From c7dc83f9a8bf330041a0eb3bea9cf757bd2431bb Mon Sep 17 00:00:00 2001
From: Chad Hanna <crh184@psu.edu>
Date: Sat, 1 Oct 2016 13:33:58 -0700
Subject: [PATCH] gstlal_ll_inspiral_aggregator: major refactoring
---
gstlal-ugly/bin/gstlal_ll_inspiral_aggregator | 329 ++++++++----------
1 file changed, 148 insertions(+), 181 deletions(-)
diff --git a/gstlal-ugly/bin/gstlal_ll_inspiral_aggregator b/gstlal-ugly/bin/gstlal_ll_inspiral_aggregator
index faec11fa00..484f5fb245 100755
--- a/gstlal-ugly/bin/gstlal_ll_inspiral_aggregator
+++ b/gstlal-ugly/bin/gstlal_ll_inspiral_aggregator
@@ -25,18 +25,16 @@ import argparse
import lal
from lal import LIGOTimeGPS
import time
-from gstlal import servicediscovery
from gi.repository import GLib
import logging
import subprocess
-import threading
-from gi.repository import GLib
-from gstlal import servicediscovery
import urllib2
import shutil
import collections
+from multiprocessing import Pool
-MIN_TIME_QUANTA = 1000
+MIN_TIME_QUANTA = 10000
+DIRS = 6
#
@@ -58,6 +56,7 @@ def parse_command_line():
parser.add_argument("--dump-period", type = float, default = 180., help = "Wait this many seconds between dumps of the URLs (default = 180., set to 0 to disable)")
parser.add_argument("--num-jobs", action="store", type=int, default=10, help="number of running jobs")
parser.add_argument("--job-tag", help = "Collect URLs for jobs reporting this job tag (default = collect all gstlal_inspiral URLs).")
+ parser.add_argument("--num-threads", type = int, default = 16, help = "Number of threads to use concurrently")
args = parser.parse_args()
@@ -93,15 +92,16 @@ def get_url(url,d):
specific route. FIXME it assumes that the routes end in .txt
"""
jobdata = urllib2.urlopen("%s%s.txt" % (url, d)).read().split("\n")
- jobtime = [float(x.split()[0]) for x in jobdata if x]
- jobdata = [float(x.split()[1]) for x in jobdata if x]
+ jobtime = numpy.array([float(x.split()[0]) for x in jobdata if x])
+ jobdata = numpy.array([float(x.split()[1]) for x in jobdata if x])
assert len(jobdata) == len(jobtime)
return jobtime, jobdata
def reduce_data(xarr, yarr, func, level = 0):
"""!
- This function does a data reduction by powers of 10
+ This function does a data reduction by powers of 10 where level
+ specifies the power. Default is 0 e.g., data reduction over 1 second
"""
datadict = collections.OrderedDict()
assert len(yarr) == len(xarr)
@@ -165,10 +165,14 @@ def get_dataset(path, base):
open a dataset at @param path with name @param base and return the data
"""
fname = os.path.join(path, "%s.hdf5" % base)
- f = h5py.File(fname, "r")
- x,y = list(f["time"]), list(f["data"])
- f.close()
- return fname, x,y
+ try:
+ f = h5py.File(fname, "r")
+ x,y = list(f["time"]), list(f["data"])
+ f.close()
+ return fname, x,y
+ except IOError:
+ fname = create_new_dataset(path, base, timedata = None, data = None, tmp = False)
+ return fname, [], []
def gps_to_minimum_time_quanta(gpstime):
@@ -199,61 +203,60 @@ def gps_to_sub_directories(gpstime, level, basedir):
return out
-def setup_dirs(gpstime, types, jobs, data, base_dir, verbose = True):
+def setup_dir_by_job_and_level(gpstime, typ, job, route, base_dir, verbose = True, level = 0):
"""!
Given a gps time, the number of jobs and data types produce an
appropriate data structure for storing the hierarchical data.
"""
str_time = str(gpstime).split(".")[0]
- digits = [int(x) for x in str_time]
- directories = [numpy.array([digits[x]]) for x in range(7)]
-
- # Setup the directory structure and put in empty files
- for dirs in [directories[:i+1] for i in range(len(directories))]:
- for path in itertools.product(*dirs):
- cur_dir = os.path.join(base_dir, "/".join(str(x) for x in path))
- makedir(cur_dir)
- for (typ,_) in types:
- type_dir = os.path.join(cur_dir, typ)
- makedir(type_dir)
- for d in data:
- create_new_dataset(type_dir, d)
- type_dir = os.path.join(cur_dir, "by_job")
- for b in jobs:
- bin_dir = os.path.join(type_dir, b)
- for (typ,_) in types:
- type_bin_dir = os.path.join(bin_dir, typ)
- makedir(type_bin_dir)
- for d in data:
- create_new_dataset(type_bin_dir, d)
-
-
-def gps_range(jobtime, dataspan):
+ str_time = str_time[:(len(str_time)-int(numpy.log10(MIN_TIME_QUANTA))-level)]
+ directory = "%s/%s/by_job/%s/%s" % (base_dir, "/".join(str_time), job, typ)
+ makedir(directory)
+ fname = create_new_dataset(directory, route)
+
+
+def setup_dir_across_job_by_level(gpstime, typ, route, base_dir, verbose = True, level = 0):
+ """!
+ Given a gps time, the number of jobs and data types produce an
+ appropriate data structure for storing the hierarchical data.
+ """
+ str_time = str(gpstime).split(".")[0]
+ str_time = str_time[:(len(str_time)-int(numpy.log10(MIN_TIME_QUANTA))-level)]
+ directory = "%s/%s/%s" % (base_dir, "/".join(str_time), typ)
+ makedir(directory)
+ fname = create_new_dataset(directory, route)
+
+
+def gps_range(jobtime):
gpsblocks = set((gps_to_minimum_time_quanta(t) for t in jobtime))
min_t, max_t = min(gpsblocks), max(gpsblocks)
- for gpstime in gpsblocks:
- dataspan.add(gpstime)
return range(min_t, max_t+MIN_TIME_QUANTA, MIN_TIME_QUANTA), range(min_t+MIN_TIME_QUANTA, max_t+2*MIN_TIME_QUANTA, MIN_TIME_QUANTA)
-def update_lowest_level_data(job, path, d, s, e, typ, self, jobtime, jobdata, func):
+def update_lowest_level_data_by_job_type_and_route(job, route, start, end, typ, base_dir, jobtime, jobdata, func):
+ path = "/".join([base_dir, gps_to_leaf_directory(start), "by_job", job, typ])
try:
- fname, prev_times, prev_data = get_dataset(path, d)
+ fname, prev_times, prev_data = get_dataset(path, route)
except:
- setup_dirs(s, self.datatypes, self.jobs, self.dataurls, self.base_dir)
- fname, prev_times, prev_data = get_dataset(path, d)
- # only get new data
+ setup_dir_by_job_and_level(start, typ, job, route, base_dir, verbose = True, level = 0)
+ fname, prev_times, prev_data = get_dataset(path, route)
+ # only get new data and assume that everything is time ordered
if prev_times:
- this_time_ix = [i for i,t in enumerate(jobtime) if s <= t < e and t > prev_times[-1]]
+ this_time_ix = numpy.logical_and(jobtime > max(start-1e-16, prev_times[-1]), jobtime < end)
else:
- this_time_ix = [i for i,t in enumerate(jobtime) if s <= t < e]
- this_time = [jobtime[i] for i in this_time_ix] + prev_times
- this_data = [jobdata[i] for i in this_time_ix] + prev_data
+ this_time_ix = numpy.logical_and(jobtime >= start, jobtime < end)
+ this_time = list(jobtime[this_time_ix]) + prev_times
+ this_data = list(jobdata[this_time_ix]) + prev_data
+ # shortcut if there are no updates
+ if len(this_time) == len(prev_times) and len(this_data) == len(prev_data):
+ print "shortcutting"
+ return []
reduced_time, reduced_data = reduce_data(this_time, this_data, func, level = 0)
- logging.info("processing job %s for data %s in span [%d,%d] of type %s: found %d" % (job, d, s, e, typ, len(reduced_time)))
- tmpfname = create_new_dataset(path, d, reduced_time, reduced_data, tmp = True)
+ #logging.info("processing job %s for data %s in span [%d,%d] of type %s: found %d" % (job, route, start, end, typ, len(reduced_time)))
+ tmpfname = create_new_dataset(path, route, reduced_time, reduced_data, tmp = True)
# copy the tmp file over the original
shutil.move(tmpfname, fname)
+ return [start, end]
def job_expanse(dataspan):
@@ -263,136 +266,87 @@ def job_expanse(dataspan):
else:
return [], []
-def reduce_data_from_lower_level(level, self, this_level_dir, job, typ, d, func, s, e):
+def reduce_data_from_lower_level_by_job_type_and_route(level, base_dir, job, typ, route, func, start, end):
+
+ this_level_dir = "/".join([base_dir, gps_to_leaf_directory(start, level = level)])
agg_data = []
agg_time = []
- for subdir in gps_to_sub_directories(s, level, self.base_dir):
+
+ # FIXME iterate over levels instead.
+ for subdir in gps_to_sub_directories(start, level, base_dir):
path = "/".join([this_level_dir, subdir, "by_job", job, typ])
try:
- fname, x, y = get_dataset(path, d)
+ fname, x, y = get_dataset(path, route)
agg_time += x
agg_data += y
except IOError as ioerr:
- logging.error(ioerr)
+ makedir(path)
+ # make an empty data set
+ create_new_dataset(path, route)
pass
reduced_time, reduced_data = reduce_data(agg_time, agg_data, func, level=level)
path = "/".join([this_level_dir, "by_job", job, typ])
- logging.info("processing reduced data %s for job %s in span [%d,%d] of type %s at level %d: found %d/%d" % (d, job, s, e, typ, level, len(reduced_time), len(agg_time)))
- tmpfname = create_new_dataset(path, d, reduced_time, reduced_data, tmp = True)
+ makedir(path)
+ #logging.info("processing reduced data %s for job %s in span [%d,%d] of type %s at level %d: found %d/%d" % (d, job, s, e, typ, level, len(reduced_time), len(agg_time)))
+ tmpfname = create_new_dataset(path, route, reduced_time, reduced_data, tmp = True)
# FIXME don't assume we can get the non temp file name this way
shutil.move(tmpfname, tmpfname.replace(".tmp",""))
-def reduce_across_jobs(self, this_level_dir, typ, d, func, level, s, e):
+def reduce_across_jobs((jobs, this_level_dir, typ, route, func, level, start, end)):
# Process this level
agg_data = []
agg_time = []
- for job in sorted(self.urls):
+ for job in sorted(jobs):
path = "/".join([this_level_dir, "by_job", job, typ])
try:
- fname, x, y = get_dataset(path, d)
+ fname, x, y = get_dataset(path, route)
agg_time += x
agg_data += y
except IOError as ioerr:
- logging.error(ioerr)
+ makedir(path)
+ create_new_dataset(path, route)
pass
reduced_time, reduced_data = reduce_data(agg_time, agg_data, func, level=level)
- logging.info("processing reduced data %s in span [%d,%d] of type %s at level %d: found %d/%d" % (d, s, e, typ, level, len(reduced_time), len(agg_time)))
+ #logging.info("processing reduced data %s in span [%d,%d] of type %s at level %d: found %d/%d" % (route, start, end, typ, level, len(reduced_time), len(agg_time)))
path = "/".join([this_level_dir, typ])
- tmpfname = create_new_dataset(path, d, reduced_time, reduced_data, tmp = True)
+ tmpfname = create_new_dataset(path, route, reduced_time, reduced_data, tmp = True)
# FIXME don't assume we can get the non temp file name this way
shutil.move(tmpfname, tmpfname.replace(".tmp",""))
-#
-# =============================================================================
-#
-# Internal Library
-#
-# =============================================================================
-#
-class Collector(servicediscovery.Listener):
- def __init__(self, mainloop, datatypes, jobs, dataurls, base_dir, job_tag = None, dump_period = 180.):
- self.datatypes = datatypes
- self.jobs = set(jobs)
- self.dataurls = dataurls
- self.base_dir = base_dir
- self.job_tag = job_tag
- self.dump_period = dump_period
- self.urls = {}
- self.lock = threading.Lock()
- # FIXME: use glib's mainloop machinery instead, implement
- # this as a timeout or whatever it's called
- logging.info("starting wget loop thread")
- self.wget_thread = threading.Thread(target = self.wget_loop, args = (mainloop,))
- self.wget_thread.start()
-
- def add_service(self, sname, stype, sdomain, host, port, properties):
- if stype != "_http._tcp" or not sname.startswith("gstlal_inspiral "):
- return
- url = "http://%s:%s/" % (host, port)
- logging.info("found '%s' server at %s for job tag '%s'" % (sname, url, properties.get("job_tag")))
- if self.job_tag is not None and properties.get("job_tag") != self.job_tag:
- logging.info("server has wrong or missing job tag, discarding")
- return
- if not properties.get("GSTLAL_LL_JOB"):
- logging.info("server has no GSTLAL_LL_JOB value, discarding")
- return
- if properties.get("GSTLAL_LL_JOB") not in self.jobs:
- logging.info("server has a GSTLAL_LL_JOB value outside of requested range, discarding")
- return
- # watch for security problems: don't let url or job ID
- # terminate the wget shell command in mid-string
- if ";" in url or ";" in properties["GSTLAL_LL_JOB"]:
- logging.warn("invalid URL and/or job ID")
- return
- logging.info("recording server at %s for GSTLAL_LL_JOB='%s'" % (url, properties["GSTLAL_LL_JOB"]))
- with self.lock:
- self.urls[properties["GSTLAL_LL_JOB"]] = url
-
- def wget_loop(self, mainloop):
- try:
- while self.dump_period:
- logging.info("sleeping")
- time.sleep(self.dump_period)
- with self.lock:
- dataspan = set()
- for job, url in sorted(self.urls.items()):
- assert job
- # FIXME Hack
- url = url.replace(".local","")
- for d in self.dataurls:
- jobtime, jobdata = get_url(url,d)
- gps1, gps2 = gps_range(jobtime, dataspan)
- for s,e in zip(gps1, gps2):
- for (typ, func) in self.datatypes:
- path = "/".join([self.base_dir, gps_to_leaf_directory(s), "by_job", job, typ])
- update_lowest_level_data(job, path, d, s, e, typ, self, jobtime, jobdata, func)
-
- # Data reduction across jobs at the lowest level
- gps1, gps2 = job_expanse(dataspan)
- for s,e in zip(gps1, gps2):
- # FIXME don't hardcode this range
- for level in range(7):
- this_level_dir = "/".join([self.base_dir, gps_to_leaf_directory(s, level = level)])
- for d in self.dataurls:
- for (typ,func) in self.datatypes:
- # Produce the data at this level by descending a level.
- if level > 0:
- for job in sorted(self.urls):
- reduce_data_from_lower_level(level, self, this_level_dir, job, typ, d, func, s, e)
- # reduce data across jobs at this level
- reduce_across_jobs(self, this_level_dir, typ, d, func, level, s, e)
- except:
- mainloop.quit()
- raise
-
- def quit(self):
- logging.info("waiting for wget loop to finish ...")
- self.dump_period = 0 # signal exit
- self.wget_thread.join()
-
+def get_data_from_job_and_reduce((job, routes, datatypes, prevdataspan, base_dir, jobs)):
+ # get the url
+ with open(os.path.join(options.job_tag, "%s_registry.txt" % job)) as f:
+ url = f.readline().strip()
+ update_time = []
+ reduce_time = []
+ dataspan = set()
+ for route in routes:
+ logging.info("processing job %s for route %s" % (job, route))
+ jobtime, jobdata = get_url(url, route)
+ gps1, gps2 = gps_range(jobtime)
+ for start, end in zip(gps1, gps2):
+ # shortcut to not reprocess data that has already been
+ # processed. Dataspan was the only thing that was
+ # previously determined to be needing to be updated
+ # anything before that is pointless
+ if prevdataspan: print end, min(prevdataspan)
+ if prevdataspan and end < min(prevdataspan):
+ continue
+ for (typ, func) in datatypes:
+ now = time.time()
+ for processed_time in update_lowest_level_data_by_job_type_and_route(job, route, start, end, typ, base_dir, jobtime, jobdata, func):
+ dataspan.add(processed_time)
+ update_time.append(time.time()-now)
+ # descend down through the levels
+ now = time.time()
+ for level in range(1,DIRS):
+ reduce_data_from_lower_level_by_job_type_and_route(level, base_dir, job, typ, route, func, start, end)
+ reduce_time.append(time.time()-now)
+ print "Updated %d with average time %f; Reduced %d with average time %f" % (len(update_time), numpy.mean(update_time), len(reduce_time), numpy.mean(reduce_time))
+ return dataspan
#
# =============================================================================
@@ -402,34 +356,47 @@ class Collector(servicediscovery.Listener):
# =============================================================================
#
-
-options = parse_command_line()
-
-# FIXME don't hardcode some of these?
-datatypes = [("min", min), ("max", max), ("median", median)]
-jobs = ["%04d" % b for b in numpy.arange(0, options.num_jobs)]
-dataurls = ["latency_history", "snr_history"]
-
-
-logging.basicConfig(level = logging.INFO, format = "%(asctime)s %(levelname)s:%(processName)s(%(process)d):%(funcName)s: %(message)s")
-
-
-mainloop = GLib.MainLoop()
-
-collector = Collector(mainloop, datatypes, jobs, dataurls, options.base_dir, job_tag = options.job_tag, dump_period = options.dump_period)
-browser = servicediscovery.ServiceBrowser(collector)
-
-try:
- mainloop.run()
-except:
- collector.quit()
- raise
-
-
-#
-# always end on an error so that condor won't think we're done and will
-# restart us
-#
-
-
-sys.exit(1)
+if __name__ == '__main__':
+
+ options = parse_command_line()
+ # FIXME don't hardcode some of these?
+ datatypes = [("min", min), ("max", max), ("median", median)]
+ jobs = ["%04d" % b for b in numpy.arange(0, options.num_jobs)]
+ routes = ["latency_history", "snr_history"]
+
+ logging.basicConfig(level = logging.INFO, format = "%(asctime)s %(levelname)s:%(processName)s(%(process)d):%(funcName)s: %(message)s")
+
+ pool = Pool(options.num_threads)
+ prevdataspan = set()
+ while True:
+ logging.info("sleeping")
+ time.sleep(options.dump_period)
+ dataspan = set()
+
+ # First get the raw and reduced data for each job in parallel
+ mapargs = [(job, routes, datatypes, prevdataspan, options.base_dir, jobs) for job in jobs]
+ for ds in pool.map(get_data_from_job_and_reduce, mapargs):
+ #for ds in map(get_data_from_job_and_reduce, mapargs):
+ dataspan.update(ds)
+ prevdataspan = dataspan.copy()
+ # Then reduce the data across jobs at each level
+ mapargs = []
+ for start, end in zip(*job_expanse(dataspan)):
+ # FIXME don't hardcode this range
+ for level in range(DIRS):
+ this_level_dir = "/".join([options.base_dir, gps_to_leaf_directory(start, level = level)])
+ logging.info("processing reduced data in span [%d,%d] at level %d" % (start, end, level))
+ mapargs = []
+ for route in routes:
+ for (typ,func) in datatypes:
+ setup_dir_across_job_by_level(start, typ, route, options.base_dir, verbose = True, level = level)
+ mapargs.append((jobs, this_level_dir, typ, route, func, level, start, end))
+ pool.map(reduce_across_jobs, mapargs)
+ #map(reduce_across_jobs, mapargs)
+
+ #
+ # always end on an error so that condor won't think we're done and will
+ # restart us
+ #
+
+ sys.exit(1)
--
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