From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Mon Feb 02 2009 - 23:26:34 CST
Hi Jose,
You are allocating an atomselection within the loop without deleting it -
atomselections take up memory so if you have to make a lot of them you
should delete them with $sel delete after you're done.
Also, there's a vmd mailing list that is better suited to vmd questions -
this one is mainly intended for namd questions.
-Grace
On Mon, Feb 2, 2009 at 10:31 PM, <fett_at_vtr.net> wrote:
>
> Dear NAMD VMD developers:
>
> I have made a tcl script for analyzing two dcd files at the same time ( a
> trajectorie file and a velocity file), I have run the script in 16gb RAM
> computer but at some point the script always crashes, if I run the same
> script in my mac (2GB of RAM) I am getting the following error:
> vmd_MACOSXX86(1476,0xa040c720) malloc: *** mmap(size=36864) failed (error
> code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> vmd_MACOSXX86(1476,0xa040c720) malloc: *** mmap(size=28672) failed (error
> code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> vmd_MACOSXX86(1476,0xa040c720) malloc: *** mmap(size=32768) failed (error
> code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): St9bad_alloc
> Abort trap
>
> If you could give some hint about it, it would be great, I have attached
> the tcl script so you can look at it.
>
>
> Regards
>
> Jose Antonio
> PhD student
>
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