Hi,
Just out of curiosity (especially for Guille): did you run amber on one of
the NCSA's machines? I'd like to know this since it might be useful for
other Amber users at NCSA. We have 64 bit version of Amber on both SGI
Origin and IBM p690 machines.
thanks,
--Dodi
http://www.ncsa.uiuc.edu/~dodi
At 11:58 AM 5/13/2003 -0700, Ioana Cozmuta wrote:
>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
> >
> >
Received on Tue May 13 2003 - 21:53:01 PDT
