It's my fault,my manual complex.prmtop was wrong.I created a new
complex.prmtop using ante-mmpbsa.
On Sat, Nov 9, 2013 at 6:33 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> For the benefit of users and developers alike, how?
>
> Thanks,
> Hannes.
>
> ________________________________________
> From: David Chen [davidchen.now.gmail.com]
> Sent: 09 November 2013 07:11
> To: jason.swails.gmail.com; AMBER Mailing List
> Subject: Re: [AMBER] help!!! I got a error when I used mmpbsa calculate
> the binding freeenergy
>
> thanks,I have resolved the problem
>
>
> On Wed, Nov 6, 2013 at 10:17 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Wed, 2013-11-06 at 13:51 +0000, Hannes Loeffler wrote:
> > > On Wed, 6 Nov 2013 08:41:31 -0500
> > > Jason Swails <jason.swails.gmail.com> wrote:
> > >
> > > > On Wed, 2013-11-06 at 21:18 +0800, David Chen wrote:
> > > > > I got error message on terminal:
> > > > > mmpbsa_py_energy: malloc.c:2451: sYSMALLOc: Assertion `(old_top ==
> > > > > (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) -
> > > > > __builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0)
> > > > > || ((unsigned long) (old_size) >= (unsigned
> > > > > long)((((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2
> > > > > * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) - 1))) &&
> > > > > ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) ==
> > > > > 0)' failed.
> > > >
> > > > Well that's a strange error message. I'm not sure why malloc would
> > > > raise an error like this in a GB calculation. GB is not very
> > > > memory-intensive, so it's highly unlikely that your machine is
> running
> > > > out of RAM unless you are using a queueing system (torque/PBS, slurm,
> > > > etc.) which has a low memory limit on the job. If this is the case,
> > > > you can try to request more memory and see if that helps.
> > >
> > > I believe that's a hint to memory corruption in whatever code caused
> it.
> >
> > It is being caused in a NAB program. There are a number of subtle ways
> > to break NAB in my experience (relocating it, copying it from one
> > machine to another, etc.). I'm certainly not ruling out a code problem,
> > but based on the available information and past experience, I'm inclined
> > to believe there is a different root cause of the memory corruption.
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
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> >
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Received on Sat Nov 09 2013 - 04:00:03 PST
