AMBER Archive (2009)

Subject: Re: [AMBER] pmemd installation in intelmpi

From: Robert Duke (
Date: Wed Feb 04 2009 - 22:34:37 CST

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

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

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" <>
To: <>
Cc: "Shan" <>
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,

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