[maker-devel] "DBD::SQLite::db locked" error; MPICH2 help

[Carson Holt]

It means that your GFF3 results will not be integrated.  Does it happen if
you start in a different directory?

The lock error is coming from SQLite, and may be the result of your working
directory being mounted on an NFS filesystem which is a known issue with
SQLite.  If you give maker a location for TMP that is not NFS mounted (I.e.
A locally mounted filesystem), then maker will try and move the SQLite
database off of the NFS mount.

You can check the mount status of the current working directory and the
directory you choose fro TMP by using the Linux df command.

df <directory>

Any NFS mount will follow the format of host:/location.

Example:
152.234.123.234:/data/research

Or 

storage.utah.edu:/data/research

If you are not running on an NFS device let me know if running in a
different directory results in the same error.

Thanks,
Carson

From:  Kipp Johnson <kippjohnson at uchicago.edu>
Date:  Thursday, 2 August, 2012 3:12 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] "DBD::SQLite::db locked" error; MPICH2 help

Hi,

     I am running Maker version 2.26. I have two questions:

1)

    When I run maker, I get errors like the following printed to STDOUT:

DBD::SQLite::db selectcol_arrayref failed: database is locked at
/home/zjiang/.mnt/kwj/maker/bin/../lib/GFFDB.pm line 107.
...
DBD::SQLite::db do failed: database is locked at
/home/zjiang/.mnt/kwj/maker/bin/../lib/GFFDB.pm line 109.
...
DBD::SQLite::db do failed: database is locked at
/home/zjiang/.mnt/kwj/maker/bin/../lib/GFFDB.pm line 497, <$IN> line 2.

     I reinstalled the indicated module via cpanm and restarted Maker from
the beginning in a new directory, and I am getting the same error. The first
time I ran maker, I ignored these and the maker run seemingly proceeded to
the process the contigs correctly. Is this something I should be worried
about?


2)

    I am running Maker on a single server with 64 processors. Would it be
faster to use MPICH2, or to simply restart Maker in the same directory ~16
times, with the # of CPUs option that gets passed to Blast set to 4 for each
restart?

    I believe that I have MPICH2 correctly compiled and installed; if it
would be faster to use MPICH2, could someone provide me with a sample
command line entry to use for Maker? I am confused about how to run MPICH2
on a single node (without a hostfile?), and searching the maker-dev-list
archive seems to give me results for older versions of MAKER and MPICH2.

Thank you,


Best,

     Kipp Johnson
     kippjohnson at uchicago.edu
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
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/20120803/5517b922/attachment-0003.html>