[gmx-users] Help with Gromacs-5.1.1 installation in Cluster

Barnett, James W jbarnet4 at tulane.edu
Fri Dec 4 13:39:15 CET 2015

On Fri, 2015-12-04 at 03:32 -0500, Ashalatha Sreshty wrote:
> Dear Gromacs Users,
> I need help with installation of gromacs-5.1.1 which is mpi enabled to run
> it in a cluster. Although, I was able to compile the the source code
> without any errors, I am unable to find the executables in the bin folder.
> Hence, I need your suggestion on how to rectify it. The step-wise commands
> are as below:

I'm guessing you're expecting to see multiple executables like "mdrun",
"grompp", etc.  Anyways, there's one executable now that prefixes every command
(started with 5.0, now required in 5.1). For most installs it is "gmx". For MPI
installs it's probably "gmx_mpi". Do you have one of those? If not, there is a
different issue.

(This question is on the mailing list about once every week or two now, so
perhaps someone with access to the wiki can put this on the FAQ?)

> Compiling fftw library
> tar xvf fftw-3.3.4.tar.gz
> cd fftw-3.3.4
> /configure --enable-threads --with-pic
> --prefix=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4 --enable-sse2
> make
> make install
> Compilation of groamcs-5.1.1
> tar xvf gromacs-5.1.1.tar.gz
> cd gromacs-5.1.1
> mkdir build
> cd build
> CMAKE_PREFIX_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4:/apps/mvapich2-
> cpu/bin/
> CMAKE_INCLUDE_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4/include
> CMAKE_LIBRARY_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4/lib
> /home1/GroupAS/ashalatha/Programs/cmake-3.1.3-Linux-x86_64/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/home1/GroupAS/ashalatha/Programs/gromacs-5.1.1
> -DCMAKE_PREFIX_PATH=/home1/GroupAS/ashalatha/Programs/fftw-3.3.4
> -DREGRESSIONTEST_PATH=/home1/GroupAS/ashalatha/Programs/regressiontests-5.1.1
> make
> make check
> make install
> make test
> Please advice.
> Thank you in advance.
> Dr. M. Asha Latha Sreshty,
> Post Doctoral Fellow,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> Bangalore

James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarnet4 at tulane.edu

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