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 <[email protected]>
To: [email protected]
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 installationprocess 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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