How big is the measured performance difference?
Each chart bar shows how many times more Time or how many times more Memory one unidentified ↓ reverse-complement program used, compared to the program that used least Time or the program that used least Memory.
reverse-complement benchmark ~240MB N=25,000,000
This table shows 5 measurements - CPU Time, Elapsed Time, Memory, Code and ~ CPU Load.
Compare how much Memory the reverse-complement programs used - sort Memory KB. Compare how much Code the programs used - sort Code B
Column × shows how many times more each program used compared to the 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 g++ #4 | 1.21 | 0.85 | 245,644 | 2275 | 37% 13% 80% 14% |
| 1.2 | Ada 2005 GNAT #2 | 1.19 | 0.98 | 197,868 | 3132 | 41% 63% 21% 0% |
| 1.2 | C++ GNU g++ #2 | 1.30 | 1.01 | 245,260 | 1098 | 98% 10% 12% 9% |
| 1.2 | ATS | 1.04 | 1.04 | 122,696 | 2077 | 0% 0% 0% 100% |
| 1.7 | C++ GNU g++ #3 | 1.40 | 1.41 | 125,420 | 810 | 100% 0% 1% 0% |
| 1.7 | C GNU gcc #4 | 1.44 | 1.44 | 125,276 | 722 | 100% 0% 1% 0% |
| 2.5 | Go 6g 8g | 2.13 | 2.13 | 160,664 | 550 | 0% 100% 0% 1% |
| 2.7 | Scala #4 | 2.37 | 2.31 | 403,140 | 505 | 97% 0% 2% 3% |
| 3.0 | OCaml #3 | 2.55 | 2.56 | 388,264 | 582 | 100% 0% 0% 0% |
| 3.1 | Haskell GHC #2 | 2.65 | 2.65 | 618,196 | 913 | 0% 1% 0% 100% |
| 3.1 | Java 6 -server #4 | 2.71 | 2.67 | 475,908 | 592 | 3% 1% 94% 3% |
| 3.2 | Lisp SBCL | 2.73 | 2.74 | 252,700 | 896 | 1% 100% 0% 1% |
| 3.3 | C# Mono | 2.82 | 2.83 | 162,192 | 1099 | 0% 1% 99% 0% |
| 3.5 | OCaml | 2.99 | 2.99 | 485,108 | 540 | 0% 100% 0% 1% |
| 3.7 | C++ GNU g++ | 3.19 | 3.19 | 245,528 | 571 | 100% 0% 1% 0% |
| 4.7 | Pascal Free Pascal #2 | 4.02 | 4.03 | 122,892 | 751 | 0% 0% 100% 0% |
| 5.5 | OCaml #2 | 4.70 | 4.70 | 209,724 | 394 | 100% 0% 0% 0% |
| 6.2 | Perl #2 | 5.25 | 5.25 | 431,496 | 298 | 100% 0% 0% 0% |
| 6.3 | Perl #4 | 5.34 | 5.35 | 124,368 | 237 | 0% 100% 0% 0% |
| 6.6 | PHP #2 | 5.60 | 5.60 | 445,220 | 343 | 9% 0% 100% 4% |
| 7.0 | Ada 2005 GNAT | 5.96 | 5.97 | 127,540 | 885 | 0% 0% 100% 0% |
| 7.4 | Python CPython #3 | 6.28 | 6.28 | 565,856 | 288 | 0% 0% 0% 100% |
| 7.9 | Fortran Intel #2 | 6.69 | 6.70 | 191,036 | 772 | 0% 0% 100% 0% |
| 8.9 | C# Mono #3 | 8.68 | 7.61 | 263,264 | 863 | 4% 6% 100% 5% |
| 9.6 | PHP | 8.15 | 8.15 | 370,760 | 297 | 0% 0% 100% 0% |
| 10 | Ruby MRI #2 | 8.50 | 8.50 | 246,712 | 255 | 0% 0% 100% 0% |
| 21 | Ruby JRuby #2 | 19.82 | 18.26 | 504,052 | 255 | 5% 42% 6% 55% |
| 23 | Lua | 19.17 | 19.17 | 538,784 | 538 | 0% 0% 100% 0% |
| 23 | Scheme PLT #2 | 19.25 | 19.24 | 465,884 | 554 | 100% 0% 0% 0% |
| 25 | Lua #3 | 21.64 | 21.65 | 155,716 | 593 | 0% 0% 0% 100% |
| 29 | Scala #5 | 25.59 | 24.88 | 712,664 | 358 | 2% 97% 2% 2% |
| 32 | Java 6 -Xint #4 | 27.09 | 27.16 | 473,140 | 592 | 0% 100% 0% 0% |
| 36 | Smalltalk VisualWorks | 30.91 | 30.92 | 299,944 | 754 | 0% 0% 0% 100% |
| 46 | JavaScript V8 #2 | 38.73 | 38.73 | 367,348 | 456 | 0% 100% 0% 0% |
| 47 | Erlang HiPE #4 | 50.21 | 40.27 | 630,108 | 1167 | 7% 27% 38% 52% |
| 52 | Perl | 44.40 | 44.40 | 398,300 | 299 | 96% 5% 0% 2% |
| 52 | JavaScript TraceMonkey #2 | 44.49 | 44.49 | 1,377,688 | 456 | 100% 0% 0% 0% |
| 74 | Erlang HiPE #3 | 66.10 | 62.92 | 815,212 | 624 | 1% 25% 0% 78% |
| Clean | Failed | 834 | ||||
| interesting alternative programs | ||||||
| Perl #3 | Bad Output | 263 | ||||
| missing programs | ||||||
| F# Mono | No program | |||||
| Java 6 steady state | No program | |||||
reverse-complement benchmark : Read DNA sequences - write their reverse-complement
diff program output for this 10KB input file (generated with the fasta program N = 1000) with this output file to check your program is correct before contributing.
We use the FASTA file generated by the fasta benchmark as input for this benchmark. Note: the file may include both lowercase and uppercase codes.
Each program should
- read line-by-line a redirected FASTA format file from stdin
- for each sequence:
- write the id, description, and the reverse-complement sequence in FASTA format to stdout
We use these code complements:
code meaning complement A A T C C G G G C T/U T A M A or C K R A or G Y W A or T W S C or G S Y C or T R K G or T M V A or C or G B H A or C or T D D A or G or T H B C or G or T V N G or A or T or C N
"by knowing the sequence of bases of one strand of DNA we immediately know the sequence of the DNA strand which will bind to it, this strand is called the reverse complement"
DNA: Structure and Function