[Lustre-discuss] MPI-Blast + Lustre

Tom.Wang Tom.Wang at Sun.COM
Wed Dec 12 21:01:20 PST 2007


Charles Taylor wrote:
> Anyone have any experience with MpiBlast and Lustre.     We have  
> MpiBlast-1.4.0-pio and lustre-1.6.3 and we are seeing some pretty  
> poor performance with most of the mpiblast threads spending 20% to  
> 50% of their time in disk wait.    We have the genbank nt database  
> split into 24 fragments (one for each of our OSTs, 3 per OSS).    The  
> individual fragments are not striped due to the ldlm_poold issue so  
> that should not be the problem.
> Should we not be using the PIO (ROM-IO) version of MPIBlast w/ lustre?
I am not familiar with MpiBlast implementation. Does it use collective I/O ?
Could you please specify its I/O pattern here?
And also it is always worth trying to adjust these hints, if  you use  

disable/enable romio_cb_write 
disable/enable romio_ds_write
ind_wr_buffer_size and ind_rd_buffer_size

> I'm wondering if there are some already discovered guidelines for  
> using MPIBlast on top of Lustre that I'm not finding via google.
> Thanks,
> Charlie Taylor
> UF HPC Center
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