<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML ><HEAD ><TITLE >Blast</TITLE ><META NAME="GENERATOR" CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK REL="HOME" TITLE="The openMosix HOWTO" HREF="index.html"><LINK REL="UP" TITLE="BioInformatics and openMosix" HREF="bio.html"><LINK REL="PREVIOUS" TITLE="Introduction" HREF="x1433.html"><LINK REL="NEXT" TITLE="openMosix Development" HREF="p1447.html"></HEAD ><BODY CLASS="SECT1" BGCOLOR="#FFFFFF" TEXT="#000000" LINK="#0000FF" VLINK="#840084" ALINK="#0000FF" ><DIV CLASS="NAVHEADER" ><TABLE SUMMARY="Header navigation table" WIDTH="100%" BORDER="0" CELLPADDING="0" CELLSPACING="0" ><TR ><TH COLSPAN="3" ALIGN="center" >The openMosix HOWTO: </TH ></TR ><TR ><TD WIDTH="10%" ALIGN="left" VALIGN="bottom" ><A HREF="x1433.html" ACCESSKEY="P" >Prev</A ></TD ><TD WIDTH="80%" ALIGN="center" VALIGN="bottom" >Chapter 17. BioInformatics and openMosix</TD ><TD WIDTH="10%" ALIGN="right" VALIGN="bottom" ><A HREF="p1447.html" ACCESSKEY="N" >Next</A ></TD ></TR ></TABLE ><HR ALIGN="LEFT" WIDTH="100%"></DIV ><DIV CLASS="SECT1" ><H1 CLASS="SECT1" ><A NAME="AEN1438" ></A >17.2. Blast</H1 ><P >One of the more frequent used application in this field is Blast, <A HREF="http://stl.bioinformatics.med.umich.edu/software/OM_BLAST_patch/openmosixpatch.html" TARGET="_top" ><I CLASS="CITETITLE" >Blast has a patch available that makes it work smoother </I ></A > with openMosix, but that's not the only alternative.</P ><P >First of all there are some known problems with this patch, and other versions of blast , blast tends to segfault sometimes, this mostly happens with the preformatted databases you download from the internet. If you run formatdb on a raw database these errors tend to go away.</P ><P >Next to the openMosix blast patch a lot of people run <A HREF="http://mpiblast.lanl.gov/" TARGET="_top" ><I CLASS="CITETITLE" >MPIBlast</I ></A > Given the fact that openMosix tends to speed up MPI, adding openMosix to this config might even give you more power for your money, however we will have to do some extra research to be able to confirm this.</P ></DIV ><DIV CLASS="NAVFOOTER" ><HR ALIGN="LEFT" WIDTH="100%"><TABLE SUMMARY="Footer navigation table" WIDTH="100%" BORDER="0" CELLPADDING="0" CELLSPACING="0" ><TR ><TD WIDTH="33%" ALIGN="left" VALIGN="top" ><A HREF="x1433.html" ACCESSKEY="P" >Prev</A ></TD ><TD WIDTH="34%" ALIGN="center" VALIGN="top" ><A HREF="index.html" ACCESSKEY="H" >Home</A ></TD ><TD WIDTH="33%" ALIGN="right" VALIGN="top" ><A HREF="p1447.html" ACCESSKEY="N" >Next</A ></TD ></TR ><TR ><TD WIDTH="33%" ALIGN="left" VALIGN="top" >Introduction</TD ><TD WIDTH="34%" ALIGN="center" VALIGN="top" ><A HREF="bio.html" ACCESSKEY="U" >Up</A ></TD ><TD WIDTH="33%" ALIGN="right" VALIGN="top" >openMosix Development</TD ></TR ></TABLE ></DIV ></BODY ></HTML >
