How big is the measured performance difference?
Each chart bar shows how many times more Time or how many times more Memory one unidentified ↓ regex-dna program used, compared to the benchmark program that used least Time or the program that used least Memory.
regex-dna benchmark ≈50MB N=5,000,000
This table shows 5 measurements - CPU Time, Elapsed Time, Memory, Code and ≈ CPU Load.
Compare how much Memory the regex-dna programs used - sort Memory KB. Compare how much Code the benchmark programs used - sort Code B
Column × shows how many times more each program used compared to the benchmark program that used least.
| sort | sort | sort | sort | |||
|---|---|---|---|---|---|---|
| × | Program Source Code | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
| 1.0 | C GNU gcc | 5.23 | 2.68 | 325,256 | 2579 | 20% 63% 67% 51% |
| 1.6 | C++ GNU g++ #4 | 13.76 | 4.37 | 111,964 | 1759 | 87% 63% 88% 76% |
| 2.3 | C++ GNU g++ | 16.50 | 6.26 | 97,472 | 1588 | 100% 0% 76% 87% |
| 2.6 | C GNU gcc #4 | 20.94 | 6.85 | 94,876 | 1525 | 55% 95% 80% 76% |
| 3.6 | Scala #4 | 26.49 | 9.54 | 698,448 | 732 | 57% 63% 85% 71% |
| 4.3 | Java 6 -server #5 | 26.34 | 11.51 | 686,076 | 929 | 58% 43% 77% 48% |
| 4.3 | OCaml | 19.24 | 11.56 | 389,516 | 1261 | 22% 25% 39% 78% |
| 4.4 | OCaml #3 | 19.43 | 11.73 | 389,524 | 892 | 24% 23% 100% 19% |
| 5.1 | Scala #3 | 31.77 | 13.71 | 979,544 | 659 | 43% 49% 55% 82% |
| 5.7 | Java 6 -server #2 | 38.52 | 15.28 | 846,044 | 1534 | 47% 51% 77% 74% |
| 5.7 | Ada 2005 GNAT | 33.18 | 15.38 | 183,064 | 3334 | 52% 19% 83% 59% |
| 7.1 | OCaml #2 | 18.91 | 18.91 | 389,548 | 615 | 0% 0% 100% 0% |
| 9.7 | Java 6 -server #4 | 26.27 | 25.87 | 931,136 | 921 | 1% 0% 2% 98% |
| 9.7 | C GNU gcc #2 | 26.04 | 26.04 | 124,920 | 1099 | 0% 0% 100% 0% |
| 10 | ATS | 26.66 | 26.67 | 166,996 | 2495 | 0% 0% 100% 0% |
| 10 | Scala #2 | 53.81 | 27.64 | 1,039,064 | 1520 | 30% 44% 35% 83% |
| 12 | C++ GNU g++ #3 | 30.93 | 30.93 | 127,268 | 1599 | 0% 0% 0% 100% |
| 12 | Scheme PLT | 32.54 | 32.54 | 621,560 | 835 | 0% 100% 0% 0% |
| 12 | Scheme PLT #2 | 33.19 | 33.19 | 633,192 | 669 | 0% 0% 0% 100% |
| 13 | C# Mono #6 | 92.27 | 35.78 | 584,876 | 638 | 56% 56% 66% 78% |
| 15 | Scala | 40.27 | 39.31 | 824,044 | 663 | 2% 2% 97% 1% |
| 20 | C# Mono #5 | 133.69 | 54.87 | 551,664 | 1647 | 76% 17% 66% 83% |
| 31 | C# Mono #3 | 84.37 | 84.37 | 2,823,520 | 607 | 0% 18% 81% 0% |
| 32 | C# Mono | 84.42 | 84.44 | 2,787,076 | 624 | 0% 100% 0% 0% |
| 54 | Java 6 -Xint #5 | 5 min | 145.60 | 705,112 | 929 | 49% 47% 39% 98% |
| 58 | C# Mono #2 | 156.68 | 156.69 | 2,726,612 | 645 | 0% 0% 0% 100% |
| 89 | Java 6 -Xint #2 | 9 min | 238.11 | 777,244 | 1534 | 1% 71% 97% 77% |
| 132 | Java 6 -Xint #4 | 5 min | 5 min | 642,844 | 921 | 0% 0% 0% 100% |
| 150 | Go 6g 8g | 6 min | 6 min | 635,920 | 624 | 0% 0% 0% 100% |
| Ada 2005 GNAT #4 | Failed | 1352 | ||||
| Ada 2005 GNAT #3 | Failed | 1233 | ||||
| Haskell GHC #4 | Make Error | 1672 | ||||
| "interesting alternative" programs | ||||||
| Haskell GHC | Make Error | 519 | ||||
| Pascal Free Pascal #3 | Make Error | 2932 | ||||
| Pascal Free Pascal | Make Error | 1199 | ||||
| 8.2 | F# Mono | 30.45 | 21.86 | 770,496 | 796 | |
| 26 | C# Mono #4 | 70.15 | 70.15 | 480,424 | 657 | |
| missing benchmark programs | ||||||
| F# Mono | No program | |||||
| Java 6 steady state | No program | |||||
| Pascal Free Pascal | No program | |||||
regex-dna benchmark : Match DNA 8-mers and substitute nucleotides for IUB codes
diff program output for this 100KB input file (generated with the fasta program N = 10000) with this output file to check your program is correct before contributing.
We use FASTA files generated by the fasta benchmark as input for this benchmark. Note: the file may include both lowercase and uppercase codes.
Each program should
- read all of a redirected FASTA format file from stdin, and record the sequence length
- use the same simple regex pattern match-replace to remove FASTA sequence descriptions and all linefeed characters, and record the sequence length
- use the same simple regex patterns, representing DNA 8-mers and their reverse complement (with a wildcard in one position), and (one pattern at a time) count matches in the redirected file
- write the regex pattern and count
- use the same simple regex patterns to make IUB code alternatives explicit, and (one pattern at a time) match-replace the pattern in the redirect file, and record the sequence length
- write the 3 recorded sequence lengths