[maker-devel] maker: SQLite database locked warning

[Chavez Montes, Ricardo Aaron]

Hello,

I've been experiencing a problem when using maker with gff3 input files. maker outputs a "database locked" warning almost always on line 525 of GFFDB.pm, sometimes on line 641. Both are $dbh->selectcol_arrayref(qq{SELECT name FROM sqlite_master WHERE type = 'table'});

I'm using a Dell 7920 standalone workstation (so, no remote or cluster hard drives of any kind; I'm using a ZFS array for data, but I set the tmp directory in maker_opts.ctl to a local, non-ZFS, ssd drive) with two Xeon processors with a total of 96 threads, and I've noticed that the number of warnings is lower and eventually disappears as I use less and less cpus at the mpiexec line. I would think that SQLite can only handle concurrency up to a certain number of processes.


Best,
Ricardo



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201124/8425b74f/attachment-0002.html>