Merge pull request #63 from duncanmmacleod/o2-replay

Improved data access for shared-memory files

bin/omicron-process

@@ -263,7 +263,6 @@ if args.gps is None and args.cache_file is not None:
 
 # extract key variables
 ifo = args.ifo
-llhoft = data.ligo_low_latency_hoft_type(ifo, use_devshm=args.use_dev_shm)
 group = args.group
 online = args.gps is None
 
@@ -478,19 +477,17 @@ segfile = os.path.join(rundir, 'segments.txt')
 keepfiles.append(segfile)
 
 if newdag and online:
-    if frametype == '%s_HOFT_C00' % ifo:
-        end = data.get_latest_data_gps(ifo, llhoft)
-    else:
-        end = data.get_latest_data_gps(ifo, frametype)
-    end -= (chunkdur + padding)
-    try:
+    # get limit of available data (allowing for padding)
+    end = data.get_latest_data_gps(ifo, frametype) - padding
+
+    try:  # start from where we got to last time
         start = segments.get_last_run_segment(segfile)[1]
-    except IOError:
-        if llhoft.endswith('llhoft'):
+    except IOError:  # otherwise start with a sensible amount of data
+        if args.use_dev_shm:  # process one chunk
             logger.debug("No online segment record, starting with "
                          "%s seconds" % chunkdur)
             start = end - chunkdur + padding
-        else:
+        else:  # process the last 4000 seconds (arbitrarily)
             logger.debug("No online segment record, starting with "
                          "4000 seconds")
             start = end - 4000
@@ -514,28 +511,6 @@ logger.info("Duration = %d seconds" % dataduration)
 
 span = (start, end)
 
-# -- double-check frametype for h(t)
-# don't use aggregated h(t) if running online
-
-if not args.cache_file:
-    try:
-        data.check_data_availability(ifo, '%s_HOFT_C00' % ifo, start, end)
-    except RuntimeError:
-        use_online_hoft = True
-        msg = "Gaps found in %s availability, turning to %s" % (
-            frametype, llhoft)
-    else:
-        use_online_hoft = False
-
-    if frametype == '%s_HOFT_C00' % ifo and use_online_hoft:
-        if online:
-            logger.debug(msg)
-        else:
-            logger.warning(msg)
-        frametype = llhoft
-    if statechannel and use_online_hoft and stateft == '%s_HOFT_C00' % ifo:
-        stateft = llhoft
-
 # -- find segments and frame files --------------------------------------------
 
 # minimum allowed duration is one full chunk
@@ -626,10 +601,11 @@ dataspan = type(segs)([segments.Segment(datastart, dataend)])
 if args.cache_file:
     with open(args.cache_file, 'r') as fobj:
         cache = Cache.fromfile(fobj)
-elif args.use_dev_shm:
+elif args.use_dev_shm and len(segs):  # only cache if we have state segments
     cache = data.find_frames(ifo, frametype, datastart, dataend,
                              on_gaps='warn', tmpdir=cachedir)
-    tempfiles.extend(cache.pfnlist())
+    # remove cached files at end of process
+    tempfiles.extend(filter(lambda p: cachedir in p, cache.pfnlist()))
 # find frames using datafind
 else:
     cache = data.find_frames(ifo, frametype, datastart, dataend,

omicron/data.py

@@ -30,7 +30,7 @@
 from glue.lal import (Cache, CacheEntry)
 from glue.segments import (segment as Segment, segmentlist as SegmentList)
 
-re_ll = re.compile('\A[HL]1_ll')
+re_ll = re.compile('_(llhoft|lldetchar)\Z')
 re_gwf_gps_epoch = re.compile('[-\/](?P<gpsepoch>\d+)$')
 
 
@@ -103,25 +103,27 @@ def get_latest_data_gps(obs, frametype, connection=None):
     gpstime : `int`
         the GPS time marking the end of the latest frame
     """
-    if re_ll.match(frametype):
-        latest = _find_ll_frames(obs, frametype)[-1]
     try:
-        latest = connection.find_latest(obs[0], frametype, urltype='file',
-                                        on_missing='error')[0]
-        try:
-            ngps = len(re_gwf_gps_epoch.search(
-                os.path.dirname(latest.path)).groupdict()['gpsepoch'])
-        except AttributeError:
-            pass
+        if re_ll.search(frametype):
+            latest = _find_ll_frames(obs, frametype)[-1]
         else:
-            while True:
-                s, e = latest.segment
-                new = latest.path.replace('-%d-' % s, '-%d-' % e)
-                new = new.replace('%s/' % str(s)[:ngps], '%s/' % str(e)[:ngps])
-                if os.path.isfile(new):
-                    latest = CacheEntry.from_T050017(new)
-                else:
-                    break
+            latest = connection.find_latest(obs[0], frametype, urltype='file',
+                                            on_missing='error')[0]
+            try:
+                ngps = len(re_gwf_gps_epoch.search(
+                    os.path.dirname(latest.path)).groupdict()['gpsepoch'])
+            except AttributeError:
+                pass
+            else:
+                while True:
+                    s, e = latest.segment
+                    new = latest.path.replace('-%d-' % s, '-%d-' % e)
+                    new = new.replace('%s/' % str(s)[:ngps],
+                                      '%s/' % str(e)[:ngps])
+                    if os.path.isfile(new):
+                        latest = CacheEntry.from_T050017(new)
+                    else:
+                        break
     except IndexError as e:
         e.args = ('No %s-%s frames found' % (obs[0], frametype),)
         raise
@@ -174,8 +176,8 @@ def check_data_availability(obs, frametype, start, end, connection=None):
     connection.find_frame_urls(obs[0], frametype, start, end, on_gaps='error')
 
 
-@with_datafind_connection
-def find_frames(obs, frametype, start, end, connection=None, **kwargs):
+def find_frames(obs, frametype, start, end, connection=None, on_gaps='warn',
+                **kwargs):
     """Find all frames for the given frametype in the GPS interval
 
     Parameters
@@ -199,46 +201,78 @@ def find_frames(obs, frametype, start, end, connection=None, **kwargs):
     cache : `~glue.lal.Cache`
         a cache of frame file locations
     """
-    if re_ll.match(frametype):
-        return find_ll_frames(obs, frametype, start, end, **kwargs)
-    else:
-        kwargs.setdefault('urltype', 'file')
-        cache = connection.find_frame_urls(obs[0], frametype, start, end,
-                                           **kwargs)
-        # use latest frame to find more recent frames that aren't in
-        # datafind yet, this is quite hacky, and isn't guaranteed to
-        # work at any point, but it shouldn't break anything
-        try:
-            latest = cache[-1]
-        except IndexError:  # no frames
-            return cache
+    ll_kw = {key: kwargs.pop(key) for key in ('tmpdir', 'root',) if
+             key in kwargs}
+
+    # find files using datafind
+    cache = _find_frames_datafind(obs, frametype, start, end,
+                                  connection=connection, on_gaps='ignore',
+                                  **kwargs)
+
+    # find more files for low-latency under /dev/shm (or similar)
+    if re_ll.search(frametype):
         try:
-            ngps = len(re_gwf_gps_epoch.search(
-                os.path.dirname(latest.path)).groupdict()['gpsepoch'])
-        except AttributeError:  # no match
-            pass
+            latest = cache[-1].segment[1]
+        except IndexError:
+            latest = start
+        if latest < end:
+            cache.extend(find_ll_frames(obs, frametype, latest, end, **ll_kw))
+
+    # handle missing files
+    if on_gaps != 'ignore':
+        seglist = SegmentList(e.segment for e in cache).coalesce()
+        missing = (SegmentList([Segment(start, end)]) - seglist).coalesce()
+        msg = "Missing segments:\n%s" % '\n'.join(map(str, missing))
+        if missing and on_gaps == 'warn':
+            warnings.warn(msg)
+        elif missing:
+            raise RuntimeError(msg)
+
+    return cache
+
+
+@with_datafind_connection
+def _find_frames_datafind(obs, frametype, start, end, connection=None,
+                          **kwargs):
+    kwargs.setdefault('urltype', 'file')
+    cache = connection.find_frame_urls(obs[0], frametype, start, end,
+                                       **kwargs)
+
+    # use latest frame to find more recent frames that aren't in
+    # datafind yet, this is quite hacky, and isn't guaranteed to
+    # work at any point, but it shouldn't break anything
+
+    try:
+        latest = cache[-1]
+    except IndexError:  # no frames
+        return cache
+
+    try:  # find number of GPS digits in paths
+        ngps = len(re_gwf_gps_epoch.search(
+            os.path.dirname(latest.path)).groupdict()['gpsepoch'])
+    except AttributeError:  # no match
+        return cache
+
+    while True:
+        s, e = latest.segment
+        if s >= end:  # dont' go beyond requested times
+            break
+        new = latest.path.replace('-%d-' % s, '-%d-' % e)
+        new = new.replace('%s/' % str(s)[:ngps], '%s/' % str(e)[:ngps])
+        if os.path.isfile(new):
+            latest = CacheEntry.from_T050017(new)
+            cache.append(latest)
         else:
-            while True:
-                s, e = latest.segment
-                if s >= end:  # dont' go beyond requested times
-                    break
-                new = latest.path.replace('-%d-' % s, '-%d-' % e)
-                new = new.replace('%s/' % str(s)[:ngps], '%s/' % str(e)[:ngps])
-                if os.path.isfile(new):
-                    latest = CacheEntry.from_T050017(new)
-                    cache.append(latest)
-                else:
-                    break
-            return cache
+            break
+    return cache
 
 
 def write_cache(cache, outfile):
     with open(outfile, 'w') as fp:
         cache.tofile(fp)
 
 
-def find_ll_frames(ifo, frametype, start, end, root='/dev/shm',
-                   on_gaps='warn', tmpdir=None):
+def find_ll_frames(ifo, frametype, start, end, root='/dev/shm', tmpdir=None):
     """Find all buffered low-latency frames in the given interval
 
     Parameters
@@ -277,14 +311,6 @@ def find_ll_frames(ifo, frametype, start, end, root='/dev/shm',
     """
     seg = Segment(start, end)
     cache = _find_ll_frames(ifo, frametype, root=root).sieve(segment=seg)
-    if on_gaps != 'ignore':
-        seglist = SegmentList(e.segment for e in cache).coalesce()
-        missing = (SegmentList([seg]) - seglist).coalesce()
-        msg = "Missing segments:\n%s" % '\n'.join(map(str, missing))
-        if missing and on_gaps == 'warn':
-            warnings.warn(msg)
-        elif missing:
-            raise RuntimeError(msg)
     if tmpdir:
         out = []
         if not os.path.isdir(tmpdir):
@@ -298,11 +324,11 @@ def find_ll_frames(ifo, frametype, start, end, root='/dev/shm',
     return cache
 
 
-def _find_ll_frames(ifo, frametype, root='/dev/shm'):
-    if frametype.startswith('%s_' % ifo):
-        frametype = frametype.split('_', 1)[1]
+def _find_ll_frames(ifo, frametype, root='/dev/shm', ext='gwf'):
     obs = ifo[0]
-    globstr = os.path.join(root, frametype, ifo,
-                           '%s-%s_%s-*-*.gwf' % (obs, ifo, frametype))
+    bits = frametype.rsplit('_', 1)
+    basedir = os.path.join(root, *bits[::-1])
+    globstr = os.path.join(basedir, '{obs}-{frametype}-*-*.{ext}'.format(
+        obs=obs, frametype=frametype, ext=ext))
     # don't return the last file, as it might not have been fully written yet
     return Cache.from_urls(sorted(glob.glob(globstr)[:-1]))

omicron/segments.py

@@ -100,11 +100,7 @@ def get_state_segments(channel, frametype, start, end, bits=[0], nproc=1,
     pend = end + pad[1]
 
     # find frame cache
-    if data.re_ll.match(frametype):
-        tmpdir = mkdtemp(prefix='tmp-pyomicron-')
-        cache = data.find_frames(ifo, frametype, pstart, pend, tmpdir=tmpdir)
-    else:
-        cache = data.find_frames(ifo, frametype, pstart, pend)
+    cache = data.find_frames(ifo, frametype, pstart, pend)
 
     # optimise I/O based on type and library
     io_kw = {}