def set_affinity(mask):
if sched_setaffinity:
sched_setaffinity(0, mask)
else:
if PsutilProcess:
p = PsutilProcess()
p.cpu_affinity(mask)
else:
if os.name == "posix":
omp_set_num_threads(len(mask))
def limit_cpu(self,
cpus: Union[int, List[int]],
logical: bool = True) -> NoReturn:
count = len(cpus)
if logical:
assert count <= self._cpu_logical_cores_count
else:
assert count <= self._cpu_physical_cores_count
logical_cores = list(range(self._cpu_logical_cores_count))
physical_cores = np.array_split(
logical_cores,
indices_or_sections=self._cpu_physical_cores_count)
cpus = list(chain(*itemgetter(*cpus)(physical_cores)))
cpus = self._force_list(cpus)
process = Process(pid=os.getpid())
process.cpu_affinity(cpus=cpus)
def configure_process(proc: psutil.Process,
cores: List[int],
infer_multi_team=False):
try:
if infer_multi_team:
existing_affinity = proc.cpu_affinity()
if len(existing_affinity) < psutil.cpu_count():
# The process in question has already been pinned to a subset of the CPUs.
# This might be a process spanning multiple teams, so we will set affinity to
# the combination of existing and newly requested cores.
cores = sorted(set(existing_affinity + cores))
proc.cpu_affinity(cores)
if platform.system() == 'Windows':
proc.nice(psutil.HIGH_PRIORITY_CLASS
) # Allow the process to run at high priority
except Exception as e:
get_logger(DEFAULT_LOGGER).info(e)
def get_affinity():
if sched_getaffinity:
return sched_getaffinity(0)
else:
if PsutilProcess:
p = PsutilProcess()
return p.cpu_affinity()
else:
return [i for i in range(cpu_count())]
def process_viewer(viewer, pid):
"""Processor for multicam view.
Runs the viewer itself as a subprocess.
Parameters
----------
viewer : utils.viewer.Viewer
The Viewer object to be run. It should be previously initialized.
pid : int
Contains an identifier of the process used to assign CPUs.
"""
p = Process()
p.cpu_affinity([pid + 1])
viewer.run()
def main(global_consensus: str,
local_consensus: str,
fasta: str,
no_write: bool = False,
cpus: int = -1,
out_prefix: str = 'A2G_aln',
remove_duplicates: bool = True):
p = Process()
n_cpus = cpus if cpus > 0 else cpu_count()
all_cpus = list(range(n_cpus))
p.cpu_affinity(all_cpus)
kwargs = dict(out_prefix=out_prefix,
no_write=no_write,
cpus=cpus,
remove_duplicates=remove_duplicates)
aln = Align(global_consensus, local_consensus, **kwargs)
aln.query = fasta
full, subset = aln.run()
if no_write:
return full, subset
def _get_process_cores(process: psutil.Process):
# cores = len(process.cpu_affinity)
try:
core = len(process.cpu_affinity())
except psutil.AccessDenied:
cores = 0
