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News
| 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.
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| 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.
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| 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." (http://www.mpiblast.org/Publications) 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.
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| 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.
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| 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.
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| 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.
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| 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.
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| 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.
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| 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
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| 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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| 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.
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| 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.
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| 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
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| 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.
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| 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.
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| mpiBLAST-1.4.0 Released
| 2005-07-05
| | mpiBLAST version 1.4.0 is released.
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| mpiBLAST.org is live
| 2005-07-05
| | mpiBLAST has moved to mpiBLAST.org and showcases a redesigned website.
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| 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.
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| 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.
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| mpiBLAST wins R&D100 award
| 2004-07-06
| | mpiBLAST receives an 2004 R&D100 award for "Speed is a BLAST".
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| 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.
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| 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.
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| 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.
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| mpiBLAST-1.1.1 Released
| 2003-06-19
| | mpiBLAST version 1.1.1 is available. This is primarily a bugfix release.
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| mpiBLAST is presented at ClusterWorld
| 2003-06-19
| | A paper describing mpiBLAST is being presented at ClusterWorld 2003.
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| mpiBLAST Sourceforge site launched
| 2003-06-18
| | We have launched a sourceforge.net project page for mpiBLAST.
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| 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.
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| mpiBLAST-1.0.1 Released
| 2003-01-28
| | mpiBLAST, version 1.0.1 is released.
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| mpiBLAST-1.0.0 Released
| 2002-12-31
| | mpiBLAST, version 1.0.0 is released.
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| mpiBLAST website is updated
| 2002-12-16
| | The new web site design & information put online.
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| mpiBLAST now has an online presence
| 2002-11-21
| | The mpiBLAST web site, mpiblast.lanl.gov, is officially launched.
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| mpiBLAST-0.9 Released
| 2002-11-15
| | The initial release of mpiBLAST, version 0.9, is available for download.
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