Building Lammps With Fftw

Building LAMMPS with FFTW

Sachin Shanbhag 488 DSL, [email protected] sandia.gov

When should you use this tutorial? ●

You use LAMMPS as you MD program

●

You have to consider long range Coulombic interaction

●

You don't know where your fft files are OR

●

You don't have permissions to access them OR

●

You simply want to create a fftw library in your local account

Download LAMMPS ●

Get the program from http://lammps.sandia.gov/download.html

●

Select C++, and hit download now

●

This gets you lammps.tar.gz

●

Untar-zip it using the command in an appropriate directory tar -zxvf lammps.tar.gz

●

mv lammps-xxx to lammps, for simplicity

Download FFTW ●

●

Download the 2.1.x version of fftw from fftw.org Untar/zip the downloaded file (I downloaded v2.1.5) tar -zxvf fftw-2.1.5.tar.gz

●

make a temporary directory called localfft

●

cd fftw-2.1.5/

●

In fftw-2.1.5/ type ./configure --prefix=[ABSPATH]/localfft

Build FFTW ●

Here [ABSPATH]is the absolute path to this directory. –

●

This really depends upon where you want to place the library in your local account

In my case it is, for now (I'll move it later), /panfs/panasas1/users/sachins/Desktop/

●

Type the following commands to build the fftw library make; make install

●

●

This will make three subdirectories in the localfft directory I moved the localfft directory into my lammps/src/ directory

Building the LAMMPS Executable ●

●

●

Detailed instructions available at: http://lammps.sandia.gov/doc/Section_sta rt.html#2_2 Right now, lets do a simple compilation: –

single processor, no MPI

–

with freely available FFTW library

cd lammps/src/STUBS/ –

●

make (builds libmpi.a)

cd lammps/src/MAKE/ –

comment out/delete LINKFORT, FORTLIB, and SYSLIB in

Makefile.g++

Building the Executable ●

●

●

The only part I changed in Makefile.g++ was CC CCFLAGS

= =

DEPFLAGS LINK LINKFLAGS USRLIB ARCHIVE ARFLAGS SIZE

= = = = = = =

g++ -g -DFFT_FFTW -I../STUBS \ -I../localfft/include $(PKGINC) -M g++ -O -L../STUBS -L../localfft/lib $(PKGPATH) -lfftw -lmpi $(PKGLIB) ar -rc size

cd lammps/src/ –

make yes-kspace

–

make g++

You should have an executable called lmp_g++

Testing if it works ●

I used the peptide example in the examples directory –

●

It needs fftw to work

cd lammps/examples/peptide

Testing if it works sachins% cat in.peptide # Solvated 5-mer peptide units atom_style

real full

pair_style 10.0 10.0 bond_style angle_style dihedral_style improper_style kspace_style

lj/charmm/coul/long 8.0

...

harmonic charmm charmm harmonic pppm 0.0001

Run the program sachins% lmp_g++ < in.peptide LAMMPS (7 Jul 2009) Scanning data file ... 3 = max bonds/atom 6 = max angles/atom 14 = max dihedrals/atom 1 = max impropers/atom PPPM initialization … G vector = 0.268721 grid = 15 15 15 stencil order = 5 RMS precision = 4.86052e-05 brick FFT buffer size/proc = 10648 3375 5808 Setting up run …