Great, that means...I can work over the weekend :/. No, seriously, thanks very much, that's great to hear :).
________________________________________ From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] Sent: Friday, November 22, 2013 5:54 PM To: denovoassembler-users@lists.sourceforge.net Subject: Re: [Denovoassembler-users] largest kmer-value? On 22/11/13 02:55 AM, Hornung, Bastian wrote: > Thanks again :). > > Any idea yet what the issue could be? I just fixed a bug that occurs when the number of MPI ranks is 1 or is a prime number (like 3). https://github.com/sebhtml/ray/commit/b5811e82a4b0fddfbe82962e77c668e69391ded9 > Seems to be rather arbitrary, especially in connection with roughly the same > problem which Jim reported. > ________________________________________ > From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] > Sent: Thursday, November 21, 2013 3:36 PM > To: Hornung, Bastian > Cc: denovoassembler-users@lists.sourceforge.net > Subject: Re: [Denovoassembler-users] largest kmer-value? > > On 17/11/13 09:14 AM, Hornung, Bastian wrote: >> Hi Sebastien, >> >> the error message is just a segmentation fault, output below: > > Hi, > > I will look at this for the 2.3.1 release. see > https://github.com/sebhtml/ray/issues/222 > >> >> 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. 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