Thanks again :). Any idea yet what the issue could be? 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. 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