[Bioclusters] Use of FPGA based BLAST accelerators?

Wed, 11 Dec 2002 12:25:09 -0800

This is a multi-part message in MIME format.

------=_NextPart_000_0037_01C2A110.583174A0
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: 7bit

Does anyone on the list have any experience with using some of the
commercially available FPGA accelerators for Bioinformatics applications
(e.g. from Timelogic)?

Based upon some of the performance claims I've seen, it seems to me that
augmenting a standard Linux cluster with one of these devices should
provide pretty compelling price/performance.  Why is this not commonly
done?

Thanks very much!

Amar

------=_NextPart_000_0037_01C2A110.583174A0
Content-Type: text/html;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Dus-ascii">

<meta name=3DProgId content=3DWord.Document>
<meta name=3DGenerator content=3D"Microsoft Word 10">
<meta name=3DOriginator content=3D"Microsoft Word 10">
<link rel=3DFile-List href=3D"cid:filelist.xml@01C2A110.5809C860">
<!--[if gte mso 9]><xml>
 <o:OfficeDocumentSettings>
  <o:DoNotRelyOnCSS/>
 </o:OfficeDocumentSettings>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <w:WordDocument>
  <w:SpellingState>Clean</w:SpellingState>
  <w:GrammarState>Clean</w:GrammarState>
  <w:DocumentKind>DocumentEmail</w:DocumentKind>
  <w:EnvelopeVis/>
  <w:Compatibility>
   <w:BreakWrappedTables/>
   <w:SnapToGridInCell/>
   <w:WrapTextWithPunct/>
   <w:UseAsianBreakRules/>
  </w:Compatibility>
  <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
 </w:WordDocument>
</xml><![endif]-->
<style>
<!--
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{mso-style-update:auto;
	mso-style-parent:"";
	margin:0in;
	margin-bottom:.0001pt;
	mso-pagination:widow-orphan;
	font-size:12.0pt;
	font-family:"Times New Roman";
	mso-fareast-font-family:"Times New Roman";}
a:link, span.MsoHyperlink
	{color:blue;
	text-decoration:underline;
	text-underline:single;}
a:visited, span.MsoHyperlinkFollowed
	{color:purple;
	text-decoration:underline;
	text-underline:single;}
span.EmailStyle17
	{mso-style-type:personal-compose;
	mso-style-noshow:yes;
	mso-ansi-font-size:10.0pt;
	mso-bidi-font-size:10.0pt;
	font-family:Arial;
	mso-ascii-font-family:Arial;
	mso-hansi-font-family:Arial;
	mso-bidi-font-family:Arial;
	color:windowtext;}
span.SpellE
	{mso-style-name:"";
	mso-spl-e:yes;}
@page Section1
	{size:8.5in 11.0in;
	margin:1.0in 1.25in 1.0in 1.25in;
	mso-header-margin:.5in;
	mso-footer-margin:.5in;
	mso-paper-source:0;}
div.Section1
	{page:Section1;}
-->
</style>
<!--[if gte mso 10]>
<style>
 /* Style Definitions */=20
 table.MsoNormalTable
	{mso-style-name:"Table Normal";
	mso-tstyle-rowband-size:0;
	mso-tstyle-colband-size:0;
	mso-style-noshow:yes;
	mso-style-parent:"";
	mso-padding-alt:0in 5.4pt 0in 5.4pt;
	mso-para-margin:0in;
	mso-para-margin-bottom:.0001pt;
	mso-pagination:widow-orphan;
	font-size:10.0pt;
	font-family:"Times New Roman";}
</style>
<![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple =
style=3D'tab-interval:.5in'>

<div class=3DSection1>

Does anyone on the list have any experience with using some of =
the
commercially available FPGA accelerators for Bioinformatics applications =
(e.g. from
Timelogic)?<o:p></o:p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Based upon some of the performance claims I&#8217;ve seen, it =
seems to
me that augmenting a standard Linux cluster with one of these devices =
should
provide pretty compelling price/performance.<span
style=3D'mso-spacerun:yes'>&nbsp; </span>Why is this not commonly =
done?<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Thanks very much!<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Amar<o:p></o:p></span></font></p>

</div>

</body>

</html>

------=_NextPart_000_0037_01C2A110.583174A0--