[From nobody Wed Aug 30 09:31:47 2006
Message-ID: &lt;44F538C4.5000203@evogene.com&gt;
Date: Wed, 30 Aug 2006 09:05:40 +0200
From: Michael Gang &lt;michael.gang@evogene.com&gt;
User-Agent: Thunderbird 1.5.0.5 (Windows/20060719)
MIME-Version: 1.0
To: David M Powers &lt;POWERS_DAVID_M@Lilly.com&gt;
Subject: Re: Fw: [Bioclusters] interpro queuing system
References: &lt;OF1770BF54.4B163B4F-ON852571D8.0066E2E8-852571D8.00672F56@EliLilly.lilly.com&gt;
In-Reply-To: &lt;OF1770BF54.4B163B4F-ON852571D8.0066E2E8-852571D8.00672F56@EliLilly.lilly.com&gt;
Content-Type: multipart/alternative;
	boundary=&quot;------------070504060102030903000702&quot;

This is a multi-part message in MIME format.
--------------070504060102030903000702
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit

Dear David,
We have the version SGE-6 (n1ge6) running on Fedora 5 core systems.
Our problem occurs when interpro  tries to  create child processes 
within themselves  and submit them via qsub. At this point (the very 
beginning) the program stops to continue it's work.

We will greatly appreciate any documentations (twiks) you have done 
combining sge6 with interpro.

Thanks in advance,
Michael

 David M Powers:
&gt;
&gt; Hi -
&gt;
&gt; The timing of your question is amazing!   I just spent the past week 
&gt; setting up interproscan version 4.2 to successfully run in our SGE-6 
&gt; environment.    We had previously been running the 3.x version of 
&gt; interproscan through our cluster using SGE-6.   Version 4.2 is a 
&gt; *huge* change from the 3.x version.   Is there a specific problem that 
&gt; you have encountered?     What version of SGE are you using?  I 
&gt; believe this latest version of interproscan also is configured for pbs.
&gt;
&gt; Dave
&gt;
&gt;
&gt; ----- Forwarded by David M Powers/AM/LLY on 08/28/2006 02:43 PM -----
&gt; *Michael Gang &lt;michael.gang@evogene.com&gt;*
&gt; Sent by: bioclusters-bounces+d_powers=lilly.com@bioinformatics.org
&gt;
&gt; 08/28/2006 10:49 AM
&gt; Please respond to
&gt; HPC in Bioinformatics &lt;bioclusters@bioinformatics.org&gt;
&gt;
&gt;
&gt; 	
&gt; To
&gt; 	bioclusters@bioinformatics.org
&gt; cc
&gt; 	
&gt; Subject
&gt; 	[Bioclusters] interpro queuing system
&gt;
&gt;
&gt;
&gt; 	
&gt;
&gt;
&gt;
&gt;
&gt;
&gt; Dear all,
&gt; I want to run interpro on an linux cluster.
&gt; We are trying to setup interpro with the queuing system qsub.
&gt; Is there another queuing system which is easier to setup (other than 
&gt; LSF) ?
&gt;
&gt; Thanks in advance,
&gt; Michael
&gt; _______________________________________________
&gt; Bioclusters maillist  -  Bioclusters@bioinformatics.org
&gt; https://bioinformatics.org/mailman/listinfo/bioclusters


--------------070504060102030903000702
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

&lt;!DOCTYPE html PUBLIC &quot;-//W3C//DTD HTML 4.01 Transitional//EN&quot;&gt;
&lt;html&gt;
&lt;head&gt;
  &lt;meta content=&quot;text/html;charset=ISO-8859-1&quot; http-equiv=&quot;Content-Type&quot;&gt;
&lt;/head&gt;
&lt;body bgcolor=&quot;#ffffff&quot; text=&quot;#000000&quot;&gt;
Dear David,&lt;br&gt;
We have the version SGE-6 (n1ge6) running on Fedora 5 core systems.&lt;br&gt;
Our problem occurs when interpro&amp;nbsp; tries to&amp;nbsp; create child processes
within themselves&amp;nbsp; and submit them via qsub. At this point (the very
beginning) the program stops to continue it's work.&lt;br&gt;
&lt;br&gt;
We will greatly appreciate any documentations (twiks) you have done
combining sge6 with interpro.&lt;br&gt;
&lt;br&gt;
Thanks in advance,&lt;br&gt;
Michael&lt;br&gt;
&lt;br&gt;
&amp;nbsp;David M Powers:
&lt;blockquote
 cite=&quot;midOF1770BF54.4B163B4F-ON852571D8.0066E2E8-852571D8.00672F56@EliLilly.lilly.com&quot;
 type=&quot;cite&quot;&gt;&lt;br&gt;
  &lt;font face=&quot;sans-serif&quot; size=&quot;2&quot;&gt;Hi -&lt;/font&gt;
  &lt;br&gt;
  &lt;br&gt;
  &lt;font face=&quot;sans-serif&quot; size=&quot;2&quot;&gt;The timing of your question is
amazing!
&amp;nbsp; I just spent the past week setting up interproscan version 4.2 to
successfully run in our SGE-6 environment. &amp;nbsp; &amp;nbsp;We had previously
been running the 3.x version of interproscan through our cluster using
SGE-6. &amp;nbsp; Version 4.2 is a *huge* change from the 3.x version. &amp;nbsp;
Is there a specific problem that you have encountered? &amp;nbsp; &amp;nbsp; What
version of SGE are you using? &amp;nbsp;I believe this latest version of
interproscan
also is configured for pbs.&lt;/font&gt;
  &lt;br&gt;
  &lt;font face=&quot;sans-serif&quot; size=&quot;2&quot;&gt;&lt;br&gt;
Dave&lt;/font&gt;
  &lt;br&gt;
  &lt;font face=&quot;sans-serif&quot; size=&quot;2&quot;&gt;&lt;br&gt;
  &lt;/font&gt;
  &lt;br&gt;
  &lt;font color=&quot;#800080&quot; face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;----- Forwarded by
David
M Powers/AM/LLY on 08/28/2006 02:43 PM -----&lt;/font&gt;
  &lt;br&gt;
  &lt;table width=&quot;100%&quot;&gt;
    &lt;tbody&gt;
      &lt;tr valign=&quot;top&quot;&gt;
        &lt;td width=&quot;40%&quot;&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;&lt;b&gt;Michael
Gang &lt;a class=&quot;moz-txt-link-rfc2396E&quot; href=&quot;mailto:michael.gang@evogene.com&quot;&gt;&amp;lt;michael.gang@evogene.com&amp;gt;&lt;/a&gt;&lt;/b&gt;
        &lt;/font&gt;&lt;br&gt;
        &lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;Sent by:
&lt;a class=&quot;moz-txt-link-abbreviated&quot; href=&quot;mailto:bioclusters-bounces+d_powers=lilly.com@bioinformatics.org&quot;&gt;bioclusters-bounces+d_powers=lilly.com@bioinformatics.org&lt;/a&gt;&lt;/font&gt;
        &lt;p&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;08/28/2006 10:49 AM&lt;/font&gt;
        &lt;table border=&quot;1&quot;&gt;
          &lt;tbody&gt;
            &lt;tr valign=&quot;top&quot;&gt;
              &lt;td bgcolor=&quot;white&quot;&gt;
              &lt;div align=&quot;center&quot;&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;Please
respond to&lt;br&gt;
HPC in Bioinformatics &lt;a class=&quot;moz-txt-link-rfc2396E&quot; href=&quot;mailto:bioclusters@bioinformatics.org&quot;&gt;&amp;lt;bioclusters@bioinformatics.org&amp;gt;&lt;/a&gt;&lt;/font&gt;&lt;/div&gt;
              &lt;/td&gt;
            &lt;/tr&gt;
          &lt;/tbody&gt;
        &lt;/table&gt;
        &lt;br&gt;
        &lt;/p&gt;
        &lt;/td&gt;
        &lt;td width=&quot;59%&quot;&gt;
        &lt;table width=&quot;100%&quot;&gt;
          &lt;tbody&gt;
            &lt;tr valign=&quot;top&quot;&gt;
              &lt;td&gt;
              &lt;div align=&quot;right&quot;&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;To&lt;/font&gt;&lt;/div&gt;
              &lt;/td&gt;
              &lt;td&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;&lt;a class=&quot;moz-txt-link-abbreviated&quot; href=&quot;mailto:bioclusters@bioinformatics.org&quot;&gt;bioclusters@bioinformatics.org&lt;/a&gt;&lt;/font&gt;
              &lt;/td&gt;
            &lt;/tr&gt;
            &lt;tr valign=&quot;top&quot;&gt;
              &lt;td&gt;
              &lt;div align=&quot;right&quot;&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;cc&lt;/font&gt;&lt;/div&gt;
              &lt;/td&gt;
              &lt;td&gt;&lt;br&gt;
              &lt;/td&gt;
            &lt;/tr&gt;
            &lt;tr valign=&quot;top&quot;&gt;
              &lt;td&gt;
              &lt;div align=&quot;right&quot;&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;Subject&lt;/font&gt;&lt;/div&gt;
              &lt;/td&gt;
              &lt;td&gt;&lt;font face=&quot;sans-serif&quot; size=&quot;1&quot;&gt;[Bioclusters]
interpro queuing system&lt;/font&gt;&lt;/td&gt;
            &lt;/tr&gt;
          &lt;/tbody&gt;
        &lt;/table&gt;
        &lt;br&gt;
        &lt;table&gt;
          &lt;tbody&gt;
            &lt;tr valign=&quot;top&quot;&gt;
              &lt;td&gt;
              &lt;br&gt;
              &lt;/td&gt;
              &lt;td&gt;&lt;br&gt;
              &lt;/td&gt;
            &lt;/tr&gt;
          &lt;/tbody&gt;
        &lt;/table&gt;
        &lt;br&gt;
        &lt;/td&gt;
      &lt;/tr&gt;
    &lt;/tbody&gt;
  &lt;/table&gt;
  &lt;br&gt;
  &lt;br&gt;
  &lt;br&gt;
  &lt;font size=&quot;2&quot;&gt;&lt;tt&gt;Dear all,&lt;br&gt;
I want to run interpro on an linux cluster.&lt;br&gt;
We are trying to setup interpro with the queuing system qsub.&lt;br&gt;
Is there another queuing system which is easier to setup (other than
LSF)
?&lt;br&gt;
  &lt;br&gt;
Thanks in advance,&lt;br&gt;
Michael&lt;br&gt;
_______________________________________________&lt;br&gt;
Bioclusters maillist &amp;nbsp;- &amp;nbsp;&lt;a class=&quot;moz-txt-link-abbreviated&quot; href=&quot;mailto:Bioclusters@bioinformatics.org&quot;&gt;Bioclusters@bioinformatics.org&lt;/a&gt;&lt;br&gt;
&lt;a class=&quot;moz-txt-link-freetext&quot; href=&quot;https://bioinformatics.org/mailman/listinfo/bioclusters&quot;&gt;https://bioinformatics.org/mailman/listinfo/bioclusters&lt;/a&gt;&lt;br&gt;
  &lt;/tt&gt;&lt;/font&gt;
&lt;/blockquote&gt;
&lt;br&gt;
&lt;/body&gt;
&lt;/html&gt;

--------------070504060102030903000702--

]