Hello, I just added the option -disable-recycling, to check if it is due to read recycling.
Can you install the last version available in git to test this ? git clone git://github.com/sebhtml/ray.git git clone git://github.com/sebhtml/RayPlatform.git cd ray make PREFIX=$(pwd)/Build make install Also, to avoid recomputing the same initial stuff over and over again, you can use checkpointing. mpiexec -n 32 \ Ray -k 31 -o Test3 -p SampleX/file1.fastq SampleX/file2.fastq \ -disable-recycling \ -read-write-checkpoints SampleX.Checkpoints Then you can re-run it again mpiexec -n 32 \ Ray -k 31 -o Test4 -p SampleX/file1.fastq SampleX/file2.fastq \ -disable-recycling.NO \ -read-write-checkpoints SampleX.Checkpoints Egon Ozer a écrit : > Just re-ran it the data set with the same settings and it got stuck in the > same loop at the same place, it seems. See following: > > Rank 2 starts on seed 285, length is 93, flow 0 [285/291] > Current peak coverage -> 164 > Rank 2 reached 0 vertices from seed 285, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 0 units/second > Rank 2: assembler memory usage: 0 KiB > ... > Rank 2 reached 8270200 vertices from seed 285, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 2195 units/second > Rank 2: assembler memory usage: 0 KiB > Rank 2 reached 8270300 vertices from seed 285, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 2670 units/second > Rank 2: assembler memory usage: 0 KiB > Rank 2 reached 8270400 vertices from seed 285, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 2545 units/second > Rank 2: assembler memory usage: 0 KiB > Rank 2 reached 8270500 vertices from seed 285, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 2874 units/second > Rank 2: assembler memory usage: 0 KiB > Rank 2 reached 8270600 vertices from seed 285, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 2742 units/second > Rank 2: assembler memory usage: 0 KiB > > > > > On Jun 14, 2012, at 10:27 AM, Sébastien Boisvert wrote: > >> Hello, >> >> >>> Rank 2 reached 76881500 vertices from seed 285, flow 1 >> As you said, there seems to be an infinite loop as 76881500 vertices is >> very long. >> >> >> I never saw this behavior before. >> >> >> >> There should be a line somewhere in your log like this: >> >> Rank 2 starts on seed 285, length is<seedLength>, flow 0 >> Current peak coverage -> <localPeakCoverage> >> >> >> What is the length of the seed 285 in your computation ? >> >> >> >> Is the problem reproducible with the same data and the same exact >> command on the >> same machine ? >> >> >> Also, the reported memory usage is 0 kb because this feature is not >> implemented >> on Mac OS. >> >> >> >> >> >> Sébastien >> >> Egon Ozer a écrit : >>> Rank 2: assembler memory usage: 0 KiB >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Denovoassembler-users mailing list >> Denovoassembler-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
