[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[Johnny Lu]

I heard that gromacs 4.6.7 is faster when compiled with the newest gnu
compilers and fftw3, than when compiled with intel compilers + mkl.

On Fri, Nov 7, 2014 at 4:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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