gprMax项目代码分解：gprMax.py
目录
1. 引言
在生成Ascan-2D.out的输出文件时用到了以下命令，这个步骤在本人《gprMax正演模拟方法》的文章中有详细讲解。
python -m gprMax user_models/cylinder_Ascan_2D.in
其中，gprMax即使我们本文中讲解的gprMax.py文件。在命令行中输入pytnon -h命令可以查看到python命令的帮助文档，其中可以看到-m mod : run library module as a script (terminates option list)这一句对于-m参数意思的解释为“将模块作为脚本运行”。user_models/cylinder_Ascan_2D.in是输入文件的路径，输入文件是需要手动编写的。
接下来，本文将对gprMax项目中的gprMax.py文件代码进行逻辑梳理和分解。
2. 代码分解
（1） 导入模块
import argparse
import datetime
import os
import platform
import sys
from enum import Enum
from io import StringIO
import h5py
import numpy as np
from gprMax._version import __version__, codename
from gprMax.constants import c
from gprMax.constants import e0
from gprMax.constants import m0
from gprMax.constants import z0
from gprMax.exceptions import GeneralError
from gprMax.model_build_run import run_model
from gprMax.utilities import detect_check_gpus
from gprMax.utilities import get_host_info
from gprMax.utilities import get_terminal_width
from gprMax.utilities import human_size
from gprMax.utilities import logo
from gprMax.utilities import open_path_file
from gprMax.utilities import timer
（2）main()函数
作为脚本运行的入口，调用了run_main()函数。
def main():
"""This is the main function for gprMax."""
# Parse command line arguments
parser = argparse.ArgumentParser(prog='gprMax', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('inputfile', help='path to, and name of inputfile or file object')
parser.add_argument('-n', default=1, type=int, help='number of times to run the input file, e.g. to create a B-scan')
parser.add_argument('-task', type=int, help='task identifier (model number) for job array on Open Grid Scheduler/Grid Engine (http://gridscheduler.sourceforge.net/index.html)')
parser.add_argument('-restart', type=int, help='model number to restart from, e.g. when creating B-scan')
parser.add_argument('-mpi', type=int, help='number of MPI tasks, i.e. master + workers')
parser.add_argument('-mpicomm', default=None, help=argparse.SUPPRESS)
parser.add_argument('--mpi-no-spawn', action='store_true', default=False, help='flag to use MPI without spawn mechanism')
parser.add_argument('--mpi-worker', action='store_true', default=False, help=argparse.SUPPRESS)
parser.add_argument('-gpu', type=int, action='append', nargs='*', help='flag to use Nvidia GPU or option to give list of device ID(s)')
parser.add_argument('-benchmark', action='store_true', default=False, help='flag to switch on benchmarking mode')
parser.add_argument('--geometry-only', action='store_true', default=False, help='flag to only build model and produce geometry file(s)')
parser.add_argument('--geometry-fixed', action='store_true', default=False, help='flag to not reprocess model geometry, e.g. for B-scans where the geometry is fixed')
parser.add_argument('--write-processed', action='store_true', default=False, help='flag to write an input file after any Python code and include commands in the original input file have been processed')
parser.add_argument('--opt-taguchi', action='store_true', default=False, help='flag to optimise parameters using the Taguchi optimisation method')
args = parser.parse_args()
run_main(args)
```
### （2）api()函数
作为模块运行的入口，调用了`run_main()函数`。
```python
def api(
inputfile,
n=1,
task=None,
restart=None,
mpi=False,
mpi_no_spawn=False,
mpicomm=None,
gpu=None,
benchmark=False,
geometry_only=False,
geometry_fixed=False,
write_processed=False,
opt_taguchi=False
):
"""If installed as a module this is the entry point."""
class ImportArguments:
pass
args = ImportArguments()
args.inputfile = inputfile
args.n = n
args.task = task
args.restart = restart
args.mpi = mpi
args.mpi_no_spawn = mpi_no_spawn
args.mpicomm = mpicomm
args.gpu = gpu
args.benchmark = benchmark
args.geometry_only = geometry_only
args.geometry_fixed = geometry_fixed
args.write_processed = write_processed
args.opt_taguchi = opt_taguchi
run_main(args)
（3）run_main()函数
run_main()函数主要作为一个宏观接口，根据所给参数调用不通的函数，进而使用指定的方法进行模拟演算。此函数调用的不同模拟演算方法函数有：run_benchmark_sim()、run_mpi_sim()、run_opt_sim()、run_mpi_no_spawn_sim() 和 run_std_sim()。默认情况下的模拟函数会使用run_std_sim()。
def run_main(args):
"""
Top-level function that controls what mode of simulation (standard/optimsation/benchmark etc...) is run.
Args:
args (dict): Namespace with input arguments from command line or api.
"""
# Print gprMax logo, version, and licencing/copyright information
logo(__version__ + ' (' + codename + ')')
with open_path_file(args.inputfile) as inputfile:
# Get information about host machine
hostinfo = get_host_info()
hyperthreading = ', {} cores with Hyper-Threading'.format(hostinfo['logicalcores']) if hostinfo['hyperthreading'] else ''
print('\nHost: {} | {} | {} x {} ({} cores{}) | {} RAM | {}'.format(hostinfo['hostname'],
hostinfo['machineID'], hostinfo['sockets'], hostinfo['cpuID'], hostinfo['physicalcores'],
hyperthreading, human_size(hostinfo['ram'], a_kilobyte_is_1024_bytes=True), hostinfo['osversion']))
# Get information/setup any Nvidia GPU(s)
if args.gpu is not None:
# Flatten a list of lists
if any(isinstance(element, list) for element in args.gpu):
args.gpu = [val for sublist in args.gpu for val in sublist]
gpus, allgpustext = detect_check_gpus(args.gpu)
print('GPU(s) detected: {}'.format(' | '.join(allgpustext)))
# If in MPI mode or benchmarking provide list of GPU objects, otherwise
# provide single GPU object
if args.mpi or args.mpi_no_spawn or args.benchmark:
args.gpu = gpus
else:
args.gpu = gpus[0]
# Create a separate namespace that users can access in any Python code blocks in the input file
usernamespace = {'c': c, 'e0': e0, 'm0': m0, 'z0': z0, 'number_model_runs': args.n, 'inputfile': os.path.abspath(inputfile.name)}
#######################################
# Process for benchmarking simulation #
#######################################
if args.benchmark:
if args.mpi or args.opt_taguchi or args.task or args.n > 1:
raise GeneralError('Benchmarking mode cannot be combined with MPI, job array, or Taguchi optimisation modes, or multiple model runs.')
run_benchmark_sim(args, inputfile, usernamespace)
####################################################
# Process for simulation with Taguchi optimisation #
####################################################
elif args.opt_taguchi:
if args.mpi_worker: # Special case for MPI spawned workers - they do not need to enter the Taguchi optimisation mode
run_mpi_sim(args, inputfile, usernamespace)
else:
from gprMax.optimisation_taguchi import run_opt_sim
run_opt_sim(args, inputfile, usernamespace)
################################################
# Process for standard simulation (CPU or GPU) #
################################################
else:
# Mixed mode MPI with OpenMP or CUDA - MPI task farm for models with each model parallelised with OpenMP (CPU) or CUDA (GPU)
if args.mpi:
if args.n == 1:
raise GeneralError('MPI is not beneficial when there is only one model to run')
if args.task:
raise GeneralError('MPI cannot be combined with job array mode')
run_mpi_sim(args, inputfile, usernamespace)
# Alternate MPI configuration that does not use MPI spawn mechanism
elif args.mpi_no_spawn:
if args.n == 1:
raise GeneralError('MPI is not beneficial when there is only one model to run')
if args.task:
raise GeneralError('MPI cannot be combined with job array mode')
run_mpi_no_spawn_sim(args, inputfile, usernamespace)
# Standard behaviour - models run serially with each model parallelised with OpenMP (CPU) or CUDA (GPU)
else:
if args.task and args.restart:
raise GeneralError('Job array and restart modes cannot be used together')
run_std_sim(args, inputfile, usernamespace)
（4）run_std_sim()函数
def run_std_sim(args, inputfile, usernamespace, optparams=None):
"""
Run standard simulation - models are run one after another and each model
is parallelised using either OpenMP (CPU) or CUDA (GPU)
Args:
args (dict): Namespace with command line arguments
inputfile (object): File object for the input file.
usernamespace (dict): Namespace that can be accessed by user in any
Python code blocks in input file.
optparams (dict): Optional argument. For Taguchi optimisation it
provides the parameters to optimise and their values.
"""
# Set range for number of models to run
if args.task:
# Job array feeds args.n number of single tasks
modelstart = args.task
modelend = args.task + 1
elif args.restart:
modelstart = args.restart
modelend = modelstart + args.n
else:
modelstart = 1
modelend = modelstart + args.n
numbermodelruns = args.n
tsimstart = timer()
for currentmodelrun in range(modelstart, modelend):
# If Taguchi optimistaion, add specific value for each parameter to
# optimise for each experiment to user accessible namespace
if optparams:
tmp = {}
tmp.update((key, value[currentmodelrun - 1]) for key, value in optparams.items())
modelusernamespace = usernamespace.copy()
modelusernamespace.update({'optparams': tmp})
else:
modelusernamespace = usernamespace
run_model(args, currentmodelrun, modelend - 1, numbermodelruns, inputfile, modelusernamespace)
tsimend = timer()
simcompletestr = '\n=== Simulation completed in [HH:MM:SS]: {}'.format(datetime.timedelta(seconds=tsimend - tsimstart))
print('{} {}\n'.format(simcompletestr, '=' * (get_terminal_width() - 1 - len(simcompletestr))))
（5）run_benchmark_sim()函数
def run_benchmark_sim(args, inputfile, usernamespace):
"""
Run standard simulation in benchmarking mode - models are run one
after another and each model is parallelised using either OpenMP (CPU)
or CUDA (GPU)
Args:
args (dict): Namespace with command line arguments
inputfile (object): File object for the input file.
usernamespace (dict): Namespace that can be accessed by user in any
Python code blocks in input file.
"""
# Get information about host machine
hostinfo = get_host_info()
hyperthreading = ', {} cores with Hyper-Threading'.format(hostinfo['logicalcores']) if hostinfo['hyperthreading'] else ''
machineIDlong = '{}; {} x {} ({} cores{}); {} RAM; {}'.format(hostinfo['machineID'], hostinfo['sockets'], hostinfo['cpuID'], hostinfo['physicalcores'], hyperthreading, human_size(hostinfo['ram'], a_kilobyte_is_1024_bytes=True), hostinfo['osversion'])
# Initialise arrays to hold CPU thread info and times, and GPU info and times
cputhreads = np.array([], dtype=np.int32)
cputimes = np.array([])
gpuIDs = []
gputimes = np.array([])
# CPU only benchmarking
if args.gpu is None:
# Number of CPU threads to benchmark - start from single thread and double threads until maximum number of physical cores
threads = 1
maxthreads = hostinfo['physicalcores']
maxthreadspersocket = hostinfo['physicalcores'] / hostinfo['sockets']
while threads < maxthreadspersocket:
cputhreads = np.append(cputhreads, int(threads))
threads *= 2
# Check for system with only single thread
if cputhreads.size == 0:
cputhreads = np.append(cputhreads, threads)
# Add maxthreadspersocket and maxthreads if necessary
if cputhreads[-1] != maxthreadspersocket:
cputhreads = np.append(cputhreads, int(maxthreadspersocket))
if cputhreads[-1] != maxthreads:
cputhreads = np.append(cputhreads, int(maxthreads))
cputhreads = cputhreads[::-1]
cputimes = np.zeros(len(cputhreads))
numbermodelruns = len(cputhreads)
# GPU only benchmarking
else:
# Set size of array to store GPU runtimes and number of runs of model required
for gpu in args.gpu:
gpuIDs.append(gpu.name)
gputimes = np.zeros(len(args.gpu))
numbermodelruns = len(args.gpu)
# Store GPU information in a temp variable
gpus = args.gpu
usernamespace['number_model_runs'] = numbermodelruns
modelend = numbermodelruns + 1
for currentmodelrun in range(1, modelend):
# Run CPU benchmark
if args.gpu is None:
os.environ['OMP_NUM_THREADS'] = str(cputhreads[currentmodelrun - 1])
cputimes[currentmodelrun - 1] = run_model(args, currentmodelrun, modelend - 1, numbermodelruns, inputfile, usernamespace)
# Run GPU benchmark
else:
args.gpu = gpus[(currentmodelrun - 1)]
os.environ['OMP_NUM_THREADS'] = str(hostinfo['physicalcores'])
gputimes[(currentmodelrun - 1)] = run_model(args, currentmodelrun, modelend - 1, numbermodelruns, inputfile, usernamespace)
# Get model size (in cells) and number of iterations
if currentmodelrun == 1:
if numbermodelruns == 1:
outputfile = os.path.splitext(args.inputfile)[0] + '.out'
else:
outputfile = os.path.splitext(args.inputfile)[0] + str(currentmodelrun) + '.out'
f = h5py.File(outputfile, 'r')
iterations = f.attrs['Iterations']
numcells = f.attrs['nx_ny_nz']
# Save number of threads and benchmarking times to NumPy archive
np.savez(os.path.splitext(inputfile.name)[0], machineID=machineIDlong, gpuIDs=gpuIDs, cputhreads=cputhreads, cputimes=cputimes, gputimes=gputimes, iterations=iterations, numcells=numcells, version=__version__)
simcompletestr = '\n=== Simulation completed'
print('{} {}\n'.format(simcompletestr, '=' * (get_terminal_width() - 1 - len(simcompletestr))))
（6）run_mpi_sim()函数
def run_mpi_sim(args, inputfile, usernamespace, optparams=None):
"""
Run mixed mode MPI/OpenMP simulation - MPI task farm for models with
each model parallelised using either OpenMP (CPU) or CUDA (GPU)
Args:
args (dict): Namespace with command line arguments
inputfile (object): File object for the input file.
usernamespace (dict): Namespace that can be accessed by user in any
Python code blocks in input file.
optparams (dict): Optional argument. For Taguchi optimisation it
provides the parameters to optimise and their values.
"""
from mpi4py import MPI
status = MPI.Status()
hostname = platform.node()
# Set range for number of models to run
modelstart = args.restart if args.restart else 1
modelend = modelstart + args.n
numbermodelruns = args.n
# Command line flag used to indicate a spawned worker instance
workerflag = '--mpi-worker'
numworkers = args.mpi - 1
##################
# Master process #
##################
if workerflag not in sys.argv:
# N.B Spawned worker flag (--mpi-worker) applied to sys.argv when MPI.Spawn is called
# See if the MPI communicator object is being passed as an argument (likely from a MPI.Split)
if args.mpicomm is not None:
comm = args.mpicomm
else:
comm = MPI.COMM_WORLD
tsimstart = timer()
mpistartstr = '\n=== MPI task farm (USING MPI Spawn)'
print('{} {}'.format(mpistartstr, '=' * (get_terminal_width() - 1 - len(mpistartstr))))
print('=== MPI master ({}, rank: {}) on {} spawning {} workers...'.format(comm.name, comm.Get_rank(), hostname, numworkers))
# Assemble a sys.argv replacement to pass to spawned worker
# N.B This is required as sys.argv not available when gprMax is called via api()
# Ignore mpicomm object if it exists as only strings can be passed via spawn
myargv = []
for key, value in vars(args).items():
if value:
# Input file name always comes first
if 'inputfile' in key:
myargv.append(value)
elif 'gpu' in key:
myargv.append('-' + key)
# Add GPU device ID(s) from GPU objects
for gpu in args.gpu:
myargv.append(str(gpu.deviceID))
elif 'mpicomm' in key:
pass
elif '_' in key:
key = key.replace('_', '-')
myargv.append('--' + key)
else:
myargv.append('-' + key)
if value is not True:
myargv.append(str(value))
# Create a list of work
worklist = []
for model in range(modelstart, modelend):
workobj = dict()
workobj['currentmodelrun'] = model
workobj['mpicommname'] = comm.name
if optparams:
workobj['optparams'] = optparams
worklist.append(workobj)
# Add stop sentinels
worklist += ([StopIteration] * numworkers)
# Spawn workers
newcomm = comm.Spawn(sys.executable, args=['-m', 'gprMax'] + myargv + [workerflag], maxprocs=numworkers)
# Reply to whoever asks until done
for work in worklist:
newcomm.recv(source=MPI.ANY_SOURCE, status=status)
newcomm.send(obj=work, dest=status.Get_source())
# Shutdown communicators
newcomm.Disconnect()
tsimend = timer()
simcompletestr = '\n=== MPI master ({}, rank: {}) on {} completed simulation in [HH:MM:SS]: {}'.format(comm.name, comm.Get_rank(), hostname, datetime.timedelta(seconds=tsimend - tsimstart))
print('{} {}\n'.format(simcompletestr, '=' * (get_terminal_width() - 1 - len(simcompletestr))))
##################
# Worker process #
##################
elif workerflag in sys.argv:
# Connect to parent to get communicator
try:
comm = MPI.Comm.Get_parent()
rank = comm.Get_rank()
except ValueError:
raise ValueError('MPI worker could not connect to parent')
# Select GPU and get info
gpuinfo = ''
if args.gpu is not None:
# Set device ID based on rank from list of GPUs
try:
args.gpu = args.gpu[rank]
# GPUs on multiple nodes where CUDA_VISIBLE_DEVICES is the same
# on each node
except:
args.gpu = args.gpu[rank % len(args.gpu)]
gpuinfo = ' using {} - {}, {} RAM '.format(args.gpu.deviceID,
args.gpu.name,
human_size(args.gpu.totalmem,
a_kilobyte_is_1024_bytes=True))
# Ask for work until stop sentinel
for work in iter(lambda: comm.sendrecv(0, dest=0), StopIteration):
currentmodelrun = work['currentmodelrun']
# If Taguchi optimisation, add specific value for each parameter to
# optimise for each experiment to user accessible namespace
if 'optparams' in work:
tmp = {}
tmp.update((key, value[currentmodelrun - 1]) for key, value in work['optparams'].items())
modelusernamespace = usernamespace.copy()
modelusernamespace.update({'optparams': tmp})
else:
modelusernamespace = usernamespace
# Run the model
print('Starting MPI spawned worker (parent: {}, rank: {}) on {} with model {}/{}{}\n'.format(work['mpicommname'], rank, hostname, currentmodelrun, numbermodelruns, gpuinfo))
tsolve = run_model(args, currentmodelrun, modelend - 1, numbermodelruns, inputfile, modelusernamespace)
print('Completed MPI spawned worker (parent: {}, rank: {}) on {} with model {}/{}{} in [HH:MM:SS]: {}\n'.format(work['mpicommname'], rank, hostname, currentmodelrun, numbermodelruns, gpuinfo, datetime.timedelta(seconds=tsolve)))
# Shutdown
comm.Disconnect()
（7）run_mpi_no_spawn_sim()函数
def run_mpi_no_spawn_sim(args, inputfile, usernamespace, optparams=None):
"""
Alternate MPI implementation that avoids using the MPI spawn mechanism.
This implementation is designed to be used as
e.g. 'mpirun -n 5 python -m gprMax user_models/mymodel.in -n 10 --mpi-no-spawn'
Run mixed mode MPI/OpenMP simulation - MPI task farm for models with
each model parallelised using either OpenMP (CPU) or CUDA (GPU)
Args:
args (dict): Namespace with command line arguments
inputfile (object): File object for the input file.
usernamespace (dict): Namespace that can be accessed by user in any
Python code blocks in input file.
optparams (dict): Optional argument. For Taguchi optimisation it
provides the parameters to optimise and their values.
"""
from mpi4py import MPI
# Define MPI message tags
tags = Enum('tags', {'READY': 0, 'DONE': 1, 'EXIT': 2, 'START': 3})
# Initializations and preliminaries
comm = MPI.COMM_WORLD
size = comm.Get_size() # total number of processes
rank = comm.Get_rank() # rank of this process
status = MPI.Status() # get MPI status object
hostname = platform.node() # get name of processor/host
# Set range for number of models to run
modelstart = args.restart if args.restart else 1
modelend = modelstart + args.n
numbermodelruns = args.n
currentmodelrun = modelstart # can use -task argument to start numbering from something other than 1
numworkers = size - 1
##################
# Master process #
##################
if rank == 0:
tsimstart = timer()
mpistartstr = '\n=== MPI task farm (WITHOUT using MPI Spawn)'
print('{} {}'.format(mpistartstr, '=' * (get_terminal_width() - 1 - len(mpistartstr))))
print('=== MPI master ({}, rank: {}) on {} using {} workers...'.format(comm.name, comm.Get_rank(), hostname, numworkers))
closedworkers = 0
while closedworkers < numworkers:
comm.recv(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG, status=status)
source = status.Get_source()
tag = status.Get_tag()
# Worker is ready, so send it a task
if tag == tags.READY.value:
if currentmodelrun < modelend:
comm.send(currentmodelrun, dest=source, tag=tags.START.value)
currentmodelrun += 1
else:
comm.send(None, dest=source, tag=tags.EXIT.value)
# Worker has completed a task
elif tag == tags.DONE.value:
pass
# Worker has completed all tasks
elif tag == tags.EXIT.value:
closedworkers += 1
tsimend = timer()
simcompletestr = '\n=== MPI master ({}, rank: {}) on {} completed simulation in [HH:MM:SS]: {}'.format(comm.name, comm.Get_rank(), hostname, datetime.timedelta(seconds=tsimend - tsimstart))
print('{} {}\n'.format(simcompletestr, '=' * (get_terminal_width() - 1 - len(simcompletestr))))
##################
# Worker process #
##################
else:
# Get info and setup device ID for GPU(s)
gpuinfo = ''
if args.gpu is not None:
# Set device ID based on rank from list of GPUs
deviceID = (rank - 1) % len(args.gpu)
args.gpu = next(gpu for gpu in args.gpu if gpu.deviceID == deviceID)
gpuinfo = ' using {} - {}, {}'.format(args.gpu.deviceID, args.gpu.name, human_size(args.gpu.totalmem, a_kilobyte_is_1024_bytes=True))
while True:
comm.send(None, dest=0, tag=tags.READY.value)
# Receive a model number to run from the master
currentmodelrun = comm.recv(source=0, tag=MPI.ANY_TAG, status=status)
tag = status.Get_tag()
# Run a model
if tag == tags.START.value:
# If Taguchi optimistaion, add specific value for each parameter
# to optimise for each experiment to user accessible namespace
if optparams:
tmp = {}
tmp.update((key, value[currentmodelrun - 1]) for key, value in optparams.items())
modelusernamespace = usernamespace.copy()
modelusernamespace.update({'optparams': tmp})
else:
modelusernamespace = usernamespace
# Run the model
print('Starting MPI worker (parent: {}, rank: {}) on {} with model {}/{}{}\n'.format(comm.name, rank, hostname, currentmodelrun, numbermodelruns, gpuinfo))
tsolve = run_model(args, currentmodelrun, modelend - 1, numbermodelruns, inputfile, modelusernamespace)
comm.send(None, dest=0, tag=tags.DONE.value)
print('Completed MPI worker (parent: {}, rank: {}) on {} with model {}/{}{} in [HH:MM:SS]: {}\n'.format(comm.name, rank, hostname, currentmodelrun, numbermodelruns, gpuinfo, datetime.timedelta(seconds=tsolve)))
# Break out of loop when work receives exit message
elif tag == tags.EXIT.value:
break
comm.send(None, dest=0, tag=tags.EXIT.value)
（8）run_opt_sim()函数
run_main()函数中调用的run_opt_sim()函数并未写在“gprMax.py”文件中，而是从“gprMax.optimisation_taguchi”中导入的，如下代码为run_main()函数中的导入run_opt_sim()函数部分。
from gprMax.optimisation_taguchi import run_opt_sim
3. 总结
本文对gprMax项目中的gprMax.py文件代码进行了逻辑梳理和分解。
Reference
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