On 27 janvier 2014 19:41, Miller, Ruth [ruth.mil...@bccdc.ca] wrote: > À : denovoassembler-users@lists.sourceforge.net > Objet : [Denovoassembler-users] Segmentation fault with -k 31 > > Hi, > > I am getting a segmentation fault when I try to analyse my data with –k31. > > The command is: > mpiexec -n 80 /global/software/ray/ray230/Ray -k 31 -i > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq –o test4 > > > The error is: > mpiexec noticed that process rank 17 with PID 30162 on node cn085 exited on > signal 11 (Segmentation fault). > > The tail of the log file I get up until then is copied in below (I would > have copied it all in, but it made the email too large to send to the mail > list). > > I wonder if it might be the same error Matthew Macmanes is seeing in his post > "_pmiu_daemon(SIGCHLD) segfault using Ray version > 2.3.1-devel<http://sourceforge.net/mailarchive/message.php?msg_id=31720108>" > ? However, it doesn't seem to happen without the –k 31 option. >
According to your log, your run failed during the loading of data whereas Matthew's issue was taking place later. Maybe there is some problem with your input file. Can you provide the first lines. > Thanks, > > Ruth > > > Rank 41 is loading sequence reads > Rank 41 : partition is [82553049;84566537], 2013489 sequence reads > Rank 59 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 40 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 15 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 69 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 39 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 24 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 74 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 14 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 32 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 31 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 79 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 57 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 46 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 13 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 33 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 29 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 72 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 60 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 42 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 12 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 34 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 28 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 73 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 58 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 45 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 9 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 38 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 25 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 76 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 56 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 41 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 11 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 77 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 61 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 10 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 75 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 63 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 62 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 78 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 67 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 71 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 64 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 70 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 68 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 70 has 0 sequence reads (completed) > Rank 68 has 0 sequence reads (completed) > Rank 67 has 0 sequence reads (completed) > Rank 71 has 0 sequence reads (completed) > Rank 64 has 0 sequence reads (completed) > Rank 50 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 55 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 53 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 49 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 49 has 0 sequence reads (completed) > Rank 53 has 0 sequence reads (completed) > Rank 50 has 0 sequence reads (completed) > Rank 55 has 0 sequence reads (completed) > Rank 43 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 44 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 47 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 51 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 54 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 48 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 52 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 51 has 0 sequence reads (completed) > Rank 54 has 0 sequence reads (completed) > Rank 48 has 0 sequence reads (completed) > Rank 52 has 0 sequence reads (completed) > Rank 43 has 0 sequence reads (completed) > Rank 44 has 0 sequence reads (completed) > Rank 47 has 0 sequence reads (completed) > Rank 16 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 16 has 0 sequence reads (completed) > Rank 23 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 23 has 0 sequence reads (completed) > Rank 21 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 21 has 0 sequence reads (completed) > Rank 22 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 22 has 0 sequence reads (completed) > Rank 19 is fetching file > HI.0946.004.Index_16.St-4_Rboth.fastq.pass_CPNHB_50.fastq with lazy loading > (please wait...) > Rank 19 has 0 sequence reads (completed) > Rank 0 has 0 sequence reads > Rank 0: assembler memory usage: 192592 KiB > Rank 0 has 100000 sequence reads > Rank 0: assembler memory usage: 192592 KiB > Rank 0 has 200000 sequence reads > Rank 0: assembler memory usage: 192592 KiB > Rank 0 has 300000 sequence reads > Rank 0: assembler memory usage: 208980 KiB > Rank 0 has 400000 sequence reads > Rank 0: assembler memory usage: 208980 KiB > Rank 17 has 0 sequence reads > Rank 17: assembler memory usage: 163460 KiB 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