[maker-devel] maker mpi failed

[Dian "Oscar" Jiao]

It is a new install.
--
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Friday, October 5, 2012 3:07 PM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

Is /work/02045/jiao/modules/Maker-GMOD/maker-dev/exe/mpich2 a new install of mpich2 or is it the install you did with 2.26 just copied over?

--Carson



From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>
Date: Friday, 5 October, 2012 4:06 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

Just default, /work/02045/jiao/modules/Maker-GMOD/maker-dev/exe/mpich2/bin/mpicc and /work/02045/jiao/modules/Maker-GMOD/maker-dev/exe/mpich2/include
--
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu> | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Friday, October 5, 2012 3:03 PM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

What were you answers to the mpicc and mpi.h questions during setup?

--Carson



From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>
Date: Friday, 5 October, 2012 3:55 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

I got problem installing the dev version Maker. Here is what I did:

./Build mpich2
perl Build.PL
(yes to MPI)
./Build clean
./Build install

The install fails while configuring Maker with MPI support:
Had problems bootstrapping Inline module 'Parallel::Application::MPI'

Can't load '/work/02045/jiao/modules/Maker-GMOD/maker-dev/src/blib/lib/auto/Parallel/Application/MPI/MPI.so' for module Parallel::Application::MPI: libifport.so.5: cannot open shared object file: No such file or directory at /work/02045/jiao/localperl/lib/5.16.1/x86_64-linux-thread-multi/DynaLoader.pm line 190.
 at /work/02045/jiao/localperl/add-on/lib/site_perl/5.16.1/Inline.pm line 536.


 at /work/02045/jiao/modules/Maker-GMOD/maker-dev/src/lib/Parallel/Application/MPI.pm line 223.


** If you are running using OpenMPI, you may have to preload object files
** for shared libraries to work. For bash, try executing a command
** similar to the following with the appropriate file location.
** Example --> export LD_PRELOAD=.../openmpi/lib/libmpi.so
** Please do this before trying to run MAKER again!!

Something wrong with my DynaLoader/Inline modules? Version 2.26 installed ok. What is the difference between 2.26 and the development version?

--
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu> | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Friday, October 5, 2012 1:19 PM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

Could you try the development version anyways with MPI using the same procedure and send me the results as you did with 2.26?

Thanks,
Carson


From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>
Date: Friday, 5 October, 2012 2:16 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

See the attached files. The command I used "/work/02045/jiao/modules/Maker-GMOD/maker2.26/exe/mpich2/bin/mpiexec -n 12 /work/02045/jiao/modules/Maker-GMOD/maker2.26/bin/maker -debug maker_exe.ctl maker_opts.ctl maker_bopts.ctl 2> mpich-maker-debug.log"

I am still using Maker 2.26. These problems I had earlier with AnyDBM_File were resolved (manually), so I did not install the development version.

~Oscar

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Friday, October 5, 2012 11:05 AM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

Are you using the subversion version of MAKER I sent?

If so send me the following.  Run under MPI with the --debug flag set on maker.  When running, supply the full path to both the maker and mpiexec executables.  Capture the STDERR to a file.

Send me that STDERR file together with the maker_opts.ctl file you are using.

Thanks,
Carson



From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>
Date: Friday, 5 October, 2012 1:06 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

I followed your instructions to compile Maker with MPICH2 (the one comes with Maker). But when I run maker with mpi, it terminates with the message:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
=========================================================================== ==========

=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=========================================================================== ==========

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

The serial version of Maker still works. I tried to install MPICH2 manually outside maker and got the same error.

--
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu> | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Thursday, October 4, 2012 3:53 PM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

You either tried to run with the -dsindex option before the log file existed or you tried to launch via MPI when not compiled for MPI or not compiled correctly.  It's as if you called MAKER serially multiple times in a row which you can do, but if you start too many before one of them gets a chance to get the log file started a race condition exists.

Which MPI flavor are you using?  MVAPICH2 won't work with MAKER, MPICH2 will, and OpenMPI may or may not (non-robust shared library behavior).

You may have to reinstall MPICH2.

MAKER can try and do this for you using necessary flags to make it easier
To do this -->
cd ./maker/src
./Build mpich2

Then reinstall maker
cd ./maker/src
perl Build.PL
<say yes to mpi question>
./Build clean
./Build install

Then use this executable to launch --> ./maker/exe/mpich2/bin/mpiexec

Note you cannot use other launchers.  You have to use the one you compiled with.

--Carson



From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>
Date: Thursday, 4 October, 2012 4:42 PM
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: [maker-devel] maker mpi failed

Hi, I was trying to run maker 2.26. It was compiled with MPI. The non-mpi executable works just fine. But I got the error below while running mpirun –n maker ……

What is this Iterator::Fasta::skip_file? Any idea what is going on here?

Oscar

STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

ERROR: Log file does not exist in Iterator::Fasta::skip_file
MPI process (rank: 8) terminated unexpectedly on c341-213.ls4.tacc.utexas.edu
Exit code -5 signaled from c341-213

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