OSError: "Unable to open file (file signature not found)" h5py/_objects.pyx:55 related error

[suniliisc]

I am experiencing the following error while saving cluster/msm etc.

Going through the tutorial 04-msm-analysis at ( http://www.emma-project.org/latest/tutorials/notebooks/04-msm-analysis.html)

I have attached the output of conda list.
(https://github.com/markovmodel/PyEMMA/files/10069918/conda_list.csv)

Executed command:
cluster.save('nb4.pyemma', model_name='doublewell_cluster', overwrite=True)

The API at (http://www.emma-project.org/latest/tutorials/notebooks/04-msm-analysis.html) also has a similar error.
I got the following error:

OSError Traceback (most recent call last)
Input In [63], in <cell line: 1>()
----> 1 cluster.save('nb4.pyemma', model_name='doublewell_cluster', overwrite=True)

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/serialization.py:238, in SerializableMixIn.save(self, file_name, model_name, overwrite, save_streaming_chain)
212 def save(self, file_name, model_name='default', overwrite=False, save_streaming_chain=False):
213 r""" saves the current state of this object to given file and name.
214
215 Parameters
(...)
236 >>> np.testing.assert_equal(m.P, inst_restored.P) # doctest: +SKIP
237 """
--> 238 from pyemma._base.serialization.h5file import H5File
239 try:
240 with H5File(file_name=file_name, mode='a') as f:

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/h5file.py:22, in
20 import numpy as np
21 from io import BytesIO
---> 22 from .pickle_extensions import HDF5PersistentPickler
24 author = 'marscher'
26 logger = logging.getLogger(name)

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/pickle_extensions.py:68, in
64 pass
67 # we cache this during runtime
---> 68 _DEFAULT_BLOSC_OPTIONS = _check_blosc_avail()
71 class HDF5PersistentPickler(Pickler):
72 # stores numpy arrays during pickling in given hdf5 group.
73 def init(self, group, file):

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/pyemma/_base/serialization/pickle_extensions.py:46, in _check_blosc_avail()
44 fid, name = tempfile.mkstemp()
45 try:
---> 46 with h5py.File(name) as h5f:
47 try:
48 h5f.create_dataset('test', shape=(1,1), **blosc_opts)

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/h5py/_hl/files.py:533, in File.init(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, **kwds)
525 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,
526 locking, page_buf_size, min_meta_keep, min_raw_keep,
527 alignment_threshold=alignment_threshold,
528 alignment_interval=alignment_interval,
529 **kwds)
530 fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy,
531 fs_persist=fs_persist, fs_threshold=fs_threshold,
532 fs_page_size=fs_page_size)
--> 533 fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
535 if isinstance(libver, tuple):
536 self._libver = libver

File ~/anaconda3/envs/MSM/lib/python3.8/site-packages/h5py/_hl/files.py:226, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
224 if swmr and swmr_support:
225 flags |= h5f.ACC_SWMR_READ
--> 226 fid = h5f.open(name, flags, fapl=fapl)
227 elif mode == 'r+':
228 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5f.pyx:106, in h5py.h5f.open()

OSError: Unable to open file (file signature not found)

---

• Pyemma 2.5.7 and python 3.8.13
• Ubuntu 18.04.6 LTS

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