def main():
proc = Popen(['docker', 'run', '-i', 'pipe_api'], stdin=PIPE, stdout=PIPE)
stdout = proc.stdout
stdin = proc.stdin
with PPE(max_workers=16) as exe:
for r in exe.map(driver, [(writer, stdin.fileno()),
(reader, stdout.fileno())]):
r
stdin.close()
def run_experiment(config_file):
with open(config_file) as f:
config = yaml.load(f)
pool = PPE()
fs = []
results = []
for dim in config['dimensions']:
for run in range(config['num_runs']):
for fevals in config['fevals_per_dim']:
for alg in config['algs']:
for variant in config[alg]:
setup = {
'dim': dim,
'fevals': min(80, fevals * dim),
'run': run + config['runs_offset'],
'variant': variant['name'],
'alg': alg,
'kwargs': variant['kwargs'],
'result_path': config['result_path']
}
if config['name'] == 'saddle':
fs.append(pool.submit(run_saddle_unit_exp, setup))
elif config['name'] == 'mop':
fs.append(pool.submit(run_mop_unit_exp, setup))
elif config['name'] == 'adhd':
if run == 0:
try:
bkp_file = os.path.join(os.path.dirname(__file__), config['result_path'].replace('.json', '_bkp.json'))
os.remove(bkp_file)
except FileNotFoundError:
pass
setup['n_init'] = config['n_init']
setup['start_seed'] = config['start_seed']
setup['result_path_bkp'] = bkp_file
fs.append(pool.submit(run_adhd_unit_exp, setup))
else:
raise Exception('unknown experiment')
results = []
for x in as_completed(fs):
try:
results.append(x.result())
except Exception as e:
print(e)
print(results)
with open(os.path.join(os.path.dirname(__file__), config['result_path']), 'w') as f:
json.dump(results, f, sort_keys=True, indent=4)
def build(self):
'''
Trigering the build function solves all models in order to
find the best model, by score, then returns it as a result.
Also generates self.all_models and self.best to store the information.
'''
with PPE() as exe:
ppe = [exe.submit(self._solve, lag) for lag in range(2, self.lags)]
for proc in as_completed(ppe):
key, spec = proc.result()
self.all_models[key] = spec
del ppe
self.best = self._check_all_models()
return self.best
async def main(*peers):
ts = []
loop = aio.get_running_loop()
bc = Blockchain.genesis(1)
heads = {h(bytes(bc.blocks[0])): bc}
if not peers:
t, protocol = await loop.create_datagram_endpoint(
lambda: Protocol(bc, heads),
local_addr=('127.0.0.1', 9999))
print('server up')
else:
for addr, port in peers:
t, protocol = await loop.create_datagram_endpoint(
lambda: Protocol(bc, heads),
remote_addr=(addr, port))
ts.append(t)
print('get chain')
protocol.getchain(0)
try:
ex = PPE(max_workers=1)
while True:
head = max(heads, key=lambda _h: len(heads[_h].blocks))
bc = heads[head]
b = await bc.mine(ex)
if bc.verify(b):
bc.add(b)
del heads[head]
heads[h(bytes(b))] = bc
for addr in Protocol.peers:
protocol.sendblock(addr, b)
print(f'MINED {b.ix}')
finally:
for t in ts:
t.close()
def main():
urls = set()
urls |= scrape(
(3, ['http://blog.livedoor.jp/geek/archives/cat_10022560.html']))
print(urls)
snapshots = sorted(glob.glob('tmp/snapshots/*'))
for snapshot in snapshots:
try:
urls |= pickle.loads(open(snapshot, 'rb').read())
except EOFError as ex:
continue
while True:
urltmp = set()
with PPE(max_workers=CPU_SIZE) as exe:
for _urlret in exe.map(scrape, chunk_urls(urls)):
if _urlret is not None:
urltmp |= _urlret
urls = urltmp
if len(urls) == 0:
break
def download(self):
while True:
try:
info = urllib.request.urlopen(self.video_url).info()
except urllib.error.HTTPError:
req = urllib.request.Request(self.video_url)
req.headers.update(headers())
info = urllib.request.urlopen(req).info()
except http.client.IncompleteRead:
continue
except AttributeError:
exit()
else:
break
self.total_length = int(info.get('content-length'))
self.file_type = info.get('content-type').split('/')[-1]
self.split_num = self.total_length // 300000
print('Use cpu thread count: ', cpu_count())
print('Split count: ', self.split_num, '\n')
l = [(self.total_length + i) // self.split_num
for i in range(self.split_num)]
args = [(i, 0 if i == 0 else sum(l[:i]) + 1, sum(l[:i]) + val)
for i, val in enumerate(l)]
with PPE(max_workers=cpu_count(),
initializer=self.pool_init,
initargs=(Value('i', 0), )) as exe:
exe.map(self.split_download, args)
with open('{}.{}'.format(self.title, self.file_type), 'wb') as f:
self.combine(f)
return str(
round(
os.path.getsize('{}.{}'.format(self.title, self.file_type)) /
(1024.0**2), 1)) + 'MB'
def run():
files = list(Path(CONFIG.HREF_PATH).glob('*'))
random.shuffle(files)
files = files[:100_0000]
args = {}
for idx, file in enumerate(files):
key = idx % 16
if args.get(key) is None:
args[key] = []
args[key].append(file)
args = [(key, files) for key, files in args.items()]
objs = set()
with PPE(max_workers=4) as exe:
for _objs in exe.map(pmap, args):
objs |= _objs
print('total size', len(objs))
with open('urls.pkl.gz', 'wb') as fp:
fp.write(gzip.compress(pickle.dumps(objs)))
for url in list(objs)[:100]:
print(url)
import asyncio, types
from concurrent.futures import ProcessPoolExecutor as PPE
ppe = PPE()
# IO bound
async def do_something(fname, data, loop):
await write(fname, data, loop)
@types.coroutine
def write(f, data, loop):
yield from loop.run_in_executor(ppe, do_write, f, data)
def do_write(f, data):
with open(f, 'w') as f:
for line in data:
f.write(line)
# CPU bound
async def do_something_else(n, loop):
await count(n, loop)
@types.coroutine
def count(n, loop):
def main():
with PPE(max_workers=16) as exe:
r = [r for r in exe.map(calc, list(range(1, 16)))]
print(r)
def football(self, begin_date="2010-01-01", end_date=None):
interval = DateHandler(begin_date).create_interval_till(end_date)
with PPE(self.cpu_count) as worker_pool:
worker_pool.map(DataCollector.fetch_day_events, interval)
return
print(os.path.exists(f'images/{hashs}.{type}'))
if os.path.exists(f'images/{hashs}.{type}'):
return
session = requests.session()
session.proxies = {
'http': 'socks5h://localhost:9050',
'https': 'socks5h://localhost:9050'
}
headers = {
'User-Agent':
'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36'
}
try:
r = session.get(img_url, headers=headers)
except Exception as ex:
print(ex)
return
bins = r.content
with open(f'images/{hashs}.{type}', 'wb') as fp:
fp.write(bins)
print('finish', img_url)
except Exception as ex:
print(ex)
from concurrent.futures import ProcessPoolExecutor as PPE
PPE(max_workers=300).map(pmap, img_urls)
try:
obj = json.load(path.open())
created_at = datetime.strptime(
obj['created_at'],
'%a %b %d %H:%M:%S +0000 %Y') + timedelta(hours=9)
day = created_at.day
hour = created_at.hour
#print(created_at)
text = obj['text']
if 'オセロニア' in text:
if time_freq.get((day, hour)) is None:
time_freq[(day, hour)] = 0
time_freq[(day, hour)] += 1
except Exception as ex:
print(ex)
return time_freq
args = [(key, paths) for key, paths in key_paths.items()]
time_freq = {}
with PPE(max_workers=12) as exe:
for _time_freq in exe.map(pmap, args):
for time, freq in _time_freq.items():
if time_freq.get(time) is None:
time_freq[time] = 0
time_freq[time] += freq
for time, freq in sorted(time_freq.items(), key=lambda x: x[0]):
day, hour = time
print(f'{day}日{hour}時', freq)
def aaf_dist(datfile,countfile,nThreads,samples,kl,long=False):
#check executables
if os.system('which fitch_kmerX > /dev/null'):
if long:
fitch = './fitch_kmerX_long'
else:
fitch = './fitch_kmerX'
if not is_exe(fitch):
print(fitch+' not found. Make sure it is in your PATH or the')
print('current directory, and that it is executable')
sys.exit()
else:
if long:
fitch = 'fitch_kmerX_long'
else:
fitch = 'fitch_kmerX'
#process the .dat.gz file
try:
iptf = smartopen(datfile,'rt')
except IOError:
print('Cannot open file', datafile)
sys.exit()
if not os.path.isfile(countfile):
print('Cannot find file', countfile)
sys.exit()
try:
total = open(countfile,'rt')
except IOError:
print('Cannot open file', countfile)
sys.exit()
try:
infile = open('infile','wt')
except IOError:
print('Cannot open infile for writing')
sys.exit()
###Read header
sl = [] #species list
line = iptf.readline()
ll = line.split()
if kl != float(ll[1]):
print("The recorded k in the shared kmer table file is not the same with the k supplied to aaf_dist; exiting now.") #kmer length
sys.exit()
while True:
line = iptf.readline()
if line.startswith('#-'):
continue
elif line.startswith('#sample'):
ll = line.split()
sl.append(ll[1])
else:
break
if sl != samples:
print("The recorded sample list in the shared kmer table file is not the same with the one supplied to aaf_dist; exiting now.") #kmer length
sys.exit()
###Initialize shared kmers matrix
sn = len(samples) #species number
nshare = [[0] * sn for i in range(sn)]
### It turns out to be very slow if we give very big chunks. So we will be
### Using only 1G of RAM intotal. As a result, we could use all the cores
### available, which was not possible for the kmer_count step.
cpu_num = psutil.cpu_count()
###Compute the number of lines to process per thread (chunk size)
line = iptf.readline()
line_size = sys.getsizeof(line)
chunkLength = int(1024 ** 3 / cpu_num / line_size)
print('chunkLength = {}'.format(chunkLength))
while True:
lines = []
for nLines in range(chunkLength):
if not line: #if empty
break
lines.append(line)
line = iptf.readline()
if not lines: #if empty
break
###Compute shared kmer matrix
with PPE(max_workers = cpu_num) as executor:
for result in executor.map(countShared_single,lines):
for i in range(sn):
for j in range(i + 1, sn):
nshare[i][j] += result[i][j]
iptf.close()
###Compute distance matrix
ntotal = [0.0] * sn
for i in range(sn):
ntotal[i] = float(total.readline().split()[1])
dist = [[0] * sn for i in range(sn)]
for i in range(sn):
for j in range(i + 1, sn):
mintotal = min(ntotal[i], ntotal[j])
if nshare[i][j] == 0:
dist[j][i] = dist[i][j] = 1
else:
distance = (-1 / float(kl) * math.log(nshare[i][j] / mintotal))
#print(mintotal,nshare[i][j])
dist[j][i] = dist[i][j] = distance
nshare[j][i] = nshare[i][j]
total.close()
###Write infile
infile.write('{} {}'.format(sn, sn))
namedic = {}
for i in range(sn):
lsl = len(sl[i])
if lsl >= 10:
ssl = sl[i][:10]
appendix = 1
while ssl in namedic:
ssl = ssl[:-len(str(appendix))] + str(appendix)
appendix += 1
if lsl < 10:
ssl = sl[i] + ' ' * (10 - lsl)
namedic[ssl] = sl[i]
infile.write('\n{}'.format(ssl))
for j in range(sn):
infile.write('\t{}'.format(dist[i][j]))
infile.close()
###Run fitch_kmer
print('{} building tree'.format(time.strftime("%c")))
if os.path.exists("./outfile"):
os.system("rm -f outfile outtree")
command = 'printf "K\n{}\nY" | {} > /dev/null'.format(int(kl),fitch)
os.system(command)
fh = open('outtree','rt')
fh1 = open(datfile.split('.')[0]+'.tre','wt')
for line in fh:
for key in namedic:
key_new = key.rstrip()+":"
if key_new in line:
newline = line.replace(key_new,namedic[key].rstrip()+":",1)
line = newline
fh1.write(line) #This can be either line or new line because when it exits
#the for loop, line==newline
fh.close()
fh1.close()
command = 'mv infile {}.dist'.format(datfile.split('.')[0])
os.system(command)
os.system('rm -f outfile outtree')
print('{} end'.format(time.strftime("%c")))
driver.get(url)
html = driver.page_source
soup = bs4.BeautifulSoup(html, 'lxml')
belements = soup.find_all('input', {'class': 'LinkButton'})
selements = driver.find_elements_by_xpath(
'//input[contains(@class,"LinkButton")]')
#print(selements)
element = selements[index]
print('try', belements[index].get('value'))
for i in range(10**10):
print('now', i + 1, belements[index].get('value'))
try:
element.click()
html = driver.page_source
save_html_with_hash(html)
except Exception as ex:
print(ex)
element = driver.find_element_by_xpath(
'//input[contains(@name,"fwListNaviBtnNext")]')
except Exception as ex:
print(ex)
driver.quit()
url = 'https://www.hellowork.go.jp/servicef/130020.do?action=initDisp&screenId=130020'
args = []
for index in range(53):
args.append((url, index))
with PPE(max_workers=53) as exe:
exe.map(run, args)
executor.submit(ocrFunc, fileListToBeScanned[i])
if __name__ == "__main__":
startTime = time.time()
imagesFolderPath_1 = getAbsFolderPath("imgP1")
imagesFolderFileList_1 = os.listdir("imgP1")
imgP1Dir = list(
map(lambda x: imagesFolderPath_1 + x, imagesFolderFileList_1))
imagesFolderPath_2 = getAbsFolderPath("imgP2")
imagesFolderFileList_2 = os.listdir("imgP2")
imgP2Dir = list(
map(lambda x: imagesFolderPath_2 + x, imagesFolderFileList_2))
imagesFolderPath_3 = getAbsFolderPath("imgP3")
imagesFolderFileList_3 = os.listdir("imgP3")
imgP3Dir = list(
map(lambda x: imagesFolderPath_3 + x, imagesFolderFileList_3))
imagesFolderPath_4 = getAbsFolderPath("imgP4")
imagesFolderFileList_4 = os.listdir("imgP4")
imgP4Dir = list(
map(lambda x: imagesFolderPath_4 + x, imagesFolderFileList_4))
#开4个进程同时处理，每个进程包含8个线程
with PPE(multiprocessing.cpu_count() * 2) as executor:
# compressImage("./imgP1","./imgP1_compressed")
submitOCRExecutor(multiProcessingDetect, imgP1Dir, imgP2Dir, imgP3Dir,
imgP4Dir)
endTime = time.time()
print(endTime - startTime, " sec used")
def initialize_pool(cls, num_processes=0):
if num_processes > 1:
if DDFacetSim.__exec_pool is None:
DDFacetSim.__exec_pool = PPE(max_workers=num_processes)
DDFacetSim.__IN_PARALLEL_INIT = True
def aaf_kmercount(dataDir,k,n,nThreads,memPerThread):
#check excutables
if k > 25:
if os.system('which kmer_countx > /dev/null'):
kmerCount = './kmer_countx'
if not is_exe(kmerCount):
print('kmer_countx not found. Make sure it is in your PATH or the')
print('current directory, and that it is executable')
sys.exit(1)
else:
kmerCount = 'kmer_countx'
else:
if os.system('which kmer_count > /dev/null'):
kmerCount = './kmer_count'
if not is_exe(kmerCount):
print('kmer_count not found. Make sure it is in your PATH or the')
print('current directory, and that it is executable')
sys.exit(1)
else:
kmerCount = 'kmer_count'
###Get sample list:
samples = []
for fileName in os.listdir(dataDir):
if os.path.isdir(os.path.join(dataDir, fileName)):
samples.append(fileName)
else:
if not fileName.startswith('.'):
sample = fileName.split(".")[0]
if sample in samples:
sample = fileName.split(".")[0]+fileName.split(".")[1]
if sample in samples:
print('Error, redundant sample or file names. Aborting!')
sys.exit(3)
os.system("mkdir {}/{}".format(dataDir,sample))
os.system("mv {}/{} {}/{}/".format(dataDir,fileName,dataDir,sample))
samples.append(sample)
samples.sort()
print(time.strftime('%c'))
print('SPECIES LIST:')
for sample in samples:
print(sample)
###Prepare kmer_count jobs
jobList = []
for sample in samples:
outFile = '{}.pkdat.gz'.format(sample)
command = '{} -l {} -n {} -G {} -o {} -f '.format(kmerCount, k, n,
memPerThread, outFile)
command1 = ''
for inputFile in os.listdir(os.path.join(dataDir, sample)):
inputFile = os.path.join(dataDir, sample, inputFile)
handle = smartopen(inputFile)
firstChar = handle.read(1)
if firstChar == '@':
seqFormat = 'FQ'
elif firstChar == '>':
seqFormat = 'FA'
else:
print('Error, file {} is not FA or FQ format. Aborting!'.format(inputFile))
sys.exit(3)
command1 += " -i '{}'".format(inputFile)
command += '{}{}> {}.wc'.format(seqFormat,command1,sample)
jobList.append(command)
###Run jobs
with PPE(max_workers = nThreads) as executor:
executor.map(run_command,jobList)
return samples
def main(): with PPE(max_workers=2) as exe: exe.map(rap, [random_sample, filter_words])
r = requests.get(simple_url)
r.encoding = r.apparent_encoding
html = r.text
open(f'darturl_clean/{link_hash}', 'w').write( simple_url )
open(f'htmls/{simple_hash}.gz', 'wb').write( gzip.compress( bytes(html,'utf8') ) )
print(simple_url)
from concurrent.futures import ProcessPoolExecutor as PPE
paths = [path for path in Path('./xml_parse').glob('*')]
def pmap(path):
#print(path)
obj = json.load(path.open())
#print( obj )
link = obj['link']
link_hash = obj['link_hash']
if 'rdsig.yahoo.co.jp' in link:
# rdsigは量が多すぎて評価できないので無視する
print(link)
rdsig((link, link_hash))
...
else:
print(link)
pickup((link, link_hash))
with PPE(max_workers=24) as exe:
exe.map(pmap, paths)
description=description, body=body, hrefs=hrefs)
ffdb.save(key=url, val=parsed)
except UnicodeError as ex:
Path(path).unlink()
except UnicodeEncodeError as ex:
Path(path).unlink()
except EOFError as ex:
Path(path).unlink()
except Exception as ex:
print(ex)
ffdb.save(key=url, val=None)
gc.collect()
print('finish batch', key)
args = {}
files = list(glob.glob('./tmp/htmls/*'))
random.shuffle(files)
size = len(files)
for idx, path in enumerate(files):
key = idx % (size//100000)
#key = idx % 16
if args.get(key) is None:
args[key] = []
args[key].append(path)
args = [(key, paths) for key, paths in args.items()]
print('made chunks')
#[pmap(arg) for arg in args]
with PPE(max_workers=8) as exe:
exe.map(pmap, args)
#href = re.sub(r'\?.*?$', '', href)
hrefs.add(a.get('href'))
except Exception as ex:
print(ex)
continue
return hrefs
if '--resume' in sys.argv:
urls = pickle.load(open('urls.pkl', 'rb') )
else:
urls = pmap((-1, [url]))
print(urls)
DIST = 1
args = { key:[] for key in range(DIST) }
[ args[index%DIST].append(url) for index, url in enumerate(urls) ]
args = [ (key,urls) for key, urls in args.items() ]
#[ pmap(arg) for arg in args ]
from concurrent.futures import ProcessPoolExecutor as PPE
while True:
with PPE(max_workers=DIST) as exe:
urls = set()
for _hrefs in exe.map(pmap, args):
urls |= _hrefs
pickle.dump( urls, open('urls.pkl', 'wb') )
args = { key:[] for key in range(DIST) }
[ args[index%DIST].append(url) for index, url in enumerate(urls) ]
args = [ (key,urls) for key, urls in args.items() ]
if os.path.exists('./'+selection_dir):
command = 'rm -r {}'.format(selection_dir)
os.system(command)
command = 'mkdir {}'.format(selection_dir)
os.system(command)
#Run ReadsSelector
reads_cmd = []
for sample in samples:
infiles = os.listdir(os.path.join(dataDir,sample))
command = '{} -k sba.kmer -fa 1 -o {}/{}_selected '.format(ReadsSelector,selection_dir,sample)
for infile in infiles:
command += '-s {}'.format(os.path.join(dataDir,sample,infile))
reads_cmd.append(command)
with PPE(max_workers = nThreads) as executor:
executor.map(run_command,reads_cmd)
#After selection
samples = aaf_kmercount(selection_dir,kl,n,options.nThreads,memSize/options.nThreads)
###Merge output wc files
divFile = selection_dir+'.wc'
handle = open(divFile, 'w')
handle.close()
for sample in samples:
countfile = sample + '.wc'
os.system('cat {} >> {}'.format(countfile, divFile))
os.remove(countfile)
