1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726
|
import itertools
import os
import pickle
import re
import shutil
import subprocess
import sys
import tempfile
from collections import defaultdict
import numpy
import brian2
from brian2.utils.stringtools import indent
__all__ = [
"FeatureTest",
"SpeedTest",
"InaccuracyError",
"Configuration",
"run_feature_tests",
"run_single_feature_test",
"run_speed_tests",
"DefaultConfiguration",
"LocalConfiguration",
"NumpyConfiguration",
"CythonConfiguration",
"CPPStandaloneConfiguration",
"CPPStandaloneConfigurationOpenMP",
]
class InaccuracyError(AssertionError):
def __init__(self, error, *args):
self.error = error
AssertionError.__init__(self, *args)
class BaseTest:
""" """
category = None # a string with the category of features
name = None # a string with the particular feature name within the category
tags = None # a list of tags (strings) of features used
# whether or not to allow the device to override the time: this can be used to remove the
# compilation overheads on certain devices (but some tests might want to include this)
allow_time_override = True
@classmethod
def fullname(cls):
return f"{cls.category}: {cls.name}"
def run(self):
"""
Runs the feature test but do not return results (some devices may
require an extra step before results are available).
"""
raise NotImplementedError
def timed_run(self, duration):
"""
Do a timed run. This means that for RuntimeDevice it will run for defaultclock.dt before running for the
rest of the duration. This means total run duration will be duration+defaultclock.dt.
For standalone devices, this feature may or may not be implemented.
"""
if isinstance(brian2.get_device(), brian2.devices.RuntimeDevice):
brian2.run(brian2.defaultclock.dt, level=1)
brian2.run(duration, level=1)
else:
brian2.run(duration, level=1)
class FeatureTest(BaseTest):
""" """
def results(self):
"""
Return the results after a run call.
"""
raise NotImplementedError
def compare(self, maxrelerr, results_base, results_test):
"""
Compare results from standard Brian run to another run.
This method or `check` should be implemented.
"""
raise NotImplementedError
def check(self, maxrelerr, results):
"""
Check results are valid (e.g. analytically).
This method or `compare` should be implemented.
"""
raise NotImplementedError
def compare_arrays(self, maxrelerr, v_base, v_test):
"""
Often you just want to compare the values of some arrays, this does that.
"""
if isinstance(v_base, dict):
for k in v_base:
self.compare_arrays(maxrelerr, v_base[k], v_test[k])
else:
I = v_base != 0
err = numpy.amax(numpy.abs(v_base[I] - v_test[I]) / v_base[I])
if err > maxrelerr:
raise InaccuracyError(err)
if (v_test[-I] != 0).any():
raise InaccuracyError(numpy.inf)
class SpeedTest(BaseTest):
n_range = [1]
n_label = "n"
n_axis_log = True
time_axis_log = True
def __init__(self, n):
self.n = n
def results(self):
return self.n
def compare(self, maxrelerr, results_base, results_test):
pass
def check(self, maxrelerr, results):
pass
def __call__(self):
return self
class Configuration:
""" """
name = None # The name of this configuration
def __init__(self, maximum_run_time=1e7 * brian2.second):
maximum_run_time = float(maximum_run_time) * brian2.second
self.maximum_run_time = maximum_run_time
def before_run(self):
pass
def after_run(self):
pass
def get_last_run_time(self):
"""
Implement this to overwrite the measured runtime (e.g. to remove overhead).
"""
if hasattr(brian2.device, "_last_run_time"):
return brian2.device._last_run_time
raise NotImplementedError
def get_last_run_completed_fraction(self):
"""
Implement this to overwrite the amount of the last run that was completed (for devices that allow breaking
early if the maximum run time is exceeded).
"""
if hasattr(brian2.device, "_last_run_completed_fraction"):
return brian2.device._last_run_completed_fraction
return 1.0
class DefaultConfiguration(Configuration):
name = "Default"
def before_run(self):
brian2.prefs.reset_to_defaults()
brian2.set_device("runtime")
class LocalConfiguration(Configuration):
name = "Local"
def before_run(self):
brian2.prefs.reset_to_defaults()
brian2.set_device("runtime")
brian2.prefs.load_preferences()
class NumpyConfiguration(Configuration):
name = "Numpy"
def before_run(self):
brian2.prefs.reset_to_defaults()
brian2.set_device("runtime")
brian2.prefs.codegen.target = "numpy"
class CythonConfiguration(Configuration):
name = "Cython"
def before_run(self):
brian2.prefs.reset_to_defaults()
brian2.set_device("runtime")
brian2.prefs.codegen.target = "cython"
class CPPStandaloneConfiguration(Configuration):
name = "C++ standalone"
def before_run(self):
brian2.prefs.reset_to_defaults()
brian2.set_device("cpp_standalone", build_on_run=False)
def after_run(self):
if os.path.exists("cpp_standalone"):
shutil.rmtree("cpp_standalone")
brian2.device.build(
directory="cpp_standalone", compile=True, run=True, with_output=False
)
class CPPStandaloneConfigurationOpenMP(Configuration):
name = "C++ standalone (OpenMP)"
def before_run(self):
brian2.prefs.reset_to_defaults()
brian2.set_device("cpp_standalone", build_on_run=False)
brian2.prefs.devices.cpp_standalone.openmp_threads = 4
def after_run(self):
if os.path.exists("cpp_standalone"):
shutil.rmtree("cpp_standalone")
brian2.device.build(
directory="cpp_standalone", compile=True, run=True, with_output=False
)
def results(configuration, feature, n=None, maximum_run_time=1e7 * brian2.second):
tempfilename = tempfile.mktemp("exception")
if n is None:
init_args = ""
else:
init_args = str(n)
code_string = """
__file__ = '{fname}'
import brian2
from {config_module} import {config_name}
from {feature_module} import {feature_name}
configuration = {config_name}()
feature = {feature_name}({init_args})
import warnings, traceback, pickle, sys, os, time
warnings.simplefilter('ignore')
try:
start_time = time.time()
configuration.before_run()
brian2.device._set_maximum_run_time({maximum_run_time})
feature.run()
configuration.after_run()
results = feature.results()
run_time = time.time()-start_time
if feature.allow_time_override:
try:
run_time = configuration.get_last_run_time()
except NotImplementedError:
pass
lrcf = configuration.get_last_run_completed_fraction()
run_time = run_time/lrcf
prof_info = brian2.magic_network.profiling_info
new_prof_info = []
for n, t in prof_info:
new_prof_info.append((n, t/lrcf))
f = open(r'{tempfname}', 'wb')
pickle.dump((None, results, run_time, new_prof_info), f, -1)
f.close()
except Exception, ex:
#traceback.print_exc(file=sys.stdout)
tb = traceback.format_exc()
f = open(r'{tempfname}', 'wb')
pickle.dump((tb, ex, 0.0, []), f, -1)
f.close()
""".format(
config_module=configuration.__module__,
config_name=configuration.__name__,
feature_module=feature.__module__,
feature_name=feature.__name__,
tempfname=tempfilename,
fname=__file__,
init_args=init_args,
maximum_run_time=float(maximum_run_time),
)
args = [sys.executable, "-c", code_string]
# Run the example in a new process and make sure that stdout gets
# redirected into the capture plugin
p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
# sys.stdout.write(stdout)
# sys.stderr.write(stderr)
with open(tempfilename, "rb") as f:
tb, res, runtime, profiling_info = pickle.load(f)
return tb, res, runtime, profiling_info
def check_or_compare(feature, res, baseline, maxrelerr):
feature = feature()
try:
feature.check(maxrelerr, res)
except NotImplementedError:
feature.compare(maxrelerr, baseline, res)
def run_single_feature_test(configuration, feature):
return results(configuration, feature)
def run_feature_tests(
configurations=None,
feature_tests=None,
strict=1e-5,
tolerant=0.05,
verbose=True,
maximum_run_time=1e7 * brian2.second,
):
if configurations is None:
# some configurations to attempt to import
try:
import brian2genn.correctness_testing
except:
pass
configurations = Configuration.__subclasses__()
if feature_tests is None:
feature_tests = FeatureTest.__subclasses__()
if DefaultConfiguration in configurations:
configurations.remove(DefaultConfiguration)
configurations = [DefaultConfiguration] + configurations
feature_tests.sort(key=lambda ft: ft.fullname())
if verbose:
print("Running feature tests")
print("Configurations:", ", ".join(c.name for c in configurations))
full_results = {}
tag_results = defaultdict(lambda: defaultdict(list))
for ft in feature_tests:
baseline = None
if verbose:
print(f"{ft.fullname()}: [", end=" ")
for configuration in configurations:
txt = "OK"
sym = "."
exc = None
tb, res, runtime, prof_info = results(
configuration, ft, maximum_run_time=maximum_run_time
)
if isinstance(res, Exception):
if isinstance(res, NotImplementedError):
sym = "N"
txt = "Not implemented"
else:
sym = "E"
txt = "Error"
if configuration is DefaultConfiguration:
raise res
else:
if configuration is DefaultConfiguration:
baseline = res
try:
check_or_compare(ft, res, baseline, strict)
except InaccuracyError as exc:
try:
check_or_compare(ft, res, baseline, tolerant)
sym = "I"
txt = f"Poor (error={100.0 * exc.error:.2f}%)"
except InaccuracyError as exc:
sym = "F"
txt = f"Fail (error={100.0 * exc.error:.2f}%)"
sys.stdout.write(sym)
full_results[configuration.name, ft.fullname()] = (
sym,
txt,
exc,
tb,
runtime,
prof_info,
)
for tag in ft.tags:
tag_results[tag][configuration.name].append(
(sym, txt, exc, tb, runtime, prof_info)
)
if verbose:
print("]")
return FeatureTestResults(full_results, tag_results, configurations, feature_tests)
class FeatureTestResults:
def __init__(self, full_results, tag_results, configurations, feature_tests):
self.full_results = full_results
self.tag_results = tag_results
self.configurations = configurations
self.feature_tests = feature_tests
@property
def test_table(self):
table = []
table.append(["Test"] + [c.name for c in self.configurations])
curcat = ""
for ft in self.feature_tests:
cat = ft.category
if cat != curcat:
table.append([cat] + [""] * len(self.configurations))
curcat = cat
row = [ft.name]
for configuration in self.configurations:
sym, txt, exc, tb, runtime, prof_info = self.full_results[
configuration.name, ft.fullname()
]
row.append(txt)
table.append(row)
return make_table(table)
@property
def tag_table(self):
table = []
table.append(["Tag"] + [c.name for c in self.configurations])
tags = sorted(self.tag_results.keys())
for tag in tags:
row = [tag]
for configuration in self.configurations:
tag_res = self.tag_results[tag][configuration.name]
syms = [sym for sym, txt, exc, tb, runtime, prof_info in tag_res]
n = len(syms)
okcount = sum(sym == "." for sym in syms)
poorcount = sum(sym == "I" for sym in syms)
failcount = sum(sym == "F" for sym in syms)
errcount = sum(sym == "E" for sym in syms)
nicount = sum(sym == "N" for sym in syms)
if okcount == n:
txt = "OK"
elif nicount == n:
txt = "Not implemented"
elif errcount == n:
txt = "Unsupported"
elif okcount + poorcount == n:
txt = f"Poor ({int(int(poorcount * 100.0 / n))}%)"
elif okcount + poorcount + failcount == n:
txt = (
f"Fail: {int(failcount * 100.0 / n)}%"
f" (poor={int(poorcount * 100.0 / n)}%)"
)
else:
txt = (
"Fail: OK={ok}%, Poor={poor}%, Fail={fail}%, NotImpl={ni}%"
" Error={err}%".format(
ok=int(okcount * 100.0 / n),
poor=int(poorcount * 100.0 / n),
fail=int(failcount * 100.0 / n),
err=int(errcount * 100.0 / n),
ni=int(nicount * 100.0 / n),
)
)
row.append(txt)
table.append(row)
return make_table(table)
@property
def tables(self):
r = ""
s = "Feature test results"
r += f"{s}\n{'-' * len(s)}\n\n{self.test_table}\n"
s = "Tag results"
r += f"{s}\n{'-' * len(s)}\n\n{self.tag_table}\n"
return r
@property
def exceptions(self):
exc_list = []
for configuration in self.configurations:
curconfig = []
for ft in self.feature_tests:
sym, txt, exc, tb, runtime, prof_info = self.full_results[
configuration.name, ft.fullname()
]
if tb is not None:
curconfig.append((ft.fullname(), tb))
if len(curconfig):
exc_list.append((configuration.name, curconfig))
if len(exc_list) == 0:
return ""
r = ""
s = "Exceptions"
r += f"{s}\n{'-' * len(s)}\n\n"
for config_name, curconfig in exc_list:
s = config_name
r += f"{s}\n{'^' * len(s)}\n\n"
for name, tb in curconfig:
r += f"{name}::\n\n{indent(tb)}\n\n"
return r
@property
def tables_and_exceptions(self):
return f"{self.tables}\n{self.exceptions}"
def __str__(self):
return self.tables
__repr__ = __str__
def run_speed_tests(
configurations=None,
speed_tests=None,
run_twice=True,
verbose=True,
n_slice=slice(None),
maximum_run_time=1e7 * brian2.second,
):
if configurations is None:
# some configurations to attempt to import
try:
import brian2genn.correctness_testing
except:
pass
configurations = Configuration.__subclasses__()
if speed_tests is None:
speed_tests = SpeedTest.__subclasses__()
speed_tests.sort(key=lambda ft: ft.fullname())
if verbose:
print("Running speed tests")
print("Configurations:", ", ".join(c.name for c in configurations))
full_results = {}
tag_results = defaultdict(lambda: defaultdict(list))
for ft in speed_tests:
if verbose:
print(f"{ft.fullname()}: ", end=" ")
for n in ft.n_range[n_slice]:
if verbose:
print(f"n={int(n)} [", end=" ")
for configuration in configurations:
sym = "."
for _ in range(1 + int(run_twice)):
tb, res, runtime, prof_info = results(
configuration, ft, n, maximum_run_time=maximum_run_time
)
if isinstance(res, Exception):
if isinstance(res, NotImplementedError):
sym = "N"
else:
sym = "E"
if configuration is DefaultConfiguration:
raise res
runtime = numpy.NAN
sys.stdout.write(sym)
full_results[configuration.name, ft.fullname(), n, "All"] = runtime
suffixtime = defaultdict(float)
overheadstime = float(runtime)
for codeobjname, proftime in prof_info:
# parts = codeobjname.split('_')
# parts = [part for part in parts if not re.match(r'\d+', part)]
# suffix = '_'.join(parts)
suffix = codeobjname
suffixtime[suffix] += proftime
overheadstime -= float(proftime)
for suffix, proftime in list(suffixtime.items()):
full_results[configuration.name, ft.fullname(), n, suffix] = (
proftime
)
full_results[configuration.name, ft.fullname(), n, "Overheads"] = (
overheadstime
)
if verbose:
print("]", end=" ")
if verbose:
print()
return SpeedTestResults(full_results, configurations, speed_tests)
class SpeedTestResults:
def __init__(self, full_results, configurations, speed_tests):
self.full_results = full_results
self.configurations = configurations
self.speed_tests = speed_tests
def get_ns(self, fullname):
L = [(cn, fn, n, s) for cn, fn, n, s in self.full_results if fn == fullname]
confignames, fullnames, n, codeobjsuffixes = zip(*L)
return numpy.array(sorted(list(set(n))))
def get_codeobjsuffixes(self, fullname):
L = [(cn, fn, n, s) for cn, fn, n, s in self.full_results if fn == fullname]
confignames, fullnames, n, codeobjsuffixes = zip(*L)
return set(codeobjsuffixes)
def plot_all_tests(self, relative=False, profiling_minimum=1.0):
if relative and profiling_minimum < 1:
raise ValueError("Cannot use relative plots with profiling")
import pylab
for st in self.speed_tests:
fullname = st.fullname()
pylab.figure()
ns = self.get_ns(fullname)
codeobjsuffixes = self.get_codeobjsuffixes(fullname)
codeobjsuffixes.remove("All")
codeobjsuffixes.remove("Overheads")
codeobjsuffixes = ["All", "Overheads"] + sorted(codeobjsuffixes)
if relative or profiling_minimum == 1:
codeobjsuffixes = ["All"]
baseline = None
havelabel = set()
markerstyles_cycle = iter(
itertools.cycle(["o", "s", "d", "v", "p", "h", "^", "<", ">"])
)
dashes = {}
markerstyles = {}
for isuffix, suffix in enumerate(codeobjsuffixes):
cols = itertools.cycle(pylab.rcParams["axes.color_cycle"])
for (iconfig, config), col in zip(enumerate(self.configurations), cols):
configname = config.name
runtimes = []
skip = True
for n in ns:
runtime = self.full_results.get(
(configname, fullname, n, "All"), numpy.nan
)
thistime = self.full_results.get(
(configname, fullname, n, suffix), numpy.nan
)
if float(thistime / runtime) >= profiling_minimum:
skip = False
runtimes.append(thistime)
if skip:
continue
runtimes = numpy.array(runtimes)
if relative:
if baseline is None:
baseline = runtimes
runtimes = baseline / runtimes
if suffix == "All":
lw = 2
label = configname
else:
lw = 1
label = suffix
plottable = sum(-numpy.isnan(runtimes[1:] + runtimes[:-1]))
if plottable:
if label in havelabel:
label = None
else:
havelabel.add(label)
dash = None
msty = None
if suffix != "All":
if suffix in dashes:
dash = dashes[suffix]
msty = markerstyles[suffix]
else:
j = len(dashes)
dash = (8, 2)
for b in bin(j)[2:]:
if b == "0":
dash = dash + (2, 2)
else:
dash = dash + (4, 2)
dashes[suffix] = dash
markerstyles[suffix] = msty = next(markerstyles_cycle)
line = pylab.plot(
ns,
runtimes,
lw=lw,
color=col,
marker=msty,
mec="none",
ms=8,
label=label,
)[0]
if dash is not None:
line.set_dashes(dash)
pylab.title(fullname)
pylab.legend(loc="best", fontsize="x-small", handlelength=8.0)
pylab.xlabel(st.n_label)
if st.n_axis_log:
pylab.gca().set_xscale("log")
if st.time_axis_log:
pylab.gca().set_yscale("log")
# Code below auto generates restructured text tables, copied from:
# http://stackoverflow.com/questions/11347505/what-are-some-approaches-to-outputting-a-python-data-structure-to-restructuredte
def make_table(grid):
max_cols = [
max(out)
for out in map(list, zip(*[[len(item) for item in row] for row in grid]))
]
rst = table_div(max_cols, 1)
for i, row in enumerate(grid):
header_flag = False
if i == 0 or i == len(grid) - 1:
header_flag = True
rst += normalize_row(row, max_cols)
rst += table_div(max_cols, header_flag)
return rst
def table_div(max_cols, header_flag=1):
out = ""
if header_flag == 1:
style = "="
else:
style = "-"
for max_col in max_cols:
out += f"{max_col * style} "
out += "\n"
return out
def normalize_row(row, max_cols):
r = ""
for i, max_col in enumerate(max_cols):
r += row[i] + (max_col - len(row[i]) + 1) * " "
return f"{r}\n"
|