[maker-devel] running maker on tacc stampede
Carson Holt
carsonhh at gmail.com
Wed Nov 6 00:53:14 MST 2013
We're also seeing core dumps on Lonestar using the same version of MAKER
already installed when we do a "fresh install". We're not sure why,
because everything should be the same. Maybe something about what we are
seeing is also related to the issue you are experiencing and maybe not.
Let me try and figure out what is happening on Lonestar and I'll send you
my install procedure, and maybe that will fix the stampede issue as well.
Thanks,
Carson
On Tue, Nov 5, 2013 at 5:53 PM, Scott Geib <smg283 at gmail.com> wrote:
> Hi,
> I was looking for help running maker on stampede at tacc. Have run in the
> past on lonestar with no issues, but am getting some errors on stampede
> (have never run before on stampede. I also tried downloading the same
> maker version on lonestar and running the same test data and had no issues.
> In both cases, used TACC module command to load more current perl into my
> environment before installing maker. On lonestar, SGE is used so
> submission script slightly different in syntax, but ran with same
> parameters. I know repbase isn't installed, but I just wanted to get
> software working
> Thanks Scott
>
>
> Using this SLURM script with the current maker beta release (30),
> submitting with sbatch on dpp test data in a copy of maker data directory:
>
> #!/bin/bash
> #SBATCH -J testmaker
> #SBATCH -o testmaker.o%J
> #SBATCH -e testmaker.e%J
> ##SBATCH -N 2
> #SBATCH -n 32
> #SBATCH -p development
> #SBATCH -t 2:00:00
> #SBATCH --mail-user=XXXXXX
> #SBATCH --mail-type=all
>
> ibrun ../maker/bin/maker -base test
>
>
> This results in the following errors in testmaker.ejobid:
>
> STATUS: Parsing control files...
> WARNING: RepBase is not installed for RepeatMasker. This limits
> RepeatMasker's functionality and makes the model_org option in the
> control files virtually meaningless. MAKER will now reconfigure
> for simple repeat masking only.
> STATUS: Processing and indexing input FASTA files...
> [c559-001.stampede.tacc.utexas.edu:mpi_rank_2][error_sighandler] Caught
> error: Segmentation fault (signal 11)
> [c559-001.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process
> (rank: 2, pid: 35423) terminated with signal 11 -> abort job
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> SIGINT received
> [c559-001.stampede.tacc.utexas.edu:mpi_rank_1][error_sighandler] Caught
> error: Segmentation fault (signal 11)
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x55efbc8)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x54f4908)', -2,
> 1111) called at /work/02726/pbarc/maker/bin/maker line 530
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/forks.pm line 609
> eval {...} called at /work/02726/pbarc/maker/bin/../perl/lib/
> forks.pm line 609
> threads::__ANON__(0.1) called at /work/02726/pbarc/maker/bin/maker
> line 586
>
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x36ffd10)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x3606080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x4d77a00)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x4c7f080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x418ece0)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x4095080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x3c05a00)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x3b0d080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x3b50a00)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x3a58080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x55cecf0)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x54d5080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x4a7ccf0)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x4983080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x53f1a00)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x52f9080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> at /work/02726/pbarc/maker/bin/../perl/lib/forks/signals.pm line 97.
> forks::signals::__ANON__('INT') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> eval {...} called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 145
> Parallel::Application::MPI::__ANON__() called at
> /work/02726/pbarc/maker/bin/../perl/lib/Perl/Unsafe/Signals.pm line 18
> Perl::Unsafe::Signals::UNSAFE_SIGNALS('CODE(0x367da00)') called at
> /work/02726/pbarc/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 146
> Parallel::Application::MPI::MPI_Recv('SCALAR(0x3585080)', 0, 4444)
> called at /work/02726/pbarc/maker/bin/maker line 578
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 23, pid: 10976) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 20, pid: 10973) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 17, pid: 10970) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 18, pid: 10971) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 19, pid: 10972) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 16, pid: 10969) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 21, pid: 10974) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 22, pid: 10975) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 24, pid: 10977) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 25, pid: 10978) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 26, pid: 10979) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 27, pid: 10980) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 28, pid: 10981) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 29, pid: 10982) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 30, pid: 10983) exited with status 2
> [c559-002.stampede.tacc.utexas.edu:mpispawn_1][child_handler] MPI process
> (rank: 31, pid: 10984) exited with status 2
>
>
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>
>
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