Comparing the pure-R implementation of the parallelism with the python script with
a simple 140 contigs input files, as described in test/speed.sh.
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
parallel-virfinder.py -i ./input.fa -o ./py.csv -f ./py.fa -n 2 |
4.682 ± 0.033 | 4.653 | 4.741 | 1.00 |
pvirfinder.R ./input.fa 2 ./ |
10.956 ± 0.095 | 10.844 | 11.082 | 2.34 ± 0.03 |
Peak memory usage:
- Python: 536,208kb
- R: 1,253,996kb
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
parallel-virfinder.py -i ./input.fa -o ./py.csv -f ./py.fa -n 4 |
4.022 ± 0.072 | 3.944 | 4.144 | 1.00 |
pvirfinder.R ./input.fa 4 ./ |
8.013 ± 0.095 | 7.909 | 8.128 | 1.99 ± 0.04 |
Peak memory usage:
- Python: 1,056,360kb
- R: 2,072,884kb
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
parallel-virfinder.py -i ./input.fa -o ./py.csv -f ./py.fa -n 8 |
4.911 ± 0.079 | 4.819 | 5.032 | 1.00 |
pvirfinder.R ./input.fa 8 ./ |
6.816 ± 0.086 | 6.714 | 6.927 | 1.39 ± 0.03 |
Peak memory usage:
- Python: 2,055,852kb
- R: 3,726,324kb