Charles Mita
ace6a46717
The HDF5 library was made thread-safe via excessive locking, so does not gain much from reads being parallelized. By using the H5DOread_chunk function (introduced in HDF5 1.10.2) we reduce the time spent the library, improving performance for when XDS uses multiple threads to process data. The decompression and type conversions have to be done manually however, and this is only used in a limited case.
Durin
XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.
See:
- https://www.nexusformat.org
- https://www.dectris.com/features/features-eiger-x/hdf5-and-nexus
- https://strucbio.biologie.uni-konstanz.de/xdswiki
Usage
In your XDS.INP add:
LIB=[path to durin-plugin.so]
NAME_TEMPLATE_OF_DATA_FRAMES=[data_path]/data_images_??????.h5
XDS will instruct the plugin to load [data_path]/data_images_master.h5 and this must be the
Eiger master file or the NeXus file for the data collection.
It is generally assumed that the files [data_path]/data_images_data_xxxxxx.h5 contain the actual
datasets and the master file contains HDF5 external links to these, but that is not required, so long as
the master file contains an NXdata or NXdetector group with either a dataset named data or a
series of datasets named data_000001, data_000002, etc.
Requirements
- HDF5 Library (https://www.hdfgroup.org/downloads)
Building
cd durin
make
Plugin file is build/durin-plugin.so