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Instructions and tips on compiling LAMMPS.
{{WIP|author=bgo}}
= Flory.usm.edu =
= Flory.usm.edu =


Compiling LAMMPS on flory.usm.edu cluster
Compiling LAMMPS on {{C|flory.usm.edu}} cluster


== Initial setup ==
== Initial setup ==


{{Cmd|source /home/bgo/shared/bin/selector-compiler -gq|source /home/bgo/shared/bin/selector-mpi -ofq|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"|export CXXFLAGS{{=}}"${CFLAGS}"|export FCFLAGS{{=}}"${CFLAGS}"|export FFLAGS{{=}}"${CFLAGS}"}}
Setup environment for using GNU compiler suite, Open MPI, and compilation flags suitable for this cluster and the version of GNU compiler currently installed.
 
{{Cmd|source /home/bgo/shared/bin/selector-compiler -gq|source /home/bgo/shared/bin/selector-mpi -i gnu-openmpi -fq|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"|export CXXFLAGS{{=}}"${CFLAGS}"|export FCFLAGS{{=}}"${CFLAGS}"|export FFLAGS{{=}}"${CFLAGS}"}}
 
For an explanation of {{C|selector-mpi}} and {{C|selector-compiler}}, see [[Selector-mpi]] and [[Initial Setup]].


== Configure LAMMPS for compilation ==
== Configure LAMMPS for compilation ==


The new Make.py of LAMMPS requires python2.7, so I installed it in my home directory.
The {{C|Make.py}} script of LAMMPS requires python2.7.
 
The python script does not accept {{C|CFLAGS}} parameters like {{C|--param l1-cache-line-size{{=}}64}}, and also expects the parameters to NOT have a '-' in front. Therefore, the {{C|CFLAGS}} environmental variable can not be directly used here.


Check the flags at the end of the first Make.py line. The python script does not accept CCFLAG 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 {{C|CFLAGS}} parameters that could not be specified on the command line can be manually added to  {{Path|MAKE/MINE/Makefile.auto}}.


{{Cmd|cd src|~/packages/bin/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} }}
== Compiling LAMMPS Libraries ==


The CCFLAGS parameters, which could not be specified on the command line, can be manually added to MAKE/MINE/Makefile.auto file.
{{Cmd|python2.7 ./Make.py -j 8 -colvars make{{=}}g++ -a lib-colvars|python2.7 ./Make.py -j 8 -meam make{{=}}gfortran -a lib-meam|python2.7 ./Make.py -j 8 -poems make{{=}}g++ -a lib-poems|python2.7 ./Make.py -j 8 -qmmm make{{=}}gfortran -a lib-qmmm|python2.7 ./Make.py -j 8 -reax make{{=}}gfortran -a lib-reax }}


== Compiling LAMMPS ==
== Compiling LAMMPS ==


=== LAMMPS Libraries ===
=== Standalone Binary (Executable) ===


{{Cmd|~/packages/bin/python2.7 ./Make.py -j 8 -colvars make{{=}}g++ -a lib-colvars|~/packages/bin/python2.7 ./Make.py -j 8 -meam make{{=}}gfortran -a lib-meam|~/packages/bin/python2.7 ./Make.py -j 8 -poems make{{=}}g++ -a lib-poems|~/packages/bin/python2.7 ./Make.py -j 8 -qmmm make{{=}}gfortran -a lib-qmmm|~/packages/bin/python2.7 ./Make.py -j 8 -reax make{{=}}gfortran -a lib-reax }}
{{Cmd|make clean-all|make -j7 auto|cp src/lmp_auto /home/bgo/shared/gnu-openmpi/bin/lmp}}


=== Standalone binary ===
=== Library ===


{{Cmd|make -j7 auto|cp src/lmp_auto /home/bgo/shared/gnu-openmpi/bin/lmp}}
Add {{C|-L/home/bgo/packages/lib}} to {{C|FFT_PATH}} in {{Path|MAKE/MINE/Makefile.auto}} so that libpython2.7.so can be found when linking. Any of the {{C|*_PATH}} variables will work, I just chose {{C|FFT_PATH}} because that was closest to where my cursor was at the time!


=== Shared library ===
==== Shared Library ====


Compile shared library using Makefile
{{Cmd|make clean-all|make -j7 mode{{=}}shlib auto}}


Each user that wants to use LAMMPS as a library should use their own lammps src. They can compile their own programs like mpic++ -I/home/bgo/lammps/src -c simple.cpp
==== Static Library ====


Add -L/home/bgo/packages/lib to FFT_PATH in MAKE/MINE/Makefile.auto so the libpython2.7.so can be found when linking. Any of the _PATH variables will work, I just choose FFT_PATH because that was closest to where my cursor was at the time!
{{Cmd|make clean-all|make -j7 mode{{=}}lib auto}}


{{Cmd|make clean-all|make -j7 mode{{=}}shlib auto
[[Category:Tutorials]]
}}

Latest revision as of 10:44, 21 April 2017

Instructions and tips on compiling LAMMPS.

Warning
This page is a work in progress by bgo (talk | contribs). Treat its contents with caution.

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
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