h5py version

As discussed in #4 , h5py 2.7.0 is required. After downgrading pip install h5py=2.7.0, I still have

$ mpirun -n 4 python test_h5py.py
hdf5_version=1.10.1
hdf5_version=1.10.1
rank 0 read and write
Traceback (most recent call last):
  File "test_h5py.py", line 10, in <module>
    f  = h5py.File('surf_file.h5', 'r+')
  File "/home/weiw/anaconda2/lib/python2.7/site-packages/h5py/_hl/files.py", line 271, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
  File "/home/weiw/anaconda2/lib/python2.7/site-packages/h5py/_hl/files.py", line 103, in make_fid
    fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
  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 (Unable to lock file, errno = 11, error message = 'resource temporarily unavailable')
hdf5_version=1.10.1
rank 0 read and write

Also seems the version plots are different here:

$ python
>>> import h5py
>>> print (h5py.version.hdf5_version)
1.10.1
>>> print h5py.__version__
2.7.0
>>>

OS: "Ubuntu 16.04.5 LTS" Python:

Python 2.7.15 |Anaconda, Inc.| (default, Oct 23 2018, 18:31:10)
[GCC 7.3.0] on linux2

[Jamesswiz]

Downgrading h5py worked for me

pip3 install --user ‘h5py==2.7.0’ --force-reinstall --no-cache-dir

[deepmo24]

I have the same problem as you. I’d like to provide my solution here.

Since the error is caused by the mode conflicts(r+ and r), we can solve this by changing the code, not depending on the version of h5py or hdf5. My idea is creating another h5 file( named surf_file_new) to store the losses and accuracies, so we only need to open the surf_file with ‘r’ mode and surf_file_new with ‘w’ mode.

For less code changing, I copy the content of surf_file to surf_file_new and after function cruch(), I let surf_file = surf_file_new, so that we don’t need to change the subsequent code.