Starting with version 2.5.0, h5py includes support for the HDF5 SWMR features.
The SWMR feature is not available in the current release (1.8 series) of HDF5 library. It is planned to be released for production use in version 1.10. Until then it is available as an experimental prototype form from development snapshot version 1.9.178 on the HDF Group ftp server or the HDF Group svn repository.
Warning
The SWMR feature is currently in prototype form and available for experimenting and testing. Please do not consider this a production quality feature until the HDF5 library is released as 1.10.
Warning
FILES PRODUCED BY THE HDF5 1.9.X DEVELOPMENT SNAPSHOTS MAY NOT BE READABLE BY OTHER VERSIONS OF HDF5, INCLUDING THE EXISTING 1.8 SERIES AND ALSO 1.10 WHEN IT IS RELEASED.
The SWMR features allow simple concurrent reading of a HDF5 file while it is being written from another process. Prior to this feature addition it was not possible to do this as the file data and meta-data would not be syncrhonised and attempts to read a file which was open for writing would fail or result in garbage data.
A file which is being written to in SWMR mode is guaranteed to always be in a valid (non-corrupt) state for reading. This has the added benefit of leaving a file in a valid state even if the writing application crashes before closing the file properly.
This feature has been implemented to work with independent writer and reader processes. No synchronisation is required between processes and it is up to the user to implement either a file polling mechanism, inotify or any other IPC mechanism to notify when data has been written.
The SWMR functionality requires use of the latest HDF5 file format: v110. In practice this implies setting the libver bounding to “latest” when opening or creating the file.
Warning
New v110 format files are not compatible with v18 format. So files, written in SWMR mode with libver=’latest’ cannot be opened with older versions of the HDF5 library (basically any version older than the SWMR feature).
The HDF Group has documented the SWMR features in details on the website: Single-Writer/Multiple-Reader (SWMR) Documentation. This is highly recommended reading for anyone intending to use the SWMR feature even through h5py. For production systems in particular pay attention to the file system requirements regarding POSIX I/O semantics.
The following basic steps are typically required by writer and reader processes:
The following snippet demonstrate a SWMR writer appending to a single dataset:
f = h5py.File("swmr.h5", 'w', libver='latest')
arr = np.array([1,2,3,4])
dset = f.create_dataset("data", chunks=(2,), maxshape=(None,), data=arr)
f.swmr_mode = True
# Now it is safe for the reader to open the swmr.h5 file
for i in range(5):
new_shape = ((i+1) * len(arr), )
dset.resize( new_shape )
dset[i*len(arr):] = arr
dset.flush()
# Notify the reader process that new data has been written
The following snippet demonstrate how to monitor a dataset as a SWMR reader:
f = h5py.File("swmr.h5", 'r', libver='latest', swmr=True)
dset = f["data"]
while True:
dset.id.refresh()
shape = dset.shape
print( shape )
In addition to the above example snippets, a few more complete examples can be found in the examples folder. These examples are described in the following sections
The inotify example demonstrate how to use SWMR in a reading application which monitors live progress as a dataset is being written by another process. This example uses the the linux inotify (pyinotify python bindings) to receive a signal each time the target file has been updated.
"""
Demonstrate the use of h5py in SWMR mode to monitor the growth of a dataset
on nofication of file modifications.
This demo uses pyinotify as a wrapper of Linux inotify.
https://pypi.python.org/pypi/pyinotify
Usage:
swmr_inotify_example.py [FILENAME [DATASETNAME]]
FILENAME: name of file to monitor. Default: swmr.h5
DATASETNAME: name of dataset to monitor in DATAFILE. Default: data
This script will open the file in SWMR mode and monitor the shape of the
dataset on every write event (from inotify). If another application is
concurrently writing data to the file, the writer must have have switched
the file into SWMR mode before this script can open the file.
"""
import asyncore
import pyinotify
import sys
import h5py
import logging
#assert h5py.version.hdf5_version_tuple >= (1,9,178), "SWMR requires HDF5 version >= 1.9.178"
class EventHandler(pyinotify.ProcessEvent):
def monitor_dataset(self, filename, datasetname):
logging.info("Opening file %s", filename)
self.f = h5py.File(filename, 'r', libver='latest', swmr=True)
logging.debug("Looking up dataset %s"%datasetname)
self.dset = self.f[datasetname]
self.get_dset_shape()
def get_dset_shape(self):
logging.debug("Refreshing dataset")
self.dset.refresh()
logging.debug("Getting shape")
shape = self.dset.shape
logging.info("Read data shape: %s"%str(shape))
return shape
def read_dataset(self, latest):
logging.info("Reading out dataset [%d]"%latest)
self.dset[latest:]
def process_IN_MODIFY(self, event):
logging.debug("File modified!")
shape = self.get_dset_shape()
self.read_dataset(shape[0])
def process_IN_CLOSE_WRITE(self, event):
logging.info("File writer closed file")
self.get_dset_shape()
logging.debug("Good bye!")
sys.exit(0)
if __name__ == "__main__":
logging.basicConfig(format='%(asctime)s %(levelname)s\t%(message)s',level=logging.INFO)
file_name = "swmr.h5"
if len(sys.argv) > 1:
file_name = sys.argv[1]
dataset_name = "data"
if len(sys.argv) > 2:
dataset_name = sys.argv[2]
wm = pyinotify.WatchManager() # Watch Manager
mask = pyinotify.IN_MODIFY | pyinotify.IN_CLOSE_WRITE
evh = EventHandler()
evh.monitor_dataset( file_name, dataset_name )
notifier = pyinotify.AsyncNotifier(wm, evh)
wdd = wm.add_watch(file_name, mask, rec=False)
# Sit in this loop() until the file writer closes the file
# or the user hits ctrl-c
asyncore.loop()
The SWMR multiprocess example starts starts two concurrent child processes: a writer and a reader. The writer process first creates the target file and dataset. Then it switches the file into SWMR mode and the reader process is notified (with a multiprocessing.Event) that it is safe to open the file for reading.
The writer process then continue to append chunks to the dataset. After each write it notifies the reader that new data has been written. Whether the new data is visible in the file at this point is subject to OS and file system latencies.
The reader first waits for the initial “SWMR mode” notification from the writer, upon which it goes into a loop where it waits for further notifications from the writer. The reader may drop some notifications, but for each one received it will refresh the dataset and read the dimensions. After a time-out it will drop out of the loop and exit.
"""
Demonstrate the use of h5py in SWMR mode to write to a dataset (appending)
from one process while monitoring the growing dataset from another process.
Usage:
swmr_multiprocess.py [FILENAME [DATASETNAME]]
FILENAME: name of file to monitor. Default: swmrmp.h5
DATASETNAME: name of dataset to monitor in DATAFILE. Default: data
This script will start up two processes: a writer and a reader. The writer
will open/create the file (FILENAME) in SWMR mode, create a dataset and start
appending data to it. After each append the dataset is flushed and an event
sent to the reader process. Meanwhile the reader process will wait for events
from the writer and when triggered it will refresh the dataset and read the
current shape of it.
"""
import sys, time
import h5py
import numpy as np
import logging
from multiprocessing import Process, Event
class SwmrReader(Process):
def __init__(self, event, fname, dsetname, timeout = 2.0):
super(SwmrReader, self).__init__()
self._event = event
self._fname = fname
self._dsetname = dsetname
self._timeout = timeout
def run(self):
self.log = logging.getLogger('reader')
self.log.info("Waiting for initial event")
assert self._event.wait( self._timeout )
self._event.clear()
self.log.info("Opening file %s", self._fname)
f = h5py.File(self._fname, 'r', libver='latest', swmr=True)
assert f.swmr_mode
dset = f[self._dsetname]
try:
# monitor and read loop
while self._event.wait( self._timeout ):
self._event.clear()
self.log.debug("Refreshing dataset")
dset.refresh()
shape = dset.shape
self.log.info("Read dset shape: %s"%str(shape))
finally:
f.close()
class SwmrWriter(Process):
def __init__(self, event, fname, dsetname):
super(SwmrWriter, self).__init__()
self._event = event
self._fname = fname
self._dsetname = dsetname
def run(self):
self.log = logging.getLogger('writer')
self.log.info("Creating file %s", self._fname)
f = h5py.File(self._fname, 'w', libver='latest')
try:
arr = np.array([1,2,3,4])
dset = f.create_dataset(self._dsetname, chunks=(2,), maxshape=(None,), data=arr)
assert not f.swmr_mode
self.log.info("SWMR mode")
f.swmr_mode = True
assert f.swmr_mode
self.log.debug("Sending initial event")
self._event.set()
# Write loop
for i in range(5):
new_shape = ((i+1) * len(arr), )
self.log.info("Resizing dset shape: %s"%str(new_shape))
dset.resize( new_shape )
self.log.debug("Writing data")
dset[i*len(arr):] = arr
#dset.write_direct( arr, np.s_[:], np.s_[i*len(arr):] )
self.log.debug("Flushing data")
dset.flush()
self.log.info("Sending event")
self._event.set()
finally:
f.close()
if __name__ == "__main__":
logging.basicConfig(format='%(levelname)10s %(asctime)s %(name)10s %(message)s',level=logging.INFO)
fname = 'swmrmp.h5'
dsetname = 'data'
if len(sys.argv) > 1:
fname = sys.argv[1]
if len(sys.argv) > 2:
dsetname = sys.argv[2]
event = Event()
reader = SwmrReader(event, fname, dsetname)
writer = SwmrWriter(event, fname, dsetname)
logging.info("Starting reader")
reader.start()
logging.info("Starting reader")
writer.start()
logging.info("Waiting for writer to finish")
writer.join()
logging.info("Waiting for reader to finish")
reader.join()
The example output below (from a virtual Ubuntu machine) illustrate some latency between the writer and reader:
python examples/swmr_multiprocess.py
INFO 2015-02-26 18:05:03,195 root Starting reader
INFO 2015-02-26 18:05:03,196 root Starting reader
INFO 2015-02-26 18:05:03,197 reader Waiting for initial event
INFO 2015-02-26 18:05:03,197 root Waiting for writer to finish
INFO 2015-02-26 18:05:03,198 writer Creating file swmrmp.h5
INFO 2015-02-26 18:05:03,203 writer SWMR mode
INFO 2015-02-26 18:05:03,205 reader Opening file swmrmp.h5
INFO 2015-02-26 18:05:03,210 writer Resizing dset shape: (4,)
INFO 2015-02-26 18:05:03,212 writer Sending event
INFO 2015-02-26 18:05:03,213 reader Read dset shape: (4,)
INFO 2015-02-26 18:05:03,214 writer Resizing dset shape: (8,)
INFO 2015-02-26 18:05:03,214 writer Sending event
INFO 2015-02-26 18:05:03,215 writer Resizing dset shape: (12,)
INFO 2015-02-26 18:05:03,215 writer Sending event
INFO 2015-02-26 18:05:03,215 writer Resizing dset shape: (16,)
INFO 2015-02-26 18:05:03,215 reader Read dset shape: (12,)
INFO 2015-02-26 18:05:03,216 writer Sending event
INFO 2015-02-26 18:05:03,216 writer Resizing dset shape: (20,)
INFO 2015-02-26 18:05:03,216 reader Read dset shape: (16,)
INFO 2015-02-26 18:05:03,217 writer Sending event
INFO 2015-02-26 18:05:03,217 reader Read dset shape: (20,)
INFO 2015-02-26 18:05:03,218 reader Read dset shape: (20,)
INFO 2015-02-26 18:05:03,219 root Waiting for reader to finish