<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0);"><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><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><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><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div style="font-size: 14px; font-family: Calibri, sans-serif;">Find the 'new' subroutine and change it from this --></div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div style="font-size: 14px;"><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></div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div style="font-size: 14px; font-family: Calibri, sans-serif;">to this --></div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div><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></div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><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><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div style="font-size: 14px; font-family: Calibri, sans-serif;">--Carson</div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><div style="font-size: 14px; font-family: Calibri, sans-serif;"><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif;"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><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></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Dear MAKER developers,</div><div><br></div><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><div><br></div><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><div><br></div><div>Thanks in advance,</div><div><br></div><div>Tim.</div><div><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></div></div></div>
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