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