Maker Error : Thread 1 terminated abnormally..

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Maker Error : Thread 1 terminated abnormally..

André Machado

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

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



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Re: Maker Error : Thread 1 terminated abnormally..

Carson Holt-2
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.

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.

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. 

—Carson


On Jun 26, 2018, at 9:36 AM, André Machado <[hidden email]> 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

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>_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org