[maker-devel] maker 2.31.8 segmentation fault when setting up GFF3 output and fasta chunks with mvapich2

[Carson Holt]

MAKER does not work with mvapich2. You must use either OpenMPI or MPICH2.

The following is from the INSTALL instructions that come with MAKER —>

If using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before even trying to install MAKER. It must also be set before running MAKER (or any program that uses OpenMPI's shared libraries), so it's best just to add it to your ~/.bash_profile. (i.e. export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so).


1.  Say yes to the 'configure for MPI' question when running 'perl Build.PL’ in step 1 of the EASY INSTALL.

2.  Give path to 'mpicc'. Note to make sure you do not give the path to ‘mpicc' from another MPI flavor that might be installed on your system.

3.  Give path to the folder containing 'mpi,h'. Note to make sure you do not give the path to a folder from another MPI flavor that might be installed on your system. Mixing MPI flavors for 'mpicc' and 'mpi.h' will cause failures. Make sure to read and confirm the auto-detected paths.

4.  Finish installation according to steps 2-4 of the EASY INSTALL

Note: For OpenMPI you may also want to set OMPI_MCA_mpi_warn_on_fork=0 in your ~/.bash_profile to turn off certain nonfatal warnings.

Note: If jobs hang or freeze when using mpiexec under OpenMPI try adding the '-mca btl ^openib' flag to mpiexec command when running MAKER.

        Example: mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


> On Dec 17, 2015, at 11:03 AM, Hua Zhong <huazhong at nmsu.edu> wrote:
> 
> Hello,
> we are using maker (2.31.8) with mvapich2, but the program terminates with a segmentation fault while setting up GFF3 output and fasta chunks. We really have no idea what the problem was. 
> 
> Below is the error message:
> 
> 
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> setting up GFF3 output and fasta chunks
> setting up GFF3 output and fasta chunks
> setting up GFF3 output and fasta chunks
> setting up GFF3 output and fasta chunks
> setting up GFF3 output and fasta chunks
> setting up GFF3 output and fasta chunks
> [fpga04.cluster:mpi_rank_111][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_107][error_sighandler] Caught error: Segmentation fault (signal 11)
> Perl exited with active threads:
>         1 running and unjoined
>         0 finished and unjoined
>         0 running and detached
> [fpga04.cluster:mpi_rank_113][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_115][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_114][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_105][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_108][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_110][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_104][error_sighandler] Caught error: Segmentation fault (signal 11)
> [fpga04.cluster:mpi_rank_106][error_sighandler] Caught error: Segmentation fault (signal 11)
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Best regards,
> 
> Hua
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20151217/f307e4eb/attachment-0003.html>