Instructions and tips on compiling LAMMPS.

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Flory.usm.edu

Compiling LAMMPS on flory.usm.edu cluster

Initial setup

Setup environment for using GNU compiler suite, Open MPI, and compilation flags suitable for this cluster and the version of GNU compiler currently installed.

user $source /home/bgo/shared/bin/selector-compiler -gq

user $source /home/bgo/shared/bin/selector-mpi -i gnu-openmpi -fq

user $

export CFLAGS="-O3 -pipe --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=15360 -march=core2 -mcx16 -msahf -mmovbe -maes -mpclmul -mpopcnt -mabm -mbmi -mavx -mtune=generic"

user $export CXXFLAGS="${CFLAGS}"

user $export FCFLAGS="${CFLAGS}"

user $export FFLAGS="${CFLAGS}"

For an explanation of selector-mpi and selector-compiler, see Selector-mpi and Initial Setup.

Configure LAMMPS for compilation

The Make.py script of LAMMPS requires python2.7.

The python script does not accept CFLAGS parameters like --param l1-cache-line-size=64, and also expects the parameters to NOT have a '-' in front. Therefore, the CFLAGS environmental variable can not be directly used here.

{{Cmd|cd src|python2.7 ./Make.py -png yes -jpg yes -s ffmpeg gzip exceptions -fft fftw3 dir=/home/bgo/shared/gnu-openmpi -a file -m none -mpi mpi dir=/home/bgo/shared/gnu-openmpi -cc /home/bgo/shared/gnu-openmpi/bin/mpiCC -flags CCFLAGS add 12 O3 march=core2 mcx16 msahf mmovbe maes mpclmul mpopcnt mabm mbmi mavx mtune=generic -j 8|make yes-all|make no-{GPU,KIM,KOKKOS,VORONOI} no-USER-{ATC,AWPMD,OMP,QUIP,H5MD,SMD,VTK} }}

The CFLAGS parameters that could not be specified on the command line can be manually added to MAKE/MINE/Makefile.auto.

Compiling LAMMPS Libraries

user $python2.7 ./Make.py -j 8 -colvars make=g++ -a lib-colvars

user $python2.7 ./Make.py -j 8 -meam make=gfortran -a lib-meam

user $python2.7 ./Make.py -j 8 -poems make=g++ -a lib-poems

user $python2.7 ./Make.py -j 8 -qmmm make=gfortran -a lib-qmmm

user $python2.7 ./Make.py -j 8 -reax make=gfortran -a lib-reax

Compiling LAMMPS

Standalone Binary (Executable)

user $make clean-all

user $make -j7 auto

user $cp src/lmp_auto /home/bgo/shared/gnu-openmpi/bin/lmp

Library

Add -L/home/bgo/packages/lib to FFT_PATH in MAKE/MINE/Makefile.auto so that libpython2.7.so can be found when linking. Any of the *_PATH variables will work, I just chose FFT_PATH because that was closest to where my cursor was at the time!

Shared Library

user $make clean-all

user $make -j7 mode=shlib auto

Static Library

user $make clean-all

user $make -j7 mode=lib auto