<html><head></head><body 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>Try changing --> <span style="font-family: Courier;">eval 'require Proc::ProcessTable';</span></div><div><span style="font-family: Courier;">to --> </span><span style="font-family: Courier;">use Proc::ProcessTable;</span></div><div><br></div><div>in .../maker/lib/Proc/ProcessTable_simple.pm.</div><div><br></div><div>That way it forces the perls import method to run incase explicitly exports something for it to function properly.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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, September 4, 2014 at 12:45 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</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></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><div>Thanks Carson.</div><div><br></div><div>I downloaded a couple of different versions of Proc::ProcessTable (v0.50 and v0.48). In each case they compiled successfully. I've copied snippets of the 'make test' below to confirm. I've scoured the source and build directories and don't see the .al
files. Nothing seems to indicate that they are generated.</div><div><br></div><div>I notice that the error occurs at line #143 in ../lib/Proc/Signal.pm of the MAKER source according to the diagnostics:</div><div><br></div><div>#142 my $obj = new Proc::ProcessTable_simple;</div><div>#143 return $obj->get_proc_by_id($id);</div><div><br></div><div>Is there a possibility that the issue is caused by $obj not having the attribute that is being referenced in line $143? I'm not a Perl expert so just throwing out ideas here. If not, how do I get the *.al files to be generated if the build says everything
built and tested ok?</div><div><br></div><div><div>> make test</div><div>make[1]: Entering directory `/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/Proc-ProcessTable-0.50/Process'</div><div>make[1]: Leaving directory `/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/Proc-ProcessTable-0.50/Process'</div><div>PERL_DL_NONLAZY=1 /tgac/software/testing/perl_activeperl/5.16.3.1603/x86_64/bin/perl-static "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t</div><div>t/process.t .. --------------------------------</div><div>uid: 10344</div><div>gid: 11995</div><div>…</div><div>cmndline: /tgac/software/testing/perl_activeperl/5.16.3.1603/x86_64/bin/perl-static t/process.t</div><div>exec: /tgac/software/testing/perl_activeperl/5.16.3.1603/x86_64/bin/perl-static</div><div>cwd: /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/Proc-ProcessTable-0.50</div><div>t/process.t .. ok</div><div>All tests successful.</div><div>Files=1, Tests=3, 0 wallclock secs ( 0.04 usr 0.02 sys + 0.08 cusr 0.07 csys = 0.21 CPU)</div><div>Result: PASS</div><div>make[1]: Entering directory `/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/Proc-ProcessTable-0.50/Process'</div><div>No tests defined for Proc::ProcessTable::Process extension.</div><div>make[1]: Leaving directory `/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/Proc-ProcessTable-0.50/Process'</div></div><div><br></div><div>Thanks,</div><div><br></div><div>Tim.</div><div><br></div><div><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></div></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span>Thursday, 4 September 2014 15:25<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></div><div><br></div><div><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>You can also try an older version from <a href="http://search.cpan.org">http://search.cpan.org</a> if you think that is the issue, but I'd try checking the directories and installation locations first.</div><div><br></div><div>--Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span>Thursday, September 4, 2014 at 8:22 AM<br><span style="font-weight:bold">To: </span>"Timothy Stitt (TGAC)" <<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></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
The error means Proc:ProcessTable didn't install and compile correctly. Any *.al files should be created during installation of Proc::ProcessTable.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
Go through these directories one at a time and check for the existence of ./Proc/ProcessTable.pm and then ./auto/Proc/ProcessTable/. If they are not there, then you installed Proc::ProcessTable somewhere else and you need to see what is wrong with your CPAN
configuration. If they are there then you may need to manually delete both before attempting to reinstall.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family: Calibri; font-size: medium;"><font face="Calibri,sans-serif">/usr/users/TGAC_ga007/stittt/Software/Perl/5.18/site/lib</font></div><div style="font-family: Calibri; font-size: medium;"><font face="Calibri,sans-serif">/usr/users/TGAC_ga007/stittt/Software/Perl/5.18/lib</font></div></div><div><font face="Calibri,sans-serif">/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../perl/lib</font></div><div><font face="Calibri,sans-serif">/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../lib</font></div><div><font face="Calibri,sans-serif">/usr/users/TGAC_ga007/stittt/Software/MAKER/UV/maker/bin/../src/inc/perl/lib</font></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
--Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><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, September 4, 2014 at 5:38 AM<br><span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</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></div><div><br></div><div><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><div><div>Hi Carson,</div><div><br></div><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><div><br></div><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><div><br></div><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><div><br></div><div>Thanks in advance for any further help with this.</div><div><br></div><div>Tim. </div><div><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></div></div></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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>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></div><div><br></div><div><div 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><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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