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1
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0
answers
119
views
Unable to load an hdf5 model file in TensorFlow / Keras
I was given an hdf5 model file that was build with tensorflow / keras. Training data is no more available.
Note: all Python code snippets shown hereunder are run against Python 3.9.23 inside a ...
0
votes
1
answer
97
views
Error when trying to access data in h5 file using h5py
I am trying to read an h5 file using python
with h5py.File(filename, 'r') as file:
print("file.keys() = ", file.keys())
a_group_key = list(file.keys())[0]
data = list(file[...
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0
votes
1
answer
52
views
How to read LZO compressed pandas HDF5 files?
Here is the situation: I have data saved into pandas HDF5 files. Some data is compressed using lzo and some using blosc:zstd. Under RHEL-7, I was able to read both types of files. Then, I was ...
0
votes
1
answer
281
views
OSError: Can't synchronously read data (can't open directory) when trying to index retrieve values from a hdf5 file
I generated a hdf5 file with the code below:
# Create forecast training data file
import h5py
import hdf5plugin
#mmap_array = np.memmap('video_prediction_224.dat', dtype='uint8', mode='w+', shape=(...
0
votes
0
answers
75
views
HDF5 Write Performance Degrades Over Time When Converting from LMDB (~3.7M entries)
I’m experiencing significant slow-downs when converting data from LMDB to HDF5 format. While the conversion starts off quickly, performance degrades substantially partway through the process.
...
1
vote
0
answers
32
views
Using HDFql to filter out groups that have specific attribute values
I am trying to use the HDFql C++ library to select groups that have attributes with specific values. There are an arbitrary number of groups in the root group, and each group has the same attribute ...
0
votes
2
answers
69
views
Write pandas df to reusable hdf5 or use other data format?
I have data that can have different sized arrays per row like:
data = {
'a': [np.array([1.,2.]), np.array([6.,7.,.6]), np.array([np.nan])],
'b': np.array([99., 66., 88.])
}
df = pd.DataFrame(...
2
votes
1
answer
77
views
Creating HDF5 attributes with 2D Dataspace in Rust
I work with HDF5 files which contain datasets aggregated from smaller HDF5 files. Using the HDF Group tool nagg I can deaggregate the larger files into their original component files. However, nagg ...
0
votes
0
answers
63
views
Issues with hyperslab in fortran HDF5
I'm trying to write two ×ばつ3 matrices (array1 and array2) into a 3D HDF5 dataset with shape (3,3,2), where each matrix occupies a different slice along the third dimension. However, the second slice ...
2
votes
0
answers
164
views
HDF5 and Standard-Compliant Fortran
I am writing Fortran code to save data to the HDF5 file format. In all the examples provided with HDF5 that I looked at, I couldn't help but notice the use of the C_LOC(x) intrinsic function with ...
0
votes
0
answers
30
views
How to setup a conda environment on a Mac laptop to compile and run a hybrid C++/Python code with MPI support
I am trying to compile a CFD code on a Mac. The code is parallelized using MPI, and is written with a combination of C++ and Fortran. In addition, it runs a Python interpreter to handle IO tasks via ...
0
votes
1
answer
65
views
Dynamically update h5py VDS from data written to in parallel -- multiple writer multiple reader case
I am trying to simulate the creation of multiple h5 files in parallel while trying to read out the results live via a dynamically updated H5 VDS in swmr mode. All h5 files are processing different ...
-4
votes
1
answer
138
views
How to save simulation parameters in HDF5 file with h5py?
I'm using H5PY to store a high number of simulations' outputs. Now of course these simulations are parametrized, hence I need to also store what parameters were used for which simulation output.
At ...
0
votes
1
answer
140
views
Writing complex Pandas DataFrame to HDF5 using h5py
I have a Pandas DataFrame with mixed scalar and array-like data of different raw types (int, float, str). The DataFrame's types look like this:
'col1', dtype('float64')
'col2', dtype('O') <-- array,...
4
votes
0
answers
75
views
How can I load an HDF5 file, including columns of strings, into R?
I have a bunch of pandas dataframes I'd like to save in one file, and each dataset gets appended to multiple times. I decided that an HD5 file would be a good way to store them, and this is code ...