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/> > 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. 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