maker: SQLite database locked warning

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

maker: SQLite database locked warning

Chavez Montes, Ricardo Aaron

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, 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.


maker-devel mailing list
[hidden email]