AMBER Archive (2009)

Subject: Re: [AMBER] pmemd installation in intelmpi

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Feb 05 2009 - 02:38:38 CST

Thanks for your kind help.
The PMEMD can be installed without any error.

Regards
Vijay

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com

--- On Thu, 5/2/09, Robert Duke <rduke_at_email.unc.edu> wrote:

> From: Robert Duke <rduke_at_email.unc.edu>
> Subject: Re: [AMBER] pmemd installation in intelmpi
> To: vjrajamany_at_yahoo.com, "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Thursday, 5 February, 2009, 12:34 PM
> I think you can just use the configure for pmemd 10 along
> with the intel mpi config_dat file (stuff attached).
> So do the following (assuming you have set the AMBERHOME
> envt variable correctly):
>
> 1) cd $AMBERHOME/src/pmemd
> 2) mv configure configure.9 (so you don't blow away the
> configure script for pmemd that shipped with amber 9)
> 3) mv the file "configure" provided here to
> $AMBERHOME/src/pmemd
> 4) mv the file "interconnect.intelmpi" to
> $AMBERHOME/src/pmemd/config_data
> 5) cd $AMBERHOME/src/pmemd
> 6) ./configure -help
> 7) follow the directions; even though this is an sgi
> machine, it will probably install as a linux_em64t with an
> ifort compiler.
> 8) if it doesn't work, thoroughly read and follow
> $AMBERHOME/src/pmemd/README
>
> Good luck; without having an exact copy of your system
> available, I can't be sure of what further grief, if any
> you might encounter.
>
> - Bob Duke
>
> ----- Original Message ----- From: "Vijay Manickam
> Achari" <vjrajamany_at_yahoo.com>
> To: <AMBER_at_ambermd.org>
> Cc: "Shan" <shan.veloo_at_aldrix.net>
> Sent: Wednesday, February 04, 2009 10:16 PM
> Subject: [AMBER] pmemd installation in intelmpi
>
>
> Dear experts
>
> We are trying to configure PMEMD in amber9 in SGI HPC
> machine running on intel Xeon X86_64. As per seen, there are
> no options to configure with intelmpi, xeon in the
> ./configure script. FYI, Intel MPI and Intel MKL are
> installed as well. Please let us know the best option for us
> to configure this. Then upon your suggestion, we will post
> any error messages if there is later.. Thanks.
>
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana_at_gmail.com
>
>
>
>
>
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