<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="">Sorry for the slow reply. Make sure you find out what flavor of MPI you are using (MPICH, MVAPICH2, Intel MPI, or OpenMPI). MAKER does not work with MVAPICH2. It can work with Intel MPI and OpenMPI with some command line modification. And it always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs.<div class=""><br class=""></div><div class=""><div class="">This command “-mca btl ^openib”, is only for OpenMPI for example. Also if using OpenMPI, set LD_PRELOAD in accordance with the INSTALL documentation. Also make sure you do not have multiple MPI flavors installed and you compiled MAKER with one then are running with a different flavor. That will cause failure shortly after starting MAKER.</div></div><div class=""><br class=""></div><div class="">Try looking further back in your STDER for the actual cause. The “Thread 1 terminated abnormally:” message is the tail end of the failure snowball, so the actual cause is often much further back. </div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 26, 2018, at 9:36 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="">
<span class=""></span><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" class="">https://groups.google.com/forum/#!msg/maker-devel/X2-76BH9gvg/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_blastdb/dna%2Efa.mpi.1/dna%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/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:4797C91C-4BE1-49A0-B4CF-0126284DD363@genetics.utah.edu"><2.log></span><span id="cid:8289D2C8-5197-4D44-A784-1C032987F333@genetics.utah.edu"><maker_exe.ctl></span><span id="cid:C4B36556-D2F2-4676-BA6C-D2A0F7BEC4FB@genetics.utah.edu"><maker_opts.ctl></span><span id="cid:9B59491A-E40D-4690-BAC5-E163EF7A4B26@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>