On 07/12/13 10:19 AM, MacManes, Matthew wrote: > Though the same thing happens with the regular release Ray-2.3.0. > > Seb- please let me know what other debugging info I can send you.
Hi Matt, Thank you for the info. That helps. I created a ticket https://github.com/sebhtml/ray/issues/223 and I included Jeff Tan's issue ( http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/735 ) and yours ( http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/739 ). They look like similar problems. I am currently working on another bug, but this one is the next in line ! Séb > > Matt > _____________________________________ > *Matthew MacManes, Ph.D. * > University of New Hampshire I Assistant Professor > Department of Molecular, Cellular, & Biomedical Sciences > Durham, NH 03824 > Phone: 603-862-4052I Twitter: @PeroMHC <https://twitter.com/PeroMHC> > Web: genomebio.org <http://genomebio.org/> > Office: 189 Rudman Hall > Laboratory: 145 Rudman Hall > > On Dec 6, 2013, at 11:03 AM, MacManes, Matthew <matthew.macma...@unh.edu > <mailto:matthew.macma...@unh.edu>> wrote: > >> This is Ray version 2.3.1-devel. I pulled from github a couple of days ago. >> >> Mat >> >> _____________________________________ >> *Matthew MacManes, Ph.D. * >> University of New Hampshire I Assistant Professor >> Department of Molecular, Cellular, & Biomedical Sciences >> Durham, NH 03824 >> Phone: 603-862-4052I Twitter: @PeroMHC <https://twitter.com/PeroMHC> >> Web: genomebio.org <http://genomebio.org/> >> Office: 189 Rudman Hall >> Laboratory: 145 Rudman Hall >> >> On Dec 6, 2013, at 10:42 AM, Sébastien Boisvert >> <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> >> wrote: >> >>> On 05/12/13 05:19 PM, MacManes, Matthew wrote: >>>> Hi All, >>>> >>>> Having problems with segfault on a Cray XE6m-200 using 480 ranks: Looks >>>> like 'Selection of optimal read markers’ had just finished. >>> >>> Which Ray version are you using ? >>> >>>> >>>> error code: >>>>> _pmiu_daemon(SIGCHLD): [NID 00285] [c1-0c2s1n3] [Thu Dec 5 16:34:07 >>>>> 2013] PE RANK 139 exit signal Segmentation fault >>>>> [NID 00285] 2013-12-05 16:34:07 Apid 54698: initiated application >>>>> termination >>>> >>>> mpiexec -n 480 Ray \ >>>> -show-memory-usage \ >>>> -read-write-checkpoints \ >>>> checkpoints \ >>>> -k \ >>>> 51 \ >>>> -p \ >>>> L1.notCombined_1.fastq \ >>>> L1.notCombined_2.fastq \ >>>> -p \ >>>> L2.notCombined_1.fastq \ >>>> L2.notCombined_2.fastq \ >>>> -p \ >>>> L3.notCombined_1.fastq \ >>>> L3.notCombined_2.fastq \ >>>> -s \ >>>> L3.extendedFrags.fastq \ >>>> -s \ >>>> L2.extendedFrags.fastq \ >>>> -s \ >>>> L3.extendedFrags.fastq \ >>>> -s \ >>>> 360.unpaired.fastq >>>> >>>> >>>> Here are last 100 lines of output: >>>> >>>> Rank 314: assembler memory usage: 3958204 KiB >>>> Rank 105: memory usage for optimal read markers= 69632 KiB >>>> Rank 105 is creating seeds [1/13097800] >>>> Rank 105: assembler memory usage: 3958204 KiB >>>> Rank 157: memory usage for optimal read markers= 69632 KiB >>>> Rank 157 is creating seeds [1/13097174] >>>> Rank 157: assembler memory usage: 3962332 KiB >>>> Rank 324: memory usage for optimal read markers= 69632 KiB >>>> Rank 324 is creating seeds [1/13103516] >>>> Rank 324: assembler memory usage: 3962332 KiB >>>> Rank 185: memory usage for optimal read markers= 69632 KiB >>>> Rank 185 is creating seeds [1/13089676] >>>> Rank 185: assembler memory usage: 3962332 KiB >>>> Rank 385: memory usage for optimal read markers= 69632 KiB >>>> Rank 385 is creating seeds [1/13101020] >>>> Rank 385: assembler memory usage: 3958204 KiB >>>> Rank 85: memory usage for optimal read markers= 69632 KiB >>>> Rank 85 is creating seeds [1/13092560] >>>> Rank 85: assembler memory usage: 3958204 KiB >>>> Rank 158: memory usage for optimal read markers= 65536 KiB >>>> Rank 158 is creating seeds [1/13093210] >>>> Rank 158: assembler memory usage: 3958204 KiB >>>> Rank 332: memory usage for optimal read markers= 69632 KiB >>>> Rank 332 is creating seeds [1/13094478] >>>> Rank 332: assembler memory usage: 3962332 KiB >>>> Rank 309: memory usage for optimal read markers= 65536 KiB >>>> Rank 309 is creating seeds [1/13102758] >>>> Rank 309: assembler memory usage: 3958204 KiB >>>> Rank 136: memory usage for optimal read markers= 69632 KiB >>>> Rank 136 is creating seeds [1/13094218] >>>> Rank 136: assembler memory usage: 3962332 KiB >>>> Rank 293: memory usage for optimal read markers= 73728 KiB >>>> Rank 293 is creating seeds [1/13090794] >>>> Rank 293: assembler memory usage: 3962332 KiB >>>> Rank 271: memory usage for optimal read markers= 73728 KiB >>>> Rank 271 is creating seeds [1/13093488] >>>> Rank 271: assembler memory usage: 3962332 KiB >>>> Rank 176: memory usage for optimal read markers= 73728 KiB >>>> Rank 176 is creating seeds [1/13107640] >>>> Rank 176: assembler memory usage: 3964384 KiB >>>> Rank 264: memory usage for optimal read markers= 69632 KiB >>>> Rank 264 is creating seeds [1/13109980] >>>> Rank 264: assembler memory usage: 3962332 KiB >>>> Rank 138: memory usage for optimal read markers= 69632 KiB >>>> Rank 138 is creating seeds [1/13093866] >>>> Rank 138: assembler memory usage: 3958204 KiB >>>> Rank 395: memory usage for optimal read markers= 69632 KiB >>>> Rank 395 is creating seeds [1/13091210] >>>> Rank 395: assembler memory usage: 3958204 KiB >>>> Rank 335: memory usage for optimal read markers= 73728 KiB >>>> Rank 335 is creating seeds [1/13095456] >>>> Rank 335: assembler memory usage: 3966460 KiB >>>> Rank 329: memory usage for optimal read markers= 73728 KiB >>>> Rank 329 is creating seeds [1/13106094] >>>> Rank 329: assembler memory usage: 3962332 KiB >>>> Rank 328: memory usage for optimal read markers= 69632 KiB >>>> Rank 328 is creating seeds [1/13100648] >>>> Rank 328: assembler memory usage: 3958204 KiB >>>> Rank 303: memory usage for optimal read markers= 69632 KiB >>>> Rank 303 is creating seeds [1/13085492] >>>> Rank 303: assembler memory usage: 3962332 KiB >>>> Rank 290: memory usage for optimal read markers= 65536 KiB >>>> Rank 290 is creating seeds [1/13091084] >>>> Rank 290: assembler memory usage: 3958204 KiB >>>> Rank 65: memory usage for optimal read markers= 69632 KiB >>>> Rank 65 is creating seeds [1/13092946] >>>> Rank 65: assembler memory usage: 3958204 KiB >>>> Rank 119: memory usage for optimal read markers= 69632 KiB >>>> Rank 119 is creating seeds [1/13096562] >>>> Rank 119: assembler memory usage: 3958204 KiB >>>> Rank 454: memory usage for optimal read markers= 69632 KiB >>>> Rank 454 is creating seeds [1/13100860] >>>> Rank 454: assembler memory usage: 3958204 KiB >>>> Rank 114: memory usage for optimal read markers= 69632 KiB >>>> Rank 114 is creating seeds [1/13091328] >>>> Rank 114: assembler memory usage: 3958204 KiB >>>> Rank 305: memory usage for optimal read markers= 69632 KiB >>>> Rank 305 is creating seeds [1/13101714] >>>> Rank 305: assembler memory usage: 3958204 KiB >>>> Rank 338: memory usage for optimal read markers= 69632 KiB >>>> Rank 338 is creating seeds [1/13099074] >>>> Rank 338: assembler memory usage: 3958204 KiB >>>> Rank 318: memory usage for optimal read markers= 65536 KiB >>>> Rank 318 is creating seeds [1/13099310] >>>> Rank 318: assembler memory usage: 3958204 KiB >>>> Rank 342: memory usage for optimal read markers= 69632 KiB >>>> Rank 342 is creating seeds [1/13096148] >>>> Rank 342: assembler memory usage: 3958204 KiB >>>> Rank 460: memory usage for optimal read markers= 69632 KiB >>>> Rank 460 is creating seeds [1/13106978] >>>> Rank 460: assembler memory usage: 4127836 KiB >>>> Rank 74: memory usage for optimal read markers= 69632 KiB >>>> Rank 74 is creating seeds [1/13087278] >>>> Rank 74: assembler memory usage: 3958204 KiB >>>> Rank 461: memory usage for optimal read markers= 73728 KiB >>>> Rank 461 is creating seeds [1/13100888] >>>> Rank 461: assembler memory usage: 4131964 KiB >>>> Application 54698 exit codes: 139 >>>> Application 54698 exit signals: Killed >>>> Application 54698 resources: utime ~11381s, stime ~63s, Rss ~809788, >>>> inblocks ~77421751, outblocks ~17677754 >>>> >>>> Any ideas? >>>> >>>> _____________________________________ >>>> *Matthew MacManes, Ph.D. * >>>> University of New Hampshire I Assistant Professor >>>> Department of Molecular, Cellular, & Biomedical Sciences >>>> Durham, NH 03824 >>>> Phone: 603-862-4052I Twitter: @PeroMHC <https://twitter.com/PeroMHC> >>>> Web:genomebio.org <http://genomebio.org/><http://genomebio.org/> >>>> Office: 189 Rudman Hall >>>> Laboratory: 145 Rudman Hall >> >> ------------------------------------------------------------------------------ >> Sponsored by Intel(R) XDK >> Develop, test and display web and hybrid apps with a single code base. >> Download it for free now! >> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk_______________________________________________ >> Denovoassembler-users mailing list >> Denovoassembler-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > 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