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

[Kipp Johnson]

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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