Tuesday, June 14, 2016

Compiling LAMMPS-14May16 with Intel-15.0.6 and Intel-MPI-5.0.3

Step 1: Remember to initialise Intel Environment. In your .bashrc
source /usr/local/intel/bin/compilervars.sh intel64
Step 2: Untar LAMMPS
# tar -zxvf lammps-stable.tar.gz
Step 3: Prepare libraries for lammps 3a. lib/reax
# make -f Makefile.gfortran
3b. lib/meam
# make -f Makefile.ifort
3c. lib/poems
# make -f Makefile.icc
Step 4: Compile required the packages. Go to src directory
# cd src
4a. Check which packages are included
# make package-status
Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package COMPRESS
Installed YES: package CORESHELL
Installed YES: package DIPOLE
Installed YES: package FLD
Installed  NO: package GPU
Installed YES: package GRANULAR
Installed  NO: package KIM
Installed YES: package KOKKOS
  src/pair_lj_sdk_kokkos.cpp does not exist
  src/pair_lj_sdk_kokkos.h does not exist
Installed YES: package KSPACE
Installed YES: package MANYBODY
Installed YES: package MC
Installed YES: package MEAM
Installed YES: package MISC
Installed YES: package MOLECULE
Installed YES: package MPIIO
Installed YES: package OPT
Installed YES: package PERI
Installed YES: package POEMS
Installed YES: package PYTHON
Installed YES: package QEQ
Installed YES: package REAX
Installed YES: package REPLICA
Installed YES: package RIGID
Installed YES: package SHOCK
Installed YES: package SNAP
Installed YES: package SRD
Installed  NO: package VORONOI
Installed YES: package XTC
.........
4b. Choose all the standard
# make yes-standard
4c. Exclude packages that are not required
# make no-voronoi
# make no-kim
# make no-gpu
# make no-kokkos
Step 5: Install User-Contributed Intel Optimised Package (user-intel) and User-Contributed OpenMP Packages (user-omp)
# make yes-user-intel
# make yes-user-omp
Step 6: Compile LAMMPS Check make options. Go to src
# make intel_cpu_intelmpi -j 16
Step 6a: If in the midst of compilation you land yourself in this error ld: unable to to locate -lompstub. This is due to Intel 2015 using depreciating ompstub to ompistub5. Just go to the Intel Directory
# cd /usr/local/intel_2015/composerxe/lib/intel64
# ln -s  libiompstubs5.so libompstub.so
Step 7: Create a /usr/local/lammps-7Dec15 and copy libraries. Go to lammps root directory
# cp -Rv bench /usr/local/lammps-14May16
# cp -Rv doc /usr/local/lammps-14May16
# cp -Rv examples /usr/local/lammps-14May16
# cp -Rv potentials /usr/local/lammps-14May16
# cp README /usr/local/lammps-14May16
# cp -Rv tools /usr/local/lammps-14May16
# cp -Rv lib /usr/local/lammps-14May16
# cp lmp_intel_cpu_intelmpi /usr/local/lammps-14May16/bin
7a. Create a softlinks
# ln -s /usr/local/lammps-7Dec15/bin/lmp_intel_cpu_intelmpi lammps
References:
  1. Quick install guide for LAMMPS on Linux cluster
  2. LAMMPS Optimized for Intel on Quad Socket Xeon

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