<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="">Seg faults will be the result of one of the programs used by MAKER or MPI itself.<div class=""><br class=""></div><div class="">If using OpenMPI, add '-mca btl ^openib’ to your command line.</div><div class="">Example: mpiexec -mca btl ^openib -n 20 maker</div><div class=""><br class=""></div><div class="">Also you nY need to do this before running MAKER —> export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so</div><div class=""><br class=""></div><div class="">Both steps are explained in the ../maker/INSTALL file.</div><div class=""><br class=""></div><div class="">MAKER is not compatible with MVAPICH2 or Intel MPI.<br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class="">For external programs that segfault. Just reinstall them or pick different versions.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Finally the error from the forks module. See the following from the devel list —> <a href="https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA" class="">https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA</a></div><div class="">It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version)</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 Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <<a href="mailto:mmacd@udel.edu" class="">mmacd@udel.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">Hi Maker,<br class="">I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds.<br class=""><br class="">sh: line 1: 34865 Segmentation fault (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate<br class="">Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/<a href="http://forks.pm/" class="">forks.pm</a> line 1736.<br class="">Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/<a href="http://forks.pm/" class="">forks.pm</a> line 1736.<br class="">ERROR: Exonerate failed<br class="">--> rank=1, hostname=biomix2.dbi.local<br class="">ERROR: Failed while polishing proteins<br class="">ERROR: Chunk failed at level:10, tier_type:3<br class="">FAILED CONTIG:picr50<br class=""><br class=""></div><div class="">I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help with this issue?<br class=""></div>Any other thoughts?<br class=""></div>Thanks<br class=""><div class=""><div class=""><br class="">-- <br class=""><div data-smartmail="gmail_signature" class=""><div dir="ltr" class=""><div class="">Madolyn Stinner (formerly Madolyn MacDonald)<div class="">UDel Bioinformatics and Systems Biology, PhD student</div><div class="">RIT Alumnus 13'</div></div></div></div>
</div></div></div>
_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></body></html>