Adk44: Created page with "* Download GMX (gromacs-4.5.4.tar.gz [http://www.gromacs.org/Downloads]) and FFTW ( fftw-3.2.2.tar.gz [http://www.fftw.org/download.html]) source codes and extract in ~/SW..."

2019-05-13T10:38:38Z

Created page with "* Download GMX (gromacs-4.5.4.tar.gz [http://www.gromacs.org/Downloads]) and FFTW ( fftw-3.2.2.tar.gz [http://www.fftw.org/download.html]) source codes and extract in ~/SW..."

New page

* Download GMX (gromacs-4.5.4.tar.gz [http://www.gromacs.org/Downloads]) and FFTW ( fftw-3.2.2.tar.gz [http://www.fftw.org/download.html]) source codes and extract in ~/SW

* '''FFTW 3.2.2'''
<pre>
cd ~/SW/fftw-3.2.2
./configure --prefix=/home/ss2029/SWins/fftw --enable-threads --enable-shared
make
make install
</pre>

GMX installation later fails if "--enable-shared" flag is not used.

Following files should be created in ~/SWins/fftw/lib:
<pre>
~/SWins/fftw/lib> ls
libfftw3.a libfftw3.so libfftw3.so.3.2.4 libfftw3_threads.la libfftw3_threads.so.3 pkgconfig
libfftw3.la libfftw3.so.3 libfftw3_threads.a libfftw3_threads.so libfftw3_threads.so.3.2.4
</pre>

* '''GROMACS 4.5.4'''

Set environment variables for configure stage of GMX
<pre>
export CPPFLAGS="-I/home/ss2029/SWins/fftw/include"
export LDFLAGS="-L/home/ss2029/SWins/fftw/lib"
</pre>

A little comment here:--[[User:Vr274|Vr274]] 17:03, 28 October 2011 (UTC)
The cleaner solution instead of manually specifying the CPPFLAGS/LDFLAGS is to add the PKG_CONFIG_PATH
<pre>
export PKG_CONFIG_PATH="/home/ss2029/SWins/fftw/lib/pkgconfig:$PKG_CONFIG_PATH"
</pre>
That also resolves the dependencies of fftw3 correctly. Check whether everything is correct by
pkg-config --libs fftw3
Should list the correct path.

'''Install serial version'''
<pre>
cd ~/SW/gromacs-4.5.4
./configure --prefix=/home/ss2029/SWins/GMX454 --disable-float --without-x --with-fft=fftw3
make
make install
</pre>

"--disable-float" installs in double precision.
If all went well, apart from a number of utility programs with prefix "g_", you should see "mdrun_d" in ~/SWins/GMX454/bin which is the main MD engine.

'''Install MPI version'''
MPI is used only by the MD engine, not by the utility programs. Following just recompiles mdrun with MPI.
<pre>
cd ~/SW/gromacs-4.5.4
module load mpi/openmpi/64/intel10/1.2.6
./configure --prefix=/home/ss2029/SWins/GMX454 --disable-float --enable-mpi --without-x --program-suffix=_mpi –with-fft=fftw3
make mdrun
make install-mdrun
</pre>

Look for "mdrun_mpi" in ~/SWins/GMX454/bin.

Note the MPI version loaded. Compilation failed with "mpi/openmpi/64/pgi71/1.2.6" and "mpi/mpich/64/gnu_/1.2.6".

The version of MPI loaded during installation must be loaded before every execution of mdrun_mpi.

I will shortly post some sample input/output to test the executables.

All set!

Some good tutorials to get started:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials

http://www.gromacs.org/Documentation/Tutorials

--[[User:Ss2029|Ss2029]] 11:19, 3 May 2011 (UTC)

Installing GROMACS on Clust - Revision history

Adk44: Created page with "* Download GMX (gromacs-4.5.4.tar.gz [http://www.gromacs.org/Downloads]) and FFTW ( fftw-3.2.2.tar.gz [http://www.fftw.org/download.html]) source codes and extract in ~/SW..."