ioerror when reading h5 file with h5py

[thorsten...@googlemail.com]

The problem: We have a pip package where during installation a .h5 file is copied to the a user environment:

 '/Users/theuser/anaconda2/envs/cryolo3/lib/python2.7/site-packages/cryolo/full_yolo_backend.h5'
 

However, h5py (version 2.8.0) cannot read it:

import h5py
h5py.h5f.open("/Users/theuser/anaconda2/envs/cryolo3/lib/python2.7/site-packages/cryolo/full_yolo_backend.h5")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 78, in h5py.h5f.open
IOError: Unable to open file (file read failed: time = Mon Jul  9 23:29:28 2018
, filename = '/Users/theuser/anaconda2/envs/cryolo3/lib/python2.7/site-packages/cryolo/full_yolo_backend.h5', file descriptor = 3, errno = 5, error message = 'Input/output error', buf = 0x7ffc467cf9b0, total read size = 8, bytes this sub-read = 8, bytes actually read = 18446744073709551615, offset = 0)

If we untar the pip package and try to load the .h5 file it works.

md5sum is equal for both files. Permissions seems to be OK. Problem occurs in Red Hat.

Any suggestions?

Best, Thorsten

[thorsten...@googlemail.com]

Here are some further information about the system:

print h5py.version.info

Summary of the h5py configuration

---------------------------------

h5py    2.8.0

HDF5    1.10.2

Python  2.7.15 |Anaconda, Inc.| (default, May  1 2018, 23:32:55) 

[GCC 7.2.0]

sys.platform    linux2

sys.maxsize     9223372036854775807

numpy   1.14.5

Red Hat Enterprise Linux Server release 7.5 (Maipo)

[Thomas Caswell]

Are you sure that the permissions are correct? 

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[thorsten...@googlemail.com]

Hi Thomas,

to make sure, that the permissions are correct we applied:

chmod -R 777 /Users/theuser/anaconda2




The error still occurs.




Best,

Thorsten


[thorsten...@googlemail.com]

Finally solved the issue. I had to deactivate file locking with

os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"