OK ! We are working on the American eel genome and I found the issue while comparing two runs with same parameters.
On 12/13/2012 12:08 PM, Louis Letourneau wrote: > Adrian had more issues than I did. I now rarely need checkpoints since my job > finish in a timely manner with X thousands of cores now. What's the value of X ? The best performance I obtain on large super computers is with the polytope for routing and with a diameter of 2. For instance: Vertices: 1024 = 32*32 Type: Polytope Degree: 62 = (32-1)*2 Diameter: 2 (32^2=1024) Options: -route-messages -connection-type polytope -routing-graph-degree 62 or Vertices: 4225 = 65*65 Type: Polytope Degree: 128 = (65-1)*2 Diameter: 2 (65^2=1024) Options: -route-messages -connection-type polytope -routing-graph-degree 4225 With OpenMPI, I use -bind-to-core -by-node -Sébastien > > It's nice that you found the issue though. > > Louis > ________________________________________ > From: Sébastien Boisvert [[email protected]] > Sent: Thursday, December 13, 2012 12:02 PM > To: Louis Letourneau > Cc: [email protected] > Subject: Regression in the checkpointing system > > Hello Louis, > > > A few months ago, you told me that Ray v1.7 was better than both Ray 2.0.0 > and Ray 2.1.0 for > your work. I also remember that you are using the checkpointing in Ray. > > I just found out that the checkpointing in Ray is broken since 2.0.0 for the > extension of seeds. > > So any job that starts from seeds that are in checkpoints won't produce any > extension and > contigs will therefore be short. > > I will cook a patch for this. > > > > -Sébastien > ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
