[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[Justin Lemkul]

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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