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.error { color:#AA0000; }</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="bloop_markdown"><p>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. </p>
<p>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 </p>
<pre><code>export LD_PRELOAD=/openmpi/lib/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0
</code></pre>
<p>and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior. </p>
<pre><code>/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><code>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>Thanks for any advice, </p>
<p>Matt</p>
<p></p></div><div class="bloop_original_html"><style>body{font-family:Avenir,Arial;font-size:13px}</style><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><br><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;"><b>Matthew MacManes, Ph.D.</b></span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;"><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;">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;"><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;">Department of Molecular, Cellular, & Biomedical Sciences</span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;"><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;">Durham, NH 03824</span><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;"><a href="tel://Phone:%20603-862-4052" style="font-family: Avenir-Book; font-size: 11px; line-height: normal;">Phone: 603-862-4052</a><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;"> | Twitter: </span><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;"><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=">@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="font-family: Avenir-Book; font-size: 11px; line-height: normal;">genomebio.org</a><br style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;"><span style="font-family: Avenir-Book; font-size: 11px; color: rgb(0, 0, 153); line-height: normal;">Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall</span></div></div><div class="bloop_markdown"><p></p></div></body></html>