Memory usage

GAT is limited by the amount of memory available. Factors affecting GAT’s memory usage are:

  • the number of segments. Memory requirements grow linearly with the number of sets and the number of intervals in the sets segments of interest, annotations and workspace. The total number of segments
  • the number of samples. For each sample, statistics on nucleotide overlap are being kept. Thus memory requirements grow linearly with the number of samples.

If memory consumption is problematic, the following might help:

Memory consumption is usually not problematic and for typical sets reaches a few Gigabytes. If memory consumption explodes it is usually a problem with the input adat.

GAT has not been optimized for memory usage. If memory consumption is a problem, please contact the developers.

Runtime performance

As with memory usage, run-time performance of GAT is linearly related to the number of segments and the number of samples.

  • the number of segments in the segments of interest. More segments require more sampling steps. Usually, an input size with twice as many segments will take twice as long. Runtime behaviour might be worse in extreme cases where the sampler has difficulties placing the last segments, for example if the segment density is high.
  • the number of samples. Each additional sample will require an additional amount of time.
  • the number of segments in the annotations. Usually less of a factor, but it becomes a factor if overlap statisticts need to be computed for many different annotations. In this case, generating a single sample might be quicker than computing overlap statisticts of that sample with

As runtime performance is a linear function of most variables, runtime can be reduced by using multiple CPUs or cores (see Using multiple CPU/cores).

Sampling performance

In order to check for biases in the sampling procedure, we run automated tests to check for even coverage of nucleotides by the sampler and absence of edge effects.