On 1/16/2013 11:41 AM, Kirill Nuzhdin wrote:
> $AMBERHOME/bin/sander.LES.MPI -O -i Rqspcfw.LES.in -p Rqspcfw.LES.prmtop
> -c Rqspcfw.LES.inpcrd -o Rqspcfw.LES.out -r Rqspcfw.LES.rst -x
> Rqspcfw.LES.crd -v Rqspcfw.LES.vel -inf Rqspcfw.LES.info -e
> Rqspcfw.LES.ext > sander_Rqspcfw.LES.out
>
> here is another problem: sander stops with the following error:
> --------------------------------------------
> * NB pairs 229 213708 exceeds capacity ( 213809) 6
> SIZE OF NONBOND LIST = 213809
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
> --------------------------------------------
>
> OK, there is probably too much of local enhancement (that is strange,
> could that be avoided without recompiling the program?), trying to run
> with smaller numbers:
> --------------------------------------------
> space numc=32 pick chem prtc H done
> space numc=8 pick chem prtc H1 | chem prtc H2 done
> --------------------------------------------
>
> In that case it was crushing with segfault:
> --------------------------------------------
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> --------------------------------------------
>
> So I thought that this could happen because the system is far from
> equilibrium, and decided to equilibrate the system before the nuclei
> quantization. That is how the question about classical simulation arose.
>
> As for "exploding", maybe you are right about failure to image the
> resulting trajectory back to the primary unit cell. I'm not very
> familiar with how that could be done - where can I find the information
> about that?
>
> Right now I think I found the reason for the last crush: it looks like
> addles starts to generate LES configuration with all beads for each
> quantized nucleus with the same coordinates! When I tried it on a very
> simple system it was creating beads with small variation in coordinates
> (as I think it should). So now I'm trying to understand what had changed
> since then.
I tried to vary coordinates of the addles prepared file manually (+-0.1
A), but I'm getting the same error
--------------------------------------------
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.LES 000000000054E910 Unknown Unknown Unknown
sander.LES 00000000005423F2 Unknown Unknown Unknown
sander.LES 00000000004FF21A Unknown Unknown Unknown
sander.LES 00000000004B1D71 Unknown Unknown Unknown
sander.LES 00000000004EA194 Unknown Unknown Unknown
sander.LES 000000000048B508 Unknown Unknown Unknown
sander.LES 00000000004860CB Unknown Unknown Unknown
sander.LES 000000000040328C Unknown Unknown Unknown
libc.so.6 00000036C881D994 Unknown Unknown Unknown
sander.LES 0000000000403199 Unknown Unknown Unknown
--------------------------------------------
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Received on Wed Jan 16 2013 - 12:00:02 PST
