Installation is “straightforward”:

1. Cluster specific settings/files:

• VSC-1:
  • mpi-selector: qlogicmpi_intel-0.1.0
    • Makefile Oct 2012 version: makefile_20oct12.vsc1
    • Makefile Sep 2013 version: makefile_9sep13.vsc1
  • mpi-selector: intel_mpi_intel64-4.1.1.036
    • Makefile Feb 2014 version: makefile_1feb14.vsc1
    • Makefile Jun 2014 version:makefile_28jun14.vsc1
• VSC-2:
  • mpi-selector: intel_mpi_intel64-4.0.3.008
  • Makefile Oct 2012 version: makefile_20oct12.vsc2
  • Makefile Feb 2013 version: makefile_3feb13.vsc2
  • Makefile Jul 2013 version: makefile_8jul13.vsc2

2. Fix the KIM_API first. It is an additional package that will be included in the standard build process later on. Watch out for the special patch to make it working with INTEL compilers. On VSC-1

su
cd /opt/src/openkim
wget http://s3.openkim.org/kim-api/kim-api-v1.6.3.tgz
gunzip kim-api-v1.6.3.tgz
tar xvf kim-api-v1.6.3.tar
cd kim-api-v1.6.3
cp Makefile.KIM_Config.example Makefile.KIM_Config
vi Makefile.KIM_Config
   KIM_DIR = /opt/src/openkim/kim-api-v1.6.3
   KIM_COMPILERSUITE = INTEL
   KIM_SYSTEMLINKER = linux
   KIM_SYSTEMARCH = 64bit
   KIM_LINK = dynamic-load
   prefix = /opt/sw/openkim-api/1.6.3
vi build_system/compiler_defaults/Makefile.INTEL   ( check general settings )
... replace the Makefile in 'src/utils/Makefile' with the one from
    https://groups.google.com/forum/#!topic/openkim/XOTVFVYVw5o
make clean
make  ( ignore all warnings regarding unresolved libifport.so... )
make install
make install-set-default-to-v1

3. Download source code from lammps homepage and confirm usage of intel_mpi_intel64-4.1.1.036:

cd /opt/src/lammps/sh_vii/
cp /from/wherever/it/is/lammps-28Jun14.tar.gz ./
gunzip lammps-28Jun14.tar.gz
tar xvf lammps-28Jun14.tar
gzip lammps-28Jun14.tar
cd lammps-28Jun14

4. Apply all the available patches known at the time of installation, ie

wget http://lammps.sandia.gov/patches/patch.11Jul14
patch -bp1 < patch.11Jul14
wget http://lammps.sandia.gov/patches/patch.22Jul14
patch -bp1 < patch.22Jul14
wget http://lammps.sandia.gov/patches/patch.29Jul14
patch -bp1 < patch.29Jul14
wget http://lammps.sandia.gov/patches/patch.1Aug14
patch -bp1 < patch.1Aug14
wget http://lammps.sandia.gov/patches/patch.6Aug14
patch -bp1 < patch.6Aug14
wget http://lammps.sandia.gov/patches/patch.8Aug14
patch -bp1 < patch.8Aug14
wget http://lammps.sandia.gov/patches/patch.15Aug14
patch -bp1 < patch.15Aug14
wget http://lammps.sandia.gov/patches/patch.27Aug14
patch -bp1 < patch.27Aug14
wget http://lammps.sandia.gov/patches/patch.28Aug14
patch -bp1 < patch.28Aug14
wget http://lammps.sandia.gov/patches/patch.29Aug14
patch -bp1 < patch.29Aug14
wget http://lammps.sandia.gov/patches/patch.5Sep14
patch -bp1 < patch.5Sep14
wget http://lammps.sandia.gov/patches/patch.8Sep14
patch -bp1 < patch.8Sep14
wget http://lammps.sandia.gov/patches/patch.11Sep14
patch -bp1 < patch.11Sep14
wget http://lammps.sandia.gov/patches/patch.18Sep14
patch -bp1 < patch.18Sep14
wget http://lammps.sandia.gov/patches/patch.25Sep14
patch -bp1 < patch.25Sep14
wget http://lammps.sandia.gov/patches/patch.30Sep14
patch -bp1 < patch.30Sep14
wget http://lammps.sandia.gov/patches/patch.7Oct14
patch -bp1 < patch.7Oct14
wget http://lammps.sandia.gov/patches/patch.8Oct14
patch -bp1 < patch.8Oct14
wget http://lammps.sandia.gov/patches/patch.9Oct14
patch -bp1 < patch.9Oct14
wget http://lammps.sandia.gov/patches/patch.21Oct14
patch -bp1 < patch.21Oct14

5. Activate most recent CUDA toolchain

export PATH=/opt/sw/cuda-6.5/bin:$PATH
export LD_LIBRARY_PATH=/opt/sw/cuda-6.5/lib64:$LD_LIBRARY_PATH

6. Compile individual optional packages in ./lib regardless of whether they will be used for the actual build of the LAMMPS executable:

cd ./lib/atc
vi Makefile.mpic++   ( set CC = mpiicpc )
make -f Makefile.mpic++
cd ../awpmd
vi Makefile.mpicc    ( set CC = mpiicpc )
make -f Makefile.mpicc
cd ../colvars
vi Makefile.g++      ( set CXX = icpc )
make -f Makefile.g++
cd ../cuda
make -n
make
cd ../gpu
vi Makefile.fermi    ( set CUDA_HOME = /opt/sw/cuda-6.5
                           EXTRAMAKE = Makefile.lammps.standard
                           CUDA_ARCH = -arch=sm_20
                           CUDA_PRECISION = -D_SINGLE_DOUBLE
                           CUDA_INCLUDE = -I$(CUDA_HOME)/include
                           CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64
                           CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
                           CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -I$(CUDA_HOME)/include
                           CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON
                     )
make -f Makefile.fermi
vi Makefile.lammps   ( set gpu_SYSPATH = -L/opt/sw/cuda-6.5/lib64  )
cd ../kokkos
vi Makefile.lammps   ( set CUDA_PATH ?= /opt/sw/cuda-6.5 )
cd ../linalg
make -f Makefile.gfortran
cd ../meam
make -f Makefile.ifort
vi Makefile.lammps   ( delete flag '-lompstub' from meam_SYSLIB )
cd ../poems
make -f Makefile.icc
cd ../qmmm
make -f Makefile.gfortran
cd ../reax
make -f Makefile.ifort

7. Copy VSC-X specific Makefile to correct directory (see list at point 1. above):

cp makefile_<version>.vscX lammps-20Oct12/src/MAKE/Makefile.vscX
... for version 28Jun14 confirm the following 
vi ./Makefile.vsc1    (  set CCFLAGS = -O3 -fno-alias -ip -unroll0 -restrict
                             LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -liomp5 -lstdc++              )

8. Change into lammps source directory and build lammps; start with the “standard” build:

cd .../wherever/it/is/lammps-28Jun14/src 
export PATH=$PATH:/opt/sw/openkim-api/1.6.3/bin
export LD_LIBRARY_PATH=/opt/sw/openkim-api/1.6.3/lib/libkim-api-v1.so:/opt/intel/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64:$LD_LIBRARY_PATH
make yes-standard
make yes-user-misc
make no-voronoi
make no-user-cuda
make no-gpu
make no-kokkos
make help
make clean-vsc1
make -j 8 vsc1
make vsc1

9. Upon successful compilation a binary called lmp_vsc1 should show up which should be copied to a save place.

cp ./lmp_vsc1   /opt/sw/lammps/lmp_vsc1

NOTE: To get information about included packages

make package-status 

1. Aiming at the KOKKOS package (see the 2014-09-04 message of A Kohlmeyer, http://sourceforge.net/p/lammps/mailman/message/32798716/)
2. Follow points 1-7 of the “standard build” described in the previous section;
3. Select different packages for the actual LAMMPS build still based on the same VSC-1-specific Makefile provided above;

cd .../wherever/it/is/lammps-28Jun14/src 
export PATH=$PATH:/opt/sw/openkim-api/1.6.3/bin
export LD_LIBRARY_PATH=/opt/sw/openkim-api/1.6.3/lib/libkim-api-v1.so:/opt/intel/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64:$LD_LIBRARY_PATH
make yes-standard
make yes-user-misc
make no-voronoi
make no-user-cuda
make yes-gpu
make yes-kokkos
make help
make clean-vsc1
make vsc1
cp ./lmp_vsc1   /opt/sw/lammps/lmp_fermi[kepler]_vsc1

NOTE: for the fermi nodes use CUDA_ARCH = -arch=sm_20, and for the kepler nodes use CUDA_ARCH = -arch=sm_35; so switching from building for 'fermi' to building for 'kepler' requires re-compilation of package gpu, ie

      cd .../wherever/it/is/lammps-28Jun14/lib/gpu
      cp Makefile.fermi Makefile.kepler
      vi Makefile.kepler   ( set CUDA_ARCH = -arch=sm_35 )
      make -f Makefile.kepler clean
      make -f Makefile.kepler
      cd ../../src
      ... continue with the above block to build lmp_vsc1

1. Change into some temporary directory and prepare the submit script for SGE.

vi ./sge_lammps_peptide.scrpt

#$ -N lammps_peptide
#$ -S /bin/bash
#$ -cwd
#$ -pe mpich 8
#$ -V
 
export LD_LIBRARY_PATH=/opt/sw/openkim-api/1.6.3/lib/libkim-api-v1.so:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64:$LD_LIBRARY_PATH
export I_MPI_FABRICS=shm:dapl 

mpirun -machinefile $TMPDIR/machines -np $NSLOTS /opt/sw/lammps/lmp_vsc1  -in  ./in.peptide

2. Submit it and compare the results - log.lammps - to the reference log files in /opt/sw/lammps/examples/peptide.

qsub ./sge_lammps_peptide.scrpt

1. Change into some temporary directory and prepare the submit script for SGE (fermi queue). Two consecutive short test runs will employ 1 GPU and 2 GPUs per node.

vi ./sge_lammps_fermi_kokkos.scrpt

#$ -N lammps_kokkos
#$ -S /bin/bash
#$ -cwd
#$ -pe smp 12
#$ -V
#$ -q fermi 
#$ -P fermi

export LD_LIBRARY_PATH=/opt/sw/openkim-api/1.6.3/lib/libkim-api-v1.so:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64:$LD_LIBRARY_PATH
export I_MPI_FABRICS=shm:dapl

# single GPU
/opt/sw/lammps/lmp_fermi_vsc1 -k on t 6  -sf kk -in ./in.kokkos
mv ./log.lammps ./log.lammps_fermi.1gpu.kokkos

# 2 x GPU
mpirun -np 2 /opt/sw/lammps/lmp_fermi_vsc1 -k on t 6 -sf kk -in ./in.kokkos
mv ./log.lammps ./log.lammps_fermi.2gpu.kokkos

2. Change into the fermi group and submit it to the appropriate queue.

sg fermi
qsub.py ./sge_lammps_fermi_kokkos.scrpt

3. Compare the results - ./log.lammps_fermi.[1,2]gpu.kokkos - to the reference log files in /opt/sw/lammps/examples/kokkos.

1. Change into some temporary directory and prepare the submit script for SGE (kepler queue). The test is analogous to the one for fermi, hence two consecutive short runs employing 1 GPU or 2 GPUs per node.

vi ./sge_lammps_kepler_kokkos.scrpt

#$ -N lammps_kokkos
#$ -S /bin/bash
#$ -cwd
#$ -pe smp 12
#$ -V
#$ -q kepler 
#$ -P fermi

export LD_LIBRARY_PATH=/opt/sw/openkim-api/1.6.3/lib/libkim-api-v1.so:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64:$LD_LIBRARY_PATH
export I_MPI_FABRICS=shm:dapl

# single GPU
/opt/sw/lammps/lmp_kepler_vsc1 -k on t 6  -sf kk -in ./in.kokkos
mv ./log.lammps ./log.lammps_kepler.1gpu.kokkos

# 2 x GPU
mpirun -np 2 /opt/sw/lammps/lmp_kepler_vsc1 -k on t 6 -sf kk -in ./in.kokkos
mv ./log.lammps ./log.lammps_kepler.2gpu.kokkos

2. Change into the fermi group and submit it to the appropriate — kepler — queue.

sg fermi
qsub.py ./sge_lammps_kepler_kokkos.scrpt

3. Compare the results - ./log.lammps_kepler.[1,2]gpu.kokkos - to the reference log files in /opt/sw/lammps/examples/kokkos.