Generated h5 files not opening on other systems


#1

Hi all,

We generate H5 files with h5py. Since recently we generate this files on a new AMD system (AMD Ryzen 5 4600G / 3.7 GHz).

However, now we are only able to open and analyse these files on the AMD system it self. If we copy the files to our own Intel laptops we are no longer able to open the h5 files. Now triple checked all of the versions of the packages that we use, reinstalled python etc… So I’m starting the believe the only difference is AMD vs Intel.

Python 3.7
h5py 3.2.1

Older versions have the same issue.

On Intel systems we get this error:

Traceback (most recent call last):
File “DOT_DAT.py”, line 505, in loadFile
dset = f[c+’/’+g][:] # ndarray
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 “C:\Users\Douwe\AppData\Local\Programs\Python\Python37-32\lib\site-packages\h5py_hl\group.py”, line 288, in getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
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\h5o.pyx”, line 190, in h5py.h5o.open
KeyError: ‘Unable to open object (bad version number for datatype message)’

Some one any idea how we can solve this? I’m still trying to get my hands on another AMD machine to be really sure this is indeed the issue.

Kind regards,

Douwe


#2

Can you look at the files w/ command-line tools, e.g.,

h5ls -r file.h5

or

h5dump -pBH file.h5

?
Can you read data

h5dump -d /path/to/dataset file.h5

?

G.


#3

What datatype do you expect the dataset to have? In particular are they very long or very short floats?


#4

Thank you gheber!

In the end we found out that we were using Python 3.7.0 32 bit, but it should have been 3.7.4 64 bit. All problems are solved now!

Kind regards,

Douwe