Changes between Initial Version and Version 2 of Ticket #29131


Ignore:
Timestamp:
Apr 14, 2011, 3:16:55 PM (13 years ago)
Author:
mf2k (Frank Schima)
Comment:

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  • Ticket #29131

    • Property Cc haroldpimentel@… removed
    • Property Owner changed from macports-tickets@… to haroldpimentel@…
    • Property Keywords malloc mmap nomem 64bit removed

  • Ticket #29131 – Description

    initial v2  
    11Running bowtie on an Xserve with 24Gb RAM, aligning against Human reference (build 37/hg19) I get this message:
    22
     3{{{
    34bowtie(16525) malloc: *** mmap(size=716197888) failed (error code=12)
    45*** error: can't allocate region
    56*** set a breakpoint in malloc_error_break to debug
    67Error: Ran out of memory allocating space for the bitpacked reference.  Please re-run on a computer with more memory.
     8}}}
    79
    810I believe this is because the -m64 (or -arch x86_64) parameter needs to be provided during compilation in order for the program to be in 64-bit, rather than 32-bit mode.  The stock version of bowtie from UMD works for me.  Below are the results of --version run on each:
    911
     12{{{
    1013/opt/local/bin/bowtie version 0.12.7
    111432-bit
    … …  
    2326Options: -O3 -m64
    2427Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
    25 
     28}}}