mpiBLAST: Open-Source Parallel BLAST
OverviewDescriptionmpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processors (SMPs). The primary advantage to using mpiBLAST versus traditional NCBI BLAST is performance. mpiBLAST can increase performance by several orders of magnitude while still retaining identical results as output from NCBI BLAST. Specifically, through the use of database fragmentation and query segmentation mpiBLAST performs a BLAST search in parallel. Database fragmentation partitions a database into multiple fragments and by distributing the fragments across many computational-resources (e.g. cluster-nodes, CPU-cores, clusters, etc.), each fragment can be searched simultaneously. Furthermore, by segmenting the query into multiple, independent searches, multiple BLAST searches can be simultaneously performed. With intelligent job scheduling, the multiple database fragments and query segments are searched in parallel with fault-tolerant execution. In short, database fragmentation reduces execution latency because each node's database fragment resides in main memory, yielding a significant speedup due to the elimination of disk I/O. Furthermore, query segmentation increases execution throughput as a single multi-sequence query is now split into separate, independent subqueries and each subquery is executed in parallel. An advanced feature found in mpiBLAST-PIO is parallel input-output optimizations. mpiBLAST-PIO offloads the formatting and writing of results from the master to the workers thereby increasing the scalability of mpiBLAST to hundreds of processors. mpiBLAST is also portable across many different operating-systems and computer-systems. mpiBLAST runs on Linux, BSD, Windows, MacOS X, and many varieties of Unix. mpiBLAST will also run on many different hardware configurations ranging from single processor PCs, to clusters of AMD Opterons, to IBM Blue Gene systems. The only requirements to executing mpiBLAST are:
For more information about mpiBLAST, please peruse this website by using the links in the menu on the left. You can find further technical information about mpiBLAST in the many papers, presentations, and posters found on the publications page. Additionally, more information regarding the usage, installation, development, and future of mpiBLAST can be found through the mailing lists. SupportersThe mpiBLAST project would like to thank the following institutions for their support: AMD Eli Lilly UsersA brief listing of known users of mpiBLAST is below:
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