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.
Matt
_____________________________________
Matthew MacManes, Ph.D.
University of New Hampshire I Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH 03824
Phone: 603-862-4052 I 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: 603-862-4052 I 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
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