<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="">You may have more than one MPI flavor. For example, the mpicc used to compile or the mpi.h referred to during maker setup and compile may be from mpich2 but your running with mpiexec from OpenMPI. Or they may be from a different OpenMPI version than the one you are running with. Also make sure LD_PRELOAD gets exported in your bash_profile or each time before running MAKER (not just during install). Finally if all else fails, you can try installing perl without pthread support, and use that version of Perl to run with instead of /usr/bin/perl. Very very rarely needed, but in cases involving /lib/x86_64-linux-gnu/libpthread.so in a seg fault it can be the source of all grief. Usually indicates that something is broken with your package manager for the MPI install, Perl install, or GNU C library install.<div class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 20, 2016, at 6:34 AM, Matthew MacManes <<a href="mailto:macmanes@gmail.com" class="">macmanes@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="bloop_markdown" style="font-family: Avenir, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);"><p style="margin: 15px 0px; -webkit-margin-before: 0px;" class="">Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5–10 contigs are processed. If I restart after a fail, another 5–10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I’m pretty confident that I’ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful.<span class="Apple-converted-space"> </span></p><p style="margin: 15px 0px;" class="">I’m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I’ve tried a few different versions), augustus–3.2, EVM 1.1.1 on a large system with lots of RAM. I set<span class="Apple-converted-space"> </span></p><pre style="margin: 15px 0px; font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(204, 204, 204); overflow: auto; padding: 4px 8px; word-break: normal; word-wrap: normal;" class=""><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 0px; margin: 0px; padding: 0px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">export LD_PRELOAD=/openmpi/lib/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0
</code></pre><p style="margin: 15px 0px;" class="">and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior.<span class="Apple-converted-space"> </span></p><pre style="margin: 15px 0px; font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(204, 204, 204); overflow: auto; padding: 4px 8px; word-break: normal; word-wrap: normal;" class=""><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 0px; margin: 0px; padding: 0px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">/openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
or
/openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
</code></pre><pre style="margin: 15px 0px; font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(204, 204, 204); overflow: auto; padding: 4px 8px; word-break: normal; word-wrap: normal;" class=""><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 0px; margin: 0px; padding: 0px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">lots of output
…
choosing best annotation set
Choosing best annotations
deleted:30 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
#-------------------------------#
processing chunk output
running blast search.
#--------- command -------------#
Widget::blastn:
/usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
-gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
_46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
#-------------------------------#
processing contig output
examining contents of the fasta file and run log
[davinci:09219] *** Process received signal ***
[davinci:09219] Signal: Segmentation fault (11)
[davinci:09219] Signal code: Address not mapped (1)
[davinci:09219] Failing at address: 0x50c
[davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
[davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 3]
--Next Contig--
/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
[davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
[davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
[davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
[davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
[davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
[davinci:09219] *** End of error message ***
SIGTERM received
SIGTERM received
Perl exited with active threads:
1 running and unjoined
0 finished and unjoined
0 running and detached
SIGTERM received
SIGTERM received
SIGTERM received
</code></pre><p style="margin: 15px 0px;" class="">Thanks for any advice,<span class="Apple-converted-space"> </span></p><p style="margin: 15px 0px;" class="">Matt</p><div style="margin: 15px 0px;" class=""><br class="webkit-block-placeholder"></div></div><div class="bloop_original_html" style="font-family: Avenir, Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);"><div id="bloop_customfont" style="font-family: Avenir, Arial; font-size: 13px; margin: 0px;" class=""><br class=""></div><br class=""><div class="bloop_sign" id="bloop_sign_1466425396475467008"><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""><b class="">Matthew MacManes, Ph.D.</b></span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class="">University of New Hampshire I Assistant Professor of Genome Enabled Biology</span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class="">Department of Molecular, Cellular, & Biomedical Sciences</span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class="">Durham, NH 03824</span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""><a href="tel://Phone:%20603-862-4052" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none; font-family: Avenir-Book; font-size: 11px; line-height: normal;" class="">Phone: 603-862-4052</a><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""> | Twitter: </span><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;" class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_macmanes&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=UqTeeQPXM6sdQU60Nu8UgU2jh30ms8LUeLT76lhbY44&e=" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;" class="">@macmanes</a> | Web: </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__genomebio.org_&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=xcTCYRLTnvXh7r_eBb-HmHZgaIA-ba7vE62iQnWHFdk&e=" style="color: rgb(65, 131, 196); 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