<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Marc,<div><br></div><div>Thanks so much for sharing the results of all your hard work! We will follow up on your feedback and incorporate the necessary updates to MAKER docs and installation procedures.</div><div><br></div><div>B</div><div><br><div><div>On Oct 26, 2013, at 5:54 AM, Marc P. Hoeppner wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear List,<br><br>after much more debugging, I found the solution myself. Here are the details:<br><br>The Maker installation instructions refer to 'mpich2' in multiple places, including weblinks (whchi are outdated btw). Some digging revealed that mpich2 has since been renamed and merged back into mpich. So the website is <a href="http://www.mpich.org">www.mpich.org</a> and the current stable version is mpich-3.0.4. Closely following the installation instruction yielded a working copy of mpiexec that Maker was willing to accept. Good news - but I suggest to update the documentation. Most importantly for either SL/CentOS users, mpich2 as packaged with e.g. Scientific Linux *does not* work with Maker. You will need to download the latest stable build and compile it yourself (the mpich2 version bundled with Maker doesn't work either btw).<br><br>Cheers,<br><br>Marc<br><br><blockquote type="cite">Dear list,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I know that MPICH2 related issues have been discussed previously, but the suggested solutions don't seem to work for me.<br></blockquote><blockquote type="cite">Briefly, I have set up a new cluster, with a fresh install of mpich2 (SL 6.4, from the yum repos) and a newly compiled build of Maker 2.28.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">When I start maker with mpiexec, I get spammed with<br></blockquote><blockquote type="cite">'WARNING: Multiple MAKER processes have been started in the same directory.'<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Here is what I have tried so far - still getting the error :-< Any suggestions would be appreciated<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--------<br></blockquote><blockquote type="cite">MPICH2<br></blockquote><blockquote type="cite">---------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">which mpiexec:<br></blockquote><blockquote type="cite">/usr/lib64/mpich2/bin/mpiexec<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Started the mpd ring as normal user across 5 nodes (bnode-01 to bnode-04, and the head node bhead)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">mpdtrace:<br></blockquote><blockquote type="cite">bhead<br></blockquote><blockquote type="cite">bnode-02<br></blockquote><blockquote type="cite">bnode-03<br></blockquote><blockquote type="cite">bnode-04<br></blockquote><blockquote type="cite">bnode-01<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">mpdringtest:<br></blockquote><blockquote type="cite">time for 1 loops = 0.00128293037415 seconds<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">mpixec -n 32 -machinefile hostfile hostname:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><long list of host names, as ecpected><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I also ran the Skampi Mpi Benchmark, which ran through just fine.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------<br></blockquote><blockquote type="cite">MAKER<br></blockquote><blockquote type="cite">-----------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">./Build status<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">PERL Dependencies: VERIFIED<br></blockquote><blockquote type="cite">External Programs: VERIFIED<br></blockquote><blockquote type="cite">External C Libraries: VERIFIED<br></blockquote><blockquote type="cite">MPI SUPPORT: ENABLED<br></blockquote><blockquote type="cite">MWAS Web Interface: DISABLED<br></blockquote><blockquote type="cite">MAKER PACKAGE: CONFIGURATION OK<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">During configuration/installation, Build.PL automatically detected all MPI data and never complained, so I have to assume that everything went fine there.<br></blockquote><blockquote type="cite"><br></blockquote><br><br>-- <br>----------<br>Marc P. Hoeppner, PhD<br>Department of Microbiology and Medical Biochemistry<br>Uppsala University, Sweden<br><a href="mailto:marc.hoeppner@imbim.uu.se">marc.hoeppner@imbim.uu.se</a><br><br><br>_______________________________________________<br>maker-devel mailing list<br>maker-devel@box290.bluehost.com<br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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