Maker Error : Thread 1 terminated abnormally.. André Machado <andremmachado25@gmail.com> AttachmentsJun 26 (8 days ago) to maker-devel 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-ini

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Maker Error : Thread 1 terminated abnormally.. André Machado <andremmachado25@gmail.com> AttachmentsJun 26 (8 days ago) to maker-devel 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-ini

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



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

2.log (51K) Download Attachment
maker_exe.ctl (1K) Download Attachment
maker_opts.ctl (6K) Download Attachment
maker_bopts.ctl (1K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Maker Error : Thread 1 terminated abnormally.. André Machado <andremmachado25@gmail.com> AttachmentsJun 26 (8 days ago) to maker-devel 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-ini

Carson Holt-2
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 <[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