Hi Sebastien, the error message is just a segmentation fault, output below:
Rank 0 registered 0/14207 Rank 0 registered 1000/14207 Rank 0 registered 2000/14207 Rank 0 registered 3000/14207 Rank 0 registered 4000/14207 Rank 0 registered 5000/14207 Rank 0 registered 6000/14207 Rank 0 registered 7000/14207 Rank 0 registered 8000/14207 Rank 0 registered 9000/14207 Rank 0 registered 10000/14207 Rank 0 registered 11000/14207 Rank 0 registered 12000/14207 Rank 0 registered 13000/14207 Rank 0 registered 14000/14207 [ssb3:10762] *** Process received signal *** [ssb3:10762] Signal: Segmentation fault (11) [ssb3:10762] Signal code: Address not mapped (1) [ssb3:10762] Failing at address: (nil) Rank 0 registered 14206/14207 Rank 0 registered its seeds [ssb3:10762] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7fbd8d667cb0] [ssb3:10762] [ 1] Ray(_ZN21SeedFilteringWorkflow14finalizeMethodEv+0x221) [0x56ef11] [ssb3:10762] [ 2] Ray(_ZN11TaskCreator8mainLoopEv+0xbe) [0x5cc3fe] [ssb3:10762] [ 3] Ray(_ZN11ComputeCore15runWithProfilerEv+0x382) [0x5cfcd2] [ssb3:10762] [ 4] Ray(_ZN11ComputeCore3runEv+0xbc) [0x5d3b8c] [ssb3:10762] [ 5] Ray(_ZN7Machine5startEv+0x19a6) [0x479416] [ssb3:10762] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x47699f] [ssb3:10762] [ 7] Ray(main+0xc7) [0x4724d7] [ssb3:10762] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fbd8d2b976d] [ssb3:10762] [ 9] Ray() [0x473f01] [ssb3:10762] *** End of error message *** (only Rank 0 because it was only running on 1 core) I first thought it could be a memory or general power problem (due to other problems with our hardware, which have been resolved in the meantime), but it now fails to run on my local machine as well as on our server, which has 256 GB of RAM. I guess that should be more than enough for a 5mb prokaryotic genome. The cutoff seems to be at 49, which still works, but it begins to crash at 51, and I have no clue why. If anyone has any idea, then I'd be very happy to hear it. Best regards, Bastian ________________________________________ From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] Sent: Friday, November 15, 2013 6:00 PM To: Hornung, Bastian Cc: denovoassembler-users@lists.sourceforge.net Subject: Re: [Denovoassembler-users] largest kmer-value? On 15/11/13 05:37 AM, Hornung, Bastian wrote: > Hi @all, > > I wonder what's the highest kmer-value, which ray can utilize. > I know that by default it's 30something. > I've compiled now versions with a way higher kmer-value (200, 500), because I > have MiSeq data with a read length of 250. > But I somehow get crashes, if I get higher than a certain kmer-value. > I began testing with 99, which doesn't work, 55 doesn't work either, 44 works > (I know, should be uneven, was my mistake), so I'm curious what's the highest > value. > And should it not work with more? Why do I get a segmentation fault with > higher values? > I personnally used MAXKMERLENGTH=96 on some of our local MiSeq data (read length is 150 I think). And it worked as far as I remember. What message are you getting ? seb > Best regards, > > Bastian > > > ------------------------------------------------------------------------------ > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
