Hello, Please use the community mailing list.
On 05/08/13 11:43 AM, Ferdinand Marlétaz wrote: > Dear Sébastien, > I read particularly nice things about your Ray assembler and I therefore > wanted to try it for the problem I am actually working on, which is the > assembly of a highly >polymorphic marine invertabrate (cephalochordate). Using SOAP and high k-mers >(67) I manage to perform the separate assembly of the two haplotypes but the >contigs are really >short (n50=400bp). My first basic question would then, how do you think Ray >would perform with such data, do you think it is a good idea to try it? It is always a good idea ot try several tools on the same data. > My second question is about the problem I had trying to run it. I tried a > first time with the whole bulk of data (~500M reads) and a high k-mer (63) > and it crashed. >I made a second attempt using a shorter k-mer and just a subset of the data >(60M paired-end reads). And it crashed again (see end of logfile attached). >The version >was the 2.3.0-devel The code in the master branch in git is not fully stable as I am working on a new plugin to make Ray run faster. > as I tried before the 2.2 of the website which seemed to cause problems that > I compiled on an ubuntu 12.04 server with 4 AMD opterons >(64 cores total) and 512GB or RAM. I therefore just ran Ray with the basic >command: I don't understand what you just said about Ray 2.2.0. > mpiexec -n 32 Ray -k 63 \ > -p \ > ../trim_reads/ATQ_BOSE_1_1.ct.fq.gz \ > ../trim_reads/ATQ_BOSE_1_2.ct.fq.gz \ > -o Bl63Ray > > I would really appreciate your feedback on these troubles with Ray, and more > generally your opinion about suitable strategy for this case. > Best Well, you are using the code from the master branch. The new plugin code is not really tested thoroughly. I should finish this code in about 2 weeks I suppose. > Ferdinand > > > *End of the logfile:* > Rank 15 processWorkerResult 137500/137959 > Rank 15 processWorkerResult 137600/137959 > Rank 15 processWorkerResult 137700/137959 > Rank 15 processWorkerResult 137800/137959 > Rank 15 processWorkerResult 137900/137959 > [DEBUG] number of relations: 18498 > VirtualProcessor: completed jobs: 137959 > Rank 15 : VirtualCommunicator (service provided by VirtualCommunicator): > 313656285 virtual messages generated 1927251 real messages (0.614447%) > Rank 2 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 0 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 3 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 14 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 8 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 13 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 9 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 6 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 1 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 11 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 12 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 7 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 15 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 4 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 10 freed 725614592 bytes from the path memory pool (chunks: 173) > Rank 5 freed 725614592 bytes from the path memory pool (chunks: 173) > [zoo-paralog:43395] *** Process received signal *** > [zoo-paralog:43395] Signal: Segmentation fault (11) > [zoo-paralog:43395] Signal code: Address not mapped (1) > [zoo-paralog:43395] Failing at address: (nil) > [zoo-paralog:43395] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7ff007cc7cb0] > [zoo-paralog:43395] [ 1] Ray(_ZNK17GraphSearchResult4dumpEPh+0x101) [0x578211] > [zoo-paralog:43395] [ 2] > Ray(_ZN23SpuriousSeedAnnihilator42call_RAY_SLAVE_MODE_PROCESS_MERGING_ASSETSEv+0xb04) > [0x567a54] > [zoo-paralog:43395] [ 3] Ray(_ZN11ComputeCore10runVanillaEv+0xf5) [0x5a7c45] > [zoo-paralog:43395] [ 4] Ray(_ZN11ComputeCore3runEv+0x89) [0x5ad459] > [zoo-paralog:43395] [ 5] Ray(_ZN7Machine5startEv+0x1846) [0x473b96] > [zoo-paralog:43395] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x47127f] > [zoo-paralog:43395] [ 7] Ray(main+0xc7) [0x46be17] > [zoo-paralog:43395] [ 8] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7ff00791976d] > [zoo-paralog:43395] [ 9] Ray() [0x46d5a1] > [zoo-paralog:43395] *** End of error message *** > -------------------------------------------------------------------------- > mpiexec noticed that process rank 15 with PID 43395 on node zoo-paralog > exited on signal 11 (Segmentation fault). > -------------------------------------------------------------------------- > ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite! 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