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-   -   BFAST malloc error (http://seqanswers.com/forums/showthread.php?t=16773)

CS Student 01-11-2012 11:12 AM

BFAST malloc error
 
Hi,

I am getting the below memory corruption error when trying to run BFAST on a 4GB RAM machine.

Could you please advise?

Thanks.
=========================================

*** glibc detected *** bfast: malloc(): memory corruption: 0x097f80a8 ***
======= Backtrace: =========
/lib/i686/nosegneg/libc.so.6[0x472dbc]
/lib/i686/nosegneg/libc.so.6(__libc_malloc+0x85)[0x473f95]
/lib/i686/nosegneg/libc.so.6(vasprintf+0x23)[0x469753]
/lib/i686/nosegneg/libc.so.6(asprintf+0x2e)[0x44f03e]
/lib/i686/nosegneg/libc.so.6(__assert_fail+0xba)[0x42b2ba]
bfast[0x8062baa]
bfast[0x8064080]
bfast[0x806f4d5]
bfast[0x8071038]
bfast[0x8078470]
bfast[0x807d7ef]
/lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x41edec]
bfast[0x8049421]
======= Memory map: ========
003eb000-00405000 r-xp 00000000 ca:01 526533 /lib/ld-2.5.so
00405000-00406000 r-xp 00019000 ca:01 526533 /lib/ld-2.5.so
00406000-00407000 rwxp 0001a000 ca:01 526533 /lib/ld-2.5.so
00409000-00549000 r-xp 00000000 ca:01 526534 /lib/i686/nosegneg/libc-2.5.so
00549000-0054b000 r-xp 00140000 ca:01 526534 /lib/i686/nosegneg/libc-2.5.so
0054b000-0054c000 rwxp 00142000 ca:01 526534 /lib/i686/nosegneg/libc-2.5.so
0054c000-0054f000 rwxp 0054c000 00:00 0
00557000-0057c000 r-xp 00000000 ca:01 526536 /lib/i686/nosegneg/libm-2.5.so
0057c000-0057d000 r-xp 00024000 ca:01 526536 /lib/i686/nosegneg/libm-2.5.so
0057d000-0057e000 rwxp 00025000 ca:01 526536 /lib/i686/nosegneg/libm-2.5.so
00580000-00593000 r-xp 00000000 ca:01 526543 /lib/i686/nosegneg/libpthread-2.5.so
00593000-00594000 r-xp 00012000 ca:01 526543 /lib/i686/nosegneg/libpthread-2.5.so
00594000-00595000 rwxp 00013000 ca:01 526543 /lib/i686/nosegneg/libpthread-2.5.so
00595000-00597000 rwxp 00595000 00:00 0
005fb000-0060d000 r-xp 00000000 ca:01 693408 /usr/lib/libz.so.1.2.3
0060d000-0060e000 rwxp 00011000 ca:01 693408 /usr/lib/libz.so.1.2.3
0061b000-00626000 r-xp 00000000 ca:01 526548 /lib/libgcc_s-4.1.2-20080102.so.1
00626000-00627000 rwxp 0000a000 ca:01 526548 /lib/libgcc_s-4.1.2-20080102.so.1
00648000-00658000 r-xp 00000000 ca:01 700448 /usr/lib/libbz2.so.1.0.3
00658000-00659000 rwxp 0000f000 ca:01 700448 /usr/lib/libbz2.so.1.0.3
08048000-08094000 r-xp 00000000 ca:01 692332 /usr/local/bin/bfast
08094000-08096000 rwxp 0004b000 ca:01 692332 /usr/local/bin/bfast
097ed000-0985f000 rwxp 097ed000 00:00 0
aff00000-aff21000 rwxp aff00000 00:00 0
aff21000-b0000000 ---p aff21000 00:00 0
b0003000-b2004000 rwxp b3f8a000 00:00 0
b204a000-b7fa1000 rwxp b204a000 00:00 0
b7fa5000-b7fa9000 rwxp b7fa5000 00:00 0
b7fa9000-b7faa000 r-xp b7fa9000 00:00 0 [vdso]
bfba6000-bfbbb000 rw-p bfba6000 00:00 0 [stack]

nilshomer 01-11-2012 05:16 PM

Could you try to find a small test case so we can debug, or run it in gdb and identify the line in the source code? Tell us your environment and other variables.


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