<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Because you truncated / removed line before the actual error (I need to see the several hundred lines that happened before "Thread 1 terminated abnormally: ../dna.maker.output/mpi_blastdb/dna%2Efa.mpi.1/dna%2Efa.mpi.1.0”), I can’t give hyou more info.<div class=""><br class=""></div><div class="">But you are getting a lot of OpenMPI complaints at the start. You may need to reinstall OpenMPI or use MPICH instead (both will require you to reinstall maker as it will need to rebuild the MPI C/Perl binding for the new installation). Also when using OpenMPI, make sure to export LD_PRELOAD in the way outlined in the …/maker/INSTALL instructions. <br class=""><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 4, 2018, at 5:16 AM, André Machado <<a href="mailto:andremmachado25@gmail.com" class="">andremmachado25@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">Hi ,</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""><br class="">
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">First
of all thanks for your efforts in Maker pipeline. Its a tremendous
help for the people that works with genomes.</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""> In the
last 4 days i have broke my head.. with an error .. but still
without a solution.
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">I found
this old thread:
<a href="https://groups.google.com/forum/#!msg/maker-devel/X2-76BH9gvg/rU4kLJ3B6tsJ" target="_blank" class="">https://groups.google.com/<wbr class="">forum/#!msg/maker-devel/X2-<wbr class="">76BH9gvg/rU4kLJ3B6tsJ</a></p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">Seems
to be a quite similar... but don't point to a specific solution.
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">I have
run maker with the data test and all runned ok. Maker finalize the
entire process without errors.
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">Recently,
i’m trying to aplly my own data on MPI cluster. But this error,
frequently occurred.</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">Thread
1 terminated abnormally:
../dna.maker.output/mpi_<wbr class="">blastdb/dna%2Efa.mpi.1/dna%<wbr class="">2Efa.mpi.1.0</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">-->
rank=8, hostname=compute-0-1.local, at
../Analysis/Geno/maker/bin/<wbr class="">maker line 1451 thread 1.</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">-->
rank=8, hostname=compute-0-1.local</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">deleted:0
hits</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">deleted:0
hits</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">preparing
ab-inits</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">deleted:0
hits</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">deleted:0
hits</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">FATAL:
Thread terminated, causing all processes to fail</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">-->
rank=8, hostname=compute-0-1.local</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">deleted:0
hits</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""><br class="">
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">Basically
im tring to run a maker with dna.fa, rna.fa, prot.fa and
my_custom_lib_of_repeats.fa, to produce raw genes models which will
be used to train SNAP.
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""><br class="">
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">I
already used several command lines and all gave me the same error..
The only change between different tests was the local of the error,
sometimes happened in compute-0-1.local other time in
compute-0-4.local or in another one.</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">mpiexec
-n 63 --hostfile Host maker 1>1.log 2>2.err</p><div class=""><br class=""></div><div class="">mpiexec
--hostfile Host maker 1>1.log 2>2.err
</div><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">mpiexec
-mca btl ^openib -n 63 --hostfile Host maker 1>1.log 2>2.err</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">nohup
mpiexec -mca btl ^openib -n 63 --hostfile Host maker -a 1>1.log
2>2.err</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""><br class="">
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">The log
file as well the option files are provided below.
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""><br class="">
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">Many
thanks in advance,</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class=""><br class="">
</p><p style="margin-bottom:0cm;line-height:100%" lang="en-US" class="">André</p><br class=""></div>
<span id="cid:3CB694AB-96F1-47AD-BEEC-788F7852FC21@genetics.utah.edu"><2.log></span><span id="cid:53141E31-20DA-4F34-9FD3-BAFBDBC74292@genetics.utah.edu"><maker_exe.ctl></span><span id="cid:36F44737-A3DA-46AF-90A9-5FC511E0EE77@genetics.utah.edu"><maker_opts.ctl></span><span id="cid:53394138-F6C5-4629-84B6-54BAF469F08D@genetics.utah.edu"><maker_bopts.ctl></span>_______________________________________________<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></body></html>