AMBER Archive (2001)

Subject: Re: shared memory

From: David Konerding (dek_at_cgl.ucsf.edu)
Date: Fri Jul 06 2001 - 11:26:43 CDT

Daniel GENEST writes:
>Hi,
>I use the serial version of sander (AMBER 5.0) on individual pc's runing
>with pentium III processors under linux. Each pc is bi-processors and I
>would like to run a parallelized version of sander using both processors on
>a single pc. However the pc works on shared memory mode and we could not
>compile the corresponding version of sander. As I see on the AMBER site
>this version is available only for CRAY or SGI. We tried to use the MPI
>version, it worked but time saving was only 30 per cent. Can we do
>something or can we expect a shared memory version for pentium III or
>pentium 4 under linux in the near future ?
>thank you,
>Daniel Genest

AMBER has pretty much switched almost entirely over to MPI-based message passing.
You can compile MPICH to support shared memory, however, this has always been
buggy for me. There is another freely available MPI library called LAM, which
I believe also supports shared-memory MPI transport. There is also a commercial
MPI implementation MPI/PRO, I don't know if it supports shared-memory yet
(last I used it, it didn't).

There are probably several other professional MPI implementations that work on
Linux, but I don't know what they are or what they support.

Dave