[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Nov 7 23:00:34 CET 2014

Dear Users

1 . I am not sure as to how to set the full path in the cmake command line.
Do I need to use the export command to set the path ?

An example will be of great help. I am also searching the web but can not
find a satisfactory answer.

As highlighted in my step 5 ( trailing mail ) , I think install_prefix will
install the gromacs version in the specified directory or am I wrong ?

2. Yes , I understand it after reading the instructions. I think mdrun will
pick up MPI threading automatically.

I have also installed FFTW 3.0 in a local folder , how do I set its path in
the cmake command line and I also have gcc in the root folder , along with

Pardon my ignorance as I think these are very basic questions related to
the linux architecture.

---------- Forwarded message ----------
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Date: Fri, 07 Nov 2014 16:26:56 -0500
Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

On 11/7/14 4:20 PM, Agnivo Gosai wrote:

> Dear Users
> I checked and found that the CMAKE version installed in my university
> cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher.
> So I installed CMAKE 2.8.11 in my local work directory :
> /work/user/GROMACS/cmake-2.8/bin/cmake
> Now I want to use Intel MKL , so after reading the GROMACS installation
> instruction I have decided to use the following workflow :-
> 1.  tar xfz gromacs-4.6.7.tar.gz
> 2. cd gromacs-4.6.7
> 3. mkdir build
> 4. cd build
> 5. cmake .. -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -
> 6. make
> 7. make install
> Now when I check install location of CMAKE it points to the old version
> located in the Cluster root directory.
> Now , I want to use the new version which I believe to have installed
> correctly. So please help in solving this problem.
Specify the full PATH of your cmake, otherwise the environment will just
pick up the default cmake on the cluster.

 Also I would request the users to check my workflow of the installation
> process and provide suggestions.

There is no point in compiling the whole suite of tools with MPI; nothing
makes use of MPI except mdrun.  So if you want to compile all the tools
(preprocessing and analysis), don't set GMX_MPI.  If you are using GMX_MPI,
then set -DGMX_BUILD_MDRUN_ONLY=ON to get MPI-enabled mdrun.  Strictly
speaking, MPI is not required, but it depends on what you want to do
whether or not you need it.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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