Skip to main content

Table 1 Drawbacks of traditional parallelization techniques

From: Scaling bioinformatics applications on HPC

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.