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<div>Hi Carson,</div>
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<div>I tried the –nolock option and it didn't have much effect. I then installed Proc:ProcessTable (which built successfully via cpan). Running MAKER though I get the following error:</div>
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<div>Can't locate auto/Proc/ProcessTable/get_proc_by.al in @INC (@INC contains: /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../perl/lib /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../lib /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../src/inc/perl/lib
/usr/users/TGAC_ga007/stittt/Software/Perl/5.18/site/lib /usr/users/TGAC_ga007/stittt/Software/Perl/5.18/lib .) at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../lib/Proc/Signal.pm line 143.</div>
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<div>I looked within the directories of the ProcessTable build but I don't see the get_<span style="font-style: italic;">proc_</span>by.al file. Should I be using an older version of ProcessTable? The one that was installed is v0.50.</div>
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<div>Thanks in advance for any further help with this.</div>
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<div>Tim. </div>
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<p style="font-size: 12px; margin: 0px; font-family: Verdana;">---</p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;"><b>Timothy Stitt PhD</b> / Head of Scientific Computing</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">The Genome Analysis Centre (TGAC)</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(4, 46, 238);"><span style="text-decoration: underline; font-size: 10px;"><a href="http://www.tgac.ac.uk/">http://www.tgac.ac.uk/</a></span></p>
<p style="margin: 0px; font-family: Cambria; min-height: 19px;"><span style="font-size: 10px;"><br>
</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">p: +44 1603 450378</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(13, 102, 213);"><span style="color: rgb(0, 0, 0); font-size: 10px;">e: <a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a></span></p>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 21 August 2014 21:17<br>
<span style="font-weight:bold">To: </span>Timothy Stitt <<a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] MAKER and large number of 'ps' processes<br>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">MAKER uses 'ps' every so often to check on certain processes to make sure they haven't failed or become zombies. On your system these 'ps' calls may be hanging which would cause them to build
up over time.</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;">You can try and run MAKER with the '-nolock' flag, since it is the NFS file locking that requires these process checks.</div>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">Alternatively you can edit .../maker/lib/Proc/ProcessTable_simple.pm and change it as follows.</div>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">Find the 'new' subroutine and change it from this --></div>
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<div><font face="Courier">sub new {</font></div>
<div><font face="Courier"> if($PS){</font></div>
<div><font face="Courier"> my $self = {};</font></div>
<div><font face="Courier"> my $class = shift;</font></div>
<div><font face="Courier"> bless($self, $class);</font></div>
<div><font face="Courier"> return $self;</font></div>
<div><font face="Courier"> }</font></div>
<div><font face="Courier"> else{</font></div>
<div><font face="Courier"> eval 'require Proc::ProcessTable';</font></div>
<div><font face="Courier"> return Proc::ProcessTable->new(@_);</font></div>
<div><font face="Courier"> }</font></div>
<div><font face="Courier">}</font></div>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">to this --></div>
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<div><font face="Courier">sub new {</font></div>
<div><font face="Courier"> eval 'require Proc::ProcessTable';</font></div>
<div><font face="Courier"> return Proc::ProcessTable->new(@_);</font></div>
<div><font face="Courier">}</font></div>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">This will access the process table directly rather than through 'ps', but it may experience the same hang as 'ps' is experiencing. Also you will need to install 'Proc::ProcessTable' via CPAN for
it to work, and that particular module may not install on some Linux systems.</div>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">--Carson</div>
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<span style="font-weight:bold">From: </span>"Timothy Stitt (TGAC)" <<a href="mailto:Timothy.Stitt@tgac.ac.uk">Timothy.Stitt@tgac.ac.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, August 21, 2014 at 2:05 PM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] MAKER and large number of 'ps' processes<br>
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<div>Dear MAKER developers,</div>
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<div>One of my users is running MAKER on our large shared-memory SGI UV2000 system (with over 2000 cores) and the application appears to be generating large amounts of 'ps' processes that are overwhelming the system and causing the system to be unusable for
other users. </div>
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<div>Can you confirm that MAKER would be generating this behaviour and if so, is there a way to prevent the application from running 'ps' repeatedly?</div>
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<div>Thanks in advance,</div>
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<div>Tim.</div>
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<p style="box-sizing: border-box; margin: 0px 0px 10px;"><font face="Helvetica,Arial,sans-serif"><span style="font-size: 10px; line-height: 11px;">—</span></font></p>
<p style="font-family: Helvetica, Arial, sans-serif; font-size: 10px; box-sizing: border-box; margin: 0px 0px 10px; line-height: 11px;">
<span class="txt" style="box-sizing: border-box;"><b>Timothy Stitt PhD</b></span><span class="txt" style="box-sizing: border-box; font-weight: bold;"> </span>| <span id="title-input" class="txt" style="box-sizing: border-box;"><b>Head of Scientific Computing</b></span><br style="box-sizing: border-box;">
<span id="mobile-input" class="txt" style="box-sizing: border-box;">+44 1603 450378</span><span class="txt" style="color: rgb(153, 153, 153); box-sizing: border-box;"> |</span><font color="#999999"> </font><a id="email-input" class="link email" href="mailto:timothy.stitt@tgac.ac.uk" style="color: rgb(0, 141, 221); box-sizing: border-box; outline: 0px;">timothy.stitt@tgac.ac.uk</a></p>
<p style="box-sizing: border-box; margin: 0px 0px 10px;"><span style="font-family: Helvetica, Arial, sans-serif; font-size: 10px; line-height: 11px;"><span id="company-input" class="txt" style="box-sizing: border-box; font-weight: bold;">The Genome Analysis
Centre</span><b> (TGAC)</b><br style="box-sizing: border-box;">
Norwich Research Park, </span><font face="Helvetica,Arial,sans-serif"><span style="font-size: 10px; line-height: 11px;">Norwich, </span></font><span style="font-size: 10px; line-height: 11px; font-family: Helvetica, Arial, sans-serif;">NR4 7UH, </span><font face="Helvetica,Arial,sans-serif"><span style="font-size: 10px; line-height: 11px;">UK</span></font><span style="color: rgb(155, 155, 155); font-family: Helvetica, Arial, sans-serif; font-size: 10px; line-height: 11px;">
| <a id="website-input" class="link" href="http://www.tgac.ac.uk/" style="box-sizing: border-box; color: rgb(0, 141, 221); text-decoration: none;">http://www.tgac.ac.uk</a></span></p>
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