[maker-devel] SQLite database locked error, maker MPI using several nodes

[Malcolm Hinsley]

Hello

I'm trying to get maker to run on MPI using several nodes.  I have an
installation set up by a colleague which includes maker 2.27 and
openmpi-1.4.3.

Previously it has only been used (here at EBI) with maker processes
running on one node only, but i find that it can wait a very long time
before being scheduled by LSF.

The command used to submit is like this (as per recommendations from
systems) (uses 8 cpus on each of 8 nodes)

|export OMP_NUM_THREADS=||64|
|bsub -q mpi -M ||40000| |-R ||"rusage[mem=40000] && span[ptile=8]"| 
|-n ||64| |-o lsf_log  -a openmpi mpirun.lsf -np ||64| |-mca btl
tcp,self  maker ||2||>&||1|

and  requires environment be set up in ~/.bashrc for openMPI.

This runs but produces a lot of errors like:

     DBD::SQLite::db do failed: database is locked at
/nfs/production/panda/ensemblgenomes/external/maker/2.27_mpi/maker/bin/../lib/GFFDB.pm
line 407.


I've looked at
https://groups.google.com/forum/#!searchin/maker-devel/database$20locked/maker-devel/TscBgbQfBX4/pae016DqlIMJ
which suggests that "It means that your GFF3 results will not be
integrated" (but i'm not sure what's meant by that, but the number of
genes i'm getting is around 2k, expect more like 15k) and that the
problem is SQLite using NFS (a known issue), and the fix is to use /tmp.

I have TMP= set as per default in maker_opts.ctl, and there are maker
directories in /tmp on the runtime nodes, but the database (i guess) is
in /nfs/...../maker/<maker_out_dir>/<prefix>.scf.db.

I don't see how i could set the working directory to a non-NFS file
systems and still use more than one node, but this error only seems to
appear (so far) with est2genome, not when running SNAP/ Augustus.

Is there a work around to stop getting the locked error or some way to
recover from it after maker has finished?  Or is it necessary to run the
est2genome step  (or maker generally) on one node?

An obvious option is to split the assembly but i was hoping to avoid that.

-- 
malcolm hinsley | EnsEMBL Genomes | +44 (0)1223 49 4669
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
United Kingdom 

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