Concatenate a large number of HDF5 files

Question

I have about 500 HDF5 files each of about 1.5 GB.

Each of the files has the same exact structure, which is 7 compound (int,double,double) datasets and variable number of samples.

Now I want to concatenate all this files by concatenating each of the datasets so that at the end I have a single 750 GB file with my 7 datasets.

Currently I am running a h5py script which:

• creates a HDF5 file with the right datasets of unlimited max
• open in sequence all the files
• check what is the number of samples (as it is variable)
• resize the global file
• append the data

this obviously takes many hours, would you have a suggestion about improving this?

I am working on a cluster, so I could use HDF5 in parallel, but I am not good enough in C programming to implement something myself, I would need a tool already written.

Answer 1

I found that most of the time was spent in resizing the file, as I was resizing at each step, so I am now first going trough all my files and get their length (it is variable).

Then I create the global h5file setting the total length to the sum of all the files.

Only after this phase I fill the h5file with the data from all the small files.

now it takes about 10 seconds for each file, so it should take less than 2 hours, while before it was taking much more.