On 07/11/13 08:27 PM, Munish Mehta wrote: > Hi Seb, (Please use the mailing list, to subscribe: https://lists.sourceforge.net/lists/listinfo/denovoassembler-users )
> > I am using RAY to do a denovo assembly of Cane Toad (Bufo Marinus). > We are using IBM Blue Gene/Q system. (65,536 PowerPC based 1.6GHz cores). > The estimated size of Genome is 4000 Million Bases roughly 30% more than > human genome. We have about 50x coverage from Illumina, 454, PacBio and Ion > Torrent platform. > > Is there any limitation on the Memory used by Ray for the nodes? What we have > found is that >apart from Rank 0 all the other Ranks do not used more than 20MB of memory. Each Blue Gene/Q node has 1 A2 CPU with 16 cores and a total of 64 threads (4 SMT threads per core). In the tests I did on this platform, I found that in general Ray needed between 400 MiB and 1 GiB of RAM per MPI rank. The 20 MB figure you are reporting is surprising. > So the job crashes after sometime. > > > Regards > > Munish Mehta > > Senior Bioinformatics officer > Western Australian Institute of Medical Research > Centre for Diabetes Research > Level 6, MRF Building > 50 Murray Street, Perth, 6000 > > ( +61-8-9224 0397 > Fax +61-8-9224 0322 > Mob +61-8-402827313 > > Email: _munish.me...@uwa.edu.au <x-msg://30/mun...@waimr.uwa.edu.au> > _Web : _www.cdr.org.au <http://www.cdr.org.au/>_ > ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
