AMBER Archive (2003)

Subject: Re: Increase lastist in the &cntrl namelist

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue May 13 2003 - 13:58:09 CDT

Hi,

You say that you have to deal with a big system so I think that only
increasing the value of lastist or MAX_ISTACK will not help. For system
the size you mention, the allocate command is normally trying to allocate
few GBytes of memory that is simply too much for the 32 bit addressing
space with which the amber7 package was built. [-n32 compiler option vs.
-64; normally 32 bit address space is plenty of address space for small
to medium problems]. Additionally, the MPI library runs out of 32 bit
memory space at about 100 or so MPI processes. So, if you want to do
problems with largish numbers of processors, you'll need to take some more
action.

So you can do the following:
1. Change in Machines/Machine.sgi_mpi all the -n32 compile
   options with -64.

2. Modify the mm_pbsa/Makefile to add a default compile line
   for C modules. Otherwise, it used the default C compile which used
   -n32.

The LEaP X11 utility is still built with -n32. Since this
is a GUI setup utility, I didn't switch it to use -64.
Then
cd amber7/src
rm -fr ../exe
make clean |& tee clean.out
make install |& tee install.out

THis is what I did in amber7 on an IRIX system.

Hope it is of help,
Ioana

On Tue, 13 May 2003, GUILLERMINA L ESTIU wrote:

>
> Hi,
> I am trying to run sander (minimization) (amber7) for a sistem of 50000
> residues (180000 atoms)
> In the first run I am minimizing only the solvent water molecules.
>
> The minimization stops with a message "Exceeding lastist in get_istack"
> The message belongs to istak.f subruitine. But it is not clear to me, if I have
> fo Increase MAX_ISTACK in sizes.h and recompile, or there is a variable
> "lastist" which I can handle from the input.
>
> Thanks
> Guille
> Dr Guillermina Estiu
> Chemistry Department
> Pennsylvania State University
> PA 16802
>
>