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

BMC Bioinformatics

Table 1 The impact of input partitions

Number of input partitions	Total execution time			Average execution time per pair
Number of input partitions	Subset100	Subset400	Subset1600	Subset100	Subset400	Subset1600
Default (2)	25.54	42.29	97.28	0.25	0.11	0.06
64	22.61	22.12	26.41	0.22	0.06	0.02
128	21.57	23.95	25.69	0.22	0.06	0.02
256	22.93	23.69	25.6	0.23	0.06	0.02

Total execution time (in s) and average execution time per pair (in s) are computed for 1-to-all PSA tests

ISSN: 1471-2105