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#+TITLE: High Resolution Trajectory Compression
* Overview
High Resolution Trajectory Compression (HRTC) is a method for
efficient storage of trajectories from particle simulators
(e.g. molecular dynamics, or agent based systems).
This code builds a stand-alone program and a library for integration
into other programs. Both are fully functional research prototypes.
* Installation
** Dependencies
- integer-encoding-library (included as sub-module)
- for the stand-alone program: libboost-program-options (part of [[https://boost.org][boost]])
- for the library: our fork of [[https://github.com/biosystemanalysis/tng][trajectory-ng]], residing in the same
parent directory as this repository
The software has only been tested on 64bit GNU/Linux systems using GCC.
** Building
First set up the integer-encoding-library:
#+BEGIN_SRC sh
git submodule init
git submodule update
(cd integer_encoding_library && make)
#+END_SRC
Then run ~make bin~, ~make lib~, or just ~make~ to build the
stand-alone program (~hrtc~), the library (~hrtc_wrapper.o~), or
both, respectively.
* Usage
As uncompressed I/O format ~hrtc~ uses either tab-separated-values
(one time-step per line) or an awkward yet-to-document binary
format.
Use
#+BEGIN_SRC sh
./hrtc --compress --format tsvfloat --numtraj 42 --bound 23 --error 0.1 \
--src original_file --dst compressed_file
#+END_SRC
to compress and
#+BEGIN_SRC sh
./hrtc --decompress --format tsvfloat --numtraj 42 --bound 23 --error 0.1 \
--src compressed_file --dst uncompressed_file
#+END_SRC
to decompress your data. The number of trajectories (rows per line)
has to be specified with ~--numtraj~ as well as the maximal absolute
value occurring in the trajectory (e.g. your bounding box) with
~--bound~. Most important is the ~--error~ which specifies the
maximal distance of a particle between compressed and original
representation.
Further parameters that can be tuned are ~--blocksize~,
~--integer-encoding~, and the ~--qp-ratio~. The last is a value
between 0 and 1 the specifies how the error budget is split between
quantization error and approximation error.
* License
The code is released under the GPL version 3 license (see file
LICENSE).
* Contact
The authors can be contacted via email and jabber at jh@sotun.de.
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