[Bioperl-l] Blast temporary open files not closed
Hilmar Lapp
hlapp at gmx.net
Sat Sep 9 12:16:05 UTC 2006
Which version of Bioperl, which version of Mac OSX?
You may also need to post your script or an equivalent script that
shows the problem. There are plenty of us who run this sort of thing
without problem, so I suspect that the way you do things in your
script has some bearing on the problem.
On Sep 9, 2006, at 4:31 AM, ende wrote:
>
> Processing a fasta file with about 500 dna seqs.. my MacOSX (that
> has the max number of opened files up to 512) crashes... You need to
> divide the problem in pieces or (in bash shell, with ulimit -n 1024)
> augment that max number of opened files.
>
> This has no sense for me since my perl program nor leave any open
> file without its corresponding closing. On the other side, the
> problem arises when the number of dnas grows _in one file_.
>
> In the code I run blast (StandAloneBlast... $blastMachine->blastall)
> for each seq.
>
>
> Then sniffing int the perl program stopped perl program I confirmed
> my suspects. BioPerl (StandAloneBlast) does not closes temporary
> opened files. Those files seems to be created to save seqs for to be
> then processed by blastall program... The output of lsof indicates
> (as MacOSX System Monitor) that those files are left opened but not
> there (!?)
>
> The output of lsof +p pidofperlprogram
>
> COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
> perl 21977 juanfc cwd VDIR 14,7 238 6835993 /Users/
> juanfc/Documents/programperl 21977 juanfc txt VREG 14,7
> 19280 1589055 /usr/bin/perl
> perl 21977 juanfc txt VREG 14,7 23476 1580272 /System/
> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/IO/IO.bundle
> perl 21977 juanfc txt VREG 14,7 17772 1580263 /System/
> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Fcntl/Fcntl.bundle
> perl 21977 juanfc txt VREG 14,7 114116 1580381 /System/
> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/POSIX/POSIX.bundle
> perl 21977 juanfc txt VREG 14,7 23684 1580265 /System/
> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/File/Glob/
> Glob.bundle
> perl 21977 juanfc txt VREG 14,7 1797788 6275687 /usr/lib/
> dyld
> perl 21977 juanfc txt VREG 14,7 4379472 6276030 /usr/lib/
> libSystem.B.dylib
> perl 21977 juanfc txt VREG 14,7 1086420 6276221 /System/
> Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/libperl.dylib
> perl 21977 juanfc 0u VCHR 4,2 0t3748 63113092 /dev/ttyp2
> perl 21977 juanfc 1u VCHR 4,2 0t3748 63113092 /dev/ttyp2
> perl 21977 juanfc 2u VCHR 4,2 0t3748 63113092 /dev/ttyp2
> perl 21977 juanfc 3u VCHR 4,2 0t3748 63113092 /dev/ttyp2
> perl 21977 juanfc 4r VREG stat(/
> private/tmp/FJPRR4sVob): No such file or directory
> perl 21977 juanfc 5r VREG stat(/
> private/tmp/MYkH56SwfZ): No such file or directory
> perl 21977 juanfc 6r VREG stat(/
> private/tmp/6mgSei6w73): No such file or directory
> perl 21977 juanfc 7r VREG stat(/
> private/tmp/VYBpVSlg59): No such file or directory
> perl 21977 juanfc 8r VREG stat(/
> private/tmp/cfMJ74N25D): No such file or directory
> perl 21977 juanfc 9r VREG stat(/
> private/tmp/M6fgaPCIXa): No such file or directory
> perl 21977 juanfc 10r VREG stat(/
> private/tmp/tMap0OjaUP): No such file or directory
> perl 21977 juanfc 11r VREG stat(/
> private/tmp/W87vtYjsCt): No such file or directory
> perl 21977 juanfc 12r VREG stat(/
> private/tmp/iHWH3bCMPC): No such file or directory
> perl 21977 juanfc 13r VREG stat(/
> private/tmp/IxcDMdaDyv): No such file or directory
> perl 21977 juanfc 14r VREG stat(/
> private/tmp/iKBhFmI6VR): No such file or directory
> perl 21977 juanfc 15r VREG stat(/
> private/tmp/8JnbRBsiTS): No such file or directory
> perl 21977 juanfc 16r VREG stat(/
> private/tmp/hZWlCYbOsY): No such file or directory
> perl 21977 juanfc 17r VREG stat(/
> private/tmp/8p1Vp3jmkV): No such file or directory
> perl 21977 juanfc 18r VREG stat(/
> private/tmp/tClGgoph8f): No such file or directory
> perl 21977 juanfc 19r VREG stat(/
> private/tmp/60BSipkClP): No such file or directory
> perl 21977 juanfc 20r VREG stat(/
> private/tmp/aWZeJiVHvV): No such file or directory
> perl 21977 juanfc 21r VREG stat(/
> private/tmp/87xqhVYjV1): No such file or directory
> perl 21977 juanfc 22r VREG stat(/
> private/tmp/06m1ko4XjK): No such file or directory
> perl 21977 juanfc 23r VREG stat(/
> private/tmp/s7P3AA6F9o): No such file or directory
> perl 21977 juanfc 24r VREG stat(/
> private/tmp/dJt3mpTS8m): No such file or directory
> perl 21977 juanfc 25r VREG stat(/
> private/tmp/xqL5jguilE): No such file or directory
> perl 21977 juanfc 26r VREG stat(/
> private/tmp/AFWKFmgBh2): No such file or directory
> perl 21977 juanfc 27r VREG stat(/
> private/tmp/zWLMrdNlv9): No such file or directory
> perl 21977 juanfc 28r VREG stat(/
> private/tmp/svOtPNyYIs): No such file or directory
> perl 21977 juanfc 29r VREG stat(/
> private/tmp/WpVvGitW33): No such file or directory
> perl 21977 juanfc 30r VREG stat(/
> private/tmp/pyoXSEsRvM): No such file or directory
> perl 21977 juanfc 31r VREG stat(/
> private/tmp/JoBSaJNqf6): No such file or directory
> perl 21977 juanfc 32r VREG stat(/
> private/tmp/Uw9ABNTqcN): No such file or directory
> perl 21977 juanfc 33r VREG stat(/
> private/tmp/wG4la2L5if): No such file or directory
> perl 21977 juanfc 34r VREG stat(/
> private/tmp/IHTz2BeDOv): No such file or directory
> perl 21977 juanfc 35r VREG stat(/
> private/tmp/t9sXizoEim): No such file or directory
> perl 21977 juanfc 36r VREG stat(/
> private/tmp/DJDliIFd30): No such file or directory
> perl 21977 juanfc 37r VREG stat(/
> private/tmp/atGFL3GEa6): No such file or directory
> perl 21977 juanfc 38r VREG stat(/
> private/tmp/PuwFdWLjw0): No such file or directory
> perl 21977 juanfc 39r VREG stat(/
> private/tmp/XoYmuh7JeD): No such file or directory
> perl 21977 juanfc 40r VREG stat(/
> private/tmp/tkXqKOoQ4L): No such file or directory
> perl 21977 juanfc 41r VREG stat(/
> private/tmp/XyQTSlDWZK): No such file or directory
> perl 21977 juanfc 42r VREG stat(/
> private/tmp/sIcuE8SxrK): No such file or directory
> perl 21977 juanfc 43r VREG stat(/
> private/tmp/lyhfZf9XlK): No such file or directory
> perl 21977 juanfc 44r VREG stat(/
> private/tmp/5XK8C6WySy): No such file or directory
> perl 21977 juanfc 45r VREG stat(/
> private/tmp/i4SUNdxxJP): No such file or directory
> perl 21977 juanfc 46r VREG stat(/
> private/tmp/sCT2jmC3Ti): No such file or directory
> perl 21977 juanfc 47r VREG stat(/
> private/tmp/eW27HGMYEH): No such file or directory
> perl 21977 juanfc 48r VREG stat(/
> private/tmp/iKDldazryA): No such file or directory
> perl 21977 juanfc 49r VREG stat(/
> private/tmp/Fim4GJg3UY): No such file or directory
> perl 21977 juanfc 50r VREG stat(/
> private/tmp/iJNWvR2ixG): No such file or directory
> perl 21977 juanfc 51r VREG stat(/
> private/tmp/U9OA0HiQgm): No such file or directory
> perl 21977 juanfc 52r VREG stat(/
> private/tmp/URFitXhlku): No such file or directory
> perl 21977 juanfc 53r VREG stat(/
> private/tmp/IauwZ1ogs6): No such file or directory
> perl 21977 juanfc 54r VREG stat(/
> private/tmp/S5pc159wKf): No such file or directory
> perl 21977 juanfc 55r VREG stat(/
> private/tmp/YENXM1G78k): No such file or directory
> perl 21977 juanfc 56r VREG stat(/
> private/tmp/uDruzEPBaM): No such file or directory
> perl 21977 juanfc 57r VREG stat(/
> private/tmp/NmW0DL9xaQ): No such file or directory
> perl 21977 juanfc 58r VREG stat(/
> private/tmp/nn5Mw2ZfGv): No such file or directory
> perl 21977 juanfc 59r VREG stat(/
> private/tmp/Pw7byHTVUb): No such file or directory
> perl 21977 juanfc 60r VREG stat(/
> private/tmp/2AXMWaFtrM): No such file or directory
> perl 21977 juanfc 61r VREG stat(/
> private/tmp/EU1vNIqLF1): No such file or directory
> perl 21977 juanfc 62r VREG stat(/
> private/tmp/uph6n3kGfL): No such file or directory
> perl 21977 juanfc 63r VREG stat(/
> private/tmp/g5WLuOEcrG): No such file or directory
> perl 21977 juanfc 64r VREG stat(/
> private/tmp/aSvXqPRW46): No such file or directory
> perl 21977 juanfc 65r VREG stat(/
> private/tmp/aJfHCcsEKx): No such file or directory
> perl 21977 juanfc 66r VREG stat(/
> private/tmp/L7vRyF2kOX): No such file or directory
> perl 21977 juanfc 67r VREG stat(/
> private/tmp/gND8bhWI9B): No such file or directory
> perl 21977 juanfc 68r VREG stat(/
> private/tmp/4hukSHCFDZ): No such file or directory
> perl 21977 juanfc 69r VREG stat(/
> private/tmp/6oKfCqu4D0): No such file or directory
> perl 21977 juanfc 70r VREG stat(/
> private/tmp/5W8jmOltQt): No such file or directory
> perl 21977 juanfc 71r VREG stat(/
> private/tmp/zJdLHNfwNb): No such file or directory
> perl 21977 juanfc 72r VREG stat(/
> private/tmp/MLuGvv77HZ): No such file or directory
> perl 21977 juanfc 73r VREG stat(/
> private/tmp/1ThCRyzfTx): No such file or directory
> perl 21977 juanfc 74r VREG stat(/
> private/tmp/pnlSoTXEhf): No such file or directory
> perl 21977 juanfc 75r VREG stat(/
> private/tmp/BYK4UnHbHF): No such file or directory
> perl 21977 juanfc 76r VREG stat(/
> private/tmp/Omp320pcne): No such file or directory
> perl 21977 juanfc 77r VREG stat(/
> private/tmp/oWgmotebi5): No such file or directory
> perl 21977 juanfc 78r VREG stat(/
> private/tmp/p5sAeD6P2S): No such file or directory
> perl 21977 juanfc 79r VREG stat(/
> private/tmp/jSTlPlrVv6): No such file or directory
> perl 21977 juanfc 80r VREG stat(/
> private/tmp/8r6Hcsd5lk): No such file or directory
> perl 21977 juanfc 81r VREG stat(/
> private/tmp/zziCynavEX): No such file or directory
> perl 21977 juanfc 82r VREG stat(/
> private/tmp/cFhq1SuNLW): No such file or directory
> perl 21977 juanfc 83r VREG stat(/
> private/tmp/dUDKQ3ylKn): No such file or directory
> perl 21977 juanfc 84r VREG stat(/
> private/tmp/gVzwuTxImT): No such file or directory
> perl 21977 juanfc 85r VREG stat(/
> private/tmp/iVMuHYGpdD): No such file or directory
> perl 21977 juanfc 86r VREG stat(/
> private/tmp/TYpIJ0XS5r): No such file or directory
> perl 21977 juanfc 87r VREG stat(/
> private/tmp/Fm8AGy6o9J): No such file or directory
> perl 21977 juanfc 88r VREG stat(/
> private/tmp/J4gj6DGGVI): No such file or directory
> perl 21977 juanfc 89r VREG stat(/
> private/tmp/Q0dKLWOJwc): No such file or directory
> perl 21977 juanfc 90r VREG stat(/
> private/tmp/N3D1bRmMyw): No such file or directory
> perl 21977 juanfc 91r VREG stat(/
> private/tmp/UajHqmaUDM): No such file or directory
> perl 21977 juanfc 92r VREG stat(/
> private/tmp/4JYJIScAdA): No such file or directory
> perl 21977 juanfc 93r VREG stat(/
> private/tmp/f6EBKb9nw9): No such file or directory
> perl 21977 juanfc 94r VREG stat(/
> private/tmp/IRuBwvfHMS): No such file or directory
> perl 21977 juanfc 95r VREG stat(/
> private/tmp/kxJdU1yPB9): No such file or directory
> perl 21977 juanfc 96r VREG stat(/
> private/tmp/m1C5ffIUVF): No such file or directory
> perl 21977 juanfc 97r VREG stat(/
> private/tmp/gcVcrpYtoT): No such file or directory
> perl 21977 juanfc 98r VREG stat(/
> private/tmp/NY19yFrBZs): No such file or directory
> perl 21977 juanfc 99r VREG stat(/
> private/tmp/mzFibP1FqR): No such file or directory
> perl 21977 juanfc 100r VREG stat(/
> private/tmp/oUZRAW6h3l): No such file or directory
> perl 21977 juanfc 101r VREG stat(/
> private/tmp/3zErWi27lP): No such file or directory
> perl 21977 juanfc 102r VREG stat(/
> private/tmp/5wrMPduqip): No such file or directory
> perl 21977 juanfc 103r VREG stat(/
> private/tmp/O5rhMCu28A): No such file or directory
>
>
>
> Please, help.
>
>
> --
> Juan Falgueras
> Profesor del Depto. de Lenguajes y Ciencias de la Computación
> Universidad de Málaga
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
--
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: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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