Not logged in
  • Log in
    Membership (41322+) Group hosting [?] Wiki
    Franklin Award

    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    All information groups
    Online databases Online analysis tools Online education tools More tools

    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1139 ] xace, tace - libraries fail to load; incompatible libraries
    03/27/11 18:32
    Submitted by:
    Assigned to:
    Ticket group:
    xace, tace - libraries fail to load; incompatible libraries
    Original submission:
    On linux-x86_64, and possibly linux-intel, xace and tace require non-standard libraries. This is something we already know, but there's a twist: one of the libraries is /lib/ld-linux, which loads ELF libraries. Even if we add this to the LD_LIBRARY_PATH, the path to /lib is hard-coded into the compiled binary.

    This can be fixed simply by installing in the /lib directory, but that would mean that anyone installing BIRCH would have to have root privileges and know how to do that.

    So to get around this we run xace or tace with a command like

    $BIRCH/lib-linux-x86_64/ $BIRCH/bin-$BIRCH_PLATFORM/xace

    That needs to be added to lbirchdb, l-gbirchdb and birchdb.

    At the same time, there still seem to be some compatibility issues. This is especially a problem on x86_64, which would be trying to read 64-bit binaries from bin-linux-x86_64 when trying to run xace or tace, which are 32-bit programs. The best solution is to create a separate directory called acedb within the lib-linux-x86_64 directory, and add that to the LD_LIBRARY_PATH.

    One consequence of this problem is that during a BIRCH install, tace won't run, so the documentation won't get localized.

    Please log in to add comments and receive followups via email.
    Comment Date By
    The fix was essentially correct for birchdb etc., but for, it had to be:

    $BIRCH/lib-linux-x86_64/acedb32/ --library-path $BIRCHLIBS

    Libraries from a Fedora 12 i686 system were written to
    lib-linux-intel and lib-linux-x86_64 in a directory called
    04/03/11 17:09 B_Fristensky
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    Other tickets that depend on this ticket
    Ticket ID Summary
    1156 birchdb, lbirchdb - can't call xace
    Ticket change history
    Field Old value Date By
    status_id Open 04/03/11 17:56 B_Fristensky
    resolution_id Not Resolved 04/03/11 17:56 B_Fristensky
    close_date 12/31/69 19:00 04/03/11 17:56 B_Fristensky
    status_id Pending 03/27/11 18:33 B_Fristensky
    priority 5 03/27/11 18:33 B_Fristensky
    assigned_to unset 03/27/11 18:33 B_Fristensky
    resolution_id Unset 03/27/11 18:33 B_Fristensky


    Copyright © 2019 · Scilico, LLC