[Bioperl-l] Blast temporary open files not closed
Brian Osborne
osborne1 at optonline.net
Sat Sep 9 13:45:06 UTC 2006
Juan,
I recall a bug like this was fixed a while back - what version Bioperl are
you using? By the way, always give version numbers when reporting a bug, the
answer "already fixed" is very common.
Brian O.
On 9/9/06 4:31 AM, "ende" <mmacho at gmail.com> 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
>
>
>
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