[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[suresh kannan]

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

I have also searched google. see this example link for building gromacs. Be
aware this is just an example for their requirement you have to chose for
your requirement. Hope this helps.

http://flakrat.blogspot.kr/2013/04/how-to-compile-gromacs-461-with-openmpi.html


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

You said you are in university. I suggest you to take help from some one
from your university.

<https://mail.google.com/mail/u/0/?ui=2&ik=4d6c0a5051&view=att&th=149643f024d7d537&attid=0.1&disp=safe&realattid=f_i1wzdfrg0&zw>

On Sat, Nov 8, 2014 at 7:00 AM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> 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
> icc.
>
> 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
> Cc:
> 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 -
> > DCMAKE_INSTALL_PREFIX=/work/user/GROMACS
> > 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.
>
> -Justin
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
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