[maker-devel] running maker on tacc stampede

Scott Geib smg283 at gmail.com
Tue Nov 5 17:53:55 MST 2013 

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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