def test_get_traced_memory(self):
# Python allocates some internals objects, so the test must tolerate
# a small difference between the expected size and the real usage
max_error = 2048
# allocate one object
obj_size = 1024 * 1024
tracemalloc.clear_traces()
obj, obj_traceback = allocate_bytes(obj_size)
size, peak_size = tracemalloc.get_traced_memory()
self.assertGreaterEqual(size, obj_size)
self.assertGreaterEqual(peak_size, size)
self.assertLessEqual(size - obj_size, max_error)
self.assertLessEqual(peak_size - size, max_error)
# destroy the object
obj = None
size2, peak_size2 = tracemalloc.get_traced_memory()
self.assertLess(size2, size)
self.assertGreaterEqual(size - size2, obj_size - max_error)
self.assertGreaterEqual(peak_size2, peak_size)
# clear_traces() must reset traced memory counters
tracemalloc.clear_traces()
self.assertEqual(tracemalloc.get_traced_memory(), (0, 0))
# allocate another object
obj, obj_traceback = allocate_bytes(obj_size)
size, peak_size = tracemalloc.get_traced_memory()
self.assertGreaterEqual(size, obj_size)
# stop() also resets traced memory counters
tracemalloc.stop()
self.assertEqual(tracemalloc.get_traced_memory(), (0, 0))
def test_task_memory_threshold(self):
diff = None
def log_func():
nonlocal diff
size, max_size = tracemalloc.get_traced_memory()
diff = (size - old_size)
obj_size = 1024 * 1024
threshold = int(obj_size * 0.75)
old_size, max_size = tracemalloc.get_traced_memory()
task = tracemalloctext.Task(log_func)
task.set_memory_threshold(threshold)
task.schedule()
# allocate
obj = allocate_bytes(obj_size)
time.sleep(MEMORY_CHECK_DELAY)
self.assertIsNotNone(diff)
self.assertGreaterEqual(diff, threshold)
# release
diff = None
old_size, max_size = tracemalloc.get_traced_memory()
obj = None
time.sleep(MEMORY_CHECK_DELAY)
size, max_size = tracemalloc.get_traced_memory()
self.assertIsNotNone(diff)
self.assertLessEqual(diff, threshold)
def check_track(self, release_gil):
nframe = 5
tracemalloc.start(nframe)
size = tracemalloc.get_traced_memory()[0]
frames = self.track(release_gil, nframe)
self.assertEqual(self.get_traceback(),
tracemalloc.Traceback(frames))
self.assertEqual(self.get_traced_memory(), self.size)
def on_epoch_end(self, last_metrics, **kwargs):
cpu_used, cpu_peak = list(map(lambda x: int(x/2**20), tracemalloc.get_traced_memory()))
self.peak_monitor_stop()
gpu_used = gpu_mem_get_used_no_cache() - self.gpu_before
gpu_peak = self.gpu_mem_used_peak - self.gpu_before
# can be negative, due to unreliable peak monitor thread
if gpu_peak < 0: gpu_peak = 0
# since we want the overhead only, subtract delta used if it's positive
elif gpu_used > 0: gpu_peak -= gpu_used
# The numbers are deltas in MBs (beginning of the epoch and the end)
return add_metrics(last_metrics, [cpu_used, cpu_peak, gpu_used, gpu_peak])
def tracemalloc_dump() -> None:
if not tracemalloc.is_tracing():
logger.warning("pid {}: tracemalloc off, nothing to dump"
.format(os.getpid()))
return
# Despite our name for it, `timezone_now` always deals in UTC.
basename = "snap.{}.{}".format(os.getpid(),
timezone_now().strftime("%F-%T"))
path = os.path.join(settings.TRACEMALLOC_DUMP_DIR, basename)
os.makedirs(settings.TRACEMALLOC_DUMP_DIR, exist_ok=True)
gc.collect()
tracemalloc.take_snapshot().dump(path)
procstat = open('/proc/{}/stat'.format(os.getpid()), 'rb').read().split()
rss_pages = int(procstat[23])
logger.info("tracemalloc dump: tracing {} MiB ({} MiB peak), using {} MiB; rss {} MiB; dumped {}"
.format(tracemalloc.get_traced_memory()[0] // 1048576,
tracemalloc.get_traced_memory()[1] // 1048576,
tracemalloc.get_tracemalloc_memory() // 1048576,
rss_pages // 256,
basename))
def add_tracemalloc_metrics(snapshot):
size, max_size = tracemalloc.get_traced_memory()
snapshot.add_metric('tracemalloc.traced.size', size, 'size')
snapshot.add_metric('tracemalloc.traced.max_size', max_size, 'size')
if snapshot.traces:
snapshot.add_metric('tracemalloc.traces', len(snapshot.traces), 'int')
size, free = tracemalloc.get_tracemalloc_memory()
snapshot.add_metric('tracemalloc.module.size', size, 'size')
snapshot.add_metric('tracemalloc.module.free', free, 'size')
if size:
frag = free / size
snapshot.add_metric('tracemalloc.module.fragmentation', frag, 'percent')
def schedule(self):
task = self._task_ref()
memory_threshold = task.get_memory_threshold()
delay = task.get_delay()
if memory_threshold is not None:
traced = tracemalloc.get_traced_memory()[0]
self.min_memory = traced - memory_threshold
self.max_memory = traced + memory_threshold
else:
self.min_memory = None
self.max_memory = None
if delay is not None:
self.timeout = _time_monotonic() + delay
else:
self.timeout = None
def once(self):
delay = None
if self.min_memory is not None:
traced = tracemalloc.get_traced_memory()[0]
if traced <= self.min_memory:
return None
if traced >= self.max_memory:
return None
delay = self.memory_delay
if self.timeout is not None:
dt = (self.timeout - _time_monotonic())
if dt <= 0:
return None
if delay is not None:
delay = min(delay, dt)
else:
delay = dt
return delay
def compute(self):
args = self.args
if args.track_memory:
if MS_WINDOWS:
from perf._win_memory import get_peak_pagefile_usage
else:
from perf._memory import PeakMemoryUsageThread
mem_thread = PeakMemoryUsageThread()
mem_thread.start()
if args.tracemalloc:
import tracemalloc
tracemalloc.start()
WorkerTask.compute(self)
if args.tracemalloc:
traced_peak = tracemalloc.get_traced_memory()[1]
tracemalloc.stop()
if not traced_peak:
raise RuntimeError("tracemalloc didn't trace any Python "
"memory allocation")
# drop timings, replace them with the memory peak
self._set_memory_value(traced_peak)
if args.track_memory:
if MS_WINDOWS:
mem_peak = get_peak_pagefile_usage()
else:
mem_thread.stop()
mem_peak = mem_thread.peak_usage
if not mem_peak:
raise RuntimeError("failed to get the memory peak usage")
# drop timings, replace them with the memory peak
self._set_memory_value(mem_peak)
def pyfaidx_fasta(n):
print('timings for pyfaidx.Fasta')
ti = []
tf = []
for _ in range(n):
t = time.time()
f = pyfaidx.Fasta(fa_file.name)
ti.append(time.time() - t)
t = time.time()
read_dict(f, headers)
tf.append(time.time() - t)
os.remove(index)
# profile memory usage and report timings
tracemalloc.start()
f = pyfaidx.Fasta(fa_file.name)
read_dict(f, headers)
os.remove(index)
print(tracemalloc.get_traced_memory())
print(mean(ti))
print(mean(tf)/nreads/10*1000*1000)
tracemalloc.stop()
def pyfaidx_bgzf_faidx(n):
print('timings for pyfaidx.Faidx with bgzf compression')
ti = []
tf = []
for _ in range(n):
t = time.time()
f = pyfaidx.Faidx(fa_file.name + '.gz')
ti.append(time.time() - t)
t = time.time()
read_faidx(f, headers)
tf.append(time.time() - t)
os.remove(index)
# profile memory usage and report timings
tracemalloc.start()
f = pyfaidx.Faidx(fa_file.name + '.gz')
read_faidx(f, headers)
os.remove(index)
print(tracemalloc.get_traced_memory())
print(mean(ti))
print(mean(tf)/nreads/10*1000*1000)
tracemalloc.stop()
def fastahack_fetch(n):
print('timings for fastahack.FastaHack')
ti = []
tf = []
for _ in range(n):
t = time.time()
f = fastahack.FastaHack(fa_file.name)
ti.append(time.time() - t)
t = time.time()
read_fastahack(f, headers)
tf.append(time.time() - t)
os.remove(index)
# profile memory usage and report timings
tracemalloc.start()
f = fastahack.FastaHack(fa_file.name)
read_fastahack(f, headers)
os.remove(index)
print(tracemalloc.get_traced_memory())
print(mean(ti))
print(mean(tf)/nreads/10*1000*1000)
tracemalloc.stop()
def loop(*, size, times):
for i in range(times):
print(len(L))
g(size)
print([t._format_size(x, False) for x in t.get_traced_memory()])
snapshot = t.take_snapshot().filter_traces(
(
t.Filter(False, "<frozen importlib._bootstrap>"),
t.Filter(False, "*tracemalloc*"),
t.Filter(False, "*linecache*"),
t.Filter(False, "*sre_*"),
t.Filter(False, "*re.py"),
t.Filter(False, "*fnmatch*"),
t.Filter(False, "*tokenize*"),
t.Filter(False, "<unknown>"),
)
)
for stat in snapshot.statistics("lineno", cumulative=False)[:3]:
print("----------------------------------------")
print(t._format_size(stat.size, False))
for line in stat.traceback.format():
print(line)
print("========================================")
def seqio_read(n):
print('timings for Bio.SeqIO')
ti = []
tf = []
for _ in range(n):
t = time.time()
fh = open(fa_file.name)
f = SeqIO.to_dict(SeqIO.parse(fh, "fasta"))
ti.append(time.time() - t)
t = time.time()
read_dict(f, headers)
tf.append(time.time() - t)
fh.close()
# profile memory usage and report timings
tracemalloc.start()
fh = open(fa_file.name)
f = SeqIO.to_dict(SeqIO.parse(fh, "fasta"))
read_dict(f, headers)
fh.close()
print(tracemalloc.get_traced_memory())
print(mean(ti))
print(mean(tf)/nreads/100*1000*1000)
tracemalloc.stop()
def pyfasta_fseek(n):
print('timings for pyfasta.Fasta (fseek)')
ti = []
tf = []
for _ in range(n):
t = time.time()
f = pyfasta.Fasta(fa_file.name, record_class=pyfasta.FastaRecord)
ti.append(time.time() - t)
t = time.time()
read_dict(f, headers)
tf.append(time.time() - t)
os.remove(fa_file.name + '.flat')
os.remove(fa_file.name + '.gdx')
# profile memory usage and report timings
tracemalloc.start()
f = pyfasta.Fasta(fa_file.name, record_class=pyfasta.FastaRecord)
read_dict(f, headers)
os.remove(fa_file.name + '.flat')
os.remove(fa_file.name + '.gdx')
print(tracemalloc.get_traced_memory())
print(mean(ti))
print(mean(tf)/nreads/10*1000*1000)
tracemalloc.stop()
self.route = route
self.date = date
self.daytype = daytype
self.rides = rides
def read_rides(filename):
'''
Read the bus ride data as a list of tuples
'''
rows = []
f = open(filename)
f_csv = csv.reader(f)
headings = next(f_csv) # Skip headers
for row in f_csv:
route = row[0]
date = row[1]
daytype = row[2]
rides = int(row[3])
record = Ride(route, date, daytype, rides)
rows.append(record)
f.close()
return rows
if __name__ == '__main__':
import tracemalloc
tracemalloc.start()
rows = read_rides('Data/ctabus.csv')
print('Memory Use: Current %d, Peak %d' % tracemalloc.get_traced_memory())
if char not in mapFinal.keys():
stack.append(char)
else:
charPop = stack.pop()
if charPop == mapPair[char]:
continue
else:
mapFinal[char] += 1
corrupted = True
break
if not corrupted:
inv_map = {v: k for k, v in mapPair.items()}
totalPoints = 0
while len(stack) > 0:
totalPoints = 5 * totalPoints + mapPoints[inv_map[stack.pop()]]
listPoints.append(totalPoints)
else:
print(len(listPoints))
print(int((len(listPoints) / 2)) + 1)
print(sorted(listPoints))
print(sorted(listPoints)[int((len(listPoints) / 2))])
#####################################################################
print("--- %s miliseconds ---" % ((time.time() - start_time) * 1000))
print("--- %s MB used ---" % (tracemalloc.get_traced_memory()[1] / 1000000))
tracemalloc.stop()
def mem_count():
if MEM_DEBUG:
logging.info("Memory: current: %s, peak: %s" % tuple(
(tracemalloc._format_size(m, False)
for m in tracemalloc.get_traced_memory())))
def on_epoch_end(self, last_metrics, **kwargs):
cpu_used, cpu_peak = list(
map(lambda x: float(x / 2**20), tracemalloc.get_traced_memory()))
self.peak_monitor_stop()
# The numbers are deltas in MBs (beginning of the epoch and the end)
return add_metrics(last_metrics, [cpu_used, cpu_peak])
elif t > M:
M = t
x1 = i
x2 = j
return M, x1, x2
#Generate an array (here size of 50000)
a = np.random.randint(-10, 10, 50000)
a = np.array(a)
#Sart tracking memory
tracemalloc.start()
#Start tracking time
begin = time.time()
max_sum_subarray_kadane = kadane_algorithm(a, len(a))
#Stop tracking time
end = time.time()
#Stopo tracking memory
snapshot = tracemalloc.take_snapshot()
for stat in snapshot.statistics("lineno"):
print("stat kadane")
print(stat)
print(stat.traceback.format())
#Print peak memory
print("\nTraced Memory (Current, Peak): ", tracemalloc.get_traced_memory())
#Print time spent
print("Time:")
print(end - begin)
def blockMerge(ALLBLOCKFILE, BLOCKSTOMERGE, BLOCKPATH, spimi_index):
print(
"=============== Merging SPIMI blocks into final inverted index... ==============="
)
tracemalloc.start()
Filewrite = open('Merge/invert_index.txt', "w+")
iterlist = []
term = ""
current_term = ""
startmerge = time.process_time()
for BLOCKFILE in ALLBLOCKFILE:
print("File Name:", BLOCKFILE)
print("-- Reading into memory... ", BLOCKFILE.split(".txt", 1)[0])
finaldict = {}
l = open(BLOCKPATH + BLOCKFILE)
Fileread = open('Merge/invert_index.txt')
Initialfile = Fileread.read()
if (Initialfile.strip()):
lst = Initialfile.strip().split('\n')
for i in range(len(lst)):
val = lst[i].split(" -----------> ")
finaldict[val[0]] = val[1]
else:
finaldict = {}
iterlist = (l.read().strip().split('\n'))
for l2 in range(len(iterlist)):
ksplit = iterlist[l2].split(
" -----------> "
) # ['aaaaaq', '[[2136, 1]]'] OR ['aam', '[[1782, 1], [1786, 1]]']
if (finaldict.get(ksplit[0]) != None):
postlingvalold = json.loads(finaldict.get(
ksplit[0])) # [[1,4],[2,5]]
newblock = json.loads(ksplit[1])
for i in range(len(newblock)):
if newblock[i] not in postlingvalold:
#print("THIS IS THE NEWBLOCK MATCHING THE CONDITION : ", newblock[i])
postlingvalold.append(newblock[i])
finaldict[ksplit[0]] = str(postlingvalold)
else:
current_term = ksplit[0]
term = term + current_term.capitalize()
finaldict[ksplit[0]] = ksplit[1]
sorted(finaldict)
Filewrite = open('Merge/invert_index.txt', "w+")
Filewrite1 = open('Merge/invert_actual_index.txt', "w+")
indexwriter1 = open('Merge/index_cp_1.txt', "w+")
indexwriter1.write(term)
for key, value in sorted(finaldict.items()):
Filewrite.write(key + " -----------> " + value + "\n")
Filewrite1.write(key + " -----------> " + value + "\n")
print("Finished merging block: ",
BLOCKFILE.split(".txt", 1)[0], " and writing to disk")
endmerge = time.process_time()
eachmerge = endmerge - startmerge
print("\n Time taken after each Block merge : ", eachmerge, "\n")
Fileread.close()
Filewrite.close()
Filewrite1.close()
indexwriter1.close()
current, peak = tracemalloc.get_traced_memory()
print(f" After merge : Current memory usage is {current / 10**6}MB")
tracemalloc.stop()
f = open(filename)
f_csv = csv.reader(f)
headings = next(f_csv) # Skip headers
for row in f_csv:
route = row[0]
date = row[1]
daytype = row[2]
rides = int(row[3])
record = (route, date, daytype, rides)
rows.append(record)
f.close()
return rows
def read_rides_into_dict() #slower
def read_rides_into_namedtuple() #medium
def read_rides_into_class() #slowest
def read_rides_into_class_w_slots() #faster
def read_rides_via_pandas() #fastest
if __name__ == '__main__':
import tracemalloc
tracemalloc.start()
rows = read_rides_into_tuple('Data/ctabus.csv')
print('Memory Use: Current %d, Peak %d' % tracemalloc.get_traced_memory())
rows = read_rides_into_dict('Data/ctabus.csv')
print('Memory Use: Current %d, Peak %d' % tracemalloc.get_traced_memory())
def post_run_cell(self, result):
logger.debug(f"post_run_cell: 1 {self.exp}")
if not self.running: return
self.time_delta = time.time() - self.time_start
if self.backend != 'cpu':
self.peak_monitoring = False
if self.gc_collect: gc.collect()
# instead of needing a peak memory monitoring thread, tracemalloc does
# the job of getting newly used and peaked memory automatically, since
# it tracks all malloc/free calls.
cpu_mem_used_delta, cpu_mem_used_peak = tracemalloc.get_traced_memory()
tracemalloc.stop() # reset accounting
with self.lock:
if self.exp is None: return
self.cpu_mem_used_new = self.exp.cpu_ram_used()
self.cpu_mem_used_delta = cpu_mem_used_delta
self.cpu_mem_peaked_delta = max(0, cpu_mem_used_peak - cpu_mem_used_delta)
if self.backend != 'cpu':
with self.lock:
if self.exp is None: return
self.gpu_mem_used_new = self.exp.gpu_ram_used()
# delta_used is the difference between current used mem and used mem at the start
self.gpu_mem_used_delta = self.gpu_mem_used_new - self.gpu_mem_used_prev
# peaked_delta is the overhead if any. It is calculated as follows:
#
# 1. The difference between the peak memory and the used memory at the
# start is measured:
# 2a. If it's negative, then peaked_delta is 0
# 2b. Otherwise, if used_delta is positive it gets subtracted from peaked_delta
# XXX: 2a shouldn't be needed once we have a reliable peak counter
self.gpu_mem_peaked_delta = self.gpu_mem_used_peak - self.gpu_mem_used_prev
if self.gpu_mem_peaked_delta <= 0:
self.gpu_mem_peaked_delta = 0
elif self.gpu_mem_used_delta > 0:
self.gpu_mem_peaked_delta -= self.gpu_mem_used_delta
if self.compact:
if 1:
out = f"CPU: {b2mb(self.cpu_mem_used_delta):0.0f}/{b2mb(self.cpu_mem_peaked_delta):0.0f}/{b2mb(self.cpu_mem_used_new):0.0f} MB"
if self.backend != 'cpu':
out += f" | GPU: {b2mb(self.gpu_mem_used_delta):0.0f}/{b2mb(self.gpu_mem_peaked_delta):0.0f}/{b2mb(self.gpu_mem_used_new):0.0f} MB"
out += f" | Time {secs2time(self.time_delta)} | (Consumed/Peaked/Used Total)"
print(out)
else:
if 1:
vals = [self.cpu_mem_used_delta, self.cpu_mem_peaked_delta, self.cpu_mem_used_new]
if self.backend != 'cpu':
vals += [self.gpu_mem_used_delta, self.gpu_mem_peaked_delta, self.gpu_mem_used_new]
w = int2width(*map(b2mb, vals)) + 1 # some air
if w < 10: w = 10 # accommodate header width
pre = '･ '
print(f"{pre}RAM: {'△Consumed':>{w}} {'△Peaked':>{w}} {'Used Total':>{w}} | Exec time {secs2time(self.time_delta)}")
if 1:
print(f"{pre}CPU: {b2mb(self.cpu_mem_used_delta):{w},.0f} {b2mb(self.cpu_mem_peaked_delta):{w},.0f} {b2mb(self.cpu_mem_used_new):{w},.0f} MB |")
if self.backend != 'cpu':
print(f"{pre}GPU: {b2mb(self.gpu_mem_used_delta):{w},.0f} {b2mb(self.gpu_mem_peaked_delta):{w},.0f} {b2mb(self.gpu_mem_used_new):{w},.0f} MB |")
# for self.data accessor
self.cpu_mem_used_prev = self.cpu_mem_used_new
if self.backend != 'cpu':
self.gpu_mem_used_prev = self.gpu_mem_used_new
self.data = CellLoggerData(
CellLoggerMemory(self.cpu_mem_used_delta, self.cpu_mem_peaked_delta, self.cpu_mem_used_prev),
CellLoggerMemory(self.gpu_mem_used_delta, self.gpu_mem_peaked_delta, self.gpu_mem_used_prev),
CellLoggerTime(self.time_delta)
)
__slots__ = ['item%s' % i for i in range(ITEM_NUM)]
def __init__(self):
for i in range(len(self.__slots__)):
setattr(self, 'item%s' % i, i)
class NoSlots:
def __init__(self):
for i in range(ITEM_NUM):
setattr(self, 'item%s' % i, i)
# 开始跟踪
tracemalloc.start()
obj = [NoSlots() for i in range(100)]
# 获取由 tracemalloc 模块跟踪的内存块的当前大小和峰值大小作为元组：(current: int, peak: int)
print(tracemalloc.get_traced_memory())
# 停止跟踪
tracemalloc.stop()
# 又开始跟踪，相当于重置
tracemalloc.start()
obj2 = [HaveSlots() for i in range(100)]
print(tracemalloc.get_traced_memory())
# (21832, 22219) # 未定义__slots__字段，创建100个对象占用的内存约为 21832 字节
# (13760, 14147) # 定义__slots__字段，创建100个对象占用的内存约为 13760 字节
def loop(*, size, times):
for i in range(times):
logger.info(
"memory (current, peak) %s",
str([t._format_size(x, False) for x in t.get_traced_memory()]))
g(size)
def test_function_memory_usage():
tracemalloc.start()
instance_list = AwsInstances()
current, peak_memory = tracemalloc.get_traced_memory()
tracemalloc.stop()
assert peak_memory / 10**6 <= 40
from main import main
import timeit
import tracemalloc
t = timeit.Timer("main(\"HDWallpaperFree\", 2)", "from main import main")
print(t.timeit(1))
tracemalloc.start()
main(screen_name="HDWallpaperFree", limit=2)
print("Current: %d, Peak %d" % tracemalloc.get_traced_memory())
def search_algo(n, maze, start, end):
tracemalloc.start()
start_time = time.time()
current, peak = tracemalloc.get_traced_memory()
print(f"Current memory usage before search {current / 10**6}MB")
search_cost = 0
pos = start
delay = 0.0
grid, rect, screen, wid = make_screen(n)
queue = [0] # BFS Queue (Pop Push function can be implemented in O(1) using 2 pointer)
row = 0
col = 0
maze[row][col] = -1
step_cost = 5
moves = []
parent = [-1]*(n*n) # stores parent of every node
while pos != end:
pos = queue.pop(0)
row = pos//n
col = pos%n
expanded = True
# try expanding current node and adding to the queue
if (col + 1 < n) and (maze[row][col + 1] not in [-1,1]) :
queue.append(row*n + col + 1)
maze[row][col+1] = -1
parent[queue[-1]] = pos
expanded = True
if queue[-1] == end:
pos = end
if (row + 1 < n) and (maze[row + 1][col] not in [-1,1]) :
queue.append((row + 1)*n + col)
maze[row+1][col] = -1
parent[queue[-1]] = pos
expanded = True
if queue[-1] == end:
pos = end
if (col - 1 >= 0) and (maze[row][col - 1] not in [-1,1]) :
queue.append(row*n + col - 1)
maze[row][col-1] = -1
parent[queue[-1]] = pos
expanded = True
if queue[-1] == end:
pos = end
if (row - 1 >= 0) and (maze[row - 1][col] not in [-1,1]) :
queue.append((row - 1)*n + col)
maze[row-1][col] = -1
parent[queue[-1]] = pos
expanded = True
if queue[-1] == end:
pos = end
redraw_maze(grid, rect, screen, n, maze, pos, delay, wid, end)
if expanded:
search_cost+=step_cost
curr_node = end
# printing the path from start to end
while parent[curr_node] != -1 :
maze[curr_node//n][curr_node%n] = 2
if parent[curr_node] == curr_node - 1 :
moves.append("Right")
elif parent[curr_node] == curr_node + 1 :
moves.append("Left")
elif parent[curr_node] == curr_node + n :
moves.append("Up")
elif parent[curr_node] == curr_node - n :
moves.append("Down")
curr_node = parent[curr_node]
#redraw_maze(grid, rect, screen, n, maze, pos, delay, wid, end)
moves = moves[::-1]
maze[0][0] = 2
redraw_maze(grid, rect, screen, n, maze, pos, delay, wid, end)
end_time = time.time()
current, peak = tracemalloc.get_traced_memory()
print("Total Search Time : {} seconds".format(end_time-start_time))
print(f"Peak Memory usage was was {peak / 10**6}MB")
print(f"Total Expanding Search Cost is {search_cost} Units")
print(f"Best Path Total Cost is {len(moves)*step_cost} Units")
tracemalloc.stop()
print(moves)
popup_win(str(len(moves)*step_cost), "Score", "./final.png" , screen)
import tracemalloc as t
print("*start")
print([t._format_size(x, False) for x in t.get_traced_memory()])
t.start()
L = [[_ for _ in range(10000)] for i in range(100)]
print("*gen")
print([t._format_size(x, False) for x in t.get_traced_memory()])
snapshot = t.take_snapshot()
for stats in snapshot.statistics("traceback")[:3]:
print(stats)
print("----------------------------------------")
snapshot = t.take_snapshot()
for stats in snapshot.statistics("lineno", cumulative=True)[:3]:
print(stats)
t.stop()
print([t._format_size(x, False) for x in t.get_traced_memory()])
def run_memleak_test(bench, iterations, report):
tracemalloc.start()
starti = min(50, iterations // 2)
endi = iterations
malloc_arr = np.empty((endi,), dtype=np.int64)
rss_arr = np.empty((endi,), dtype=np.int64)
rss_peaks = np.empty((endi,), dtype=np.int64)
nobjs_arr = np.empty((endi,), dtype=np.int64)
garbage_arr = np.empty((endi,), dtype=np.int64)
open_files_arr = np.empty((endi,), dtype=np.int64)
rss_peak = 0
p = psutil.Process()
for i in range(endi):
bench()
gc.collect()
rss = p.memory_info().rss
malloc, peak = tracemalloc.get_traced_memory()
nobjs = len(gc.get_objects())
garbage = len(gc.garbage)
open_files = len(p.open_files())
print("{0: 4d}: pymalloc {1: 10d}, rss {2: 10d}, nobjs {3: 10d}, garbage {4: 4d}, files: {5: 4d}".format(
i, malloc, rss, nobjs, garbage, open_files))
malloc_arr[i] = malloc
rss_arr[i] = rss
if rss > rss_peak:
rss_peak = rss
rss_peaks[i] = rss_peak
nobjs_arr[i] = nobjs
garbage_arr[i] = garbage
open_files_arr[i] = open_files
print('Average memory consumed per loop: %1.4f bytes\n' %
(np.sum(rss_peaks[starti+1:] - rss_peaks[starti:-1]) / float(endi - starti)))
from matplotlib import pyplot as plt
fig, (ax1, ax2, ax3) = plt.subplots(3)
ax1b = ax1.twinx()
ax1.plot(malloc_arr, 'r')
ax1b.plot(rss_arr, 'b')
ax1.set_ylabel('pymalloc', color='r')
ax1b.set_ylabel('rss', color='b')
ax2b = ax2.twinx()
ax2.plot(nobjs_arr, 'r')
ax2b.plot(garbage_arr, 'b')
ax2.set_ylabel('total objects', color='r')
ax2b.set_ylabel('garbage objects', color='b')
ax3.plot(open_files_arr)
ax3.set_ylabel('open file handles')
if not report.endswith('.pdf'):
report = report + '.pdf'
fig.tight_layout()
fig.savefig(report, format='pdf')
def tick():
while True:
logger.info(
"%s",
str([t._format_size(x, False) for x in t.get_traced_memory()]))
time.sleep(0.2)
def do_benchmark(name, num_freq_bins, num_samples, dtype):
print("###################################################")
print("Starting benchmark '%s' (%d freq bins, %d samples, dtype=%s)" %
(name, num_freq_bins, num_samples, dtype))
print("###################################################")
###################################
# DATASET SETUP
###################################
dataset = Dataset("./", name)
dataset.device.name = "Benchmark Data Generator"
dataset.device.version = "1.0"
freq_bins = np.logspace(3, 9, num_freq_bins)
if not "test" in dataset:
dataset.create_subset("test", freq_bins, False, dtype=dtype)
###################################
# WRITE
###################################
print("Start writing %d Samples with %d bins each" %
(num_samples, num_freq_bins))
tracemalloc.start()
start_time = time.perf_counter()
for i in range(num_samples):
dataset["test"].append_sample(
time=np.datetime64("now"),
spectrum=np.random.random(num_freq_bins) * 30 - 80)
stop_time = time.perf_counter()
(current, peak) = tracemalloc.get_traced_memory()
print("Peak memory consumption: %.3f MiB" % (peak / 1048576))
print("Done. Took %.3f seconds" % (stop_time - start_time))
print()
tracemalloc.stop()
###################################
# READ AND SUM
###################################
print("Start reading all samples (%d) and summing up the spectrum" %
dataset["test"].len())
tracemalloc.start()
start_time = time.perf_counter()
sum = dataset["test"].spectrum[:].sum(1)
stop_time = time.perf_counter()
(current, peak) = tracemalloc.get_traced_memory()
print("Peak memory consumption: %.3f MiB" % (peak / 1048576))
print("Done. Took %.3f seconds" % (stop_time - start_time))
print()
tracemalloc.stop()
###################################
# READ AND SUM (Chunked)
###################################
print(
"Start reading all (chunked) samples (%d) and summing up the spectrum"
% dataset["test"].len())
tracemalloc.start()
start_time = time.perf_counter()
chunk_size = 100
for i in range(int(dataset["test"].len() / chunk_size)):
sum = dataset["test"].spectrum[i * chunk_size:i * chunk_size +
chunk_size].sum(1)
stop_time = time.perf_counter()
(current, peak) = tracemalloc.get_traced_memory()
print("Peak memory consumption: %.3f MiB" % (peak / 1048576))
print("Done. Took %.3f seconds" % (stop_time - start_time))
print()
tracemalloc.stop()
dataset.close()
def train_and_predict(
config,
# Functions to not import all modules
preprocess_data_inverse,
fitted_power_transform,
# Other
iterated_model_train,
iterated_model_predict,
iterated_model_name,
iterated_model_index,
optimization_index,
optimization_value,
model_train_input,
model_predict_input,
model_test_inputs,
models_test_outputs,
models_test_outputs_unstandardized,
data_abs_max,
data_mean,
data_std,
last_undiff_value=None,
final_scaler=None,
pipe=None,
semaphor=None,
) -> None | dict[str, Any]:
"""Inner function, that can run in parallel with multiprocessing.
Note:
config is just a dictionary passed as param, so cannot use dot syntax here.
Args:
Some values from predictit configuration.
Returns:
None | dict[str, Any]: Return dict of results or send data via multiprocessing.
"""
logs_list = []
warnings_list = []
if config["multiprocessing"]:
mylogging._misc.filter_warnings()
mylogging.outer_warnings_filter(config["ignored_warnings"],
config["ignored_warnings_class_type"])
mylogging.config.BLACKLIST = config["ignored_warnings"]
mylogging.config.OUTPUT = config["logger_output"]
mylogging.config.LEVEL = config["logger_level"]
mylogging.config.FILTER = config["logger_filter"]
mylogging.config.COLORIZE = config["logger_color"]
logs_redirect = mylogging.redirect_logs_and_warnings_to_lists(
logs_list, warnings_list)
if config["is_tested"]:
import mypythontools
mypythontools.tests.setup_tests(matplotlib_test_backend=True)
if semaphor:
semaphor.acquire()
if config["trace_processes_memory"]:
import tracemalloc
tracemalloc.start()
model_results = {"Name": iterated_model_name}
result_name = (f"{iterated_model_name} - {optimization_value}"
if config["optimization"] else f"{iterated_model_name}")
if (config["optimizeit"] and optimization_index == 0
and iterated_model_name in config["models_parameters_limits"]):
start_optimization = time.time()
try:
model_results[
"Best optimized parameters"] = predictit.best_params.optimize(
iterated_model_train,
iterated_model_predict,
config["models_parameters"].get(iterated_model_name),
config["models_parameters_limits"][iterated_model_name],
model_train_input=model_train_input,
model_test_inputs=model_test_inputs,
models_test_outputs=models_test_outputs,
time_limit=config["optimizeit_limit"],
error_criterion=config["error_criterion"],
name=iterated_model_name,
iterations=config["iterations"],
fragments=config["fragments"],
details=config["optimizeit_details"],
plot=config["optimizeit_plot"],
)
except TimeoutError:
model_results["Best optimized parameters"] = {}
mylogging.traceback(
f"Hyperparameters optimization of {iterated_model_name} didn't finished"
)
for k, l in model_results["Best optimized parameters"].items():
if iterated_model_name not in config["models_parameters"]:
config["models_parameters"][iterated_model_name] = {}
config["models_parameters"][iterated_model_name][k] = l
stop_optimization = time.time()
model_results[
"Hyperparameter optimization time"] = stop_optimization - start_optimization
start = time.time()
try:
# If no parameters or parameters details, add it so no index errors later
if iterated_model_name not in config["models_parameters"]:
config["models_parameters"][iterated_model_name] = {}
# Train all models
trained_model = iterated_model_train(
model_train_input,
**config["models_parameters"][iterated_model_name])
# Create predictions - out of sample
one_reality_result = iterated_model_predict(model_predict_input,
trained_model,
config["predicts"])
if np.isnan(np.sum(one_reality_result)) or one_reality_result is None:
raise ValueError("NaN predicted from model.")
# Remove wrong values out of scope to not be plotted
one_reality_result[abs(one_reality_result) > 3 * data_abs_max] = np.nan
# Do inverse data preprocessing
if config["power_transformed"]:
one_reality_result = fitted_power_transform(
one_reality_result, data_std, data_mean)
one_reality_result = preprocess_data_inverse(
one_reality_result,
final_scaler=final_scaler,
last_undiff_value=last_undiff_value,
standardizeit=config["standardizeit"],
data_transform=config["data_transform"],
)
tests_results = np.zeros((config["repeatit"], config["predicts"]))
test_errors_unstandardized = np.zeros(
(config["repeatit"], config["predicts"]))
test_errors = np.zeros(config["repeatit"])
# Predict many values in test inputs to evaluate which models are best - do not inverse data preprocessing,
# because test data are processed
for repeat_iteration in range(config["repeatit"]):
# Create in-sample predictions to evaluate if model is good or not
tests_results[repeat_iteration] = iterated_model_predict(
model_test_inputs[repeat_iteration],
trained_model,
predicts=config["predicts"],
)
if config["power_transformed"]:
tests_results[repeat_iteration] = fitted_power_transform(
tests_results[repeat_iteration], data_std, data_mean)
test_errors[
repeat_iteration] = predictit.evaluate_predictions.compare_predicted_to_test(
tests_results[repeat_iteration],
models_test_outputs[repeat_iteration],
error_criterion=config["error_criterion"],
)
tests_results[repeat_iteration] = preprocess_data_inverse(
tests_results[repeat_iteration],
final_scaler=final_scaler,
last_undiff_value=last_undiff_value,
standardizeit=config["standardizeit"],
data_transform=config["data_transform"],
)
test_errors_unstandardized[
repeat_iteration] = predictit.evaluate_predictions.compare_predicted_to_test(
tests_results[repeat_iteration],
models_test_outputs_unstandardized[repeat_iteration],
error_criterion=config["error_criterion"],
)
model_results["Model error"] = test_errors.mean()
model_results["Unstandardized model error"] = test_errors.mean()
model_results["Results"] = one_reality_result
model_results["Test errors"] = test_errors
# For example tensorflow is not pickleable, so sending model from process would fail.
# Trained models only if not multiprocessing
if not ["multiprocessing"]:
model_results["Trained model"] = trained_model
except (Exception, ):
results_array = np.zeros(config["predicts"])
results_array.fill(np.nan)
test_errors = np.zeros((config["repeatit"], config["predicts"]))
test_errors.fill(np.nan)
model_results["Model error"] = np.inf
model_results["Unstandardized model error"] = np.inf
model_results["Results"] = results_array
model_results["Test errors"] = test_errors
error_message = (
f"Error in '{result_name}' model"
if not config["optimization"] else
f"Error in {iterated_model_name} model with optimized value: {optimization_value}"
)
mylogging.traceback(caption=error_message)
finally:
model_results["Index"] = (optimization_index, iterated_model_index)
model_results["warnings_list"] = warnings_list
model_results["logs_list"] = logs_list
model_results["Model time [s]"] = time.time() - start
if config["optimization_variable"]:
model_results["Optimization value"] = optimization_value
if config["trace_processes_memory"]:
_, memory_peak_MB = tracemalloc.get_traced_memory()
model_results["Memory Peak\n[MB]"] = memory_peak_MB / 10**6
tracemalloc.stop()
if config["multiprocessing"]:
logs_redirect.close_redirect()
if semaphor:
semaphor.release()
if config["multiprocessing"] == "process":
pipe.send({f"{result_name}": model_results})
pipe.close()
else:
return {f"{result_name}": model_results}
def run_memleak_test(bench, iterations, report):
tracemalloc.start()
starti = min(50, iterations // 2)
endi = iterations
malloc_arr = np.empty((endi, ), dtype=np.int64)
rss_arr = np.empty((endi, ), dtype=np.int64)
rss_peaks = np.empty((endi, ), dtype=np.int64)
nobjs_arr = np.empty((endi, ), dtype=np.int64)
garbage_arr = np.empty((endi, ), dtype=np.int64)
open_files_arr = np.empty((endi, ), dtype=np.int64)
rss_peak = 0
p = psutil.Process()
for i in range(endi):
bench()
gc.collect()
rss = p.memory_info().rss
malloc, peak = tracemalloc.get_traced_memory()
nobjs = len(gc.get_objects())
garbage = len(gc.garbage)
open_files = len(p.open_files())
print("{0: 4d}: pymalloc {1: 10d}, rss {2: 10d}, nobjs {3: 10d}, "
"garbage {4: 4d}, files: {5: 4d}".format(i, malloc, rss, nobjs,
garbage, open_files))
malloc_arr[i] = malloc
rss_arr[i] = rss
if rss > rss_peak:
rss_peak = rss
rss_peaks[i] = rss_peak
nobjs_arr[i] = nobjs
garbage_arr[i] = garbage
open_files_arr[i] = open_files
print('Average memory consumed per loop: {:1.4f} bytes\n'.format(
np.sum(rss_peaks[starti + 1:] - rss_peaks[starti:-1]) /
(endi - starti)))
from matplotlib import pyplot as plt
fig, (ax1, ax2, ax3) = plt.subplots(3)
ax1b = ax1.twinx()
ax1.plot(malloc_arr, 'r')
ax1b.plot(rss_arr, 'b')
ax1.set_ylabel('pymalloc', color='r')
ax1b.set_ylabel('rss', color='b')
ax2b = ax2.twinx()
ax2.plot(nobjs_arr, 'r')
ax2b.plot(garbage_arr, 'b')
ax2.set_ylabel('total objects', color='r')
ax2b.set_ylabel('garbage objects', color='b')
ax3.plot(open_files_arr)
ax3.set_ylabel('open file handles')
if not report.endswith('.pdf'):
report = report + '.pdf'
fig.tight_layout()
fig.savefig(report, format='pdf')
get_factors_from_state(state, tb) for state in marked_states
]
tracemalloc.start()
qstate = grover_candecomp(marked_states,
backend=backend,
rank_threshold=rank_threshold,
compress_ratio=compress_ratio,
cp_tol=cp_tol,
cp_maxiter=cp_maxiter,
cp_inneriter=cp_inneriter,
num_als_init=num_als_init,
init_als=init_als,
mode=mode,
debug=debug)
current_memory, peak_memory = tracemalloc.get_traced_memory()
tracemalloc.stop()
print(f'current_memory is {current_memory / (1024 * 1024)} MB')
print(f'peak_memory is {peak_memory / (1024 * 1024)} MB')
overall_item_fidelity = 0.
for i in range(num_marked_states):
item_fidelity = candecomp.fidelity(marked_states_factors[i],
qstate.factors, tb)**2
print(f"Fidelity for {i} is {item_fidelity}")
overall_item_fidelity += item_fidelity
print(f"Overall item fidelity is {overall_item_fidelity}")
print(f"Fidelity average is {qstate.fidelity_avg ** 2}")
n_outputs = len(set([row[-1] for row in train]))
network = initialize_network(n_inputs, n_hidden, n_outputs)
train_network(network, train, l_rate, n_epoch, n_outputs)
predictions = list()
for row in test:
prediction = predict(network, row)
predictions.append(prediction)
return (predictions)
# Test Backprop on Seeds dataset
seed(1)
memoryuse = 0
tracemalloc.start()
current1, peak1 = tracemalloc.get_traced_memory()
# load and prepare data
filename = 'seeds_dataset.csv'
dataset = load_csv(filename)
for i in range(len(dataset[0]) - 1):
str_column_to_float(dataset, i)
# convert class column to integers
str_column_to_int(dataset, len(dataset[0]) - 1)
# normalize input variables
minmax = dataset_minmax(dataset)
normalize_dataset(dataset, minmax)
# evaluate algorithm
n_folds = 5
l_rate = 0.3
# n_epoch = 10
# n_hidden = 3
def loop(self):
if self.cntr % 60 == 0:
tracker = messaging.MsgTrack()
stats_obj = stats.APRSDStats()
pl = packets.PacketList()
thread_list = APRSDThreadList()
now = datetime.datetime.now()
last_email = stats_obj.email_thread_time
if last_email:
email_thread_time = utils.strfdelta(now - last_email)
else:
email_thread_time = "N/A"
last_msg_time = utils.strfdelta(now - stats_obj.aprsis_keepalive)
current, peak = tracemalloc.get_traced_memory()
stats_obj.set_memory(current)
stats_obj.set_memory_peak(peak)
try:
login = self.config["aprs"]["login"]
except KeyError:
login = self.config["ham"]["callsign"]
keepalive = (
"{} - Uptime {} RX:{} TX:{} Tracker:{} Msgs TX:{} RX:{} "
"Last:{} Email: {} - RAM Current:{} Peak:{} Threads:{}"
).format(
login,
utils.strfdelta(stats_obj.uptime),
pl.total_recv,
pl.total_tx,
len(tracker),
stats_obj.msgs_tx,
stats_obj.msgs_rx,
last_msg_time,
email_thread_time,
utils.human_size(current),
utils.human_size(peak),
len(thread_list),
)
LOG.info(keepalive)
# See if we should reset the aprs-is client
# Due to losing a keepalive from them
delta_dict = utils.parse_delta_str(last_msg_time)
delta = datetime.timedelta(**delta_dict)
if delta > self.max_delta:
# We haven't gotten a keepalive from aprs-is in a while
# reset the connection.a
if not client.KISSClient.is_enabled(self.config):
LOG.warning("Resetting connection to APRS-IS.")
client.factory.create().reset()
# Check version every hour
delta = now - self.checker_time
if delta > datetime.timedelta(hours=1):
self.checker_time = now
level, msg = utils._check_version()
if level:
LOG.warning(msg)
self.cntr += 1
time.sleep(1)
return True
if __name__ == '__main__':
import glb
import objgraph
import gc,tracemalloc
tracemalloc.start()
b_snapshot = tracemalloc.take_snapshot()
for i in range(10):
with glb.db_connect() as conn:
with conn.cursor(as_dict=True) as cursor:
cursor.execute("SELECT * FROM zhanbao_tbl WHERE id=4274 order by id asc")
row = cursor.fetchone()
while row:
b1_snapshot = tracemalloc.take_snapshot()
try:
print('worker_no:'+ row['worker_no']+"\t"+ str(row['id']) +" "+ str(tracemalloc.get_traced_memory()))
files_template_exec(row['id'],json.loads(row['config_txt']),row['worker_no'],glb.config['UPLOAD_FOLDER'] ,wx_queue=glb.msg_queue)
print("====================================")
print('worker_no:'+ row['worker_no']+"\t"+ str(row['id']) +" "+ str(tracemalloc.get_traced_memory()))
print("====================================")
snapshot2 = tracemalloc.take_snapshot()
top_stats = snapshot2.compare_to(b1_snapshot, 'lineno')
for stat in top_stats[:10]:
print(stat)
print("====================================")
except Exception as e:
print(e)
row = cursor.fetchone()
gc.collect()
objgraph.show_most_common_types(limit=5)
### 打印出对象数目最多的 50 个类型信息
def launch_model(images,
labels,
adam_coef=0.01,
t_size=0.2,
batch_s=100,
nb_epoches=10):
print(
'------------------------------------------------------------------------------------------------\n'
)
print(
'{0}\nAdam coef: {4}\tTrain size: {5}%\tPercentage of test data:{1}\tBatch size: {2}\tNb epoches:{3}'
.format(os.path.basename(__file__), t_size, batch_s, nb_epoches,
adam_coef, t_size))
# Split dataset = % training dataset 20% test_dataset
X_train, X_test, y_train, y_test = train_test_split(images,
labels,
test_size=t_size,
random_state=11)
# Transform training and test datasets into PyTorch dataset
## Tensors
tensor_x_train = torch.Tensor(X_train)
tensor_y_train = torch.Tensor(y_train)
tensor_x_test = torch.Tensor(X_test)
tensor_y_test = torch.Tensor(y_test)
## Convert labels float type into long type (labels need to be type long)
tensor_y_train = tensor_y_train.long()
tensor_y_test = tensor_y_test.long()
## Create TensorDataset
tensorDataset_train = TensorDataset(tensor_x_train, tensor_y_train)
tensorDataset_test = TensorDataset(tensor_x_test, tensor_y_test)
## Create dataloaders
train_loader = DataLoader(tensorDataset_train,
batch_size=batch_s) # batch_s samples / batch
test_loader = DataLoader(tensorDataset_test, batch_size=batch_s)
# Start timer and save memory capacity
start = time.time()
tracemalloc.start()
# Init model
network = cnn.CNN()
optimizer = optim.Adam(network.parameters(), lr=adam_coef)
# Launch epoches
for epoch in range(nb_epoches):
total_loss = 0
total_correct = 0
for batch in train_loader: # Get batch
images, labels = batch
preds = network(images) # Pass Batch
loss = F.cross_entropy(preds, labels) # Calculate Loss
# Update hyperparameters
optimizer.zero_grad()
loss.backward() # Calculate Gradients
optimizer.step() # Update Weights
# Save loss and number of good prediction / batch
total_loss += loss.item()
total_correct += get_num_correct(preds, labels)
print("Epoch:", epoch, "Total_correct:", total_correct, "Loss:",
total_loss)
# Calculate accurancy for test dataset
with torch.no_grad():
test_preds = get_all_preds(network, test_loader)
all_labels = tensor_y_test
preds_correct = get_num_correct(test_preds, all_labels)
print('Total correct:{0}/{1}'.format(preds_correct, len(y_test)))
accuracy = preds_correct * 100 / len(y_test)
timer = time.time() - start
current, peak = tracemalloc.get_traced_memory()
diff = peak - current
print('Accuracy: {0} %'.format(accuracy))
print(
'------------------------------------------------------------------------------------------------\n'
)
return network, {
'Epoches': nb_epoches,
'Batchs': batch_s,
'Accuracies': float("{:.2f}".format(accuracy)),
'Test_size': t_size,
'Adam_coef': adam_coef,
'Timer': float("{:.4f}".format(timer)),
'Mem_current': current,
'Mem_peak': peak,
'Mem_diff': diff
}
print(len(word))
obj.insert(word)
print(obj.search(word))
prefix1 = 'asdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwf'
print(obj.startsWith(prefix1))
prefix2 = 'asdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefh'
print(obj.startsWith(prefix2))
prefix3 = 'asdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxgtyeuyriwpasdksdklfnsdmvncxmvnjdgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviue'
print(obj.startsWith(prefix3))
word2 = 'jnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfiddsdfsdfsdfsdfiddsdfsdfidjdksdndvlndslfwoiefhowfcslmnvdslfwoiefhowfcslmnvkjsdhowfcslmnvkjsdbfkjcslmnvkjsdbfkjsdbfjsdhfiuwefgquyvrgquyvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhtxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqasdfsddsvrtgbdidddddytjnhgdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvasdfsddsvrtgbdidddddytjnhgtfgghdddddrfeferdhtyjretyjnddsdfsdfidjdksdndvlndslfwoiefhowfcdslmnvkjsdbfkjsdbfjsdhfiuwefgquywesdfsdfliwopfihwlfcnsdvccjbvhsdfjhsfiqoqghasgfsagdstxfzxgcvgquyrwfeutyqwreuywdksdklfnsdmvncxmvnjdgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuefqoqwjpowqpqoiwjdjksbjdnbcnmxbvhfdgvgjghasgfsagdstxfzxgcvgquyrwfeutyqwreuywqtduhsvajvzbxbxbxbhshsdfgtyeuyriwpasdksdklfnsdmvncxmvnfjdgviuef'
print(len(word2))
obj.insert(word2)
word3 = 'dewoidhdslknforhgferiubgvkjfbvkasdjdbfkjasdfjksdbfkjsabhfuiweihfiuqwegfihbvhsbvmnxcbncnndhjdhxcycywioqwiskkdfbnsdkjhfreifgiwreuhfdsjbvckcjbvkjsdfkujshfiuwegfiweufedjihfdskjfnsdkjbfviuerhbvyrefbvifdhbsdkjfbvksdubfiweufhiewuhasdjkcaskjdqiuqwiqwouwiudhwiudbsutcdstytdtcrsfytcrsadtycfasdgcvsd'
print(len(word3))
obj.insert(word3)
prefix4 = 'dewoidhdslknforhgferiubgvkjfbvkasdjdbfkjasdfjksdbfkjsabhfuiweihfiuqwegfihbvhsbvmnxcbncnndhjdhxcycywioqwiskkdfbnsdkjhfreifgiwreuhfdsjbvckcjbvkjsdfkujshfiuwegfiweufedjihfdskjfnsdkjbfviuerhbvyrefbvifdhbsdkjfbvksdubfiweufhiewuhasdjkcaskjdqiuqwiqwouwiudhwiudbsutcdstytdtcrsfytcrsadtycfasdcxvdsfdv'
print(obj.startsWith(prefix4))
prefix5 = 'dewoidhdslknforhgferiubgvkjfbvkasdjdbfkjasdfjksdbfkjsabhfuiweihfiuqwegfihbvhsbvmnxcbncnndhjdhxcycywioqwiskkdfbnsdkjhfreifgiwreuhfdsjbvckcjbvkjsdfkujshfiuwegfiweufedjihfdskjfnsdkjbfviuerhbvyrefbvifdhbsdkjfbvksdubfiweufhiewuhasdjkcaskjdqiuqwiqwouwiudhwiudbsutcdstytdtcrsfytcrsadtycfasd'
print(obj.startsWith(prefix5))
current, peak = tracemalloc.get_traced_memory()
print(
f"Current memory usage is {current / 10**6}MB; Peak was {peak / 10**6}MB")
snapshot = tracemalloc.take_snapshot()
top_stats = snapshot.statistics('traceback')
""" print("[ Top 10 ]")
for stat in top_stats[:10]:
print('메모리 블록이 할당된 곳:', stat.traceback, '/ 메모리 블록 수(int):', stat.count, '/ 총 메모리 블록의 바이트 단위 크기 (int):', stat.size) """
display_top(snapshot)
tracemalloc.stop()
def tick():
while True:
logger.info("%s", str([t._format_size(x, False) for x in t.get_traced_memory()]))
time.sleep(0.2)
# ------------------------------------------------------------
# Part 4: Thinking in functions
# ------------------------------------------------------------
import tracemalloc
tracemalloc.start()
import readrides
rows = readrides.read_as_instances('ctabus.csv')
# 1. How many bus routes exist?
# Solution: Read into a set
routes = {row.route for row in rows}
print(len(routes), 'routes')
# 2. How many people rode route 22 on 9-Apr-2007?
# Solution: Build an index mapping routes, dates to ride totals.
# You'll use (route,date) as a composite key.
by_route_and_date = {(row.route, row.date): row.rides for row in rows}
print('Route 22 on 9-Apr-2007:', by_route_and_date['22', '04/09/2007'])
# 3. Find out what day the route 22 bus had the highest ridership
rt22 = [(row.rides, row.date) for row in rows if row.route == '22']
print('Max ridership:', max(rt22))
print('Current %s, Peak %s' % tracemalloc.get_traced_memory())
def dump_memory(what):
print("***** %s *****" % what)
size, peak_size = tracemalloc.get_traced_memory()
print("traced: %.1f KB (peak: %.1f KB)" % (size / 1024., peak_size / 1024.))
os.chdir(script_path)
#
n = "\n"
print(
# unvivtool.__doc__, n,
unvivtool, n,
dir(unvivtool), n,
flush=True
)
# tracemalloc -- BEGIN ---------------------------------------------------------
# tracemalloc.stop()
first_size, first_peak = tracemalloc.get_traced_memory()
if sys.version_info[0:2] >= (3, 9):
tracemalloc.reset_peak()
tracemalloc.start()
# tracemalloc -- END -----------------------------------------------------------
count_successful_tests = 0
print("")
# Decode
if args.cmd[0] == "d":
vivfile = "tests/car.viv"
outdir = "tests"
def main():
config = ConfigParser.ConfigParser()
my_path = Path(__file__).parent.parent
ini_path = os.path.join(my_path, 'config', 'server.ini')
config.read(ini_path)
YAML_DIR = config['SERVICE']['yaml_directory']
METRIC_YAML = config['SERVICE']['metrics_yaml']
METRIC_YML_PATH = os.path.join(my_path, YAML_DIR, METRIC_YAML)
SPDX_URL = config['EXTERNAL']['spdx_license_github']
DATACITE_API_REPO = config['EXTERNAL']['datacite_api_repo']
RE3DATA_API = config['EXTERNAL']['re3data_api']
METADATACATALOG_API = config['EXTERNAL']['metadata_catalog']
isDebug = config.getboolean('SERVICE', 'debug_mode')
data_files_limit = int(config['SERVICE']['data_files_limit'])
metric_specification = config['SERVICE']['metric_specification']
preproc = Preprocessor()
preproc.retrieve_metrics_yaml(METRIC_YML_PATH, data_files_limit,
metric_specification)
print('Total metrics defined: {}'.format(preproc.get_total_metrics()))
isDebug = config.getboolean('SERVICE', 'debug_mode')
preproc.retrieve_licenses(SPDX_URL, isDebug)
preproc.retrieve_datacite_re3repos(RE3DATA_API, DATACITE_API_REPO, isDebug)
preproc.retrieve_metadata_standards(METADATACATALOG_API, isDebug)
preproc.retrieve_science_file_formats(isDebug)
preproc.retrieve_long_term_file_formats(isDebug)
print('Total SPDX licenses : {}'.format(preproc.get_total_licenses()))
print('Total re3repositories found from datacite api : {}'.format(
len(preproc.getRE3repositories())))
print('Total subjects area of imported metadata standards : {}'.format(
len(preproc.metadata_standards)))
start = False
usedatacite = True
tracemalloc.start()
n = 1
for identifier in testpids:
print(identifier)
print(n)
n += 1
if identifier == startpid or not startpid:
start = True
if start:
ft = FAIRCheck(uid=identifier,
test_debug=debug,
metadata_service_url=metadata_service_endpoint,
metadata_service_type=metadata_service_type,
use_datacite=usedatacite)
#ft = FAIRCheck(uid=identifier, test_debug=True, use_datacite=usedatacite)
uid_result, pid_result = ft.check_unique_persistent()
ft.retrieve_metadata_embedded(ft.extruct_result)
include_embedded = True
if ft.repeat_pid_check:
uid_result, pid_result = ft.check_unique_persistent()
ft.retrieve_metadata_external()
core_metadata_result = ft.check_minimal_metatadata()
content_identifier_included_result = ft.check_content_identifier_included(
)
access_level_result = ft.check_data_access_level()
license_result = ft.check_license()
relatedresources_result = ft.check_relatedresources()
check_searchable_result = ft.check_searchable()
data_content_metadata = ft.check_data_content_metadata()
data_file_format_result = ft.check_data_file_format()
community_standards_result = ft.check_community_metadatastandards()
data_provenance_result = ft.check_data_provenance()
formal_representation_result = ft.check_formal_metadata()
semantic_vocabulary_result = ft.check_semantic_vocabulary()
metadata_preserved_result = ft.check_metadata_preservation()
standard_protocol_metadata_result = ft.check_standardised_protocol_metadata(
)
standard_protocol_data_result = ft.check_standardised_protocol_data(
)
results = [
uid_result, pid_result, core_metadata_result,
content_identifier_included_result, check_searchable_result,
access_level_result, formal_representation_result,
semantic_vocabulary_result, license_result,
data_file_format_result, data_provenance_result,
relatedresources_result, community_standards_result,
data_content_metadata, metadata_preserved_result,
standard_protocol_data_result,
standard_protocol_metadata_result
]
#results=[core_metadata_result,uid_result, pid_result]
#print(ft.metadata_merged)
debug_messages = ft.get_log_messages_dict()
ft.logger_message_stream.flush()
ft.get_assessment_summary(results)
for res_k, res_v in enumerate(results):
if ft.isDebug:
debug_list = debug_messages.get(res_v['metric_identifier'])
#debug_list= ft.msg_filter.getMessage(res_v['metric_identifier'])
if debug_list is not None:
results[res_k]['test_debug'] = debug_messages.get(
res_v['metric_identifier'])
else:
results[res_k]['test_debug'] = [
'INFO: No debug messages received'
]
else:
results[res_k]['test_debug'] = ['INFO: Debugging disabled']
debug_messages = {}
print(json.dumps(results, indent=4, sort_keys=True))
#remove unused logger handlers and filters to avoid memory leaks
ft.logger.handlers = [ft.logger.handlers[-1]]
#ft.logger.filters = [ft.logger.filters]
current, peak = tracemalloc.get_traced_memory()
print(
f"Current memory usage is {current / 10 ** 6}MB; Peak was {peak / 10 ** 6}MB"
)
snapshot = tracemalloc.take_snapshot()
top_stats = snapshot.statistics('traceback')
# pick the biggest memory block
stat = top_stats[0]
print("%s memory blocks: %.1f KiB" %
(stat.count, stat.size / 1024))
for line in stat.traceback.format():
print(line)
for i, stat in enumerate(snapshot.statistics('filename')[:5], 1):
print(i, str(stat))
#preproc.logger.
gc.collect()
tracemalloc.stop()
def func():
size, max_size = tracemalloc.get_traced_memory()
print("Traced memory: %.1f MB"
% (size / 1024.0 ** 2))
def _worker(self, bench, sample_func):
args = self.args
loops = args.loops
metadata = dict(self.metadata)
start_time = perf.monotonic_clock()
calibrate = (not loops)
if calibrate:
loops, calibrate_warmups = self._calibrate(bench, sample_func)
else:
if perf.python_has_jit():
# With a JIT, continue to calibrate during warmup
calibrate = True
calibrate_warmups = None
if args.track_memory:
if MS_WINDOWS:
from perf._win_memory import get_peak_pagefile_usage
else:
from perf._memory import PeakMemoryUsageThread
mem_thread = PeakMemoryUsageThread()
mem_thread.start()
if args.tracemalloc:
import tracemalloc
tracemalloc.start()
if args.warmups:
loops, warmups = self._run_bench(bench, sample_func, loops,
args.warmups,
is_warmup=True, calibrate=calibrate)
else:
warmups = []
if calibrate_warmups:
warmups = calibrate_warmups + warmups
loops, samples = self._run_bench(bench, sample_func, loops,
args.samples)
if args.tracemalloc:
traced_peak = tracemalloc.get_traced_memory()[1]
tracemalloc.stop()
if not traced_peak:
raise RuntimeError("tracemalloc didn't trace any Python "
"memory allocation")
# drop timings, replace them with the memory peak
metadata['unit'] = 'byte'
warmups = None
samples = (float(traced_peak),)
if args.track_memory:
if MS_WINDOWS:
mem_peak = get_peak_pagefile_usage()
else:
mem_thread.stop()
mem_peak = mem_thread.peak_usage
if not mem_peak:
raise RuntimeError("failed to get the memory peak usage")
# drop timings, replace them with the memory peak
metadata['unit'] = 'byte'
warmups = None
samples = (float(mem_peak),)
duration = perf.monotonic_clock() - start_time
metadata['duration'] = duration
metadata['name'] = self.name
metadata['loops'] = loops
if self.inner_loops is not None and self.inner_loops != 1:
metadata['inner_loops'] = self.inner_loops
run = perf.Run(samples, warmups=warmups, metadata=metadata)
bench.add_run(run)
self._display_result(bench, check_unstable=False)
# Save loops into args
args.loops = loops
def test_reproject_3D_memory():
pytest.importorskip('reproject')
tracemalloc.start()
snap1 = tracemalloc.take_snapshot()
# create a 64 MB cube
cube,_ = utilities.generate_gaussian_cube(shape=[200,200,200])
sz = _.dtype.itemsize
# check that cube is loaded into memory
snap2 = tracemalloc.take_snapshot()
diff = snap2.compare_to(snap1, 'lineno')
diffvals = np.array([dd.size_diff for dd in diff])
# at this point, the generated cube should still exist in memory
assert diffvals.max()*u.B >= 200**3*sz*u.B
wcs_in = cube.wcs
wcs_out = wcs_in.deepcopy()
wcs_out.wcs.ctype = ['GLON-SIN', 'GLAT-SIN', cube.wcs.wcs.ctype[2]]
wcs_out.wcs.crval = [0.001, 0.001, cube.wcs.wcs.crval[2]]
wcs_out.wcs.crpix = [2., 2., cube.wcs.wcs.crpix[2]]
header_out = (wcs_out.to_header())
header_out['NAXIS'] = 3
header_out['NAXIS1'] = int(cube.shape[2]/2)
header_out['NAXIS2'] = int(cube.shape[1]/2)
header_out['NAXIS3'] = cube.shape[0]
# First the unfilled reprojection test: new memory is allocated for
# `result`, but nowhere else
result = cube.reproject(header_out, filled=False)
snap3 = tracemalloc.take_snapshot()
diff = snap3.compare_to(snap2, 'lineno')
diffvals = np.array([dd.size_diff for dd in diff])
# result should have the same size as the input data, except smaller in two dims
# make sure that's all that's allocated
assert diffvals.max()*u.B >= 200*100**2*sz*u.B
assert diffvals.max()*u.B < 200*110**2*sz*u.B
# without masking the cube, nothing should change
result = cube.reproject(header_out, filled=True)
snap4 = tracemalloc.take_snapshot()
diff = snap4.compare_to(snap3, 'lineno')
diffvals = np.array([dd.size_diff for dd in diff])
assert diffvals.max()*u.B <= 1*u.MB
assert result.wcs.wcs.crval[0] == 0.001
assert result.wcs.wcs.crpix[0] == 2.
# masking the cube will force the fill to create a new in-memory copy
mcube = cube.with_mask(cube > 0.1*cube.unit)
# `_is_huge` would trigger a use_memmap
assert not mcube._is_huge
assert mcube.mask.any()
# take a new snapshot because we're not testing the mask creation
snap5 = tracemalloc.take_snapshot()
tracemalloc.stop()
tracemalloc.start() # stop/start so we can check peak mem use from here
current_b4, peak_b4 = tracemalloc.get_traced_memory()
result = mcube.reproject(header_out, filled=True)
current_aftr, peak_aftr = tracemalloc.get_traced_memory()
snap6 = tracemalloc.take_snapshot()
diff = snap6.compare_to(snap5, 'lineno')
diffvals = np.array([dd.size_diff for dd in diff])
# a duplicate of the cube should have been created by filling masked vals
# (this should be near-exact since 'result' should occupy exactly the
# same amount of memory)
assert diffvals.max()*u.B <= 1*u.MB #>= 200**3*sz*u.B
# the peak memory usage *during* reprojection will have that duplicate,
# but the memory gets cleaned up afterward
assert (peak_aftr-peak_b4)*u.B >= (200**3*sz*u.B + 200*100**2*sz*u.B)
assert result.wcs.wcs.crval[0] == 0.001
assert result.wcs.wcs.crpix[0] == 2.
def log_func():
nonlocal diff
size, max_size = tracemalloc.get_traced_memory()
diff = (size - old_size)
def printMem(self):
current, peak = tracemalloc.get_traced_memory()
print(f"Current memory usage is {current / 10**6}MB;")
return
def handle_traceback(sig, frame):
logger.info(
"memory (current, peak) %s", str([t._format_size(x, False) for x in t.get_traced_memory()])
)
import traceback
traceback.print_stack(limit=5)
def read_write(plot=False):
# mesh = generate_tetrahedral_mesh()
mesh = generate_triangular_mesh()
print(mesh)
mem_size = mesh.points.nbytes + mesh.cells[0].data.nbytes
mem_size /= 1024.0 ** 2
print(f"mem_size: {mem_size:.2f} MB")
formats = {
"Abaqus": (meshio.abaqus.write, meshio.abaqus.read, ["out.inp"]),
"Ansys (ASCII)": (
lambda f, m: meshio.ansys.write(f, m, binary=False),
meshio.ansys.read,
["out.ans"],
),
# "Ansys (binary)": (
# lambda f, m: meshio.ansys.write(f, m, binary=True),
# meshio.ansys.read,
# ["out.ans"],
# ),
"AVS-UCD": (meshio.avsucd.write, meshio.avsucd.read, ["out.ucd"]),
# "CGNS": (meshio.cgns.write, meshio.cgns.read, ["out.cgns"]),
"Dolfin-XML": (meshio.dolfin.write, meshio.dolfin.read, ["out.xml"]),
"Exodus": (meshio.exodus.write, meshio.exodus.read, ["out.e"]),
# "FLAC3D": (meshio.flac3d.write, meshio.flac3d.read, ["out.f3grid"]),
"Gmsh 4.1 (ASCII)": (
lambda f, m: meshio.gmsh.write(f, m, binary=False),
meshio.gmsh.read,
["out.msh"],
),
"Gmsh 4.1 (binary)": (
lambda f, m: meshio.gmsh.write(f, m, binary=True),
meshio.gmsh.read,
["out.msh"],
),
"MDPA": (meshio.mdpa.write, meshio.mdpa.read, ["out.mdpa"]),
"MED": (meshio.med.write, meshio.med.read, ["out.med"]),
"Medit": (meshio.medit.write, meshio.medit.read, ["out.mesh"]),
"MOAB": (meshio.h5m.write, meshio.h5m.read, ["out.h5m"]),
"Nastran": (meshio.nastran.write, meshio.nastran.read, ["out.bdf"]),
"OBJ": (meshio.obj.write, meshio.obj.read, ["out.obj"]),
"OFF": (meshio.off.write, meshio.off.read, ["out.off"]),
"Permas": (meshio.permas.write, meshio.permas.read, ["out.dato"]),
"PLY (binary)": (
lambda f, m: meshio.ply.write(f, m, binary=True),
meshio.ply.read,
["out.ply"],
),
"PLY (ASCII)": (
lambda f, m: meshio.ply.write(f, m, binary=False),
meshio.ply.read,
["out.ply"],
),
"STL (binary)": (
lambda f, m: meshio.stl.write(f, m, binary=True),
meshio.stl.read,
["out.stl"],
),
"STL (ASCII)": (
lambda f, m: meshio.stl.write(f, m, binary=False),
meshio.stl.read,
["out.stl"],
),
# "TetGen": (meshio.tetgen.write, meshio.tetgen.read, ["out.node", "out.ele"],),
"VTK (binary)": (
lambda f, m: meshio.vtk.write(f, m, binary=True),
meshio.vtk.read,
["out.vtk"],
),
"VTK (ASCII)": (
lambda f, m: meshio.vtk.write(f, m, binary=False),
meshio.vtk.read,
["out.vtk"],
),
"VTU (binary, uncompressed)": (
lambda f, m: meshio.vtu.write(f, m, binary=True, compression=None),
meshio.vtu.read,
["out.vtu"],
),
"VTU (binary, zlib)": (
lambda f, m: meshio.vtu.write(f, m, binary=True, compression="zlib"),
meshio.vtu.read,
["out.vtu"],
),
"VTU (binary, LZMA)": (
lambda f, m: meshio.vtu.write(f, m, binary=True, compression="lzma"),
meshio.vtu.read,
["out.vtu"],
),
"VTU (ASCII)": (
lambda f, m: meshio.vtu.write(f, m, binary=False),
meshio.vtu.read,
["out.vtu"],
),
"Wavefront .obj": (meshio.obj.write, meshio.obj.read, ["out.obj"]),
# "wkt": ".wkt",
"XDMF (binary)": (
lambda f, m: meshio.xdmf.write(f, m, data_format="Binary"),
meshio.xdmf.read,
["out.xdmf", "out0.bin", "out1.bin"],
),
"XDMF (HDF, GZIP)": (
lambda f, m: meshio.xdmf.write(f, m, data_format="HDF", compression="gzip"),
meshio.xdmf.read,
["out.xdmf", "out.h5"],
),
"XDMF (HDF, uncompressed)": (
lambda f, m: meshio.xdmf.write(f, m, data_format="HDF", compression=None),
meshio.xdmf.read,
["out.xdmf", "out.h5"],
),
"XDMF (XML)": (
lambda f, m: meshio.xdmf.write(f, m, data_format="XML"),
meshio.xdmf.read,
["out.xdmf"],
),
}
# formats = {
# # "VTK (ASCII)": formats["VTK (ASCII)"],
# # "VTK (binary)": formats["VTK (binary)"],
# # "VTU (ASCII)": formats["VTU (ASCII)"],
# # "VTU (binary)": formats["VTU (binary)"],
# # "Gmsh 4.1 (binary)": formats["Gmsh 4.1 (binary)"],
# # "FLAC3D": formats["FLAC3D"],
# "MDPA": formats["MDPA"],
# }
# max_key_length = max(len(key) for key in formats)
elapsed_write = []
elapsed_read = []
file_sizes = []
peak_memory_write = []
peak_memory_read = []
print()
print(
"format "
+ "write (s) "
+ "read(s) "
+ "file size "
+ "write mem "
+ "read mem "
)
print()
with tempfile.TemporaryDirectory() as directory:
directory = pathlib.Path(directory)
for name, (writer, reader, filenames) in formats.items():
filename = directory / filenames[0]
tracemalloc.start()
t = time.time()
writer(filename, mesh)
# snapshot = tracemalloc.take_snapshot()
elapsed_write.append(time.time() - t)
peak_memory_write.append(tracemalloc.get_traced_memory()[1])
tracemalloc.stop()
file_sizes.append(sum(os.stat(directory / f).st_size for f in filenames))
tracemalloc.start()
t = time.time()
reader(filename)
elapsed_read.append(time.time() - t)
peak_memory_read.append(tracemalloc.get_traced_memory()[1])
tracemalloc.stop()
print(
"{:<26} {:e} {:e} {:e} {:e} {:e}".format(
name,
elapsed_write[-1],
elapsed_read[-1],
file_sizes[-1] / 1024.0 ** 2,
peak_memory_write[-1] / 1024.0 ** 2,
peak_memory_read[-1] / 1024.0 ** 2,
)
)
names = list(formats.keys())
# convert to MB
file_sizes = np.array(file_sizes)
file_sizes = file_sizes / 1024.0 ** 2
peak_memory_write = np.array(peak_memory_write)
peak_memory_write = peak_memory_write / 1024.0 ** 2
peak_memory_read = np.array(peak_memory_read)
peak_memory_read = peak_memory_read / 1024.0 ** 2
if plot:
plot_speed(names, elapsed_write, elapsed_read)
plot_file_sizes(names, file_sizes, mem_size)
plot_memory_usage(names, peak_memory_write, peak_memory_read, mem_size)
def main():
tracemalloc.start()
print(createDict(50000))
current, peak = tracemalloc.get_traced_memory()
print(f"Current memory usage is {current / 10**6}MB; Peak was {peak / 10**6}MB")
tracemalloc.stop()
def compute(polygon,
polygon_id,
s_id,
t_id,
s,
t,
algorithm_list,
run_timeout=3600,
max_time=5,
min_runs=5,
max_runs=20):
"""Compute the benchmark for one start/end pair in one polygon with all known algorithms."""
from socket import gethostname
from datetime import datetime
from gsp import makestep_shortest_path, delaunay_shortest_path, lee_preparata_shortest_path, \
trapezoid_shortest_path
import gc
import tracemalloc
import sys
import traceback
from time import process_time as timer
m_run = model.Run.create(
polygon_id=polygon_id,
host=model.Host.create_or_get(name=gethostname())[0],
start=datetime.now(),
end=datetime.now(),
s=model.PolygonPoint.get(id=s_id),
t=model.PolygonPoint.get(id=t_id),
version=model.Version.get())
logging.debug('Created run "%s"', m_run)
for algorithm, sp in dict(
delaunay=delaunay_shortest_path,
makestep=makestep_shortest_path,
trapezoid=trapezoid_shortest_path,
lee_preparata=lee_preparata_shortest_path).items():
if algorithm not in algorithm_list:
continue
m_algorithm, _ = model.Algorithm.create_or_get(name=algorithm)
logging.info('Running algorithm "%s"', m_algorithm)
gc.collect()
tracemalloc.start()
try:
signal.alarm(run_timeout)
path = list(sp(polygon, s, t))
signal.alarm(0)
except BaseException:
traceback.print_exc(file=sys.stderr)
continue
else:
memory = tracemalloc.get_traced_memory()
gc.collect()
tracemalloc.stop()
m_instance = model.Instance.create(run=m_run,
algorithm=m_algorithm,
memory=memory[1] - memory[0],
path_length=len(path))
logging.debug('Saved instance "%s"', m_instance)
logging.debug('Creating resulting path: "%s"', path)
for i, point in enumerate(path):
try:
m_point = model.Point.get(x=point.x, y=point.y)
except model.Point.DoesNotExist:
for tmp_polygon_point in m_run.polygon.polygon_points:
if tmp_polygon_point.point.as_geometry() == point:
m_polygon_point = tmp_polygon_point
break
else:
m_polygon_point = model.PolygonPoint.get(
point=m_point,
polygon_id=polygon_id,
is_vertex=isinstance(point, PolygonPoint))
model.PathPoint.create(instance=m_instance,
index=i,
polygon_point=m_polygon_point)
for property, value in sp.properties.items():
m_property, _ = model.PropertyName.create_or_get(name=property)
if isinstance(value, int):
model.IntegerProperty.create(instance=m_instance,
name=m_property,
value=value)
total_time = 0
runs = 0
times = []
while runs < min_runs or max_time > total_time and runs < max_runs:
try:
signal.alarm(run_timeout)
gc.disable()
start = timer()
list(sp(polygon, s, t))
time = timer() - start
gc.enable()
signal.alarm(0)
except BaseException:
traceback.print_exc(file=sys.stderr)
break
else:
times.append(time)
total_time += time
runs += 1
if len(times) > 0:
with model.db.atomic():
model.Time.insert_many(
dict(instance=m_instance, time=t)
for t in times).execute()
m_instance.median_time = median(times)
m_instance.save()
m_run.end = datetime.now()
m_run.save()
return (polygon_id, s_id, t_id)
def measure(self):
import tracemalloc
current, peak = tracemalloc.get_traced_memory()
snap = tracemalloc.take_snapshot()
return current, snap
path = Depth_First_Search(InitNode)
elif Search == "BFS":
path = Breadth_First_Search(InitNode)
elif Search == "GBS":
path = Greedy_Best_Search(InitNode)
else:
path = A_Star_Search(InitNode)
# if a solution was found
if path != False and Goal(path.state):
# PathPrint(InitNode.state, path.moveSet)
File.write("S," + str(nodesSearched) + ",") # solved (S), #moves
else:
File.write("F," + str(nodesSearched) + ",") # failed (F), #move = 0
curr_mem, max_mem = tracemalloc.get_traced_memory()
# save execution time, curr memory and max memory usage
File.write(str(time.process_time()) + "," + str(2*curr_mem / 10**6) + "MB," + str(2*max_mem/ 10**6) + "MB\n")
File.close()
print("DENE w/" + Search + "," + str(sys.argv[1]) + "x" + str(sys.argv[1]) +"\n\n")
# InitNode = Node()
# # initializing pegboard
# InitNode.state = ExperimentState(9)
# # # letting global size variables
# cMax = len(InitNode.state[0])
# rMax = len(InitNode.state)
# path = A_Star_Search(InitNode)
#!/usr/bin/env python
"""
exercise2_1.py
"""
import tracemalloc
f = open('Data/ctabus.csv')
tracemalloc.start()
data = f.read()
d = len(data)
print(d)
current, peak = tracemalloc.get_traced_memory()
print(current)
print(peak)
