pmTM-align: scalable pairwise and multiple structure alignment with Apache Spark and OpenMP

BMC Bioinformatics

Table 2 The impact of partition fusion

Number of partitions after fusion	Total execution time			Average execution time per pair
Number of partitions after fusion	Subset100	Subset400	Subset1600	Subset100	Subset400	Subset1600
64	93.69	936.09	14,128.78	0.02	0.01	0.01
128	35.60	234.91	13,136.66	0.01	0.003	0.01
320	35.02	145.92	1702.24	0.01	0.002	0.001
640	36.71	135.97	1666.90	0.01	0.002	0.001
960	39.89	140.88	1696.40	0.01	0.002	0.001
1280	37.89	140.74	1652.48	0.01	0.002	0.001
Default^a	42.46	144.38	1728.53	0.01	0.002	0.001

Total execution time (in s) and average execution time per pair (in s) are computed for all-to-all PSA tests
^aThe default number of partitions are 2025, 3364 and 3969 for subset 100, 400 and 1600 respectively

ISSN: 1471-2105