mpiBLAST: Open-Source Parallel BLAST

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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.

Software Architecture of mpiBLAST-2.0 presented at IEEE ICSM 2007-10-02
The software engineering methodology and analysis of mpiBLAST-2.0 was presented at 23rd IEEE International Conference for Software Maintenance (ICSM 2007). The presentation was well received and catalyzed several future collaborations. The paper and presentation are available here.

SC|07 Storage Challenge Finalist: ParaMEDIC Environment for mpiBLAST 2007-08-28
MPICH2 (Argonne National Laboratory) and mpiBLAST (Virginia Tech) collaborate using the ParaMEDIC framework to land a finalist slot in the SC|07 storage challenge. ParaMEDIC, short for Parallel Meta-data Environment for Distributed I/O and Computing, accelerates the I/O in mpiBLAST by as much as 25-fold in a distributed I/O and computing environment. For additional information, see the SC07 entry here.

Next-generation mpiBLAST framework presented at IEEE EMBC 2007-08-23
A high-level overview of a new pluggable software architecture for mpiBLAST was presented at the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2007) in Lyon, France. The publication can be found here.

mpiBLAST project and website rejuvenated 2007-07-07
Just as the website sports a newly revamped look, the mpiBLAST project is also undergoing a renaissance. For the first time since its inception, several developers are co-located at the same place spurring development. Furthermore, a new development model is also emerging more closely resembling the successful open-source models of established projects.

Massively Parallel Sequence Search presented at ACM-CF 2007-05-07
"Parallel Genomic Sequence-Search on a Massively Parallel System" is presented by Virginia Tech, IBM, and North Carolina State University at ACM International Conference on Computing Frontiers. This paper describes a novel approach to executing mpiBLAST-PIO on IBM BlueGene/L that improves scalability to 8192 nodes (with 2 processors per node). The modifications will be either be released as a patch or incorporated into mpiBLAST-1.5.0-PIO shortly.

GreenGene Ad-hoc Grid presented at SC|06 2006-11-15
Virginia Tech, the University of Utah, and North Carolina State University present the following Best Paper Nominee at SC06: "Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications". The paper describes a multi-disciplinary effort from SC05 that used 458 lines of Perl code to form an ad-hoc grid to run mpiBLAST-1.4.0-PIO. The "GreenGene" ad-hoc grid used over 3000 CPU cores to compare the NT database against itself.

mpiBLAST-1.4.0-PIO Released 2006-01-22
mpiBLAST-1.4.0-PIO, an effort led by North Carolina State University and Oak Ridge National Laboratory with support from Los Alamos National Laboratory, is available for download. mpiBLAST-1.4.0-PIO incorporates the parallel-I/O performance enhancements of pioBLAST into mpiBLAST. Documentation is here: mpiBLAST-PIO-design.pdf

mpiBLAST can run on IBM Blue Gene/L 2006-01-20
Patches are available to allow mpiBLAST to run on IBM BlueGene machines. No source code changes are required, but the build process is slightly modified.

GreenGene runs at SC|05 2005-11-12
The GreenGene distributed system runs mpiBLAST on more than 3000 CPU cores to compare the NT database against itself during SC05.

mpiBLAST-1.4.0 Released 2005-07-05
mpiBLAST version 1.4.0 is released. is live 2005-07-05
mpiBLAST has moved to and showcases a redesigned website.

mpiBLAST and GreenDestiny win FLC award 2005-05-04
mpiBLAST and Green Destiny win an FLC Award with "Hardware & Software for Super Efficient Supercomputing".

mpiBLAST is gridified 2005-04-28
mpiBLAST-g2 is available thanks to Academia Sinica Computing Centre (ASCC), Taiwan. mpiBLAST-g2 allows the parallel execution of mpiBLAST over a grid environment based on Globus Toolkits 2.x and MPICH-g2. ISGC 2004 slides (PowerPoint format) can be found here.

pioBLAST presented at IPDPS 2005 2005-04-06
North Carolina State University and Oak Ridge National Laboratory prototype pioBLAST, a parallelization and optimization of the serial I/O-processing in mpiBLAST. For additional information, please see "Efficient Data Access for Parallel BLAST" which appeared in the IEEE International Parallel & Distributed Processing Symposium, April 2005.

mpiBLAST-1.3.0 Released 2004-12-08
mpiBLAST version 1.3.0 is available. This releases incorporates many changes and performance improvements. E-value scores are now identical to those reported by NCBI. Database pipelining lessens the load on the central shared storage server by limiting the number of concurrent accesses. Results pipelining collects results throughout the life of a search instead of only at the end. Better query distribution improves memory usage for large query sets. Read the ChangeLog for more improvements.

mpiBLAST wins R&D100 award 2004-07-06
mpiBLAST receives an 2004 R&D100 award for "Speed is a BLAST".

mpiBLAST can run on 64-bit SuSE Linux 2004-05-13
mpiBLAST (with NCBI) binaries for AMD x86_64 for SuSE SLES 8 are available as well as instructions to compile from source.

mpiBLAST-1.2.1 Released 2004-02-06
mpiBLAST version 1.2.1 is available. This release fixes a memory deallocation bug during result output, and includes a 1000 fragments patch for the November 2003 NCBI toolbox release.

mpiBLAST-1.2.0 Released 2003-11-05
mpiBLAST version 1.2.0 is available. New features include alignments in translated searches, distributed sequence lookup during result output, and database updates.

mpiBLAST-1.1.1 Released 2003-06-19
mpiBLAST version 1.1.1 is available. This is primarily a bugfix release.

mpiBLAST is presented at ClusterWorld 2003-06-19
A paper describing mpiBLAST is being presented at ClusterWorld 2003.

mpiBLAST Sourceforge site launched 2003-06-18
We have launched a project page for mpiBLAST.

mpiBLAST-1.1.0 Released 2003-04-07
mpiBLAST, version 1.1.0 is released. mpiBLAST now runs on Windows and Unix.

Thanks to everybody who sent in bug reports.

mpiBLAST-1.0.1 Released 2003-01-28
mpiBLAST, version 1.0.1 is released.

mpiBLAST-1.0.0 Released 2002-12-31
mpiBLAST, version 1.0.0 is released.

mpiBLAST website is updated 2002-12-16
The new web site design & information put online.

mpiBLAST now has an online presence 2002-11-21
The mpiBLAST web site,, is officially launched.

mpiBLAST-0.9 Released 2002-11-15
The initial release of mpiBLAST, version 0.9, is available for download.

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