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

[Kipp Johnson]

It does happen if I start in a different directory. My current working
directory is NFS. I changed the tmp directory in maker_opts from the NFS to
a local partition (tmpfs), and I'm still getting this error. Does the
working directory also have to be locally mounted?

On Fri, Aug 3, 2012 at 8:27 AM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
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>
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