Opened 10 years ago

Closed 9 years ago

#29131 closed defect (fixed)

bowtie does not obey build_arch

Reported by: pchines@… Owned by: haroldpimentel@…
Priority: Normal Milestone:
Component: ports Version: 1.9.2
Keywords: Cc:
Port: bowtie

Description (last modified by mf2k (Frank Schima))

Running bowtie on an Xserve with 24Gb RAM, aligning against Human reference (build 37/hg19) I get this message:

bowtie(16525) malloc: *** mmap(size=716197888) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error: Ran out of memory allocating space for the bitpacked reference.  Please re-run on a computer with more memory.

I 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:

/opt/local/bin/bowtie version 0.12.7
32-bit
Built on zeus.nhgri.nih.gov
Tue Apr 12 10:33:33 EDT 2011
Compiler: gcc version 4.0.1 (Apple Inc. build 5490)
Options: -O3
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 4, 8, 4, 4, 8}

/usr/local/bin/bowtie version 0.12.7
64-bit
Built on Franklin.local
Tue Sep  7 14:27:57 PDT 2010
Compiler: gcc version 4.0.1 (Apple Inc. build 5493)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Change History (4)

comment:1 Changed 10 years ago by pchines@…

Cc: pchines@… added

Cc Me!

comment:2 Changed 10 years ago by mf2k (Frank Schima)

Cc: haroldpimentel@… pchines@… removed
Description: modified (diff)
Keywords: malloc mmap nomem 64bit removed
Owner: changed from macports-tickets@… to haroldpimentel@…

comment:3 Changed 10 years ago by jmroot (Joshua Root)

Summary: bowtie cannot align to large genomesbowtie does not obey build_arch

What OS are you running? 10.5? I assume you have build_arch set to x86_64 in macports.conf?

comment:4 Changed 9 years ago by jmroot (Joshua Root)

Resolution: fixed
Status: newclosed
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