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 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
