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h5rnd

A random HDF5 container generator based on Prüfer sequence. In development often the need arises for a complex HDF5 dataset with atributes and certain properties to test, measure some charaterestics of a software package. A real life dataset may be restritive in licensing or size, possibly diverting focus from the main work -- h5rnd fills in this gap by providing scalable random datasets, with predictive characteristics for serial and parallel HDF5.

usage:

Usage: h5rnd [options] 

Optional arguments:
-h --help       shows help message and exits
-v --version    prints version information and exits
-o --output     the new hdf5 will be created/or opened rw [required]
-d --data-sets  number of datasets [default: 100]
-g --groups     number of groups [default: 10]
--hdf5          flag for HDF5 output [default: false]
--graphviz      flag for graphviz output [default: false]

example output

HDF5 container h5ls -r tree.h5

/                        Group
/AkWTsmZmlndfbRhKWywY    Dataset {1000}
/luSQtFEs                Group
/luSQtFEs/EcdhmBaFpNoplYIqUGHuVZj Group
/luSQtFEs/EcdhmBaFpNoplYIqUGHuVZj/ORmqQLNnWtDSQhfexAyrczVolGPY Dataset {1000}
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv Group
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/BtuejM Dataset {1000}
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/YSdbCOyP Group
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/YSdbCOyP/DNrnKgcxo Group
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/YSdbCOyP/DNrnKgcxo/CudEjqyaFtBGqcrFenMUhA Dataset {1000}
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/YSdbCOyP/VDorTtsiEIwtZ Dataset {1000}
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/YSdbCOyP/fuLsrYEurcvdOXWickWKFXLyMGY Dataset {1000}
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/qyHzilzoCyZlTaMcqZQ Dataset {1000}
/luSQtFEs/pOnCmrTKREyihDZBHmDyJDpiLv/wfXkhrapzAB Dataset {1000}
/luSQtFEs/yGnBRCmSxyrPv  Group
/luSQtFEs/yGnBRCmSxyrPv/bZPYDqZmhSXwunlyCwGMLu Group
/luSQtFEs/yGnBRCmSxyrPv/bZPYDqZmhSXwunlyCwGMLu/PnHPAPgjWqfkhBHeR Dataset {1000}
/luSQtFEs/yGnBRCmSxyrPv/bZPYDqZmhSXwunlyCwGMLu/QmNJYWKrrEXsqVxDAqkFQRPVHwaD Dataset {1000}
/luSQtFEs/yGnBRCmSxyrPv/rtaEOCMRrqKzAcRBEHQjFQ Dataset {1000}
/snWTGjtKQva             Dataset {1000}
/zzxgLfDdtDtViDnSLtrEzVpYKVZzr Dataset {1000}

graphviz: cat tree.gv sets defaults for datasets, then lists the folders, use dot directed graph for rendering, see: Makefile for details

digraph prufer {
	node [shape=note color=orange fontcolor=purple fontname="times bold" fillcolor=violet width=0.01 height=0.1 fontsize=9.0 labelloc=b style=bold];
	1 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	2 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	3 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	4 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	5 [shape=cylinder color=purple fillcolor=orange style=filled label=HDF5 weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	6 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	7 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]
	8 [shape=folder color=purple weight=2.0 width=0.75 height=0.5 fontsize=14.0 labelloc=c]

6 -> 0;
2 -> 9;
1 -> 2;
4 -> 10;
3 -> 4;
7 -> 11;
1 -> 12;
6 -> 13;
8 -> 14;
8 -> 15;
7 -> 8;
3 -> 7;
5 -> 16;
5 -> 17;
6 -> 18;
1 -> 19;
6 -> 1;
3 -> 6;
5 -> 3;
5 -> 20;
}

requirements:

  • h5cpp v1.10.6-2 included with this project
  • argparse included with this project
  • HDF5 C base library, no high level API or built in C++ API is needed works with: serial|parallel
  • c++17 or higher compiler

visualization:

  • graphviz
  • xviewer
h5rnd --graphviz -o tree.gv -d 30 -g 11  # create a graphviz output
dot -Tsvg tree.gv -o tree.svg            # convert `dot` file to `svg`
xviewer -wf  tree.svg                    # view it on screen

known bugs:

  • data size should allow a range for random values
  • in addition to random strings, should pick values from dictionary: /usr/share/dict/words
  • use the included/shipped h5cpp header files until I update the original h5cpp distribution with h5::gr_t support for read|write|create operators.