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


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Setup environment for using GNU compiler suite, Open MPI, and compilation flags suitable for this cluster and the version of GNU compiler currently installed.
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 -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{{=}}"${CFLAGS}"}}
{{Cmd|source /home/bgo/shared/bin/selector-compiler -gq|source /home/bgo/shared/bin/selector-mpi -i gnu-openmpi -fq|export CFLAGS{{=}}"-O3 -pipe --param l1-cache-size{{=}}32 --param l1-cache-line-size{{=}}64 --param l2-cache-size{{=}}15360 -march{{=}}core2 -mcx16 -msahf -mmovbe -maes -mpclmul -mpopcnt -mabm -mbmi -mavx -mtune{{=}}generic"|export CXXFLAGS{{=}}"${CFLAGS}"|export FCFLAGS{{=}}"${CFLAGS}"|export FFLAGS{{=}}"${CFLAGS}"}}


For an explanation of {{C|selector-mpi}} and {{C|selector-compiler}} see [[Initial Setup]].
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 ==
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The {{C|Make.py}} script of LAMMPS requires python2.7.
The {{C|Make.py}} script of LAMMPS requires python2.7.


The python script does not accept CFLAG parameters like {{C|--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.
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.


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


== Compiling LAMMPS Libraries ==
== Compiling LAMMPS Libraries ==


{{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|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 ==
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=== Library ===
=== 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!
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 ====
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{{Cmd|make clean-all|make -j7 mode{{=}}lib auto}}
{{Cmd|make clean-all|make -j7 mode{{=}}lib 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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