[Bioperl-l] Blast temporary open files not closed

Brian Osborne osborne1 at optonline.net
Sat Sep 9 09:45:06 EDT 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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