Month: June 2016

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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/impi/5.0.3.049/bin64/mpivars.sh intel64
source /usr/local/intel/composerxe/bin/compilervars.sh intel64
source /usr/local/intel/mkl/bin/mklvars.sh intel64

Step 2: Untar LAMMPS

# tar -zxvf lammps-stable.tar.gz

Step 3: Prepare selected libraries for lammps

3a. lib/reax

# make -f Makefile.gfortran

3b. lib/meam

# make -f Makefile.ifort

3c. lib/poems

# make -f Makefile.icc

3d. lib/colvars

# make -f Makefile.g++

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 src/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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Compiling Quantum ESPRESSO-2.4.0 with Intel Parallel Studio 2016 on CentOS 6

Before Compilation,

Step 1: Download Quantum ESPRESSO 5.4.0 from Quantum ESPRESSO Download Site

Step 2: Remember to source the Intel Compilers and indicate MKLROOT in your .bashrc

export MKLROOT=/usr/local/intel_2016/mkl/lib
source /usr/local/intel_2016/bin/compilervars.sh intel64

Compilation QE-5.40

Step 3: Make a file call setup.sh and copy the contents inside.

export F90=mpiifort
export F77=mpiifort
export MPIF90=mpiifort
export CC=mpiicc
export CPP="icc -E"
export CFLAGS="-g O3"
export AR=xiar
export BLAS_LIBS=""
export LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64"
export SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
export FFT_LIBS="-L$MKLROOT/intel64"
./configure  --enable-parallel --prefix=/usr/local/espresso-5.4.0
# ./setup.sh
# make all -j 16
# make install

References:

  1. [Pw_forum] Compilation with intel compiler and MKL
  2. Quantum ESPRESSO: Compiling and Choice of Libraries