Thu Jul 12 14:05:00 MDT 2018

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.

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. 

—Carson

> On Jul 4, 2018, at 5:16 AM, André Machado <andremmachado25 at gmail.com> wrote:
> 
> Hi ,
> 
> First of all thanks for your efforts in Maker pipeline. Its a tremendous help for the people that works with genomes.
> In the last 4 days i have broke my head.. with an error .. but still without a solution.
> I found this old thread: https://groups.google.com/forum/#!msg/maker-devel/X2-76BH9gvg/rU4kLJ3B6tsJ <https://groups.google.com/forum/#!msg/maker-devel/X2-76BH9gvg/rU4kLJ3B6tsJ>
> Seems to be a quite similar... but don't point to a specific solution.
> I have run maker with the data test and all runned ok. Maker finalize the entire process without errors.
> Recently, i’m trying to aplly my own data on MPI cluster. But this error, frequently occurred.
> Thread 1 terminated abnormally: ../dna.maker.output/mpi_blastdb/dna%2Efa.mpi.1/dna%2Efa.mpi.1.0
> --> rank=8, hostname=compute-0-1.local, at ../Analysis/Geno/maker/bin/maker line 1451 thread 1.
> --> rank=8, hostname=compute-0-1.local
> deleted:0 hits
> deleted:0 hits
> preparing ab-inits
> deleted:0 hits
> deleted:0 hits
> FATAL: Thread terminated, causing all processes to fail
> --> rank=8, hostname=compute-0-1.local
> deleted:0 hits
> 
> 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.
> 
> 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.
> mpiexec -n 63 --hostfile Host maker 1>1.log 2>2.err
> 
> mpiexec --hostfile Host maker 1>1.log 2>2.err
> mpiexec -mca btl ^openib -n 63 --hostfile Host maker 1>1.log 2>2.err
> nohup mpiexec -mca btl ^openib -n 63 --hostfile Host maker -a 1>1.log 2>2.err
> 
> The log file as well the option files are provided below.
> 
> Many thanks in advance,
> 
> André
> 
> <2.log><maker_exe.ctl><maker_opts.ctl><maker_bopts.ctl>_______________________________________________
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