[gmx-users] errors due to genbox

[Mark Abraham]

On 09/21/09, wuxiao  <xiaowu759 at hotmail.com> wrote:
> 
> 
> .hmmessage P{margin:0px;padding:0px}body.hmmessage{font-size: 10pt;font-family:Verdana}
> 
> Dear GMXers,
>    I try to generate gro file using genbox, but fail with some errors. Command lines are:
>    genbox -ci B.gro -o Bb.gro -nmol 200 -box 3 3 3
>    where B.gro is the coordinate file of vinyl alcohol residue.
>    The errors are given as bellows. Please give me some hints to cope with these problem. Thanks a lot for any reply.
>  
>    Sincerely,
>    Chaofu Wu
>  
> ........
>     success (now 1400 atoms)!
> 
All the following material is being generated by the operating system in response to some failure of GROMACS in allocating memory, or such. Providing more of the text before here may help developers assess what you're doing wrong.

Mark

> 
> 
> *** glibc detected *** genbox: realloc(): invalid old size: 0x083e6a70 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0xb7db8cb1]
> /lib/libc.so.6[0xb7dbb928]
> /lib/libc.so.6(__libc_realloc+0x100)[0xb7dbca40]
> genbox[0x815bd6c]
> ======= Memory map: ========
> 08048000-083d2000 r-xp 00000000 08:09 358678     /usr/local/gromacs/bin/genbox
> 083d2000-083d9000 rwxp 00389000 08:09 358678     /usr/local/gromacs/bin/genbox
> 083d9000-21bc3000 rwxp 083d9000 00:00 0          [heap]
> b7c00000-b7c21000 rwxp b7c00000 00:00 0
> b7c21000-b7d00000 ---p b7c21000 00:00 0
> b7d50000-b7d51000 rwxp b7d50000 00:00 0
> b7d51000-b7d53000 r-xp 00000000 08:09 17118      /lib/libdl-2.4.so
> b7d53000-b7d55000 rwxp 00001000 08:09 17118      /lib/libdl-2.4.so
> b7d55000-b7e70000 r-xp 00000000 08:09 17112       /lib/libc-2.4.so
> b7e70000-b7e72000 r-xp 0011a000 08:09 17112      /lib/libc-2.4.so
> b7e72000-b7e74000 rwxp 0011c000 08:09 17112      /lib/libc-2.4.so
> b7e74000-b7e77000 rwxp b7e74000 00:00 0
> b7e77000-b7f6b000 r-xp 00000000 08:09 33645      /usr/X11R6/lib/libX11.so.6.2
> b7f6b000-b7f6e000 rwxp 000f4000 08:09 33645      /usr/X11R6/lib/libX11.so.6.2
> b7f6e000-b7f6f000 rwxp b7f6e000 00:00 0
> b7f6f000-b7f84000 r-xp 00000000 08:09 33639      /usr/X11R6/lib/libICE.so.6.4
> b7f84000-b7f85000 rwxp 00014000 08:09 33639      /usr/X11R6/lib/libICE.so.6.4
> b7f85000-b7f87000 rwxp b7f85000 00:00 0
> b7f87000-b7f8f000 r-xp 00000000 08:09 33641      /usr/X11R6/lib/libSM.so.6.0
> b7f8f000-b7f90000 rwxp 00007000 08:09 33641      /usr/X11R6/lib/libSM.so. 6.0
> b7f90000-b7fb3000 r-xp 00000000 08:09 17120      /lib/libm-2.4.so
> b7fb3000-b7fb5000 rwxp 00022000 08:09 17120      /lib/libm-2.4.so
> b7fb5000-b7fc6000 r-xp 00000000 08:09 17123      /lib/libnsl-2.4.so
> b7fc6000-b7fc8000 rwxp 00010000 08:09 17123      /lib/libnsl-2.4.so
> b7fc8000-b7fca000 rwxp b7fc8000 00:00 0
> b7fd6000-b7fe2000 r-xp 00000000 08:09 331626     /usr/local/lib/libgcc_s.so.1
> b7fe2000-b7fe3000 rwxp 0000c000 08:09 331626     /usr/local/lib/libgcc_s.so.1
> b7fe3000-b7fe5000 rwxp b7fe3000 00:00 0
> b7fe5000-b7fff000 r-xp 00000000 08:09 17105      /lib/ld-2.4.so
> b7fff000-b8001000 rwxp 0001a000 08:09 17105      /lib/ld-2.4.so
> bffb3000-bffca000 rwxp bffb3000 00:00 0          [stack]
> ffffe000-fffff000 ---p 00 000000 00:00 0          [vdso]
> Aborted
> 
> 
> 
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