def __init__(self, parameters, poly_file):
self.parameters = parameters
params = self.parameters.myparams(
{
"name": str,
"workdir": str,
"batch_size": int
}, ['tasks', 'sieve'])
self.name = params.get("name")
self.workdir = params.get("workdir")
self.batch_size = params.get("batch_size")
# variables that are accessed from multiple threads
self.stage = 'sieve'
self.stage_lock = threading.Lock()
self.finished = False
self.finished_lock = threading.Lock()
self.queue = deque()
self.queue_lock = threading.Lock()
self.rels_total = 0
self.rels_total_lock = threading.Lock()
# if rels_wanted is not set, then specify a default initial value based on the large prime bounds
self.rels_wanted = parameters.myparams({
"rels_wanted": 0
}, ["tasks", "sieve", "sieving", "las"]).get("rels_wanted")
if self.rels_wanted == 0:
# taking into account duplicates, the initial value
# pi(2^lpbr) + pi(2^lpba) should be good
paths = ["tasks", "sieve", "sieving", "las"]
nr = 2**self.parameters.myparams({"lpbr": int}, paths).get("lpbr")
na = 2**self.parameters.myparams({"lpba": int}, paths).get("lpba")
nra = int(nr / log(nr) + na / log(na))
self.rels_wanted = nra
self.rels_wanted_lock = threading.Lock()
# compile regular expressions here for speed
self.relation_re = re.compile("(-?\d*),(\d*):(.*)")
self.relation_total_re = re.compile("# Total (\d+) reports")
self.relation_file_re = re.compile("%s[.]sieving[.](\d+)-(\d+)[.]gz" %
self.name)
self.completed_factorization = False
self.poly_file = poly_file
self.poly = None
with open(self.poly_file, 'r') as f:
self.poly = Polynomials(f.readlines())
self.reldir = os.path.join(self.workdir, self.name + ".upload")
self.msieve_dat_file = os.path.join(self.workdir, self.name + ".dat")
# The relation files that we will pass on to filtering
# TODO: we might not need this variable
self.relation_files = []
# The set of files that we have already seen and processed
self.seen_files = set()
self.fb_paths = None
self.freerel_output = None
self.generator = None
self.start_time = None
def parse_poly(input):
block = []
for line in input.split("\n"):
line = line.strip()
if line:
block.append(line)
else:
if block:
try:
yield Polynomials(block)
except Exception as e:
pass
block = []
if block:
try:
yield Polynomials(block)
except Exception as e:
pass
def __init__(self, parameters, poly_file):
self.parameters = parameters
params = self.parameters.myparams({
"name": str,
"workdir": str,
"batch_size": int
}, ['tasks', 'sieve'])
self.name = params.get("name")
self.workdir = params.get("workdir")
self.batch_size = params.get("batch_size")
# variables that are accessed from multiple threads
self.stage = 'sieve'
self.stage_lock = threading.Lock()
self.finished = False
self.finished_lock = threading.Lock()
self.queue = deque()
self.queue_lock = threading.Lock()
self.rels_total = 0
self.rels_total_lock = threading.Lock()
# if rels_wanted is not set, then specify a default initial value based on the large prime bounds
self.rels_wanted = parameters.myparams({"rels_wanted": 0}, ["tasks", "sieve", "sieving", "las"]).get("rels_wanted")
if self.rels_wanted == 0:
# taking into account duplicates, the initial value
# pi(2^lpbr) + pi(2^lpba) should be good
paths = ["tasks", "sieve", "sieving", "las"]
nr = 2 ** self.parameters.myparams({"lpbr": int}, paths).get("lpbr")
na = 2 ** self.parameters.myparams({"lpba": int}, paths).get("lpba")
nra = int(nr / log(nr) + na / log(na))
self.rels_wanted = nra
self.rels_wanted_lock = threading.Lock()
# compile regular expressions here for speed
self.relation_re = re.compile("(-?\d*),(\d*):(.*)")
self.relation_total_re = re.compile("# Total (\d+) reports")
self.relation_file_re = re.compile("%s[.]sieving[.](\d+)-(\d+)[.]gz" % self.name)
self.completed_factorization = False
self.poly_file = poly_file
self.poly = None
with open(self.poly_file, 'r') as f:
self.poly = Polynomials(f.readlines())
self.reldir = os.path.join(self.workdir, self.name + ".upload")
self.msieve_dat_file = os.path.join(self.workdir, self.name + ".dat")
# The relation files that we will pass on to filtering
# TODO: we might not need this variable
self.relation_files = []
# The set of files that we have already seen and processed
self.seen_files = set()
self.fb_paths = None
self.freerel_output = None
self.generator = None
self.start_time = None
class Sieve:
def __init__(self, parameters, poly_file):
self.parameters = parameters
params = self.parameters.myparams({
"name": str,
"workdir": str,
"batch_size": int
}, ['tasks', 'sieve'])
self.name = params.get("name")
self.workdir = params.get("workdir")
self.batch_size = params.get("batch_size")
# variables that are accessed from multiple threads
self.stage = 'sieve'
self.stage_lock = threading.Lock()
self.finished = False
self.finished_lock = threading.Lock()
self.queue = deque()
self.queue_lock = threading.Lock()
self.rels_total = 0
self.rels_total_lock = threading.Lock()
# if rels_wanted is not set, then specify a default initial value based on the large prime bounds
self.rels_wanted = parameters.myparams({"rels_wanted": 0}, ["tasks", "sieve", "sieving", "las"]).get("rels_wanted")
if self.rels_wanted == 0:
# taking into account duplicates, the initial value
# pi(2^lpbr) + pi(2^lpba) should be good
paths = ["tasks", "sieve", "sieving", "las"]
nr = 2 ** self.parameters.myparams({"lpbr": int}, paths).get("lpbr")
na = 2 ** self.parameters.myparams({"lpba": int}, paths).get("lpba")
nra = int(nr / log(nr) + na / log(na))
self.rels_wanted = nra
self.rels_wanted_lock = threading.Lock()
# compile regular expressions here for speed
self.relation_re = re.compile("(-?\d*),(\d*):(.*)")
self.relation_total_re = re.compile("# Total (\d+) reports")
self.relation_file_re = re.compile("%s[.]sieving[.](\d+)-(\d+)[.]gz" % self.name)
self.completed_factorization = False
self.poly_file = poly_file
self.poly = None
with open(self.poly_file, 'r') as f:
self.poly = Polynomials(f.readlines())
self.reldir = os.path.join(self.workdir, self.name + ".upload")
self.msieve_dat_file = os.path.join(self.workdir, self.name + ".dat")
# The relation files that we will pass on to filtering
# TODO: we might not need this variable
self.relation_files = []
# The set of files that we have already seen and processed
self.seen_files = set()
self.fb_paths = None
self.freerel_output = None
self.generator = None
self.start_time = None
def generate_sieving_task_commands(self):
paths = ["tasks", "sieve", "sieving", "las"]
program_to_run = cadoprograms.Las
progparams = self.parameters.myparams(program_to_run.get_accepted_keys(), paths)
progparams.pop("q0", None)
progparams.pop("q1", None)
progparams.pop("factorbase", None)
progparams.pop("out", None)
progparams.pop("poly", None)
progparams.pop("stats-stderr", None)
params = self.parameters.myparams({
"alim": int,
"rlim": int,
"qrange": int,
"lpba": int,
"qmin": [int],
"execpath": str,
}, paths)
start = 0
if "qmin" in params:
start = params.get("qmin")
else:
start = params.get("alim")
last_q1 = start
qrange = params.get("qrange")
qmax = 2 ** params.get("lpba")
while (True):
q0 = last_q1
q1 = q0 + qrange
last_q1 = q1
# the special q values should always remain below 2^lpba
if (q0 >= qmax):
logger.debug("Stopping attempt to create tasks with special q values greater than 2**lpba")
break
# allow q1 to be at most the algebraic large prime bound
q1 = min(q1, qmax)
out_file = os.path.join(self.reldir, self.name + '.sieving.' + str(q0) + '-' + str(q1) + '.gz')
# check if out_file is one of our previously seen files
if out_file in self.seen_files:
continue
if len(self.fb_paths) > 1: # is twoalgosides
program = cadoprograms.Las(q0=q0, q1=q1, factorbase0=self.fb_paths[0], factorbase1=self.fb_paths[1], out=out_file, poly=self.poly_file, stats_stderr=True, **progparams)
else:
program = cadoprograms.Las(q0=q0, q1=q1, factorbase=self.fb_paths[0], out=out_file, poly=self.poly_file, stats_stderr=True, **progparams)
cmd = program.make_command_line()
cmd_logger.debug(cmd)
yield (out_file, cmd)
def submit_batch(self):
jobs = []
for i in range(self.batch_size):
try:
jobs.append(next(self.generator))
except StopIteration:
logger.debug("Unable to generate any more tasks")
# we cannot generate any more commands
break
logger.info("Submitting %d additional jobs", len(jobs))
i = 0
num_submitted = 0
batch_file = str(os.path.join(self.workdir, 'sieving.sh'))
for filen, cmd in jobs:
with open(batch_file, 'w') as f:
f.write("#!/bin/sh\n")
f.write("#SBATCH -p factor\n")
f.write("#SBATCH -J %s\n" % filen.split('/')[-1])
f.write("#SBATCH -n 1\n")
f.write("#SBATCH -c 2\n")
f.write("#SBATCH -s\n")
f.write("#SBATCH --requeue\n")
f.write("#SBATCH --output=/dev/null\n")
f.write("srun --output=%s.out %s 2>&1\n" % (filen, cmd))
f.write("wait\n")
os.chmod(batch_file, 0o755)
utils.run_command('sbatch ' + batch_file)
if i >= 100:
logger.debug("Submitted %d/%d sieve jobs", num_submitted, len(jobs))
i = 0
if self.is_finished():
return
num_submitted += 1
i += 1
def verify_relation(self, line):
""" Check that the primes listed for a relation divide the value of
the polynomials """
match = self.relation_re.match(line)
if match:
a, b, rest = match.groups()
a, b = int(a), int(b)
sides = rest.split(":")
assert len(sides) == 2
for side, primes_as_str in enumerate(sides):
value = self.poly.get_polynomial(side).eval_h(a, b)
primes = [int(s, 16) for s in primes_as_str.split(",")]
for prime in primes:
if value % prime != 0:
return False
return True
return None
def process_relation_file(self, filename):
if not os.path.isfile(filename):
logger.warning("File '%s' does not exist", filename)
return 0
try:
relations = []
count = 0
# check some relations in the file before importing
relations_to_check = 10
with gzip.open(filename, 'rt', encoding='utf-8') as f:
for line in f:
if relations_to_check > 0:
result = self.verify_relation(line)
if result is True:
relations_to_check -= 1
elif result is False:
return 0
else: # Did not match: try again
pass
if line[0] != '#':
relations.append(line)
count += 1
if relations_to_check == 0:
with open(self.msieve_dat_file, 'at', encoding='utf-8') as f:
f.write(''.join(relations))
# return the relation count in this file
return count
except Exception as e:
logger.warning("Exception in file '%s': %s", filename, e)
# This will be reached on an exception or if at least 10 relations do not check out
return 0
def check_relation_file(self, filename):
# check that the .out file exists (otherwise, the .gz file might not be complete)
outfile = filename + '.out'
outfile_count = 0
relfile_count = 0
match = None
if not os.path.isfile(outfile):
return 0
outfile_count = 0
with open(outfile, 'rt', encoding='utf-8') as f:
# Check for line matching '# Total 12377 reports [0.00429s/r, 18.0r/sq]'
match = self.relation_total_re.findall(f.read())
if match:
outfile_count = int(match[0])
return outfile_count
def import_relations(self, location):
gz_files = []
if os.path.isfile(location):
with open(location, 'r') as f:
gz_files = [i for i in f if self.relation_file_re.match(i) ]
elif os.path.isdir(location):
d = os.listdir(location)
all_gz_files = [ str(os.path.join(location, i)) for i in d if self.relation_file_re.match(i) ]
unseen_gz_files = [ i for i in all_gz_files if i not in self.seen_files ]
gz_files = [ i for i in unseen_gz_files if self.check_relation_file(i) ]
self.seen_files.update(set(gz_files))
return gz_files
def set_stage(self, stage):
with self.stage_lock:
self.stage = stage
def get_stage(self):
with self.stage_lock:
return self.stage
def set_finished(self):
with self.finished_lock:
self.finished = True
def is_finished(self):
with self.finished_lock:
return self.finished
def run_slurm_thread(self):
while not self.is_finished():
# check if there are enough jobs running
jobs_out = utils.run_command("squeue -t PENDING,RUNNING,COMPLETING").strip().split('\n')
logger.info("Number of queued jobs: %d", len(jobs_out) - 1)
if len(jobs_out) < 2 * self.batch_size:
self.submit_batch()
sleep(10)
def run_sieving(self):
logger.info("Starting Sieving...")
self.start_time = time.time()
if os.path.isfile(self.msieve_dat_file):
logger.info("Removing existing .dat file for msieve")
os.remove(self.msieve_dat_file)
with open(self.msieve_dat_file, 'wt', encoding='utf-8') as f:
f.write(str(self.parameters.myparams({'N': int}, [])['N']))
f.write('\n')
# check if we should import relations
import_relation_file = self.parameters.myparams({'import': None}, ['tasks', 'sieve']).get('import')
if import_relation_file:
logger.info("Importing relations from file '%s'", import_relation_file)
imported_files = self.import_relations(import_relation_file)
self.queue_extend(imported_files)
logger.info("Found %d relation files in file '%s'", len(imported_files), self.reldir)
if not os.path.exists(self.reldir):
# create the directory for relations if it does not yet exist
logger.info("Creating directory for relations %s", self.reldir)
os.makedirs(self.reldir)
else:
# check if there are relations in the directory already and add them to the import queue.
# We do this check once outside the loop so that we know which tasks not to regenerate
logger.info("Importing relations files from directory '%s;", self.reldir)
imported_files = self.import_relations(self.reldir)
self.queue_extend(imported_files)
logger.info("Found %d relation files in directory '%s'", len(imported_files), self.reldir)
# generate sieving task commands, skipping files that have already been generated
self.generator = self.generate_sieving_task_commands()
# spawn a thread to launch sieving tasks until sieving is finished
slurm_thread = threading.Thread(target=self.run_slurm_thread)
slurm_thread.start()
# spawn a thread to print out a status message periodically
status_thread = threading.Thread(target=self.run_status_thread)
status_thread.start()
# spawn a thread to filter periodically until sieving is finished
filter_thread = threading.Thread(target=self.run_filter_thread)
filter_thread.start()
# wait until filter thread completes
try:
filter_thread.join()
slurm_thread.join()
status_thread.join()
finally:
utils.run_command("scancel -p factor")
def queue_empty(self):
with self.queue_lock:
return False if self.queue else True
def queue_pop(self):
with self.queue_lock:
return self.queue.popleft()
def queue_extend(self, elements):
with self.queue_lock:
self.queue.extend(elements)
def get_rels_total(self):
with self.rels_total_lock:
return self.rels_total
def set_rels_total(self, value):
with self.rels_total_lock:
self.rels_total = value
def get_rels_wanted(self):
with self.rels_wanted_lock:
return self.rels_wanted
def set_rels_wanted(self, value):
with self.rels_wanted_lock:
self.rels_wanted = value
def run_filter_thread(self):
# first, initialize filtering state
filtering.init(self.parameters, self.freerel_output)
# a list of new files to be passed in to filtering
new_files = []
while True:
# check if there are relations in the directory already and add them to the import deque
imported_files = self.import_relations(self.reldir)
self.queue_extend(imported_files)
# process files from queue until we reach rels_wanted or the queue is empty
while not self.queue_empty():
filename = self.queue_pop()
count = self.process_relation_file(filename)
self.set_rels_total(self.get_rels_total() + count)
self.relation_files.append(filename)
new_files.append(filename)
logger.info("Found %d new relations in %s. Total %d/%d (%.2f%%)",\
count, filename, self.get_rels_total(), self.get_rels_wanted(), 100 * self.get_rels_total() / self.get_rels_wanted())
if self.get_rels_total() >= self.get_rels_wanted():
logger.info("Reached rels_wanted with %d/%d relations", self.get_rels_total(), self.get_rels_wanted())
# stop processing output files when we've reached our target
break
if self.get_rels_total() >= self.get_rels_wanted():
self.set_stage('filter')
rels_additional = filtering.run(new_files)
new_files = []
if rels_additional == 0:
break
elif rels_additional == -1:
rels_addtional = math.ceil(self.get_rels_wanted() * 0.1)
elif rels_additional == -2:
self.completed_factorization = True
break
elif rels_additional > 0:
self.set_rels_wanted(self.get_rels_wanted() + rels_additional)
else:
logger.error('unexpected value for rels_additional: ', rels_additional)
sys.exit(1)
else:
self.set_stage('sieve')
sleep(10)
self.set_finished()
def run_status_thread(self):
while not self.is_finished():
# give the user a status update
stage = self.get_stage()
if stage == 'sieve':
elapsed = time.time() - self.start_time
rels_total = self.get_rels_total()
rels_wanted = self.get_rels_wanted()
rate = rels_total / elapsed
eta = 0
if rate > 0:
eta = (rels_wanted - rels_total) / rate
logger.info("Status: %d/%d relations at %d rels/sec - elapsed: %s, ETA: %s", rels_total, rels_wanted, int(rate), utils.str_time(elapsed), utils.str_time(eta))
elif stage == 'filter':
logger.info("Status: performing filtering")
sleep(10)
def run_factor_base(self):
logger.info("Starting FactorBase...")
paths = ["tasks", "sieve", "factorbase", "makefb"]
fb_params = self.parameters.myparams({"gzip": True, "I": int, "rlim": int, "alim": int}, paths)
program_to_run = cadoprograms.MakeFB
progparams = self.parameters.myparams(program_to_run.get_accepted_keys(), paths)
progparams.setdefault("maxbits", fb_params["I"] - 1)
input_files = {"poly": self.poly_file}
merged_args = dict(progparams.items() | input_files.items())
use_gz = ".gz" if fb_params["gzip"] else ""
twoalgsides = self.poly.polyg.degree > 1
outpath = os.path.join(self.workdir, "factorbase")
if not os.path.exists(outpath):
logger.info("Creating directory for factorbase %s", outpath)
os.makedirs(outpath)
outputfiles = ["%s/roots%d%s" % (outpath, i, use_gz) for i in range(1 + twoalgsides)]
if not twoalgsides:
p = cadoprograms.MakeFB(out=outputfiles[0], lim=fb_params["alim"], **merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
utils.run_command(command_line)
logger.info("FactorBase: Created outputfile %s", outputfiles[0])
else:
p = cadoprograms.MakeFB(out=outputfiles[1], side=0, lim=fb_params["rlim"], **merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
utils.run_command(command_line)
logger.info("FactorBase: Created outputfile %s", outputfiles[1])
p = cadoprograms.MakeFB(out=outputfiles[0], side=1, lim=self.params["alim"], **merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
utils.run_command(command_line)
logger.info("FactorBase: Created outputfile %s", outputfiles[0])
self.fb_paths = outputfiles
def parse_freerel_output(self, text):
wanted_regex = {
'nfree': (r'# Free relations: (\d+)', int),
'nprimes': (r'Renumbering struct: nprimes=(\d+)', int)
}
found = {}
for line in text.split("\n"):
for (key, (regex, datatype)) in wanted_regex.items():
match = re.match(regex, line)
if match:
found[key] = datatype(match.group(1))
return found
def run_freerel(self):
logger.info("Starting FreeRel...")
paths = ["tasks", "sieve", "freerel"]
program_to_run = cadoprograms.FreeRel
progparams = self.parameters.myparams(program_to_run.get_accepted_keys(), paths)
progparams.setdefault("addfullcol", True)
input_files = {"poly": self.poly_file}
merged_args = dict(progparams.items() | input_files.items())
use_gz = ".gz" if self.parameters.myparams({"gzip": True}, paths) else ""
outpath = os.path.join(self.workdir, "freerel")
if not os.path.exists(outpath):
logger.info("Creating directory for freerel %s", outpath)
os.makedirs(outpath)
freerelfilename = "%s/freerel%s" % (outpath, use_gz)
renumberfilename = "%s/renumber%s" % (outpath, use_gz)
p = cadoprograms.FreeRel(renumber=renumberfilename, out=freerelfilename, **merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
stdout, stderr = utils.run_command(command_line, include_stdout=True, include_stderr=True, logger=logger)
freerel_output = self.parse_freerel_output(stderr)
freerel_output["freerelfilename"] = freerelfilename
freerel_output["renumberfilename"] = renumberfilename
logger.info("FreeRel: Created outputfile %s", freerelfilename)
logger.info("FreeRel: Created outputfile %s", renumberfilename)
self.freerel_output = freerel_output
def run(self):
self.run_factor_base()
self.run_freerel()
self.run_sieving()
return self.relation_files
class Sieve:
def __init__(self, parameters, poly_file):
self.parameters = parameters
params = self.parameters.myparams(
{
"name": str,
"workdir": str,
"batch_size": int
}, ['tasks', 'sieve'])
self.name = params.get("name")
self.workdir = params.get("workdir")
self.batch_size = params.get("batch_size")
# variables that are accessed from multiple threads
self.stage = 'sieve'
self.stage_lock = threading.Lock()
self.finished = False
self.finished_lock = threading.Lock()
self.queue = deque()
self.queue_lock = threading.Lock()
self.rels_total = 0
self.rels_total_lock = threading.Lock()
# if rels_wanted is not set, then specify a default initial value based on the large prime bounds
self.rels_wanted = parameters.myparams({
"rels_wanted": 0
}, ["tasks", "sieve", "sieving", "las"]).get("rels_wanted")
if self.rels_wanted == 0:
# taking into account duplicates, the initial value
# pi(2^lpbr) + pi(2^lpba) should be good
paths = ["tasks", "sieve", "sieving", "las"]
nr = 2**self.parameters.myparams({"lpbr": int}, paths).get("lpbr")
na = 2**self.parameters.myparams({"lpba": int}, paths).get("lpba")
nra = int(nr / log(nr) + na / log(na))
self.rels_wanted = nra
self.rels_wanted_lock = threading.Lock()
# compile regular expressions here for speed
self.relation_re = re.compile("(-?\d*),(\d*):(.*)")
self.relation_total_re = re.compile("# Total (\d+) reports")
self.relation_file_re = re.compile("%s[.]sieving[.](\d+)-(\d+)[.]gz" %
self.name)
self.completed_factorization = False
self.poly_file = poly_file
self.poly = None
with open(self.poly_file, 'r') as f:
self.poly = Polynomials(f.readlines())
self.reldir = os.path.join(self.workdir, self.name + ".upload")
self.msieve_dat_file = os.path.join(self.workdir, self.name + ".dat")
# The relation files that we will pass on to filtering
# TODO: we might not need this variable
self.relation_files = []
# The set of files that we have already seen and processed
self.seen_files = set()
self.fb_paths = None
self.freerel_output = None
self.generator = None
self.start_time = None
def generate_sieving_task_commands(self):
paths = ["tasks", "sieve", "sieving", "las"]
program_to_run = cadoprograms.Las
progparams = self.parameters.myparams(
program_to_run.get_accepted_keys(), paths)
progparams.pop("q0", None)
progparams.pop("q1", None)
progparams.pop("factorbase", None)
progparams.pop("out", None)
progparams.pop("poly", None)
progparams.pop("stats-stderr", None)
params = self.parameters.myparams(
{
"alim": int,
"rlim": int,
"qrange": int,
"lpba": int,
"qmin": [int],
"execpath": str,
}, paths)
start = 0
if "qmin" in params:
start = params.get("qmin")
else:
start = params.get("alim")
last_q1 = start
qrange = params.get("qrange")
qmax = 2**params.get("lpba")
while (True):
q0 = last_q1
q1 = q0 + qrange
last_q1 = q1
# the special q values should always remain below 2^lpba
if (q0 >= qmax):
logger.debug(
"Stopping attempt to create tasks with special q values greater than 2**lpba"
)
break
# allow q1 to be at most the algebraic large prime bound
q1 = min(q1, qmax)
out_file = os.path.join(
self.reldir,
self.name + '.sieving.' + str(q0) + '-' + str(q1) + '.gz')
# check if out_file is one of our previously seen files
if out_file in self.seen_files:
continue
if len(self.fb_paths) > 1: # is twoalgosides
program = cadoprograms.Las(q0=q0,
q1=q1,
factorbase0=self.fb_paths[0],
factorbase1=self.fb_paths[1],
out=out_file,
poly=self.poly_file,
stats_stderr=True,
**progparams)
else:
program = cadoprograms.Las(q0=q0,
q1=q1,
factorbase=self.fb_paths[0],
out=out_file,
poly=self.poly_file,
stats_stderr=True,
**progparams)
cmd = program.make_command_line()
cmd_logger.debug(cmd)
yield (out_file, cmd)
def submit_batch(self):
jobs = []
for i in range(self.batch_size):
try:
jobs.append(next(self.generator))
except StopIteration:
logger.debug("Unable to generate any more tasks")
# we cannot generate any more commands
break
logger.info("Submitting %d additional jobs", len(jobs))
i = 0
num_submitted = 0
batch_file = str(os.path.join(self.workdir, 'sieving.sh'))
for filen, cmd in jobs:
with open(batch_file, 'w') as f:
f.write("#!/bin/sh\n")
f.write("#SBATCH -p factor\n")
f.write("#SBATCH -J %s\n" % filen.split('/')[-1])
f.write("#SBATCH -n 1\n")
f.write("#SBATCH -c 2\n")
f.write("#SBATCH -s\n")
f.write("#SBATCH --requeue\n")
f.write("#SBATCH --output=/dev/null\n")
f.write("srun --output=%s.out %s 2>&1\n" % (filen, cmd))
f.write("wait\n")
os.chmod(batch_file, 0o755)
utils.run_command('sbatch ' + batch_file)
if i >= 100:
logger.debug("Submitted %d/%d sieve jobs", num_submitted,
len(jobs))
i = 0
if self.is_finished():
return
num_submitted += 1
i += 1
def verify_relation(self, line):
""" Check that the primes listed for a relation divide the value of
the polynomials """
match = self.relation_re.match(line)
if match:
a, b, rest = match.groups()
a, b = int(a), int(b)
sides = rest.split(":")
assert len(sides) == 2
for side, primes_as_str in enumerate(sides):
value = self.poly.get_polynomial(side).eval_h(a, b)
primes = [int(s, 16) for s in primes_as_str.split(",")]
for prime in primes:
if value % prime != 0:
return False
return True
return None
def process_relation_file(self, filename):
if not os.path.isfile(filename):
logger.warning("File '%s' does not exist", filename)
return 0
try:
relations = []
count = 0
# check some relations in the file before importing
relations_to_check = 10
with gzip.open(filename, 'rt', encoding='utf-8') as f:
for line in f:
if relations_to_check > 0:
result = self.verify_relation(line)
if result is True:
relations_to_check -= 1
elif result is False:
return 0
else: # Did not match: try again
pass
if line[0] != '#':
relations.append(line)
count += 1
if relations_to_check == 0:
with open(self.msieve_dat_file, 'at', encoding='utf-8') as f:
f.write(''.join(relations))
# return the relation count in this file
return count
except Exception as e:
logger.warning("Exception in file '%s': %s", filename, e)
# This will be reached on an exception or if at least 10 relations do not check out
return 0
def check_relation_file(self, filename):
# check that the .out file exists (otherwise, the .gz file might not be complete)
outfile = filename + '.out'
outfile_count = 0
relfile_count = 0
match = None
if not os.path.isfile(outfile):
return 0
outfile_count = 0
with open(outfile, 'rt', encoding='utf-8') as f:
# Check for line matching '# Total 12377 reports [0.00429s/r, 18.0r/sq]'
match = self.relation_total_re.findall(f.read())
if match:
outfile_count = int(match[0])
return outfile_count
def import_relations(self, location):
gz_files = []
if os.path.isfile(location):
with open(location, 'r') as f:
gz_files = [i for i in f if self.relation_file_re.match(i)]
elif os.path.isdir(location):
d = os.listdir(location)
all_gz_files = [
str(os.path.join(location, i)) for i in d
if self.relation_file_re.match(i)
]
unseen_gz_files = [
i for i in all_gz_files if i not in self.seen_files
]
gz_files = [
i for i in unseen_gz_files if self.check_relation_file(i)
]
self.seen_files.update(set(gz_files))
return gz_files
def set_stage(self, stage):
with self.stage_lock:
self.stage = stage
def get_stage(self):
with self.stage_lock:
return self.stage
def set_finished(self):
with self.finished_lock:
self.finished = True
def is_finished(self):
with self.finished_lock:
return self.finished
def run_slurm_thread(self):
while not self.is_finished():
# check if there are enough jobs running
jobs_out = utils.run_command(
"squeue -t PENDING,RUNNING,COMPLETING").strip().split('\n')
logger.info("Number of queued jobs: %d", len(jobs_out) - 1)
if len(jobs_out) < 2 * self.batch_size:
self.submit_batch()
sleep(10)
def run_sieving(self):
logger.info("Starting Sieving...")
self.start_time = time.time()
if os.path.isfile(self.msieve_dat_file):
logger.info("Removing existing .dat file for msieve")
os.remove(self.msieve_dat_file)
with open(self.msieve_dat_file, 'wt', encoding='utf-8') as f:
f.write(str(self.parameters.myparams({'N': int}, [])['N']))
f.write('\n')
# check if we should import relations
import_relation_file = self.parameters.myparams({
'import': None
}, ['tasks', 'sieve']).get('import')
if import_relation_file:
logger.info("Importing relations from file '%s'",
import_relation_file)
imported_files = self.import_relations(import_relation_file)
self.queue_extend(imported_files)
logger.info("Found %d relation files in file '%s'",
len(imported_files), self.reldir)
if not os.path.exists(self.reldir):
# create the directory for relations if it does not yet exist
logger.info("Creating directory for relations %s", self.reldir)
os.makedirs(self.reldir)
else:
# check if there are relations in the directory already and add them to the import queue.
# We do this check once outside the loop so that we know which tasks not to regenerate
logger.info("Importing relations files from directory '%s;",
self.reldir)
imported_files = self.import_relations(self.reldir)
self.queue_extend(imported_files)
logger.info("Found %d relation files in directory '%s'",
len(imported_files), self.reldir)
# generate sieving task commands, skipping files that have already been generated
self.generator = self.generate_sieving_task_commands()
# spawn a thread to launch sieving tasks until sieving is finished
slurm_thread = threading.Thread(target=self.run_slurm_thread)
slurm_thread.start()
# spawn a thread to print out a status message periodically
status_thread = threading.Thread(target=self.run_status_thread)
status_thread.start()
# spawn a thread to filter periodically until sieving is finished
filter_thread = threading.Thread(target=self.run_filter_thread)
filter_thread.start()
# wait until filter thread completes
try:
filter_thread.join()
slurm_thread.join()
status_thread.join()
finally:
utils.run_command("scancel -p factor")
def queue_empty(self):
with self.queue_lock:
return False if self.queue else True
def queue_pop(self):
with self.queue_lock:
return self.queue.popleft()
def queue_extend(self, elements):
with self.queue_lock:
self.queue.extend(elements)
def get_rels_total(self):
with self.rels_total_lock:
return self.rels_total
def set_rels_total(self, value):
with self.rels_total_lock:
self.rels_total = value
def get_rels_wanted(self):
with self.rels_wanted_lock:
return self.rels_wanted
def set_rels_wanted(self, value):
with self.rels_wanted_lock:
self.rels_wanted = value
def run_filter_thread(self):
# first, initialize filtering state
filtering.init(self.parameters, self.freerel_output)
# a list of new files to be passed in to filtering
new_files = []
while True:
# check if there are relations in the directory already and add them to the import deque
imported_files = self.import_relations(self.reldir)
self.queue_extend(imported_files)
# process files from queue until we reach rels_wanted or the queue is empty
while not self.queue_empty():
filename = self.queue_pop()
count = self.process_relation_file(filename)
self.set_rels_total(self.get_rels_total() + count)
self.relation_files.append(filename)
new_files.append(filename)
logger.info("Found %d new relations in %s. Total %d/%d (%.2f%%)",\
count, filename, self.get_rels_total(), self.get_rels_wanted(), 100 * self.get_rels_total() / self.get_rels_wanted())
if self.get_rels_total() >= self.get_rels_wanted():
logger.info("Reached rels_wanted with %d/%d relations",
self.get_rels_total(), self.get_rels_wanted())
# stop processing output files when we've reached our target
break
if self.get_rels_total() >= self.get_rels_wanted():
self.set_stage('filter')
rels_additional = filtering.run(new_files)
new_files = []
if rels_additional == 0:
break
elif rels_additional == -1:
rels_addtional = math.ceil(self.get_rels_wanted() * 0.1)
elif rels_additional == -2:
self.completed_factorization = True
break
elif rels_additional > 0:
self.set_rels_wanted(self.get_rels_wanted() +
rels_additional)
else:
logger.error('unexpected value for rels_additional: ',
rels_additional)
sys.exit(1)
else:
self.set_stage('sieve')
sleep(10)
self.set_finished()
def run_status_thread(self):
while not self.is_finished():
# give the user a status update
stage = self.get_stage()
if stage == 'sieve':
elapsed = time.time() - self.start_time
rels_total = self.get_rels_total()
rels_wanted = self.get_rels_wanted()
rate = rels_total / elapsed
eta = 0
if rate > 0:
eta = (rels_wanted - rels_total) / rate
logger.info(
"Status: %d/%d relations at %d rels/sec - elapsed: %s, ETA: %s",
rels_total, rels_wanted, int(rate),
utils.str_time(elapsed), utils.str_time(eta))
elif stage == 'filter':
logger.info("Status: performing filtering")
sleep(10)
def run_factor_base(self):
logger.info("Starting FactorBase...")
paths = ["tasks", "sieve", "factorbase", "makefb"]
fb_params = self.parameters.myparams(
{
"gzip": True,
"I": int,
"rlim": int,
"alim": int
}, paths)
program_to_run = cadoprograms.MakeFB
progparams = self.parameters.myparams(
program_to_run.get_accepted_keys(), paths)
progparams.setdefault("maxbits", fb_params["I"] - 1)
input_files = {"poly": self.poly_file}
merged_args = dict(progparams.items() | input_files.items())
use_gz = ".gz" if fb_params["gzip"] else ""
twoalgsides = self.poly.polyg.degree > 1
outpath = os.path.join(self.workdir, "factorbase")
if not os.path.exists(outpath):
logger.info("Creating directory for factorbase %s", outpath)
os.makedirs(outpath)
outputfiles = [
"%s/roots%d%s" % (outpath, i, use_gz)
for i in range(1 + twoalgsides)
]
if not twoalgsides:
p = cadoprograms.MakeFB(out=outputfiles[0],
lim=fb_params["alim"],
**merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
utils.run_command(command_line)
logger.info("FactorBase: Created outputfile %s", outputfiles[0])
else:
p = cadoprograms.MakeFB(out=outputfiles[1],
side=0,
lim=fb_params["rlim"],
**merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
utils.run_command(command_line)
logger.info("FactorBase: Created outputfile %s", outputfiles[1])
p = cadoprograms.MakeFB(out=outputfiles[0],
side=1,
lim=self.params["alim"],
**merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
utils.run_command(command_line)
logger.info("FactorBase: Created outputfile %s", outputfiles[0])
self.fb_paths = outputfiles
def parse_freerel_output(self, text):
wanted_regex = {
'nfree': (r'# Free relations: (\d+)', int),
'nprimes': (r'Renumbering struct: nprimes=(\d+)', int)
}
found = {}
for line in text.split("\n"):
for (key, (regex, datatype)) in wanted_regex.items():
match = re.match(regex, line)
if match:
found[key] = datatype(match.group(1))
return found
def run_freerel(self):
logger.info("Starting FreeRel...")
paths = ["tasks", "sieve", "freerel"]
program_to_run = cadoprograms.FreeRel
progparams = self.parameters.myparams(
program_to_run.get_accepted_keys(), paths)
progparams.setdefault("addfullcol", True)
input_files = {"poly": self.poly_file}
merged_args = dict(progparams.items() | input_files.items())
use_gz = ".gz" if self.parameters.myparams({"gzip": True},
paths) else ""
outpath = os.path.join(self.workdir, "freerel")
if not os.path.exists(outpath):
logger.info("Creating directory for freerel %s", outpath)
os.makedirs(outpath)
freerelfilename = "%s/freerel%s" % (outpath, use_gz)
renumberfilename = "%s/renumber%s" % (outpath, use_gz)
p = cadoprograms.FreeRel(renumber=renumberfilename,
out=freerelfilename,
**merged_args)
command_line = p.make_command_line()
cmd_logger.debug(command_line)
stdout, stderr = utils.run_command(command_line,
include_stdout=True,
include_stderr=True,
logger=logger)
freerel_output = self.parse_freerel_output(stderr)
freerel_output["freerelfilename"] = freerelfilename
freerel_output["renumberfilename"] = renumberfilename
logger.info("FreeRel: Created outputfile %s", freerelfilename)
logger.info("FreeRel: Created outputfile %s", renumberfilename)
self.freerel_output = freerel_output
def run(self):
self.run_factor_base()
self.run_freerel()
self.run_sieving()
return self.relation_files
