<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Did it die or did you just get a warning?<div class=""><br class=""></div><div class="">Here is a list of flags to add that suppress warnings and other issues with OpenMPI. You can add them all or one at a time depending on issues you get.</div><div class=""><br class=""></div><div class="">#add if MPI not using all CPU given</div><div class="">--oversubscribe --bind-to none</div><div class=""><br class=""></div><div class="">#workaround for infinaband (use instead of --mca ^openib)</div><div class="">--mca btl vader,tcp,self --mca btl_tcp_if_include ib0</div><div class=""><br class=""></div><div class="">#add to stop certain other warnings</div><div class="">--mca orte_base_help_aggregate 0</div><div class=""><br class=""></div><div class="">#stop fork warnings</div><div class="">--mca btl_openib_want_fork_support 1 --mca mpi_warn_on_fork 0</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 15, 2017, at 9:34 AM, zl c <<a href="mailto:chzelin@gmail.com" class="">chzelin@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_extra">Here are some latest message:<div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[cn3360:57176] 1 more process has sent help message help-opal-runtime.txt / opal_init:warn-fork</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">[cn3360:57176] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages</span></div></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><div class="m_-1862143133597923131gmail-m_5723736450607837839gmail_signature"><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class="">------------------------------<wbr class="">--------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>]<br class=""><br class=""></div><div class=""><br class=""></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Tue, Aug 15, 2017 at 10:39 AM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="auto" class=""><div class="">You may need to delete the .../maker/perl directory before doing the reinstall if not doing a brand new installation. Otherwise you can ignore the subroutine redefined warnings during compile.</div><div class=""><br class=""></div><div class="">Have you been able to test the alternate flags on the command line for MPI? How about an alternate perl without threads?<br class=""><br class=""><div class=""><div class=""><span style="font-size:13pt" class="">--Carson</span></div><div class=""><br class=""></div><div class="">Sent from my iPhone</div></div></div><div class=""><br class="">On Aug 15, 2017, at 8:27 AM, zl c <<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>> wrote:<br class=""><br class=""></div><blockquote type="cite" class=""><div class=""><div dir="ltr" class="">When I installed by './Build install', I got following some messages:<div class=""><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Configuring MAKER with MPI support</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Installing MAKER...</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Configuring MAKER with MPI support</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine dl_load_flags redefined at (eval 125) line 8.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_ANY_SOURCE redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_ANY_TAG redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_SUCCESS redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_Init redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_Finalize redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_Comm_rank redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_Comm_size redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_Send redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::C_<wbr class="">MPI_Recv redefined at (eval 125) line 9.</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Menlo; background-color: rgb(255, 222, 150);" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Subroutine Parallel::Application::MPI::_c<wbr class="">omment redefined at (eval 125) line 9.</span></div></div><div class="gmail_extra"><br class=""></div><div class="gmail_extra">I'm not sure whether it's correctly installed.</div><div class="gmail_extra"><br class=""></div><div class="gmail_extra">Thanks,</div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-1862143133597923131gmail-m_5723736450607837839m_-7744257814608198508gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">------------------------------<wbr class="">--------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>]<br class=""><br class=""></div><div class=""><div class="">NIH/NHGRI</div><div class=""><span style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class="">Building 50, Room 5531</span><br style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class=""><span style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class="">50 SOUTH DR, MSC 8004 </span><br style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class=""><span style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class="">BETHESDA, MD 20892-8004</span></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Aug 14, 2017 at 9:23 PM, Fields, Christopher J <span dir="ltr" class=""><<a href="mailto:cjfields@illinois.edu" target="_blank" class="">cjfields@illinois.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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<div class="m_-1862143133597923131gmail-m_5723736450607837839m_-7744257814608198508m_-5812194475710527082WordSection1"><p class="MsoNormal">Carson,<u class=""></u><u class=""></u></p><p class="MsoNormal"><u class=""></u> <u class=""></u></p><p class="MsoNormal">It was attached to the initial message (named ‘run05.mpi.o47346077’). It looks like a Perl issue with threads, though I don’t see why this would crash a cluster. The fact there is a log file would suggest it just ended the job.<u class=""></u><u class=""></u></p><p class="MsoNormal"><u class=""></u> <u class=""></u></p><p class="MsoNormal">chris<u class=""></u><u class=""></u></p><p class="MsoNormal"><u class=""></u> <u class=""></u></p>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0in 0in" class=""><p class="MsoNormal" style="margin-left:0.5in"><b class=""><span style="font-size: 12pt;" class="">From:
</span></b><span style="font-size: 12pt;" class="">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank" class="">maker-devel-bounces@yandell-l<wbr class="">ab.org</a>> on behalf of Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>><br class="">
<b class="">Date: </b>Monday, August 14, 2017 at 2:18 PM<br class="">
<b class="">To: </b>zl c <<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>><br class="">
<b class="">Cc: </b>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank" class="">maker-devel@yandell-lab.org</a>><br class="">
<b class="">Subject: </b>Re: [maker-devel] maker MPI problem<u class=""></u><u class=""></u></span></p>
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<div class=""><p class="MsoNormal" style="margin-left:0.5in"><u class=""></u> <u class=""></u></p>
</div><p class="MsoNormal" style="margin-left:0.5in">This is rather vague —> “crashed the computer cluster”
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<div class=""><p class="MsoNormal" style="margin-left:0.5in">Do you have a specific error?<u class=""></u><u class=""></u></p>
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<div class=""><p class="MsoNormal" style="margin-left:0.5in">—Carson<u class=""></u><u class=""></u></p>
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<div class=""><p class="MsoNormal" style="margin-left:0.5in">On Aug 14, 2017, at 12:59 PM, zl c <<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>> wrote:<u class=""></u><u class=""></u></p>
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Hello,<u class=""></u><u class=""></u></p>
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I ran maker 3.0 with openmpi 2.0.2 and it crashed the computer cluster. I attached the log file. Could you help me to solve the problem?<u class=""></u><u class=""></u></p>
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CMD:<u class=""></u><u class=""></u></p><p class="MsoNormal" style="margin-left:0.5in">
export LD_PRELOAD=/usr/local/OpenMPI/<wbr class="">2.0.2/gcc-6.3.0/lib/libmpi.so<u class=""></u><u class=""></u></p><p class="MsoNormal" style="margin-left:0.5in">
export OMPI_MCA_mpi_warn_on_fork=0<u class=""></u><u class=""></u></p><p class="MsoNormal" style="margin-left:0.5in">
mpiexec -mca btl ^openib -n $SLURM_NTASKS maker -c 1 –base genome -g genome.fasta<u class=""></u><u class=""></u></p>
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Thanks,<u class=""></u><u class=""></u></p><p class="MsoNormal" style="margin-left:0.5in">
Zelin Chen<u class=""></u><u class=""></u></p>
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<div class=""><p class="MsoNormal" style="margin-left:0.5in">------------------------------<wbr class="">--------------<u class=""></u><u class=""></u></p>
</div><p class="MsoNormal" style="margin-left:0.5in">Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>] Ph.D.<u class=""></u><u class=""></u></p>
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<div class=""><p class="MsoNormal" style="margin-left:0.5in">NIH/NHGRI<u class=""></u><u class=""></u></p>
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<div class=""><p class="MsoNormal" style="margin-left:0.5in"><span style="font-size:9pt;font-family:Verdana,sans-serif" class="">Building 50, Room 5531<br class="">
50 SOUTH DR, MSC 8004 <br class="">
BETHESDA, MD 20892-8004</span><u class=""></u><u class=""></u></p>
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</div><p class="MsoNormal" style="margin-left:0.5in"><run05.mpi.o47346077>_________<wbr class="">______________________________<wbr class="">________<br class="">
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