AMBER Archive (2008)

Subject: Re: AMBER: Amber 10 on the BlueGene

From: Carlos Simmerling (
Date: Mon Jul 28 2008 - 13:37:59 CDT

also update your compilers, we had a compiler bug on our BG that
caused the compiler to segfault just during a sander build. works ok now.

On Mon, Jul 28, 2008 at 1:17 PM, Robert Duke <> wrote:
> I think the pmemd config stuff for pmemd 9 should work for pmemd 10 for BG/L
> - Ross and I both have some config info posted there; mine was for an IBM
> bluegene facility, Ross' was for the bluegene at SDSC. These may not be
> absolutely correct for your installation, but should provide you with a
> good starting point (this is under "Tips for running Amber 8 or 9 on various
> architectures").
> Best Regards - Bob Duke
> ----- Original Message -----
> From: Mike Hanby
> To:
> Sent: Monday, July 28, 2008 12:15 PM
> Subject: AMBER: Amber 10 on the BlueGene
> Has anyone compiled Amber 10 (I guess pmemd to be precise) for the Blue
> Gene, and if so wouldn't mind sharing the config file and instructions?
> Also, I've read a thread or two about the difficulties of getting NetCDF
> support built into the Blue Gene binary, has anyone had any success with
> this? My Amber users are reluctant to use bintraj for their non Blue Gene
> jobs if the BGL will have to use the old format.
> Thanks for any help,
> Mike

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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