Segmentation fault with large nucleotide databases and many alignments

torognes / swipe

Smith-Waterman database searches with inter-sequence SIMD parallelisation

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Segmentation fault with large nucleotide databases and many alignments #16

Closed torognes closed 10 years ago

torognes commented 10 years ago

When a large (>3GB) nucleotide database is searched and many alignments (-b 1000000) are requested, SWIPE may crash with a segmentation fault.

torognes commented 10 years ago

See email dated 13 February 2014.

torognes commented 10 years ago

This is probably because SWIPE allocates enough memory to hold all the hits requested in memory even though the database may contain fewer sequences than the number of alignments requested with the -b option. Can probably be fixed by limiting the allocated memory for hits to the actual number of sequences in the database.

torognes commented 10 years ago

I believe this problem is resolved with SWIPE version 2.0.11. Specifying a very high number with options -v or -b does not anymore cause very large amounts of memory to be allocated.