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Fix numpy pickle for versions less than 1.9 #243
Fix #236. There were two bugs conflated in one:
Python 3 writer, Python 2 reader
That's the direction reported in #236. Standard pickle of dtype created with python 3 and numpy 1.9 can not be read with python 2.
Writer script (python 3, numpy 1.9)
import pickle import numpy as np dt = np.dtype('>f8') with open('/tmp/test.pkl', 'wb') as f: pickle.Pickler(f, protocol=2).dump(dt)
Reader script (python 2, numpy 1.8)
import pickle pickle.load(open('/tmp/test.pkl', 'rb'))
Python 2 writer, Python 3 reader
Related to NumpyPickler/NumpyUnPickler cycle. The likely culprit is that we use encoding=bytes for performance reasons, but that also means that all python2 strings are loaded as bytes in python3. This seems a bit iffy to say the least ... @GaelVaroquaux @ogrisel any opinions ?
Writer script (python 2, numpy 1.9)
import joblib pickler = joblib.numpy_pickle.NumpyPickler('/tmp/test.pkl') import numpy as np pickler = joblib.numpy_pickle.NumpyPickler('/tmp/test.pkl') pickler.save(np.dtype('f8')) # Don't forget to quit ipython here in order to flush to file ...
Reader script (python 3, numpy 1.8)
import joblib unpickler = joblib.numpy_pickle.NumpyUnpickler('/tmp/test.pkl', open('/tmp/test.pkl', 'rb')) unpickler.load()
Full disclosure: at the moment the python 2/3 compatibility for non compressed pickles is actually broken because of this iffyness. An instance of NDArrayWrapper ends up with keys that are bytes rather than str.
Olivier Grisel Revert back to the fork start method (instead of forkserver) as the latter was found to cause crashes in interactive Python sessions. Release 0.9.2 Lo?c Est?ve Joblib hashing now uses the default pickle protocol (2 for Python 2 and 3 for Python 3). This makes it very unlikely to get the same hash for a given object under Python 2 and Python 3. In particular, for Python 3 users, this means that the output of joblib.hash changes when switching from joblib 0.8.4 to 0.9.2 . We strive to ensure that the output of joblib.hash does not change needlessly in future versions of joblib but this is not officially guaranteed. Lo?c Est?ve Joblib pickles generated with Python 2 can not be loaded with Python 3 and the same applies for joblib pickles generated with Python 3 and loaded with Python 2. During the beta period 0.9.0b2 to 0.9.0b4, we experimented with a joblib serialization that aimed to make pickles serialized with Python 3 loadable under Python 2. Unfortunately this serialization strategy proved to be too fragile as far as the long-term maintenance was concerned (For example see joblib/joblib#243). That means that joblib pickles generated with joblib 0.9.0bN can not be loaded under joblib 0.9.2. Joblib beta testers, who are the only ones likely to be affected by this, are advised to delete their joblib cache when they upgrade from 0.9.0bN to 0.9.2. Arthur Mensch Fixed a bug with joblib.hash that used to return unstable values for strings and numpy.dtype instances depending on interning states. Olivier Grisel Make joblib use the 'forkserver' start method by default under Python 3.4+ to avoid causing crash with 3rd party libraries (such as Apple vecLib / Accelerate or the GCC OpenMP runtime) that use an internal thread pool that is not not reinitialized when a fork system call happens. Olivier Grisel New context manager based API (with block) to re-use the same pool of workers across consecutive parallel calls. Vlad Niculae and Olivier Grisel Automated batching of fast tasks into longer running jobs to hide multiprocessing dispatching overhead when possible. Olivier Grisel FIX make it possible to call joblib.load(filename, mmap_mode='r') on pickled objects that include a mix of arrays of both memmory memmapable dtypes and object dtype. Release 0.8.4 2014-11-20 Olivier Grisel OPTIM use the C-optimized pickler under Python 3 This makes it possible to efficiently process parallel jobs that deal with numerous Python objects such as large dictionaries. Release 0.8.3 2014-08-19 Olivier Grisel FIX disable memmapping for object arrays 2014-08-07 Lars Buitinck MAINT NumPy 1.10-safe version comparisons 2014-07-11 Olivier Grisel FIX #146: Heisen test failure caused by thread-unsafe Python lists This fix uses a queue.Queue datastructure in the failing test. This datastructure is thread-safe thanks to an internal Lock. This Lock instance not picklable hence cause the picklability check of delayed to check fail. When using the threading backend, picklability is no longer required, hence this PRs give the user the ability to disable it on a case by case basis. Release 0.8.2 2014-06-30 Olivier Grisel BUG: use mmap_mode='r' by default in Parallel and MemmapingPool The former default of mmap_mode='c' (copy-on-write) caused problematic use of the paging file under Windows. 2014-06-27 Olivier Grisel BUG: fix usage of the /dev/shm folder under Linux Release 0.8.1 2014-05-29 Gael Varoquaux BUG: fix crash with high verbosity Release 0.8.0 2014-05-14 Olivier Grisel Fix a bug in exception reporting under Python 3 2014-05-10 Olivier Grisel Fixed a potential segfault when passing non-contiguous memmap instances. 2014-04-22 Gael Varoquaux ENH: Make memory robust to modification of source files while the interpreter is running. Should lead to less spurious cache flushes and recomputations. 2014-02-24 Philippe Gervais New Memory.call_and_shelve API to handle memoized results by reference instead of by value. Release 0.8.0a3 2014-01-10 Olivier Grisel & Gael Varoquaux FIX #105: Race condition in task iterable consumption when pre_dispatch != 'all' that could cause crash with error messages "Pools seems closed" and "ValueError: generator already executing". 2014-01-12 Olivier Grisel FIX #72: joblib cannot persist "output_dir" keyword argument. Release 0.8.0a2 2013-12-23 Olivier Grisel ENH: set default value of Parallel's max_nbytes to 100MB Motivation: avoid introducing disk latency on medium sized parallel workload where memory usage is not an issue. FIX: properly handle the JOBLIB_MULTIPROCESSING env variable FIX: timeout test failures under windows Release 0.8.0a 2013-12-19 Olivier Grisel FIX: support the new Python 3.4 multiprocessing API 2013-12-05 Olivier Grisel ENH: make Memory respect mmap_mode at first call too ENH: add a threading based backend to Parallel This is low overhead alternative backend to the default multiprocessing backend that is suitable when calling compiled extensions that release the GIL. Author: Dan Stahlke <firstname.lastname@example.org> Date: 2013-11-08 FIX: use safe_repr to print arg vals in trace This fixes a problem in which extremely long (and slow) stack traces would be produced when function parameters are large numpy arrays. 2013-09-10 Olivier Grisel ENH: limit memory copy with Parallel by leveraging numpy.memmap when possible Release 0.7.1 2013-07-25 Gael Varoquaux MISC: capture meaningless argument (n_jobs=0) in Parallel 2013-07-09 Lars Buitinck ENH Handles tuples, sets and Python 3's dict_keys type the same as lists. in pre_dispatch 2013-05-23 Martin Luessi ENH: fix function caching for IPython Release 0.7.0 This release drops support for Python 2.5 in favor of support for Python 3.0 2013-02-13 Gael Varoquaux BUG: fix nasty hash collisions 2012-11-19 Gael Varoquaux ENH: Parallel: Turn of pre-dispatch for already expanded lists Gael Varoquaux 2012-11-19 ENH: detect recursive sub-process spawning, as when people do not protect the __main__ in scripts under Windows, and raise a useful error. Gael Varoquaux 2012-11-16 ENH: Full python 3 support Release 0.6.5 2012-09-15 Yannick Schwartz BUG: make sure that sets and dictionnaries give reproducible hashes 2012-07-18 Marek Rudnicki BUG: make sure that object-dtype numpy array hash correctly 2012-07-12 GaelVaroquaux BUG: Bad default n_jobs for Parallel Release 0.6.4 2012-05-07 Vlad Niculae ENH: controlled randomness in tests and doctest fix 2012-02-21 GaelVaroquaux ENH: add verbosity in memory 2012-02-21 GaelVaroquaux BUG: non-reproducible hashing: order of kwargs The ordering of a dictionnary is random. As a result the function hashing was not reproducible. Pretty hard to test Release 0.6.3 2012-02-14 GaelVaroquaux BUG: fix joblib Memory pickling 2012-02-11 GaelVaroquaux BUG: fix hasher with Python 3 2012-02-09 GaelVaroquaux API: filter_args: *args, **kwargs -> args, kwargs Release 0.6.2 2012-02-06 Gael Varoquaux BUG: make sure Memory pickles even if cachedir=None Release 0.6.1 Bugfix release because of a merge error in release 0.6.0 Release 0.6.0 Beta 3 2012-01-11 Gael Varoquaux BUG: ensure compatibility with old numpy DOC: update installation instructions BUG: file semantic to work under Windows 2012-01-10 Yaroslav Halchenko BUG: a fix toward 2.5 compatibility Beta 2 2012-01-07 Gael Varoquaux ENH: hash: bugware to be able to hash objects defined interactively in IPython 2012-01-07 Gael Varoquaux ENH: Parallel: warn and not fail for nested loops ENH: Parallel: n_jobs=-2 now uses all CPUs but one 2012-01-01 Juan Manuel Caicedo Carvajal and Gael Varoquaux ENH: add verbosity levels in Parallel Release 0.5.7 2011-12-28 Gael varoquaux API: zipped -> compress 2011-12-26 Gael varoquaux ENH: Add a zipped option to Memory API: Memory no longer accepts save_npy 2011-12-22 Kenneth C. Arnold and Gael varoquaux BUG: fix numpy_pickle for array subclasses 2011-12-21 Gael varoquaux ENH: add zip-based pickling 2011-12-19 Fabian Pedregosa Py3k: compatibility fixes. This makes run fine the tests test_disk and test_parallel Release 0.5.6 2011-12-11 Lars Buitinck ENH: Replace os.path.exists before makedirs with exception check New disk.mkdirp will fail with other errnos than EEXIST. 2011-12-10 Bala Subrahmanyam Varanasi MISC: pep8 compliant Release 0.5.5 2011-19-10 Fabian Pedregosa ENH: Make joblib installable under Python 3.X Release 0.5.4 2011-09-29 Jon Olav Vik BUG: Make mangling path to filename work on Windows 2011-09-25 Olivier Grisel FIX: doctest heisenfailure on execution time 2011-08-24 Ralf Gommers STY: PEP8 cleanup. Release 0.5.3 2011-06-25 Gael varoquaux API: All the usefull symbols in the __init__ Release 0.5.2 2011-06-25 Gael varoquaux ENH: Add cpu_count 2011-06-06 Gael varoquaux ENH: Make sure memory hash in a reproducible way Release 0.5.1 2011-04-12 Gael varoquaux TEST: Better testing of parallel and pre_dispatch Yaroslav Halchenko 2011-04-12 DOC: quick pass over docs -- trailing spaces/spelling Yaroslav Halchenko 2011-04-11 ENH: JOBLIB_MULTIPROCESSING env var to disable multiprocessing from the environment Alexandre Gramfort 2011-04-08 ENH : adding log message to know how long it takes to load from disk the cache Release 0.5.0 2011-04-01 Gael varoquaux BUG: pickling MemoizeFunc does not store timestamp 2011-03-31 Nicolas Pinto TEST: expose hashing bug with cached method 2011-03-26...2011-03-27 Pietro Berkes BUG: fix error management in rm_subdirs BUG: fix for race condition during tests in mem.clear() Gael varoquaux 2011-03-22...2011-03-26 TEST: Improve test coverage and robustness Gael varoquaux 2011-03-19 BUG: hashing functions with only *var **kwargs Gael varoquaux 2011-02-01... 2011-03-22 BUG: Many fixes to capture interprocess race condition when mem.cache is used by several processes on the same cache. Fabian Pedregosa 2011-02-28 First work on Py3K compatibility Gael varoquaux 2011-02-27 ENH: pre_dispatch in parallel: lazy generation of jobs in parallel for to avoid drowning memory. GaelVaroquaux 2011-02-24 ENH: Add the option of overloading the arguments of the mother 'Memory' object in the cache method that is doing the decoration. Gael varoquaux 2010-11-21 ENH: Add a verbosity level for more verbosity Release 0.4.6 Gael varoquaux 2010-11-15 ENH: Deal with interruption in parallel Gael varoquaux 2010-11-13 BUG: Exceptions raised by Parallel when n_job=1 are no longer captured. Gael varoquaux 2010-11-13 BUG: Capture wrong arguments properly (better error message) Release 0.4.5 Pietro Berkes 2010-09-04 BUG: Fix Windows peculiarities with path separators and file names BUG: Fix more windows locking bugs Gael varoquaux 2010-09-03 ENH: Make sure that exceptions raised in Parallel also inherit from the original exception class ENH: Add a shadow set of exceptions Fabian Pedregosa 2010-09-01 ENH: Clean up the code for parallel. Thanks to Fabian Pedregosa for the patch. Release 0.4.4 Gael varoquaux 2010-08-23 BUG: Fix Parallel on computers with only one CPU, for n_jobs=-1. Gael varoquaux 2010-08-02 BUG: Fix setup.py for extra setuptools args. Gael varoquaux 2010-07-29 MISC: Silence tests (and hopefuly Yaroslav :P) Release 0.4.3 Gael Varoquaux 2010-07-22 BUG: Fix hashing for function with a side effect modifying their input argument. Thanks to Pietro Berkes for reporting the bug and proving the patch. Release 0.4.2 Gael Varoquaux 2010-07-16 BUG: Make sure that joblib still works with Python2.5. => release 0.4.2 Release 0.4.1