AMBER Archive (2004)

Subject: Re: AMBER: Problems in Amber MPI version (64 bits machine)

From: Haijun Yang (
Date: Wed Jun 23 2004 - 12:33:49 CDT

Hi, Dr. Case:

 Thanks for your immediately reply!

 We successfully compiled the AMBER7 using MPICH_GM MPI and G77 compiler on
AMD 64 OPTERON (Suse OS) system. And it can run some benchmark jobs well.
At the same time, we can run another GB job smoothly . We didn't use
configure (this is for AMBER8?).

The weird thing is that: when we recompiled AMBER7 using MPICH and G77 on
this X86-64 system, and ran benchmark jobs, for all benchmark jobs, it is
okay if we used 1 cpu ( "mpirun -np 1 ../../sander ....."). But if we used
2 cpus, gb_mb could go through, and other benchmark jobs failed due to the
exceeding of vlimit (like my original post).

 Can you explain the problem which is normally due to high VDW energy? Is
it due to MPI system?

 Many thanks in advance!


----- Original Message -----
From: "David A. Case" <>
To: <>
Sent: Tuesday, June 22, 2004 8:31 PM
Subject: Re: AMBER: Problems in Amber MPI version (64 bits machine)

> On Tue, Jun 22, 2004, Haijun Yang wrote:
> > I just compiled Amber MPI version for 64 bits machine.
> >
> >
> > But I can run with the exact restart file using single CPU at the same
> > bits machine, and it works fine. Also I can run with MPI version at
> > machine. (32 bits)
> You don't say much about what kind of machine you have, and so on. But as
> a guess, don't use the "-big" flag with configure. An incompatibility
> between that flag and your MPI library can easily occur. Without more
> information, I don't think anyone can be of much help.
> ...dac

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