AMBER Archive (2004)

Subject: Re: AMBER: memory problem in NMODE

From: xhu1_at_memphis.edu
Date: Mon Apr 19 2004 - 18:43:47 CDT

Dear David Case,

Thank you very much for your reply.

Yes, when a protein has 10 residues, 184 atoms, it works under the
original parameter(MAXMEMX=15000000), because the required memory for
real words is just 467183. When a protein has more than 20 residues,
346 atoms, it doesn't work under the original parameter. The output
stopped at "increase the real memory by xxxxxxxxx words"

the sysinfo about "limit" as following

cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked unlimited
maxproc 7168

My workstation has dual intel xeon 3.06G CPU,and the OS is redhat 9.0

Thanks again

All the best

Shawn

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Monday, April 19, 2004 4:54 pm
Subject: Re: AMBER: memory problem in NMODE

> On Mon, Apr 19, 2004, xhu1_at_memphis.edu wrote:
> >
> > I am doing normal mode analysis of protein by nmode of amber 7.
> The
> > protein has 198 residues(1520 atoms). I got a memory problem:
> >
> > >Total memory required : 132758715 real words
> > >Total memory avail : 15000000 real words
> > >Total memory required : 202865 integer words
> > >Total memory avail : 4000000 integer words
> >
> > >Maximum nonbond pairs 3797134
> > >increase the real memory by 117758715 words
> >
> > I increased the real memory to 140000000 at sizes.h file, and
> tried
> > again. This time I got "Segmentation fault...(core dumped)".
>
> Was there any output? Do smaller problems work on your system?
>
> Check your shell limits (use the "limits" command). You may have
> to
> invoke commands like
>
> limit datasize unlimited
> limit memoryuse unlimited
>
> (These are just guesses since you don't say what cpu or operating
> systemyou are using....)
>
> ...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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