[maker-devel] Maker jobs hanging

[Carson Holt]

Use 2.31.  It has been tested to work without issue on several thousand
cpus.  Also use OpenMPI for any jobs greater than 100 cpus. In addition,
OpenMPI can freeze on some systems without the following flag when using
perl based MPI programs --> -mca btl ^openib

Example --> mpiexec -mca btl ^openib -n 200 maker


Finally, never use MVAPICH2.  It doesn't play well with perl, and freezes
whenever perl based MPI jobs extend across nodes (they run fine within a
single node though).

—Carson



On 2/21/14, 11:48 AM, "Greg Taylor" <gtaylor at bcgsc.ca> wrote:

>Hello,
> I'm having a problem with Maker_2.28 jobs hanging. I am annotating a 3Gb
>genome with predictors SNAP and Genemark, and using ABySS assembled
>RNA-seq data. To do this I am using 480 processors on our local cluster.
>Once a run begins, 479 contigs are started, as noted in the
>*_master_datastore_index.log file, the standard error log for the whole
>job looks normal, as do the run.log and run.log.child.0 for the daughter
>processes. This seems to be sequence dependent, as re-running contigs
>that hang doesn't help, the same contigs will always hang. I'm still
>looking into this myself, but it seems most if not all the jobs are stuck
>at the Blastx stage. If you have any suggestions, your help would be
>greatly appreciated.
>
>sincerely,
>Greg Taylor
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