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# -*- coding: utf-8 -*-
"""
Utilities that assist in computation
Created on Tue Nov 3 21:14:25 2015
@author: Suhas Somnath, Chris Smith
"""
from __future__ import print_function, division, unicode_literals, \
absolute_import
import joblib
import numpy as np
from multiprocessing import cpu_count
from psutil import virtual_memory as vm
def get_MPI():
"""
Returns the mpi4py.MPI object if mpi4py is available and size > 1.
Returns None otherwise
Returns
-------
MPI : :class:`mpi4py.MPI` object or None
"""
try:
from mpi4py import MPI
if MPI.COMM_WORLD.Get_size() == 1:
# mpi4py available but NOT called via mpirun or mpiexec => single node
MPI = None
except ImportError:
# mpi4py not even present! Single node by default:
MPI = None
return MPI
def group_ranks_by_socket(verbose=False):
"""
Groups MPI ranks in COMM_WORLD by socket. Another way to think about this
is that it assigns a master rank for each rank such that there is a single
master rank per socket (CPU). The results from this function can be used to
split MPI communicators based on the socket for intra-node communication.
Parameters
----------
verbose : bool, optional
Whether or not to print debugging statements
Returns
-------
master_ranks : 1D unsigned integer :class:`numpy.ndarray`
Array with values that signify which rank a given rank should consider
its master.
Notes
-----
This is necessary when wanting to carve up the memory for all ranks within
a socket. This is also relevant when trying to bring down the number of
ranks that are writing to the HDF5 file. This is all based on the premise
that data analysis involves a fair amount of file writing and writing with
3 ranks is a lot better than writing with 100 ranks. An assumption is made
that the communication between the ranks within each socket would be faster
than communicating across nodes / scokets. No assumption is made about the
names of each socket
"""
MPI = get_MPI()
comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
# Step 1: Gather all the socket names:
sendbuf = MPI.Get_processor_name()
if verbose:
print('Rank: ', rank, ', sendbuf: ', sendbuf)
recvbuf = comm.allgather(sendbuf)
if verbose and rank == 0:
print('Rank: ', rank, ', recvbuf received: ', recvbuf)
# Step 2: Find all unique socket names:
recvbuf = np.array(recvbuf)
unique_sockets = np.unique(recvbuf)
if verbose and rank == 0:
print('Unique sockets: {}'.format(unique_sockets))
master_ranks = np.zeros(size, dtype=np.uint16)
for item in unique_sockets:
temp = np.where(recvbuf == item)[0]
master_ranks[temp] = temp[0]
if verbose and rank == 0:
print('Parent rank for all ranks: {}'.format(master_ranks))
return master_ranks
def parallel_compute(data, func, cores=None, lengthy_computation=False,
func_args=None, func_kwargs=None, verbose=False,
joblib_backend='multiprocessing'):
"""
Computes the provided function using multiple cores using the joblib
library
Parameters
----------
data : numpy.ndarray
Data to map function to. Function will be mapped to the first axis of
data
func : callable
Function to map to data
cores : uint, optional
Number of logical cores to use to compute
Default - All cores - 1 (total cores <= 4) or - 2 (cores > 4) depending
on number of cores.
Ignored in the MPI context - each rank will execute serially
lengthy_computation : bool, optional
Whether or not each computation is expected to take substantial time.
Sometimes the time for adding more cores can outweigh the time per core
Default - False
func_args : list, optional
arguments to be passed to the function
func_kwargs : dict, optional
keyword arguments to be passed onto function
joblib_backend : str, optional
Backend to use for parallel computation with Joblib.
The older paradigm - "multiprocessing" is the default in pyUSID.
Set to None to use the joblib default - "loky"
verbose : bool, optional. default = False
Whether or not to print statements that aid in debugging
Returns
-------
results : list
List of computational results
"""
if not callable(func):
raise TypeError('Function argument is not callable')
if not isinstance(data, np.ndarray):
raise TypeError('data must be a numpy array')
if func_args is None:
func_args = list()
else:
if isinstance(func_args, tuple):
func_args = list(func_args)
if not isinstance(func_args, list):
raise TypeError('Arguments to the mapped function should be '
'specified as a list')
if func_kwargs is None:
func_kwargs = dict()
else:
if not isinstance(func_kwargs, dict):
raise TypeError('Keyword arguments to the mapped function should '
'be specified via a dictionary')
req_cores = cores
MPI = get_MPI()
if MPI is not None:
rank = MPI.COMM_WORLD.Get_rank()
# Was unable to get the MPI + joblib framework to work.
# Did not compute anything at all. Just froze
cores = 1
else:
rank = 0
cores = recommend_cpu_cores(data.shape[0],
requested_cores=cores,
lengthy_computation=lengthy_computation,
verbose=verbose)
if verbose:
print('Rank {} starting computing on {} cores (requested {} cores)'
''.format(rank, cores, req_cores))
if cores > 1:
values = [joblib.delayed(func)(x, *func_args, **func_kwargs) for x in data]
results = joblib.Parallel(n_jobs=cores, backend=joblib_backend)(values)
# Finished reading the entire data set
print('Rank {} finished parallel computation'.format(rank))
else:
if verbose:
print("Rank {} computing serially ...".format(rank))
# List comprehension vs map vs for loop?
# https://stackoverflow.com/questions/1247486/python-list-comprehension-vs-map
results = [func(vector, *func_args, **func_kwargs) for vector in data]
return results
def get_available_memory():
"""
Returns the available memory in bytes
Chris Smith -- csmith55@utk.edu
Returns
-------
mem : unsigned int
Memory in bytes
"""
import sys
mem = vm().available
if sys.maxsize <= 2 ** 32:
mem = min([mem, sys.maxsize])
return mem
def recommend_cpu_cores(num_jobs, requested_cores=None, min_free_cores=None,
lengthy_computation=False, verbose=False):
"""
Decides the number of cores to use for parallel computing
Parameters
----------
num_jobs : unsigned int
Number of times a parallel operation needs to be performed
requested_cores : unsigned int (Optional. Default = None)
Number of logical cores to use for computation
lengthy_computation : Boolean (Optional. Default = False)
Whether or not each computation takes a long time.
min_free_cores : uint (Optional, default = 1 if number of logical cores
< 5 and 2 otherwise)
Number of CPU cores that should not be used)
verbose : Boolean (Optional. Default = False)
Whether or not to print statements that aid in debugging
Returns
-------
requested_cores : unsigned int
Number of logical cores to use for computation
Notes
-----
If each computation is quick, the overhead of starting and using a larger
number of cores would defeat the benefits of parallel computation, so use
fewer cores instead.
Eg- Band Excitation (BE) simple harmonic fitting is fast
(~ few msec/spectrum) so set ``lengthy_computation`` to False,
Eg- Bayesian Inference is very slow (~ 10-20 sec) so set
``lengthy_computation`` to True
"""
logical_cores = cpu_count()
if min_free_cores is not None:
if not isinstance(min_free_cores, int):
raise TypeError('min_free_cores should be an unsigned integer')
if min_free_cores < 0 or min_free_cores >= logical_cores:
raise ValueError('min_free_cores should be an unsigned integer '
'less than the number of logical cores')
if verbose:
print('Number of requested free CPU cores: {} was accepted'.format(min_free_cores))
else:
if logical_cores > 4:
min_free_cores = 2
elif logical_cores == 1:
min_free_cores = 0
else:
min_free_cores = 1
if verbose:
print('Number of CPU free cores set to: {} given that the CPU has '
'{} logical cores.'.format(min_free_cores, logical_cores))
max_cores = max(1, logical_cores - min_free_cores)
if requested_cores is None:
# conservative allocation
if verbose:
print('No requested_cores given. Using estimate of {}.'
''.format(max_cores))
requested_cores = max_cores
else:
if not isinstance(requested_cores, int):
raise TypeError('requested_cores should be an unsigned integer')
if verbose:
print('{} cores requested.'.format(requested_cores))
if requested_cores < 0 or requested_cores > logical_cores:
# Respecting the explicit request
requested_cores = max(min(int(abs(requested_cores)),
logical_cores), 1)
if verbose:
print('Clipped explicit request for CPU cores to: {}'
''.format(requested_cores))
if not isinstance(num_jobs, int):
raise TypeError('num_jobs should be an unsigned integer')
if num_jobs < 1:
raise ValueError('num_jobs should be greater than 0')
jobs_per_core = max(int(num_jobs / requested_cores), 1)
# I don't like to hard-code things here but I don't have a better idea for now
min_jobs_per_core = 20
if verbose:
print('computational jobs per core = {}. For short computations, each '
'core must have at least {} jobs to warrant parallel computation'
'.'.format(jobs_per_core, min_jobs_per_core))
if not lengthy_computation:
if verbose:
print('Computations are not lengthy.')
if requested_cores > 1 and jobs_per_core < min_jobs_per_core:
# cut down the number of cores if there are too few jobs
jobs_per_core = 2 * min_jobs_per_core
# intelligently set the cores now.
requested_cores = max(1, min(requested_cores, int(num_jobs / jobs_per_core)))
if verbose:
print('Not enough jobs per core. Reducing cores to {}'
''.format(requested_cores))
return int(requested_cores)
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