On 11/12/13 12:08 AM, Sucheta Tripathy wrote: > Here are the last lines of the stdout:
[Please use the mailing list] Do you also have a standard error log (stderr) because there are no errors in what you provided. > > --- > Rank 37 starts on seed 1009, length is 487, flow 0 [1009/7123] > Rank 37 starts on seed 1010, length is 487, flow 0 [1010/7123] > Rank 37 starts on seed 1011, length is 487, flow 0 [1011/7123] > Rank 37 starts on seed 1012, length is 486, flow 0 [1012/7123] > Rank 37 starts on seed 1013, length is 485, flow 0 [1013/7123] > Rank 37 starts on seed 1014, length is 485, flow 0 [1014/7123] > Rank 37 starts on seed 1015, length is 485, flow 0 [1015/7123] > Rank 37 starts on seed 1016, length is 484, flow 0 [1016/7123] > Rank 37 starts on seed 1017, length is 483, flow 0 [1017/7123] > Rank 37 starts on seed 1018, length is 483, flow 0 [1018/7123] > Rank 37 starts on seed 1019, length is 483, flow 0 [1019/7123] > Rank 37 starts on seed 1020, length is 483, flow 0 [1020/7123] > Rank 37 starts on seed 1021, length is 482, flow 0 [1021/7123] > Rank 37 starts on seed 1022, length is 481, flow 0 [1022/7123] > Rank 37 starts on seed 1023, length is 480, flow 0 [1023/7123] > Rank 13: assembler memory usage: 811760 KiB > Rank 13 starts on seed 724, length is 616, flow 0 [724/7163] > Rank 13 starts on seed 725, length is 616, flow 0 [725/7163] > Rank 33 traversed 1858264 nucleotide symbols > Rank 33: assembler memory usage: 787912 KiB > Rank 33 starts on seed 1051, length is 441, flow 0 [1051/7179] > Rank 33 starts on seed 1052, length is 441, flow 0 [1052/7179] > Rank 33 starts on seed 1053, length is 441, flow 0 [1053/7179] > Rank 33 starts on seed 1054, length is 441, flow 0 [1054/7179] > Rank 23 reached 2363 vertices from seed 1065, flow 2 > Speed RAY_SLAVE_MODE_EXTENSION 1255 units/second > Rank 23: assembler memory usage: 794512 KiB > Rank 23 is changing direction. > Rank 27: assembler memory usage: 826720 KiB > Rank 27 starts on seed 796, length is 561, flow 0 [796/7089] > Rank 27 starts on seed 797, length is 560, flow 0 [797/7089] > Rank 27 starts on seed 798, length is 559, flow 0 [798/7089] > Rank 45 traversed 1827563 nucleotide symbols > Rank 45 reached 2036 vertices from seed 1003, flow 3 > Speed RAY_SLAVE_MODE_EXTENSION 967 units/second > Rank 45: assembler memory usage: 802196 KiB > Rank 45 (extension done) NumberOfFlows: 3 > Rank 45 FlowedVertices: 0 488 1 1142 2 2036 3 2036 > Rank 45: assembler memory usage: 798096 KiB > Rank 45 starts on seed 1004, length is 487, flow 0 [1004/7303] > Rank 20 traversed 1511593 nucleotide symbols > Rank 20 reached 1472 vertices from seed 781, flow 3 > Speed RAY_SLAVE_MODE_EXTENSION 1480 units/second > Rank 20: assembler memory usage: 809988 KiB > Rank 20 (extension done) NumberOfFlows: 3 > Rank 20 FlowedVertices: 0 542 1 1173 2 1472 3 1472 > Rank 20: assembler memory usage: 805888 KiB > Rank 20 starts on seed 782, length is 542, flow 0 [782/7064] > Rank 26 reached 1439 vertices from seed 806, flow 2 > Speed RAY_SLAVE_MODE_EXTENSION 1509 units/second > Rank 26: assembler memory usage: 806404 KiB > Rank 26 is changing direction. > Terminated > > > > On Mon, Dec 9, 2013 at 9:02 PM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> > wrote: > > Can you provide the last lines of the standard output ? > > > On 06/12/13 10:15 PM, Sucheta Tripathy wrote: > > Thanks Sebastian! I tried fixing that as well! Now both my libraries > have good quality equal number of sequences: Here is the content of > NumberOfSequences file: > > Files: 2 > > FileNumber: 0 > FilePath: /scratch/sucheta/out1.fastq > NumberOfSequences: 69393976 > FirstSequence: 0 > LastSequence: 69393975 > > FileNumber: 1 > FilePath: /scratch/sucheta/out2.fastq > NumberOfSequences: 69393976 > FirstSequence: 69393976 > LastSequence: 138787951 > > > Summary > NumberOfSequences: 138787952 > FirstSequence: 0 > LastSequence: 138787951 > ~ > > In the output directory, I see the following files: Where the > parallelPaths.txt file has 0 content. I am not sure what is making this crash. > > -rw-r--r-- 1 sucheta iicb 332 Dec 6 07:48 > CoverageDistributionAnalysis.__txt > -rw-r--r-- 1 sucheta iicb 259819 Dec 6 07:48 CoverageDistribution.txt > -rw-r--r-- 1 sucheta iicb 672 Dec 6 09:28 degreeDistribution.txt > -rw-r--r-- 1 sucheta iicb 1541 Dec 6 15:41 ElapsedTime.txt > -rw-r--r-- 1 sucheta iicb 164 Dec 6 06:23 FilePartition.txt > -rw-r--r-- 1 sucheta iicb 3545 Dec 6 09:27 GraphPartition.txt > -rw-r--r-- 1 sucheta iicb 6496 Dec 6 15:41 LibraryData.xml > -rw-r--r-- 1 sucheta iicb 389 Dec 6 15:41 LibraryStatistics.txt > -rw-r--r-- 1 sucheta iicb 2388 Dec 6 06:18 NetworkTest.txt > -rw-r--r-- 1 sucheta iicb 352 Dec 6 06:23 NumberOfSequences.txt > -rw-r--r-- 1 sucheta iicb 0 Dec 6 15:42 ParallelPaths.txt > drwxr-x--- 2 sucheta iicb 4096 Dec 6 16:20 Plugins > -rw-r--r-- 1 sucheta iicb 116 Dec 6 06:18 RayCommand.txt > -rw-r--r-- 1 sucheta iicb 18 Dec 6 06:18 RayPlatform_Version.txt > -rw-r--r-- 1 sucheta iicb 10 Dec 6 06:18 RayVersion.txt > drwxr-x--- 2 sucheta iicb 4096 Dec 6 06:18 Scheduling > -rw-r--r-- 1 sucheta iicb 25434 Dec 6 15:02 > SeedLengthDistribution.txt > -rw-r--r-- 1 sucheta iicb 2859 Dec 6 06:23 SequencePartition.txt > > Here is my commandline: > mpiexec -n 96 Ray \ > -k \ > 21 \ > -p \ > /scratch/sucheta/out1.fastq \ > /scratch/sucheta/out2.fastq \ > -o \ > rayTest1 > ~ > > > > On Fri, Dec 6, 2013 at 9:10 PM, Sébastien Boisvert > <sebastien.boisvert.3@ulaval.__ca <mailto:sebastien.boisver...@ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>> wrote: > > On 01/12/13 04:12 AM, Sucheta Tripathy wrote: > > > I am trying to run Ray for a while now on our Illumina data. > It is run in parallel mode and memory is not a constraint now because we have > a cluster with 16 X 16 GB memory in each node. > > > The problem is this: tmp1 and tmp2 don't contain the same number > of sequences. > > Using paired files with different number of sequences will cause > crash in Ray 2.2.0 and earlier versions. > If you use Ray 2.3.0, Ray will throw an error. > > > Also, lane1_1b and lane_1_2b are empty (0 sequences). You may > want to check that out too. > > > my Command: > mpiexec -n 64 Ray \ > -k \ > 31 \ > -disable-recycling \ > -p \ > /scratch/sucheta/tmp1.fastq \ > /scratch/sucheta/tmp2.fastq \ > -p \ > /scratch/sucheta/lane1_1b.fq \ > /scratch/sucheta/lane1_2b.fq \ > -o \ > rayTest > > Content of NumberOfSequences.txt > Files: 4 > > FileNumber: 0 > FilePath: /scratch/sucheta/tmp1.fastq > NumberOfSequences: 73013670 > FirstSequence: 0 > LastSequence: 73013669 > > FileNumber: 1 > FilePath: /scratch/sucheta/tmp2.fastq > NumberOfSequences: 72339350 > FirstSequence: 73013670 > LastSequence: 145353019 > > FileNumber: 2 > FilePath: /scratch/sucheta/lane1_1b.fq > NumberOfSequences: 0 > > FileNumber: 3 > FilePath: /scratch/sucheta/lane1_2b.fq > NumberOfSequences: 0 > > Summary > NumberOfSequences: 145353020 > FirstSequence: 0 > LastSequence: 145353019 > > > However, after running for a while Ray terminates: This is > the last few lines of STDOUT: > > --- > > Speed RAY_SLAVE_MODE_EXTENSION 1183 units/second > Rank 9: assembler memory usage: 850432 KiB > Rank 9 is changing direction. > Rank 12: assembler memory usage: 826944 KiB > Rank 12 starts on seed 1200, length is 477, flow 0 > [1200/6451] > Rank 12 starts on seed 1201, length is 476, flow 0 > [1201/6451] > Rank 10 traversed 1273646 nucleotide symbols > Rank 10: assembler memory usage: 869460 KiB > Rank 10 starts on seed 534, length is 906, flow 0 [534/6579] > Rank 31 reached 2270 vertices from seed 491, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 1174 units/second > Rank 31: assembler memory usage: 866768 KiB > Rank 31 is changing direction. > Rank 2 traversed 1910058 nucleotide symbols > Rank 2 reached 1269 vertices from seed 1007, flow 2 > Speed RAY_SLAVE_MODE_EXTENSION 1435 units/second > Rank 2: assembler memory usage: 843432 KiB > Rank 2 (extension done) NumberOfFlows: 2 > Rank 2 FlowedVertices: 0 576 1 1269 2 1269 > Rank 2: assembler memory usage: 839332 KiB > Rank 2 starts on seed 1008, length is 576, flow 0 [1008/6537] > Terminated > --- > > It creates the following output files before crashing: > > CoverageDistributionAnalysis.____txt NumberOfSequences.txt > > CoverageDistribution.txt ParallelPaths.txt > degreeDistribution.txt Plugins > ElapsedTime.txt RayCommand.txt > FilePartition.txt RayPlatform_Version.txt > GraphPartition.txt RayVersion.txt > LibraryData.xml Scheduling > LibraryStatistics.txt SeedLengthDistribution.txt > NetworkTest.txt SequencePartition.txt > > > Any help in this regard will be much appreciated! > > > -- > Sucheta Tripathy, Ph.D > Scientist, Ramalingaswamy Fellow, > Indian Institute of Chemical Biology, > Kolkata, India. > https://sites.google.com/site/____suchetalab/ > <https://sites.google.com/site/__suchetalab/> > <https://sites.google.com/__site/suchetalab/ > <https://sites.google.com/site/suchetalab/>> > > https://twitter.com/tsucheta > > > > > > -- > Sucheta Tripathy, Ph.D > Scientist, Ramalingaswamy Fellow, > Indian Institute of Chemical Biology, > Kolkata, India. > https://sites.google.com/site/__suchetalab/ > <https://sites.google.com/site/suchetalab/> > https://twitter.com/tsucheta > > > > > > -- > Sucheta Tripathy, Ph.D > Scientist, Ramalingaswamy Fellow, > Indian Institute of Chemical Biology, > Kolkata, India. > https://sites.google.com/site/suchetalab/ > https://twitter.com/tsucheta ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. 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