<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=""><div class="">Hi Justin,</div><div class=""><br class=""></div><div class="">You need to set LD_PRELOAD to the proper location and add the '-mca btl ^openib’ flag to your command line.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">The following is from the INSTALL file that should be included with MAKER —></div><div class=""><br class=""></div>If using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before even trying to install MAKER. <b class="">It must also be set before running MAKER</b> (or any program that uses OpenMPI's shared libraries), so it's best just to add it to your ~/.bash_profile. (i.e. export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so).<br class=""><br class=""><br class="">1. Say yes to the 'configure for MPI' question when running 'perl Build.PL’ in step 1 of the EASY INSTALL.<br class=""><br class="">2. Give path to 'mpicc'. Note to make sure you do not give the path to ‘mpicc' from another MPI flavor that might be installed on your system.<br class=""><br class="">3. Give path to the folder containing 'mpi,h'. Note to make sure you do not give the path to a folder from another MPI flavor that might be installed on your system. Mixing MPI flavors for 'mpicc' and 'mpi.h' will cause failures. Make sure to read and confirm the auto-detected paths.<br class=""><br class="">4. Finish installation according to steps 2-4 of the EASY INSTALL<br class=""><br class=""> Note: For OpenMPI you may also want to set OMPI_MCA_mpi_warn_on_fork=0 in your ~/.bash_profile to turn off certain nonfatal warnings.<br class=""><br class=""> Note: If jobs hang or freeze when using mpiexec under OpenMPI try adding the '-mca btl ^openib' flag to mpiexec command when running MAKER.<br class=""><br class=""> Example: mpiexec -mca btl ^openib -n 20 maker<div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 27, 2014, at 7:59 PM, Justin Peyton <<a href="mailto:cognitiveshrapnel@gmail.com" class="">cognitiveshrapnel@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">I am working on getting maker running on a system running ubuntu 14.04. I have installed maker and it runs great on a small but real data set. When I try it with openmpi with the exact same inputs, however, I get the below error almost instantly. <div class=""><br class=""></div><div class=""><div class="">STATUS: Parsing control files...</div><div class="">STATUS: Processing and indexing input FASTA files...</div><div class="">[molybdenum:23241] *** Process received signal ***</div><div class="">[molybdenum:23241] Signal: Segmentation fault (11)</div><div class="">[molybdenum:23241] Signal code: Address not mapped (1)</div><div class="">[molybdenum:23241] Failing at address: 0x50c</div><div class="">[molybdenum:23241] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7f99bd0e8c30]</div><div class="">[molybdenum:23241] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f99bd5155a2]</div><div class="">[molybdenum:23241] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7f99bd0e8c30]</div><div class="">[molybdenum:23241] [ 3] /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f99bd19fbad]</div><div class="">[molybdenum:23241] [ 4] /usr/local/openmpi/lib/libopen-pal.so.6(+0x72156)[0x7f99bcbcc156]</div><div class="">[molybdenum:23241] [ 5] /usr/local/openmpi/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x13b)[0x7f99bcbc34bb]</div><div class="">[molybdenum:23241] [ 6] /usr/local/openmpi/lib/libopen-rte.so.7(+0x3897e)[0x7f99bce6e97e]</div><div class="">[molybdenum:23241] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f99bc944182]</div><div class="">[molybdenum:23241] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f99bd1acefd]</div><div class="">[molybdenum:23241] *** End of error message ***</div><div class="">SIGTERM received</div><div class="">SIGTERM received</div><div class="">SIGTERM received</div><div class="">SIGTERM received</div><div class="">SIGTERM received</div><div class="">[molybdenum:23252] *** Process received signal ***</div><div class="">[molybdenum:23252] Signal: Segmentation fault (11)</div><div class="">[molybdenum:23252] Signal code: Address not mapped (1)</div><div class="">[molybdenum:23252] Failing at address: 0x50c</div><div class="">[molybdenum:23252] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7fb191b31c30]</div><div class="">[molybdenum:23252] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7fb191f5e5a2]</div><div class="">[molybdenum:23252] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7fb191b31c30]</div><div class="">[molybdenum:23252] [ 3] /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7fb191be8bad]</div><div class="">[molybdenum:23252] [ 4] /usr/local/openmpi/lib/libopen-pal.so.6(+0x72156)[0x7fb191615156]</div><div class="">[molybdenum:23252] [ 5] /usr/local/openmpi/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x13b)[0x7fb19160c4bb]</div><div class="">[molybdenum:23252] [ 6] /usr/local/openmpi/lib/libopen-rte.so.7(+0x3897e)[0x7fb1918b797e]</div><div class="">[molybdenum:23252] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7fb19138d182]</div><div class="">[molybdenum:23252] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fb191bf5efd]</div><div class="">[molybdenum:23252] *** End of error message ***</div><div class="">SIGTERM received</div><div class="">--------------------------------------------------------------------------</div><div class="">mpiexec noticed that process rank 2 with PID 23241 on node molybdenum exited on signal 11 (Segmentation fault).</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">I have tried reinstalling both maker and openmpi. I have tried two different versions of both maker and openmpi. I am curenlty working with maker 2.31.6 and openmpi 1.8.3 because I have had those work together on another system. I have triple checked that LD_PRELOAD is properly set. I have a feeling that I am pissing something small. I appreciate all the help.</div><div class=""><br class=""></div><div class="">Justin Peyton</div><div class="">The Ohio State University</div></div>
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