AMBER Archive (2003)

Subject: Re: AMBER: a problem with memory size

From: David A. Case (case_at_scripps.edu)
Date: Sun Nov 16 2003 - 16:49:30 CST

On Sun, Nov 16, 2003, Ye Mei wrote:
>
> I met a problem with memory size. In my job, lastist = 36283950 is needed.
> But when I increase lastist to 37000000, it failed with Segmentation
> fault(core dump). My computer is XEON 1.8G with 1GB memory. And OS is
> SuSE8.2. Does anyone know how to solve it?

> The following is the error message in mdout.
> Exceeding lastist in get_istack
> lastist = 30000000
> top_stk= 18497700
> isize = 17786250
> request= 36283950
> Increase MAX_ISTACK in sizes.h and recompile
> ????????????
>

You are using a static-memory version of sander (i.e. without -DMEM_ALLOC
set when you compiled.) This means that the value of lastist you enter
is not used. As the message above indicates, you need to edit sizes.h
and recompile.

Given the message above, I have no idea why you should get a core dump: that
message should lead to a graceful error exit, with no segmentation faults.
But try to changes the sizes.h file and see if that helps.

..good luck...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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu