[gmx-users] Error with editconf 4.0

Berk Hess gmx3 at hotmail.com
Thu Nov 6 11:07:18 CET 2008 

Hi,



That is another small bug in the 4.0 release.

I had already fixed this for 4.0.1.



Berk


> Date: Wed, 5 Nov 2008 17:19:34 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Error with editconf 4.0
> 
> 
> Hi all,
> 
> I was trying to dump out a .gro file from a .tpr under Gromacs 4.0, but editconf 
> gave a Segmentation Fault.  The complete output is below:
> 
> editconf -f npt.tpr -o in.gro
> 
> <snip>
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
>           this can deviate from the real mass of the atom type
> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
>           this can deviate from the real mass of the atom type
> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 31
> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading file npt.tpr, VERSION 4.0 (single precision)
> Reading file npt.tpr, VERSION 4.0 (single precision)
> editconf(12411) malloc: *** error for object 0x1006e00: incorrect checksum for 
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x100ce00: incorrect checksum for 
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x9070b0: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x1002400: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x100ce00: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x907330: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x907ad0: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x907ba0: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x907c40: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x130000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> Read 138271 atoms
> Volume: 1701.6 nm^3, corresponds to roughly 765700 electrons
> Velocities found
> editconf(12411) malloc: *** error for object 0x100ce00: incorrect checksum for 
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> editconf(12411) malloc: *** error for object 0x907c50: incorrect checksum for 
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> Segmentation fault
> 
> No output is generated, obviously.  Interestingly, if I issue the same command 
> with editconf 4.0 on a .tpr file generated under Gromacs 3.3.3, I get the following:
> 
> <snip>
> 
> Reading file npt.tpr, VERSION 3.3.3 (single precision)
> Reading file npt.tpr, VERSION 3.3.3 (single precision)
> editconf(12421) malloc: *** error for object 0x2316000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0xf8c000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x27d6000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x2cee000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x296e000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x29f6000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x2bde000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x1006a00: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0xfb4000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x2c34000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x180000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0xfdd000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x2c66000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x2ca1000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x1002400: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x9071c0: double free
> *** set a breakpoint in malloc_error_break to debug
> editconf(12421) malloc: *** error for object 0x2d24000: pointer being freed was 
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> Read 138271 atoms
> Volume: 2001.49 nm^3, corresponds to roughly 900600 electrons
> Velocities found
> 
> gcq#163: "If You Don't Like Cool Quotes Check Your GMXRC File" (Your Sysadmin)
> 
> The result is that in.gro is generated from the 3.3.3 .tpr file.  Any ideas 
> what's going on?
> 
> Thanks,
> Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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