AMBER Archive (2009)

Subject: Re: [AMBER] Asking help for parallel installation of Amber9

From: David Watson (
Date: Wed Nov 18 2009 - 07:23:17 CST

On Nov 18, 2009, at 7:00 AM, nicholus bhattacharjee wrote:

> Dear David,
> Thanx for your help. But I am unable to understand much
> of your suggestions. Can you please elaborate. I am not much pro in linux.

OK, I take from your previous message that you successfully compiled Amber in serial with ifort.
Some time before this happened you must have run the script.
I don't know where your intel compilers are installed, but usually they are in /opt/intel/.
If you have updated with newer intel fortran releases, these will be found along with your initial ifort installation in subdirectories of /opt/intel/ such as
In my case, I would then run the command
    . /opt/intel/Compiler/11.0/074/bin/
and then I would receive a warning that I didn't specify the architecture of my computer.
In that case, I would run it again with the appropriate architecture for my computer (yours will likely be ia32)
    . /opt/intel/Compiler/11.0/074/bin/ intel64

Once this is done, you can go ahead with the amber9
    make parallel
instructions. But, since you have gone through the trouble of installing intel fortran, you also have the MKL headers installed, so why not take advantage of them?
You will find them in some other location than I will, but you will need to run a script to set up your MKL environment properly.
For me, this is done by running
    . /Library/Frameworks/Intel_MKL.framework/Versions/Current/tools/environment/
and setting MKL_HOME for amber9 by
    export MKL_HOME=/Library/Frameworks/Intel_MKL.framework/Versions/Current

You are using a different operating system and apparently the ia32 architecture, and so the details of which script to use are up to you.
Again, you don't have to set MKL_HOME or run the mklvars*sh script in order to successfully compile amber9, but some have suggested that certain amber routines run more efficiently if you do.

On another related note, if you try to
    su root
in order to compile amber9, you will lose all of these environment settings, so you may want to 'su root' before running the other scripts.

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