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.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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Received on Fri Apr 18 2008 - 21:13:59 PDT
