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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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MPI_IO=y with large datasets sometimes fail #178

Closed sebhtml closed 11 years ago

sebhtml commented 11 years ago

With Illumina data at k=31, it got stuck at

Rank 329 requires 4213508 bytes for storage. Rank 81 requires 4296342 bytes for storage. Rank 301 requires 3819954 bytes for storage. Rank 397 requires 3935799 bytes for storage. Rank 206 requires 4269500 bytes for storage. Rank 73 requires 4391855 bytes for storage. Rank 365 requires 3992411 bytes for storage. Rank 429 requires 4180933 bytes for storage. Rank 109 requires 4229076 bytes for storage. Rank 213 requires 3975706 bytes for storage. Rank 334 requires 4650353 bytes for storage. Rank 205 requires 4503802 bytes for storage. Rank 237 requires 4540413 bytes for storage. Rank 85 requires 4332618 bytes for storage. Rank 201 requires 5113335 bytes for storage. Rank 333 requires 5052987 bytes for storage.

Bird-11 is -k 57

see #174

sebhtml commented 11 years ago

Evaluation: 5 human-hours

sebhtml commented 11 years ago

Probably fixed by this one:

https://github.com/sebhtml/RayPlatform/commit/d78e7ec5037c9c9e8a08160cb83864bbe67f658c