[mira_talk] Developer build internal bug

  • From: Artemus Harper <subanark@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 4 Oct 2011 14:29:33 -0700

Any update on this? I would like to know if there is any data I should
retain for further analysis, or anything I can do as a temporary workaround.

On Mon, Oct 3, 2011 at 8:48 AM, Artemus Harper <subanark@xxxxxxxxx> wrote:

> Mira stopped this morning. Please tell me if you need anything else from
> the output file. It is taking up 167G of HD space right now.
>
> GOOD: 165481297 0 0
> GOOD: 165481298 0 0
> GOOD: 165481299 0 0
>
>
> ========================== Memory self assessment
> ==============================
> Running in 64 bit mode.
>
> Dump from /proc/meminfo
>
> --------------------------------------------------------------------------------
> MemTotal:     528624708 kB
> MemFree:      302086772 kB
> Buffers:        222388 kB
> Cached:        1874972 kB
> SwapCached:          0 kB
> Active:       224022116 kB
> Inactive:      1580080 kB
> HighTotal:           0 kB
> HighFree:            0 kB
> LowTotal:     528624708 kB
> LowFree:      302086772 kB
> SwapTotal:     8289532 kB
> SwapFree:      8289532 kB
> Dirty:             156 kB
> Writeback:           0 kB
> AnonPages:    223504776 kB
> Mapped:         113260 kB
> Slab:           199664 kB
> PageTables:     511132 kB
> NFS_Unstable:        0 kB
> Bounce:              0 kB
> CommitLimit:  272601884 kB
> Committed_AS: 262788128 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed:    361348 kB
> VmallocChunk: 34359376347 kB
> HugePages_Total:     0
> HugePages_Free:      0
> HugePages_Rsvd:      0
> Hugepagesize:     2048 kB
>
> --------------------------------------------------------------------------------
>
> Dump from /proc/self/status
>
> --------------------------------------------------------------------------------
> Name: mira
> State: R (running)
> SleepAVG: 78%
> Tgid: 9648
> Pid: 9648
> PPid: 9644
> TracerPid: 0
> Uid: 5018 5018 5018 5018
> Gid: 5005 5005 5005 5005
> FDSize: 256
> Groups: 5005
> VmPeak: 262164656 kB
> VmSize: 261867580 kB
> VmLck:       0 kB
> VmHWM: 258686184 kB
> VmRSS: 222888736 kB
> VmData: 261862184 kB
> VmStk:      88 kB
> VmExe:    5272 kB
> VmLib:       0 kB
> VmPTE:  505312 kB
> StaBrk: 06fa8000 kB
> Brk: 3e73c8c000 kB
> StaStk: 7fff449a6770 kB
> Threads: 1
> SigQ: 0/4210688
> SigPnd: 0000000000000000
> ShdPnd: 0000000000000000
> SigBlk: 0000000000000000
> SigIgn: 0000000000001000
> SigCgt: 0000000180000000
> CapInh: 0000000000000000
> CapPrm: 0000000000000000
> CapEff: 0000000000000000
> Cpus_allowed:
> 00000000,00000000,00000000,00000000,00000000,00000000,ffffffff,ffffffff
> Mems_allowed: 00000000,0000000f
>
> --------------------------------------------------------------------------------
>
> Information on current assembly object:
>
> AS_readpool: 165481300 reads.
> AS_contigs: 0 contigs.
> AS_bbcontigs: 0 contigs.
> Mem used for reads: 141753391872 (132.0 GiB)
>
> Memory used in assembly structures:
>                                            Eff. Size   Free cap.
> LostByAlign
>      AS_writtenskimhitsperid:  165481300     631 MiB         0 B         0
> B
>                AS_skim_edges:  563714456    16.8 GiB        32 B         0
> B
>                  AS_adsfacts:          0        24 B         0 B         0
> B
>           AS_confirmed_edges:          0        24 B         0 B         0
> B
>    AS_permanent_overlap_bans:          1        24 B         0 B         0
> B
>               AS_readhitmiss:          0        24 B         0 B         0
> B
>             AS_readhmcovered:          0        24 B         0 B         0
> B
>                 AS_count_rhm:          0        24 B         0 B         0
> B
>                  AS_clipleft:  165481300     631 MiB         0 B         0
> B
>                 AS_clipright:  165481300     631 MiB         0 B         0
> B
>                  AS_used_ids:  165481300     158 MiB         0 B         4
> B
>               AS_multicopies:          0     158 MiB     158 MiB         4
> B
>             AS_hasmcoverlaps:          0     158 MiB     158 MiB         4
> B
>        AS_maxcoveragereached:  165481300     631 MiB         0 B         0
> B
>        AS_coverageperseqtype:          0        24 B         0 B         0
> B
>            AS_istroublemaker:  165481300     158 MiB         0 B         4
> B
>                  AS_isdebris:  165481300     158 MiB         0 B         4
> B
>           AS_needalloverlaps:  165481300     158 MiB        44 B         0
> B
>     AS_readsforrepeatresolve:          0        40 B         0 B         0
> B
>                 AS_allrmbsok:          0     631 MiB     631 MiB         0
> B
>         AS_probablermbsnotok:          0     631 MiB     631 MiB         0
> B
>             AS_weakrmbsnotok:          0     631 MiB     631 MiB         0
> B
>           AS_readmaytakeskim:  165481300     158 MiB        44 B         0
> B
>                AS_skimstaken: 5226841530     4.9 GiB         6 B         0
> B
>           AS_numskimoverlaps:  165481300     631 MiB         0 B         0
> B
>        AS_numleftextendskims:  165481300     631 MiB         0 B         0
> B
>          AS_rightextendskims:  165481300     631 MiB         0 B         0
> B
>       AS_skimleftextendratio:  165481300     158 MiB         0 B         4
> B
>      AS_skimrightextendratio:  165481300     158 MiB         0 B         4
> B
>              AS_usedtmpfiles:         10       336 B         0 B         0
> B
> Total: 173127680944 (161.2 GiB)
>
>
> ================================================================================
> Dynamic allocs: 0
> Align allocs: 0
>
> Internal logic/programming/debugging error (*sigh* this should not have
> happened).
> Please file a bug report on
> http://sourceforge.net/apps/trac/mira-assembler/
>
> "Would extend memory of AS_skim_edges? Shouldn't be. File:
> Chemdawg_mira_1_assembly/Chemdawg_mira_1_d_tmp/Chemdawg_mira_1_int_posmatchc_pass.1.bin
>  Line:
> 854458193
> SE: 62697086 103812658 24 10890 2177922329 1 -1 33 0 0 0 0 1
>
> "
>
> ->Thrown: uint32 Assembly::rsh4_loadSkimHitBlock(const string & filename,
> int32 blockstartid, int32 blockendid, int8 rid1dir, int8 rid2dir)
> ->Caught: main
>
> Aborting process, probably due to an internal error.
>
> If you want to report the error, please do so on
> http://sourceforge.net/apps/trac/mira-assembler/
> and also give a short notice on the mira talk mailing list.
>
> If reporting, please do not delete the log and checkpoint directories,
> there may
> be files in them which could be needed to find the problem.
>
> Subscribing / unsubscribing to mira talk, see:
> //www.freelists.org/list/mira_talk
>
> CWD: /home/dhingralab/artemus_harper
> Thank you for noticing that this is *NOT* a crash, but a
> controlled program stop.
> --
> Artemus Harper
>



-- 
Artemus Harper

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