mpiBLAST: Open-Source Parallel BLAST

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mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community. More...

Key Features of mpiBLAST: Awards:
  • Perfect scaling across tens of thousands of compute cores

  • Superlinear speedup for huge sequence databases

  • Exact NCBI e-value scores

  • Increased per-query throughput

  • Improved query response time

  • Portable across all major operating systems

  • Scalable parallel input/output

  • High-performance on desktops, clusters, and HPC systems

Recent News:

mpiBLAST Development 2012-11-28
mpiBLAST development continues as resources permit and demand from the community dictates. At the present time, development around the new NCBI engine has been put on hold. In the meantime, you may wish to look into AbokiaBLAST, a re-factored parallel BLAST that is 10 times faster than mpiBLAST and includes professional service support and updates.

mpiBLAST-1.6.0 Officially Released 2010-07-13
We are pleased to announce the availability of mpiBLAST-1.6.0 for public download. This release enables users to leverage advanced supercomputers with tens of thousands of processors to accelerate BLAST search. Get mpiBLAST-1.6.0 here.

Paper Accepted to IEEE Transactions on Parallel and Distributed Systems 2010-05-01
Heshan Lin and Wu Feng of Virginia Tech have an accepted paper, co-authored with Xiaosong Ma and Nagiza Samatova of North Carolina State University, in the IEEE Transactions on Parallel and Distributed Systems (TPDS). The work, entitled "Coordinating Computation and I/O in Massively Parallel Sequence Search", detailed the design of the updated mpiBLAST 1.6.0 release.

mpiBLAST-1.6.0-Beta1 Released 2009-11-20
We are pleased to release mpiBLAST-1.6.0 for beta testing. This release incorporates performance optimizations that enable mpiBLAST to scale efficiently on petascale parallel computers. Part of the optimizations are presented in H. Lin et. al.'s SC08 publication "Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture." ( The efficacy of the newly designed algorithm core has been tested on up to 32,768 compute cores on a Blue Gene/P system. Get mpiBLAST-1.6.0-beta1 here.

SC|08: mpiBLAST Scales to 32K cores on Blue Gene/P with 93% Efficiency 2008-11-19
At SC|08, Heshan Lin of North Carolina State University presented, "Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture", showcasing the scalability and performance of mpiBLAST. The collaboration between North Carolina State University, Argonne National Laboratory, IBM, and Virginia Tech enabled mpiBLAST to scale to 32,768 cores of the IBM Blue Gene/P system with 93% efficiency.

WINNER ISC08 Distinguished Paper Award 2008-06-17
The 2008 International Supercomputing Conference awarded the Distinguished Paper Award to "Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer," which recounted the experiences of an international team in finding missing genes in genomes and in constructing a genome similarity tree from the SC07 International Storage Challenge.

Paper Accepted to ACM/IEEE International Symposium on High-Performance Distributed Computing 2008-04-11
Wu Feng of Virginia Tech has an accepted paper, co-authored with Pavan Balaji and Heshan Lin of Argonne National Laboratory and North Carolina State University, respectively, in the ACM/IEEE International Symposium on High-Performance Distributed Computing (HPDC). The work, entitled "Semantic-based Distributed I/O with the ParaMEDIC Framework", will be presented in Boston, MA, on June 23-27, 2008.

mpiBLAST-1.5.0-PIO Released 2008-01-17
After almost a year in development, we are pleased to release version 1.5.0-PIO for production use. Although labeled as "PIO", this version is capable of running on both parallel (e.g. PVFS) and serial (e.g. NFS) file-systems achieving significant performance improvements over prior versions of mpiBLAST. Additionally, this release is able to quickly generate exact e-value scores for large query sets. Also of interest, this version was used in our winning entry for the SC|07 Storage Challenge. Get mpiBLAST-1.5.0-PIO here.

mpiBLAST Turns 5 Years Old 2007-12-31
Today is an important day for the mpiBLAST project as it marks 5 years since the initial 1.0 release back in 2002. The mpiBLAST project would like to thank all its users and developers for helping make mpiBLAST what it is today: one of the most popular parallel BLAST applications in use and the de facto standard against which all parallel BLAST applications are compared.

WINNER SC|07 Storage Challenge: ParaMEDIC Environment for mpiBLAST 2007-11-15
The collaboration between Virginia Tech (mpiBLAST), Argonne National Laboratory (MPICH2), and North Carolina State University (mpiBLAST-PIO) was chosen as the Winner of the SC|07 Storage Challenge. ParaMEDIC used 12,000 cores, performed 256 Trillion searches, and generated 1 Petabyte of data. The winning announcement is here: SC07 Award Winners

ParaMEDIC Enables Worldwide Supercomputer for Bioinformatics 2007-11-08
Utilizing the combined resources of five supercomputer centers distributed across the continental United States and a single high-performance storage center more than 10,000 kilometers away in Tokyo, Japan, a worldwide supercomputer to benefit genomics performed more than 256 Trillion searches and generated 1 Petabyte of data. Newswise reports that this high-performance worldwide supercomputer and ParaMEDIC, a general software-based framework for large-scale distributed computing developed by Argonne National Laboratory (ANL) and Virginia Tech, will have a significant impact on the study of genomics.

mpiBLAST-2.0 presented at the Microsoft eScience Workshop 2007 at RENCI 2007-10-21
As part of the poster session highlighting novel research, mpiBLAST was presented at the Microsoft eScience Workshop 2007 at RENCI. Showcasing the novel mixin layers software architecture, the poster was well received and fostered future collaborations with large medical and bioinformatics institutions. The poster is available for download on the Publications page.

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