[Bioperl-l] Blast temporary open files not closed

Hilmar Lapp hlapp at gmx.net
Sat Sep 9 08:16:05 EDT 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
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================








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