cannot be specified along with --gpu")
# set the mode to gpu if the gpu # was set
if cmd_options.gpu is not None and cmd_options.mode == 'auto':
cmd_options.mode = "gpu"
# convert gpu to an integer
if cmd_options.gpu is not None:
try:
cmd_options.gpu = int(cmd_options.gpu)
except ValueError:
parser.error('--gpu must be an integer')
# convert notice_level to an integer
if cmd_options.notice_level is not None:
try:
cmd_options.notice_level = int(cmd_options.notice_level)
except ValueError:
parser.error('--notice-level must be an integer')
# Convert nx to an integer
if cmd_options.nx is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error(
"The --nx option is only avaible in MPI builds.\n")
raise RuntimeError('Error setting option')
try:
cmd_options.nx = int(cmd_options.nx)
except ValueError:
parser.error('--nx must be an integer')
# Convert ny to an integer
if cmd_options.ny is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error(
"The --ny option is only avaible in MPI builds.\n")
raise RuntimeError('Error setting option')
try:
cmd_options.ny = int(cmd_options.ny)
except ValueError:
parser.error('--ny must be an integer')
# Convert nz to an integer
if cmd_options.nz is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error(
"The --nz option is only avaible in MPI builds.\n")
raise RuntimeError('Error setting option')
try:
cmd_options.nz = int(cmd_options.nz)
except ValueError:
parser.error('--nz must be an integer')
# Convert nthreads to an integer
if cmd_options.nthreads is not None:
if not _hoomd.is_TBB_available():
hoomd.context.msg.error(
"The --nthreads option is only avaible in TBB-enabled builds.\n"
)
raise RuntimeError('Error setting option')
try:
cmd_options.nthreads = int(cmd_options.nthreads)
except ValueError:
parser.error('--nthreads must be an integer')
# copy command line options over to global options
hoomd.context.options.mode = cmd_options.mode
hoomd.context.options.gpu = cmd_options.gpu
hoomd.context.options.gpu_error_checking = cmd_options.gpu_error_checking
hoomd.context.options.min_cpu = cmd_options.min_cpu
hoomd.context.options.ignore_display = cmd_options.ignore_display
hoomd.context.options.nx = cmd_options.nx
hoomd.context.options.ny = cmd_options.ny
hoomd.context.options.nz = cmd_options.nz
hoomd.context.options.linear = cmd_options.linear
hoomd.context.options.onelevel = cmd_options.onelevel
hoomd.context.options.single_mpi = cmd_options.single_mpi
hoomd.context.options.nthreads = cmd_options.nthreads
if cmd_options.notice_level is not None:
hoomd.context.options.notice_level = cmd_options.notice_level
hoomd.context.msg.setNoticeLevel(hoomd.context.options.notice_level)
if cmd_options.msg_file is not None:
hoomd.context.options.msg_file = cmd_options.msg_file
hoomd.context.msg.openFile(hoomd.context.options.msg_file)
if cmd_options.shared_msg_file is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error(
"Shared log files are only available in MPI builds.\n")
raise RuntimeError('Error setting option')
hoomd.context.options.shared_msg_file = cmd_options.shared_msg_file
hoomd.context.msg.setSharedFile(hoomd.context.options.shared_msg_file)
if cmd_options.nrank is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error(
"The --nrank option is only avaible in MPI builds.\n")
raise RuntimeError('Error setting option')
# check validity
nrank = int(cmd_options.nrank)
if (_hoomd.ExecutionConfiguration.getNRanksGlobal() % nrank):
hoomd.context.msg.error(
"Total number of ranks is not a multiple of --nrank\n")
raise RuntimeError('Error checking option')
hoomd.context.options.nrank = nrank
if cmd_options.user is not None:
hoomd.context.options.user = shlex.split(cmd_options.user)
def _parse_command_line(arg_string=None):
parser = OptionParser();
parser.add_option("--mode", dest="mode", help="Execution mode (cpu or gpu)", default='auto');
parser.add_option("--gpu", dest="gpu", help="GPU or comma-separated list of GPUs on which to execute");
parser.add_option("--gpu_error_checking", dest="gpu_error_checking", action="store_true", default=False, help="Enable error checking on the GPU");
parser.add_option("--minimize-cpu-usage", dest="min_cpu", action="store_true", default=False, help="Enable to keep the CPU usage of HOOMD to a bare minimum (will degrade overall performance somewhat)");
parser.add_option("--ignore-display-gpu", dest="ignore_display", action="store_true", default=False, help="Attempt to avoid running on the display GPU");
parser.add_option("--notice-level", dest="notice_level", help="Minimum level of notice messages to print");
parser.add_option("--msg-file", dest="msg_file", help="Name of file to write messages to");
parser.add_option("--shared-msg-file", dest="shared_msg_file", help="(MPI only) Name of shared file to write message to (append partition #)");
parser.add_option("--nrank", dest="nrank", help="(MPI) Number of ranks to include in a partition");
parser.add_option("--nx", dest="nx", help="(MPI) Number of domains along the x-direction");
parser.add_option("--ny", dest="ny", help="(MPI) Number of domains along the y-direction");
parser.add_option("--nz", dest="nz", help="(MPI) Number of domains along the z-direction");
parser.add_option("--linear", dest="linear", action="store_true", default=False, help="(MPI only) Force a slab (1D) decomposition along the z-direction");
parser.add_option("--onelevel", dest="onelevel", action="store_true", default=False, help="(MPI only) Disable two-level (node-local) decomposition");
parser.add_option("--single-mpi", dest="single_mpi", action="store_true", help="Allow single-threaded HOOMD builds in MPI jobs");
parser.add_option("--user", dest="user", help="User options");
parser.add_option("--nthreads", dest="nthreads", help="Number of TBB threads");
input_args = None;
if arg_string is not None:
input_args = shlex.split(arg_string);
(cmd_options, args) = parser.parse_args(args=input_args);
# check for valid mode setting
if cmd_options.mode is not None:
if not (cmd_options.mode == "cpu" or cmd_options.mode == "gpu" or cmd_options.mode == "auto"):
parser.error("--mode must be either cpu, gpu, or auto");
# check for sane options
if cmd_options.mode == "cpu" and (cmd_options.gpu is not None):
parser.error("--mode=cpu cannot be specified along with --gpu")
# set the mode to gpu if the gpu # was set
if cmd_options.gpu is not None and cmd_options.mode == 'auto':
cmd_options.mode = "gpu"
# convert gpu to an integer
if cmd_options.gpu is not None:
try:
cmd_options.gpu = [int(gpu) for gpu in str(cmd_options.gpu).split(',')]
except ValueError:
parser.error('--gpu must be an integer or comma-separated list of integers')
# convert notice_level to an integer
if cmd_options.notice_level is not None:
try:
cmd_options.notice_level = int(cmd_options.notice_level);
except ValueError:
parser.error('--notice-level must be an integer')
# Convert nx to an integer
if cmd_options.nx is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error("The --nx option is only available in MPI builds.\n");
raise RuntimeError('Error setting option');
try:
cmd_options.nx = int(cmd_options.nx);
except ValueError:
parser.error('--nx must be an integer')
# Convert ny to an integer
if cmd_options.ny is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error("The --ny option is only available in MPI builds.\n");
raise RuntimeError('Error setting option');
try:
cmd_options.ny = int(cmd_options.ny);
except ValueError:
parser.error('--ny must be an integer')
# Convert nz to an integer
if cmd_options.nz is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error("The --nz option is only available in MPI builds.\n");
raise RuntimeError('Error setting option');
try:
cmd_options.nz = int(cmd_options.nz);
except ValueError:
parser.error('--nz must be an integer')
# Convert nthreads to an integer
if cmd_options.nthreads is not None:
if not _hoomd.is_TBB_available():
hoomd.context.msg.error("The --nthreads option is only available in TBB-enabled builds.\n");
raise RuntimeError('Error setting option');
try:
cmd_options.nthreads = int(cmd_options.nthreads);
except ValueError:
parser.error('--nthreads must be an integer')
# copy command line options over to global options
hoomd.context.options.mode = cmd_options.mode;
hoomd.context.options.gpu = cmd_options.gpu;
hoomd.context.options.gpu_error_checking = cmd_options.gpu_error_checking;
hoomd.context.options.min_cpu = cmd_options.min_cpu;
hoomd.context.options.ignore_display = cmd_options.ignore_display;
hoomd.context.options.nx = cmd_options.nx;
hoomd.context.options.ny = cmd_options.ny;
hoomd.context.options.nz = cmd_options.nz;
hoomd.context.options.linear = cmd_options.linear
hoomd.context.options.onelevel = cmd_options.onelevel
hoomd.context.options.single_mpi = cmd_options.single_mpi
hoomd.context.options.nthreads = cmd_options.nthreads
if cmd_options.notice_level is not None:
hoomd.context.options.notice_level = cmd_options.notice_level;
hoomd.context.msg.setNoticeLevel(hoomd.context.options.notice_level);
if cmd_options.msg_file is not None:
hoomd.context.options.msg_file = cmd_options.msg_file;
hoomd.context.msg.openFile(hoomd.context.options.msg_file);
if cmd_options.shared_msg_file is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error("Shared log files are only available in MPI builds.\n");
raise RuntimeError('Error setting option');
hoomd.context.options.shared_msg_file = cmd_options.shared_msg_file;
hoomd.context.msg.setSharedFile(hoomd.context.options.shared_msg_file);
if cmd_options.nrank is not None:
if not _hoomd.is_MPI_available():
hoomd.context.msg.error("The --nrank option is only available in MPI builds.\n");
raise RuntimeError('Error setting option');
# check validity
nrank = int(cmd_options.nrank)
if (_hoomd.ExecutionConfiguration.getNRanksGlobal() % nrank):
hoomd.context.msg.error("Total number of ranks is not a multiple of --nrank\n");
raise RuntimeError('Error checking option');
hoomd.context.options.nrank = nrank
if cmd_options.user is not None:
hoomd.context.options.user = shlex.split(cmd_options.user);
def initialize(args=None, memory_traceback=False, mpi_comm=None):
R""" Initialize the execution context
Args:
args (str): Arguments to parse. When *None*, parse the arguments passed on the command line.
memory_traceback (bool): If true, enable memory allocation tracking (*only for debugging/profiling purposes*)
mpi_comm: Accepts an mpi4py communicator. Use this argument to perform many independent hoomd simulations
where you communicate between those simulations using your own mpi4py code.
:py:func:`hoomd.context.initialize()` parses the command line arguments given, sets the options and initializes MPI and GPU execution
(if any). By default, :py:func:`hoomd.context.initialize()` reads arguments given on the command line. Provide a string to :py:func:`hoomd.context.initialize()`
to set the launch configuration within the job script.
:py:func:`hoomd.context.initialize()` can be called more than once in a script. However, the execution parameters are fixed on the first call
and *args* is ignored. Subsequent calls to :py:func:`hoomd.context.initialize()` create a new :py:class:`SimulationContext` and set it current. This
behavior is primarily to support use of hoomd in jupyter notebooks, so that a new clean simulation context is
set when rerunning the notebook within an existing kernel.
Example::
from hoomd import *
context.initialize();
context.initialize("--mode=gpu --nrank=64");
context.initialize("--mode=cpu --nthreads=64");
world = MPI.COMM_WORLD
comm = world.Split(world.Get_rank(), 0)
hoomd.context.initialize(mpi_comm=comm)
"""
global exec_conf, msg, options, current, _prev_args
if exec_conf is not None:
if args != _prev_args:
msg.warning("Ignoring new options, cannot change execution mode after initialization.\n");
current = SimulationContext();
return current
_prev_args = args;
options = hoomd.option.options();
hoomd.option._parse_command_line(args);
# Check to see if we are built without MPI support and the user used mpirun
if (not _hoomd.is_MPI_available() and not options.single_mpi
and ( 'OMPI_COMM_WORLD_RANK' in os.environ
or 'MV2_COMM_WORLD_LOCAL_RANK' in os.environ
or 'PMI_RANK' in os.environ
or 'ALPS_APP_PE' in os.environ)
):
print('HOOMD-blue is built without MPI support, but seems to have been launched with mpirun');
print('exiting now to prevent many sequential jobs from starting');
raise RuntimeError('Error launching hoomd')
# output the version info on initialization
msg.notice(1, _hoomd.output_version_info())
# ensure creation of global bibliography to print HOOMD base citations
cite._ensure_global_bib()
exec_conf = _create_exec_conf(mpi_comm);
# set memory tracing option
exec_conf.setMemoryTracing(memory_traceback)
current = SimulationContext();
return current
def _create_exec_conf(mpi_comm):
global exec_conf, options, msg
# use a cached execution configuration if available
if exec_conf is not None:
return exec_conf
mpi_available = _hoomd.is_MPI_available()
if options.mode == 'auto':
exec_mode = _hoomd.ExecutionConfiguration.executionMode.AUTO
elif options.mode == "cpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.CPU
elif options.mode == "gpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.GPU
else:
raise RuntimeError("Invalid mode")
# convert None options to defaults
if options.gpu is None:
gpu_id = -1
else:
gpu_id = int(options.gpu)
if options.nrank is None:
nrank = 0
else:
nrank = int(options.nrank)
# create the specified configuration
if mpi_comm is None:
exec_conf = _hoomd.ExecutionConfiguration(exec_mode, gpu_id,
options.min_cpu,
options.ignore_display, msg,
nrank)
else:
if not mpi_available:
msg.error(
"mpi_comm provided, but MPI support was disabled at compile time\n"
)
raise RuntimeError("mpi_comm is not supported in serial builds")
handled = False
# pass in pointer to MPI_Comm object provided by mpi4py
try:
import mpi4py
if isinstance(mpi_comm, mpi4py.MPI.Comm):
addr = mpi4py.MPI._addressof(mpi_comm)
exec_conf = _hoomd.ExecutionConfiguration._make_exec_conf_mpi_comm(
exec_mode, gpu_id, options.min_cpu, options.ignore_display,
msg, nrank, addr)
handled = True
except ImportError:
# silently ignore when mpi4py is missing
pass
# undocumented case: handle plain integers as pointers to MPI_Comm objects
if not handled and isinstance(mpi_comm, int):
exec_conf = _hoomd.ExecutionConfiguration._make_exec_conf_mpi_comm(
exec_mode, gpu_id, options.min_cpu, options.ignore_display,
msg, nrank, mpi_comm)
handled = True
if not handled:
msg.error("unknown mpi_comm object: {}.\n".format(mpi_comm))
raise RuntimeError("Invalid mpi_comm object")
# if gpu_error_checking is set, enable it on the GPU
if options.gpu_error_checking:
exec_conf.setCUDAErrorChecking(True)
if _hoomd.is_TBB_available():
# set the number of TBB threads as necessary
if options.nthreads != None:
exec_conf.setNumThreads(options.nthreads)
exec_conf = exec_conf
return exec_conf
def _create_exec_conf(mpi_comm):
global exec_conf, options, msg
# use a cached execution configuration if available
if exec_conf is not None:
return exec_conf
mpi_available = _hoomd.is_MPI_available();
if options.mode == 'auto':
exec_mode = _hoomd.ExecutionConfiguration.executionMode.AUTO;
elif options.mode == "cpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.CPU;
elif options.mode == "gpu":
exec_mode = _hoomd.ExecutionConfiguration.executionMode.GPU;
else:
raise RuntimeError("Invalid mode");
# convert None options to defaults
if options.gpu is None:
gpu_id = [];
else:
gpu_id = options.gpu;
if options.nrank is None:
nrank = 0;
else:
nrank = int(options.nrank);
gpu_vec = _hoomd.std_vector_int()
for gpuid in gpu_id:
gpu_vec.append(gpuid)
# create the specified configuration
if mpi_comm is None:
exec_conf = _hoomd.ExecutionConfiguration(exec_mode, gpu_vec, options.min_cpu, options.ignore_display, msg, nrank);
else:
if not mpi_available:
msg.error("mpi_comm provided, but MPI support was disabled at compile time\n");
raise RuntimeError("mpi_comm is not supported in serial builds");
handled = False;
# pass in pointer to MPI_Comm object provided by mpi4py
try:
import mpi4py
if isinstance(mpi_comm, mpi4py.MPI.Comm):
addr = mpi4py.MPI._addressof(mpi_comm);
exec_conf = _hoomd.ExecutionConfiguration._make_exec_conf_mpi_comm(exec_mode, gpu_vec, options.min_cpu, options.ignore_display, msg, nrank, addr);
handled = True
except ImportError:
# silently ignore when mpi4py is missing
pass
# undocumented case: handle plain integers as pointers to MPI_Comm objects
if not handled and isinstance(mpi_comm, int):
exec_conf = _hoomd.ExecutionConfiguration._make_exec_conf_mpi_comm(exec_mode, gpu_vec, options.min_cpu, options.ignore_display, msg, nrank, mpi_comm);
handled = True
if not handled:
msg.error("unknown mpi_comm object: {}.\n".format(mpi_comm));
raise RuntimeError("Invalid mpi_comm object");
# if gpu_error_checking is set, enable it on the GPU
if options.gpu_error_checking:
exec_conf.setCUDAErrorChecking(True);
if _hoomd.is_TBB_available():
# set the number of TBB threads as necessary
if options.nthreads != None:
exec_conf.setNumThreads(options.nthreads)
exec_conf = exec_conf;
return exec_conf;
util.unquiet_status();
def get_step():
""" Get the current simulation time step.
Returns:
The current simulation time step.
Example::
print(hoomd.get_step())
"""
# check if initialization has occurred
if not init.is_initialized():
context.msg.error("Cannot get step before initialization\n");
raise RuntimeError('Error getting step');
return context.current.system.getCurrentTimeStep();
# Check to see if we are built without MPI support and the user used mpirun
if (not _hoomd.is_MPI_available()
and ( 'OMPI_COMM_WORLD_RANK' in os.environ
or 'MV2_COMM_WORLD_LOCAL_RANK' in os.environ
or 'PMI_RANK' in os.environ
or 'ALPS_APP_PE' in os.environ)
):
print('HOOMD-blue is built without MPI support, but seems to have been launched with mpirun');
print('exiting now to prevent many sequential jobs from starting');
raise RuntimeError('Error launching hoomd')
def _get_proc_name():
if _hoomd.is_MPI_available():
return _hoomd.get_mpi_proc_name()
else:
return platform.node()
def _get_proc_name():
if _hoomd.is_MPI_available():
return _hoomd.get_mpi_proc_name()
else:
return platform.node()