Parallelization Technique | Application | Drawback |
---|---|---|
Multi-threading | BLAST+ | Scaling is limited to cores on one computing node. |
MPI | mpiBLAST, tntBLAST | • Scaling is limited by the master/core bottleneck - one master core serves all worker cores, which may number in the thousands. • Cannot scale beyond the available cores in the cluster. |
Any of the above | Any of the above | Performance degrades drastically if the sequences in queries and database cannot completely fit in the memory of the computing node. |
Any of the above | Any of the above | No checkpointing. Failures during long job runs can mean serious schedule setbacks, a risk that can negatively affect research design and dilute research objectives. |