Frequently Asked Questions (FAQ)

Why don’t you use HDF5 as a container for all data?

HDF5 is a great format with efficient I/O under certain conditions, but there are some issues:

  • Datasets within a file cannot be deleted. They are only unlinked, but still occupy disk space. This makes the format not well suited for dynamic data that changes frequently.
  • I/O performance drops significantly when compression filters are used. Performance becomes comparible to that of PNG files at similar compression levels.
  • I/O performance also drops dramatically upon random access, i.e. when only small subsets of datasets are accessed. This becomes a bottleneck with complex access patterns.
  • No support for concurrent writes. As with every file format, locks prevent multiple processes from writing to a file in parallel. Ok, there is Parallel HDF5, but it relies on MPI and who want’s to use it these days? We don’t! It wouldn’t play nice with architectures like Spark. In a distributed environment one would consequently have to use a separate file for each batch job (already a nightmare from a data consistency point of view).

There is a nice blog on this topic called Moving away from HDF5.

We still use HDF5 files, but only for large binary persistent data. However, we will probably also move to other formats for this use case in the future.

Does TissueMAPS run on GPUs?