# Benchmarks of different implementations
* macOS 10.14
* i7-8700k
* oracleJDK8
* rustc 1.37.0
* Perl 5.30.0
## IntSpan 1
* Rust
```text
$ pushd ~/Scripts/rust/intspan &&
cargo build --release --examples &&
command time -l target/release/examples/benchmark &&
popd
["target/release/examples/benchmark"]
step 2
duration: 0.024120771000000003 s
step 3
duration: 0.028843299 s
step 4
duration: 0.067436723 s
step 5
duration: 0.26832116899999997 s
step 6
duration: 0.470739197 s
0.86 real 0.85 user 0.00 sys
1073152 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
271 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
42 involuntary context switches
```
* Java
```text
$ pushd ~/Scripts/java/jintspan &&
mvn clean verify &&
command time -l java -jar target/jintspan-*-jar-with-dependencies.jar benchmark &&
popd
step 2
duration 0.015188
step 3
duration 0.023388
step 4
duration 0.042441
step 5
duration 0.212403
step 6
duration 0.365264
0.78 real 0.93 user 0.05 sys
182984704 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
46445 page reclaims
1 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
5 voluntary context switches
654 involuntary context switches
```
* C
```text
$ pushd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark &&
make &&
command time -l ./test_c benchmark &&
popd
step 2
duration 0.022875
step 3
duration 0.032172
step 4
duration 0.057164
step 5
duration 0.294729
step 6
duration 0.525069
0.93 real 0.93 user 0.00 sys
1085440 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
274 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
176 involuntary context switches
```
* Perl
```text
$ pushd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark &&
command time -l perl test_ai.pl benchmark &&
popd
step 2
duration 1.749132
step 3
duration 1.951063
step 4
duration 2.060910
step 5
duration 32.967968
step 6
duration 68.138299
106.89 real 106.77 user 0.05 sys
6500352 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
1596 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
6303 involuntary context switches
```
* Perl XS
```text
$ pushd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark &&
command time -l perl test_ai.pl benchmark xs &&
popd
step 2
step 2
duration 0.195549
step 3
duration 0.205843
step 4
duration 0.271525
step 5
duration 1.440861
step 6
duration 6.663916
8.79 real 8.78 user 0.00 sys
6586368 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
1617 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
609 involuntary context switches
```
## IntSpan 2
* Rust
```text
$ pushd ~/Scripts/rust/intspan &&
cargo build --release --examples &&
command time -l target/release/examples/file &&
popd
["target/release/examples/file"]
step 1 create
duration: 0.014380602999999999 s
step 2 intersect
duration: 0.523088785 s
step 3 intersect runlist
duration: 0.611574268 s
1.15 real 1.14 user 0.00 sys
2699264 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
668 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
243 involuntary context switches
```
* Java
```text
$ pushd ~/Scripts/java/jintspan &&
mvn clean verify &&
command time -l java -jar target/jintspan-*-jar-with-dependencies.jar file &&
popd
step 1 create
duration 0.053408
step 2 intersect
duration 0.347398
step 3 intersect runlist
duration 0.555934
1.06 real 1.17 user 0.12 sys
582258688 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
143954 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
0 voluntary context switches
1194 involuntary context switches
```
* C
```text
$ pushd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark &&
make &&
command time -l ./test_c file &&
popd
step 1 create
duration 0.118375
step 2 intersect
duration 2.174462
step 3 intersect runlist
duration 18.218233
20.51 real 20.42 user 0.05 sys
2121728 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
521 page reclaims
6 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
1 voluntary context switches
6360 involuntary context switches
```
* Perl
```text
$ pushd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark &&
command time -l perl test_ai.pl file &&
popd
==> test against large sets
step 1 create
duration 4.548069
step 2 intersect
duration 61.313397
step 3 intersect runlist
duration 61.335031
127.25 real 126.56 user 0.38 sys
11943936 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
2924 page reclaims
1 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
6 voluntary context switches
45869 involuntary context switches
```
* Perl XS
```text
$ pushd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark &&
command time -l perl test_ai.pl file xs &&
popd
==> test against large sets
step 1 create
duration 0.116019
step 2 intersect
duration 8.530752
step 3 intersect runlist
duration 8.677303
17.37 real 17.26 user 0.05 sys
9822208 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
2407 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
7011 involuntary context switches
```
## linkr
```bash
brew install jrange
cargo install intspan
cpanm App::Rangeops
brew install hyperfine
```
### sort
```bash
hyperfine --warmup 1 --export-markdown sort.md.tmp \
'gzip -dcf tests/Atha/links.lastz.tsv.gz tests/Atha/links.blast.tsv.gz | linkr sort stdin -o /dev/null' \
'gzip -dcf tests/Atha/links.lastz.tsv.gz tests/Atha/links.blast.tsv.gz | jrange sort stdin -o /dev/null' \
'gzip -dcf tests/Atha/links.lastz.tsv.gz tests/Atha/links.blast.tsv.gz | rangeops sort stdin -o /dev/null'
```
| linkr | 143.4 ± 1.4 | 141.5 | 147.2 | 1.0 |
| jrange | 604.3 ± 4.0 | 599.9 | 613.2 | 4.2 |
| rangeops | 1399.3 ± 14.6 | 1380.5 | 1423.1 | 9.8 |
### clean
```bash
hyperfine --min-runs 3 --export-markdown clean.md.tmp \
'linkr clean tests/Atha/sort.tsv -o /dev/null' \
'jrange clean tests/Atha/sort.tsv -o /dev/null' \
'rangeops clean tests/Atha/sort.tsv -o /dev/null'
```
| linkr | 5.896 ± 0.045 | 5.864 | 5.948 | 1.2 |
| jrange | 4.881 ± 0.049 | 4.831 | 4.929 | 1.0 |
| rangeops | 122.840 ± 1.813 | 120.871 | 124.442 | 25.2 |
### merge
```bash
hyperfine --min-runs 3 --export-markdown merge.md.tmp \
'linkr merge tests/Atha/sort.clean.tsv -c 0.95 -o /dev/null' \
'jrange merge tests/Atha/sort.clean.tsv -c 0.95 -o /dev/null' \
'rangeops merge tests/Atha/sort.clean.tsv -c 0.95 -p 4 -o /dev/null'
```
| linkr | 5.278 ± 0.026 | 5.255 | 5.305 | 2.4 |
| jrange | 2.228 ± 0.020 | 2.206 | 2.246 | 1.0 |
| rangeops | 64.090 ± 0.267 | 63.783 | 64.273 | 28.8 |
### clean2
```bash
hyperfine --min-runs 3 --export-markdown clean2.md.tmp \
'linkr clean tests/Atha/sort.clean.tsv -r tests/Atha/merge.tsv --bundle 500 -o /dev/null' \
'jrange clean tests/Atha/sort.clean.tsv -r tests/Atha/merge.tsv --bundle 500 -o /dev/null' \
'rangeops clean tests/Atha/sort.clean.tsv -r tests/Atha/merge.tsv --bundle 500 -o /dev/null'
```
| linkr | 3.208 ± 0.019 | 3.186 | 3.220 | 1.0 |
| jrange | 4.170 ± 0.047 | 4.119 | 4.212 | 1.3 |
| rangeops | 54.888 ± 0.244 | 54.651 | 55.139 | 17.1 |
### connect
```bash
hyperfine --export-markdown connect.md.tmp \
'linkr connect tests/Atha/clean.tsv -o /dev/null' \
'rangeops connect tests/Atha/clean.tsv -o /dev/null'
```
| linkr | 196.9 ± 1.9 | 194.5 | 200.6 | 1.0 |
| rangeops | 2497.3 ± 11.5 | 2477.2 | 2513.0 | 12.7 |
### filter
```bash
hyperfine --warmup 1 --export-markdown filter.md.tmp \
'linkr filter tests/Atha/connect.tsv -r 0.8 -o /dev/null' \
'jrange filter tests/Atha/connect.tsv -r 0.8 -o /dev/null' \
'rangeops filter tests/Atha/connect.tsv -r 0.8 -o /dev/null'
```
| linkr | 31.0 ± 0.6 | 30.1 | 33.0 | 1.0 |
| jrange | 109.6 ± 1.9 | 105.4 | 114.2 | 3.5 |
| rangeops | 415.7 ± 6.4 | 409.3 | 429.2 | 13.4 |