From: Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
JA ALGO | ParBiConstruct | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
P | k | U(sec) | S(sec) | R(mm:ss) | U(sec) | speedup | S(sec) | speedup | R(mm:ss) | Speedup |
8 | 21 | 6388.08 | 21.54 | 13:26.42 | 1028.61 | 6.21 | 8.08 | 2.67 | 2:10.77 | 6.17 |
8 | 27 | 2220.41 | 14.85 | 5:47.71 | 500.22 | 4.44 | 3.72 | 3.99 | 1:04.12 | 5.42 |
8 | 33 | 1662.14 | 6.63 | 3:29.89 | 288.14 | 5.77 | 2.47 | 2.68 | 0:37.46 | 5.60 |
8 | 35 | 496.89 | 3.81 | 1:03.77 | 159.59 | 3.11 | 1.03 | 3.70 | 0:21.19 | 3.01 |
12 | 21 | 9116.72 | 20.31 | 12:43.14 | 985.97 | 9.25 | 6.91 | 2.94 | 1:23.95 | 9.09 |
12 | 27 | 2626.30 | 13.94 | 3:59.85 | 479.10 | 5.48 | 3.20 | 4.36 | 0:41.32 | 5.80 |
12 | 33 | 2320.07 | 6.14 | 3:15.15 | 317.08 | 7.32 | 2.35 | 2.61 | 0:27.76 | 7.03 |
12 | 35 | 561.02 | 3.47 | 0:48.19 | 166.06 | 3.38 | 1.13 | 3.07 | 0:15.04 | 3.20 |
16 | 21 | 11943.18 | 19.91 | 12:29.49 | 1044.31 | 11.44 | 7.42 | 2.68 | 1:06.91 | 11.20 |
16 | 27 | 2889.32 | 12.95 | 3:50.81 | 498.36 | 5.80 | 3.42 | 3.79 | 0:32.48 | 7.11 |
16 | 33 | 2971.37 | 6.49 | 3:07.41 | 357.63 | 8.31 | 2.53 | 2.57 | 0:23.64 | 7.93 |
16 | 35 | 580.08 | 3.67 | 0:37.63 | 170.56 | 3.40 | 1.33 | 2.76 | 0:11.85 | 3.18 |
24 | 21 | 17744.55 | 20.26 | 12:21.94 | 1205.51 | 14.72 | 8.00 | 2.53 | 0:51.74 | 14.34 |
24 | 27 | 3399.06 | 15.24 | 2:39.02 | 658.02 | 5.17 | 4.00 | 3.81 | 0:28.72 | 5.54 |
24 | 33 | 4981.96 | 7.89 | 6:25.41 | 652.80 | 7.63 | 3.69 | 2.14 | 0:51.65 | 7.46 |
24 | 35 | 750.26 | 5.57 | 0:37.30 | 295.58 | 2.54 | 2.23 | 2.50 | 0:14.19 | 2.63 |
32 | 21 | 23119.80 | 20.95 | 12:04.89 | 1070.31 | 21.60 | 8.40 | 2.49 | 0:34.90 | 20.77 |
32 | 27 | 3897.63 | 15.20 | 2:12.96 | 464.24 | 8.40 | 5.21 | 2.92 | 0:15.81 | 8.41 |
32 | 33 | 5132.44 | 9.33 | 3:11.64 | 534.38 | 9.60 | 4.84 | 1.93 | 0:21.01 | 9.12 |
32 | 35 | 973.78 | 5.35 | 0:37.30 | 324.23 | 3.00 | 3.35 | 1.60 | 0:13.16 | 2.83 |
48 | 21 | 37116.65 | 26.37 | 13:03.67 | 2422.83 | 15.32 | 13.46 | 1.96 | 0:55.33 | 14.16 |
48 | 27 | 4932.47 | 21.70 | 1:48.76 | 1112.72 | 4.43 | 10.51 | 2.06 | 0:26.11 | 4.17 |
48 | 33 | 6658.10 | 13.72 | 3:11.84 | 1157.33 | 5.75 | 9.41 | 1.46 | 0:34.33 | 5.59 |
48 | 35 | 1020.88 | 10.95 | 0:30.47 | 447.84 | 2.28 | 8.18 | 1.34 | 0:14.08 | 2.16 |
64 | 21 | 51443.09 | 35.46 | 16:25.33 | 1938.25 | 26.54 | 25.05 | 1.42 | 0:39.57 | 24.90 |
64 | 27 | 6304.66 | 33.49 | 2:05.96 | 1029.89 | 6.12 | 21.80 | 1.54 | 0:21.64 | 5.82 |
64 | 33 | 15314.25 | 23.95 | 5:57.82 | 673.55 | 22.74 | 21.31 | 1.12 | 0:17.08 | 20.95 |
64 | 35 | 1048.56 | 20.71 | 0:25.93 | 358.62 | 2.92 | 18.86 | 1.10 | 0:09.87 | 2.63 |