AMBER Archive (2008)

Subject: Re: AMBER: Nmode segmentation fault

From: James Thomas (james.protein_at_googlemail.com)
Date: Tue Mar 25 2008 - 14:00:44 CDT

The input file:
&data
     ntrun=4,
     nsave=2,
     ndiag=2,
     cut=95.0,
     nprint=100,
     drms=0.00001,
     maxcyc=100,
     bdwnhl=0.01,
     dfpred=0.1,
     scnb=2.0,
     scee=2.0,
     nvect=200,
     ntxo=1,
 &end

The machine:
I run it on Opteron-based compute cluster, it has a head node with dual
Opteron 246 CPUs, 4GB RAM and mirrored 160GB SATA disks.
The OS is SuSE Linux 9.3

Thanks a lot!

On Tue, Mar 25, 2008 at 6:44 PM, David A. Case <case_at_scripps.edu> wrote:

> On Tue, Mar 25, 2008, James Thomas wrote:
> >
> > Test protein: 1382 atoms (successful)
> > Interest protein: 5780 atoms (segmentation fault error)
> >
> > I did not do any CG minimisation before starting NR.
> >
> > I look forward to your advice on how to solve the segmentation fault
> problem
>
> No real advice. You have to check how much memory you have on your
> system,
> but nmode should report an allocation failure, not a segfault even in that
> case. But the error checking for allocation failures might not be robust,
> and it could be that you just have a lack of memory.
>
>
> For 5780 atoms, you will need (5780*3)*(5730*3)*8 = 2.4 Gbytes of
> available
> memory. But you haven't give much to go on: we don't know what sort of
> job
> you are running (i.e. ntrun), the type of machine, and so on.
>
> ...dac
>
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