Sorry, me again :/. Again, another problem, and again no idea what could cause it. Besides that I'm running ray on another server.
I started ray with: mpiexec -n 3 Ray -k 49 -p /home/bastian/data/XXX/Raw_data/NG-XXX_1.fastq /home/bastian/data/XXX/Raw_data/NG-XXX_2.fastq -o /home/bastian/data/XXX/NG-XXX_rayk49 -write-kmers -enable-neighbourhoods -write-seeds -write-read-markers -write-extensions -write-contig-paths As error message I get: Rank 2: assembler memory usage: 781872 KiB Got a seed, peak coverage: 72, adding seed. Rank 2 has 547 seeds Rank 2 is creating seeds [5258290/5258290] (completed) Rank 2: peak number of workers: 179, maximum: 32768 Rank 2 : VirtualCommunicator (service provided by VirtualCommunicator): 35999329 virtual messages generated 1263205 real messages (3.50897%) Rank 2 runtime statistics for seeding algorithm: Rank 2 Skipped paths because of dead end for head: 0 Rank 2 Skipped paths because of dead end for tail: 0 Rank 2 Skipped paths because of two dead ends: 0 Rank 2 Skipped paths because of bubble weak component: 0 Rank 2 Skipped paths because of short length: 5257176 Rank 2 Skipped paths because of bad ownership: 567 Rank 2 Skipped paths because of low coverage: 0 Rank 2 Eligible paths: 547 Rank 2: assembler memory usage: 781872 KiB Rank 0 has 556 seeds to register. Rank 1 has 573 seeds to register. Rank 2 has 547 seeds to register. Rank 1 registered 0/573 Rank 2 registered 0/547 Rank 0 registered 0/556 Rank 1 registered 572/573 Rank 1 registered its seeds Rank 2 registered 546/547 Rank 2 registered its seeds Rank 0 registered 555/556 Rank 0 registered its seeds VirtualProcessor: completed jobs: 0 Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) VirtualProcessor: completed jobs: 0 Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) VirtualProcessor: completed jobs: 0 Rank 2 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) Rank 2 freed 62914560 bytes from the path memory pool (chunks: 15) Rank 0 freed 62914560 bytes from the path memory pool (chunks: 15) Rank 1 freed 62914560 bytes from the path memory pool (chunks: 15) Fatal error in PMPI_Isend: Invalid rank, error stack: PMPI_Isend(148): MPI_Isend(buf=0x7fa36f4e4250, count=8, MPI_BYTE, dest=3, tag=224, MPI_COMM_WORLD, request=0x1082eb0) failed PMPI_Isend(95).: Invalid rank has value 3 but must be nonnegative and less than 3 Fatal error in PMPI_Isend: Invalid rank, error stack: PMPI_Isend(148): MPI_Isend(buf=0x7f738c14bd10, count=8, MPI_BYTE, dest=3, tag=224, MPI_COMM_WORLD, request=0x2301ec8) failed PMPI_Isend(95).: Invalid rank has value 3 but must be nonnegative and less than 3 Fatal error in PMPI_Isend: Invalid rank, error stack: PMPI_Isend(148): MPI_Isend(buf=0x7f0534dc9350, count=8, MPI_BYTE, dest=3, tag=224, MPI_COMM_WORLD, request=0x10d1c70) failed PMPI_Isend(95).: Invalid rank has value 3 but must be nonnegative and less than 3 Only difference to my previous runs: As from the email before, this time I correctly wrote "-write-kmers". I just ran the assembly again, this time without this option (and with 9 cores instead of 3), and it finished. I doubt it's an issue with 3 cores (...well...you never know...as you've seen with 2 cores), so I guess there's something wrong with that option. Best regards, Bastian ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
