LAMMPS 2Aug23 (intel oneapi classic)
Webpagehttps://www.lammps.org

Version2Aug23

Build EnvironmentIntel oneAPI Compiler Classic 2023.2.0
Intel MKL 2023.2.0
Intel MPI 2021.10.0

Files Required
lammps-stable_2Aug2023.tar.gz(many packages will be downloaded in the procedure below.)

Build Procedure#!/bin/sh
VERSION=2Aug23
NAME=lammps-stable_2Aug2023
INSTALL_PREFIX=/apl/lammps/2023-Aug2-intel
BASEDIR=/home/users/${USER}/Software/LAMMPS/${VERSION}LAMMPS_TARBALL=${BASEDIR}/${NAME}.tar.gz
WORKDIR=/gwork/users/${USER}LAMMPS_WORKDIR=${WORKDIR}/${NAME}
VMD_MOLFILE_INC=/home/users/${USER}/Software/VMD/1.9.4/vmd-1.9.4a57/plugins/include
PARALLEL=12#-----------------------------------------------------------------umask 0022
export LANG=C
ulimit -s unlimited
module -s purge# load intel env (2023.2.0). ~/intel/oneapi/compiler/latest/env/vars.sh
module -s load intelmpi/2021.10.0
module -s load mkl/2023.2.0
PYTHONEXE=/usr/bin/python3.6m
PYTHONINC=/usr/include/python3.6mcd ${WORKDIR}
if [ -d ${NAME} ]; thenmv ${NAME} lammps_erase
rm -rf lammps_erase &fitar zxf ${LAMMPS_TARBALL}
cd ${NAME}

sed -i -e "s/xHost/march=core-avx2/" cmake/CMakeLists.txt
mkdir build && cd build# Disabled PKGs:# FFMPEG, ADIOS, MDI, VTK: noavail# QUIP: no avail# ML-HDNNP: failed to build# ML-IAP: failed to build# KIM: CDDL is imcompatible with GPL# MPIIO: not maintained?
cmake ../cmake \-DLAMMPS_MACHINE=rccs \-DENABLE_TESTING=on \-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \-DCMAKE_C_COMPILER=icc \-DCMAKE_CXX_COMPILER=icpc \-DCMAKE_Fortran_COMPILER=ifort \-DCMAKE_MPI_C_COMPILER=mpiicc \-DCMAKE_MPI_CXX_COMPILER=mpiicpc \-DCMAKE_MPI_Fortran_COMPILER=mpiifort \-DCMAKE_C_FLAGS_RELEASE="-O3 -DNDEBUG" \-DCMAKE_CXX_FLAGS_RELEASE="-O3 -DNDEBUG" \-DCMAKE_Fortran_FLAGS_RELEASE="-O3 -DNDEBUG" \-DPython_EXECUTABLE=${PYTHONEXE} \-DPython_INCLUDE_DIR=${PYTHONINC} \-DLAMMPS_EXCEPTIONS=on \-DBUILD_SHARED_LIBS=on \-DBUILD_TOOLS=on \-DBUILD_MPI=on \-DBUILD_OMP=on \-DBUILD_LAMMPS_GUI=off \-DFFT=MKL \-DFFT_SINGLE=on \-DFFT_MKL_THREADS=on \-DWITH_JPEG=on \-DWITH_PNG=on \-DWITH_GZIP=on \-DPKG_ADIOS=off \-DPKG_AMOEBA=on \-DPKG_ASPHERE=on \-DPKG_ATC=on \-DPKG_AWPMD=on \-DPKG_BOCS=on \-DPKG_BODY=on \-DPKG_BPM=on \-DPKG_BROWNIAN=on \-DPKG_CG-DNA=on \-DPKG_CG-SPICA=on \-DPKG_CLASS2=on \-DPKG_COLLOID=on \-DPKG_COLVARS=on \-DPKG_COMPRESS=on \-DPKG_CORESHELL=on \-DPKG_DIELECTRIC=on \-DPKG_DIFFRACTION=on \-DPKG_DIPOLE=on \-DPKG_DPD-BASIC=on \-DPKG_DPD-MESO=on \-DPKG_DPD-REACT=on \-DPKG_DPD-SMOOTH=on \-DPKG_DRUDE=on \-DPKG_ELECTRODE=on \-DPKG_EFF=on \-DPKG_EXTRA-COMPUTE=on \-DPKG_EXTRA-DUMP=on \-DPKG_EXTRA-FIX=on \-DPKG_EXTRA-MOLECULE=on \-DPKG_EXTRA-PAIR=on \-DPKG_FEP=on \-DPKG_GPU=off \-DPKG_GRANULAR=on \-DPKG_H5MD=on \-DPKG_INTEL=on \-DPKG_INTERLAYER=on \-DPKG_KIM=off \-DDOWNLOAD_KIM=off \-DPKG_KOKKOS=off \-DKokkos_ARCH_ZEN3=off \-DKokkos_ENABLE_OPENMP=off \-DPKG_KSPACE=on \-DPKG_LATBOLTZ=on \-DPKG_LEPTON=on \-DPKG_MACHDYN=on \-DDOWNLOAD_EIGEN3=on \-DPKG_MANIFOLD=on \-DPKG_MANYBODY=on \-DPKG_MC=on \-DPKG_MDI=on \-DPKG_MEAM=on \-DPKG_MESONT=on \-DPKG_MGPT=on \-DPKG_MISC=on \-DPKG_ML-HDNNP=off \-DDOWNLOAD_N2P2=off \-DPKG_ML-IAP=off \-DPKG_ML-PACE=on \-DPKG_ML-QUIP=off \-DDOWNLOAD_QUIP=off \-DPKG_ML-RANN=on \-DPKG_ML-SNAP=on \-DPKG_MOFFF=on \-DPKG_MOLECULE=on \-DPKG_MOLFILE=on \-DMOLFILE_INCLUDE_DIR=${VMD_MOLFILE_INC} \-DPKG_MPIIO=off \-DPKG_MSCG=on \-DPKG_NETCDF=on \-DPKG_OPENMP=on \-DPKG_OPT=on \-DPKG_ORIENT=on \-DPKG_PERI=on \-DPKG_PHONON=on \-DPKG_PLUGIN=on \-DPKG_PLUMED=on \-DDOWNLOAD_PLUMED=on \-DPKG_POEMS=on \-DPKG_PTM=on \-DPKG_PYTHON=on \-DPKG_QEQ=on \-DPKG_QMMM=on \-DPKG_QTB=on \-DPKG_REACTION=on \-DPKG_REAXFF=on \-DPKG_REPLICA=on \-DPKG_RIGID=on \-DPKG_SCAFACOS=on \-DDOWNLOAD_SCAFACOS=on \-DPKG_SHOCK=on \-DPKG_SMTBQ=on \-DPKG_SPH=on \-DPKG_SPIN=on \-DPKG_SRD=on \-DPKG_TALLY=on \-DPKG_UEF=on \-DPKG_VORONOI=on \-DDOWNLOAD_VORO=on \-DPKG_VTK=off \-DPKG_YAFF=on \-DBLAS_LIBRARIES="-qmkl" \-DCMAKE_BUILD_TYPE=Release
make VERBOSE=1 -j ${PARALLEL}
export OMP_NUM_THREADS=2
make test # will put error...
make install
cp -a ../examples ${INSTALL_PREFIX}
cd ${INSTALL_PREFIX}
for f in etc/profile.d/*; doln -s $f .
done
cd lib64
if [ -f liblammps_rccs.so ]; thenln -s liblammps_rccs.so liblammps.sofi
if [ -f liblammps_rccs.so.0 ]; thenln -s liblammps_rccs.so.0 liblammps.so.0fiList of Available Packages
AMOEBA ASPHERE ATC AWPMD BOCS BODY BPM BROWNIAN CG-DNA CG-SPICA CLASS2 COLLOID COLVARS COMPRESS CORESHELL DIELECTRICDIFFRACTION DIPOLE DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH DRUDE EFF ELECTRODE EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX EXTRAMOLECULE EXTRA-PAIR FEP GRANULAR H5MD INTEL INTERLAYER KSPACE LATBOLTZ LEPTON MACHDYN MANIFOLD MANYBODY MC MDI MEAMMESONT MGPT MISC ML-PACE ML-RANN ML-SNAP MOFFF MOLECULE MOLFILE MSCG NETCDF OPENMP OPT ORIENT PERI PHONON PLUGIN PLUMEDPOEMS PTM PYTHON QEQ QMMM QTB REACTION REAXFF REPLICA RIGID SCAFACOS SHOCK SMTBQ SPH SPIN SRD TALLY UEF VORONOI YAFF

Tests
Copy of test results are available at /apl/lammps/2023-Aug2-intel/Testing/. Please see there for details.
(Although there are so many failed tests, most of them are caused by minor numerical errors. Some of failures might not
be negligible.)
13 - AtomStyles (Failed)
37 - SimpleCommands (SEGFAULT)
39 - Groups (Failed)
40 - Regions (Subprocess aborted)
118 - MolPairStyle:coul_diel (Failed)
125 - MolPairStyle:coul_shield (Failed)
127 - MolPairStyle:coul_slater_long (Failed)
169 - MolPairStyle:lj_class2_soft (Failed)
188 - MolPairStyle:lj_cut_soft (Failed)
194 - MolPairStyle:lj_expand_coul_long (Failed)
211 - MolPairStyle:lj_spica_coul_long (Failed)
212 - MolPairStyle:lj_spica_coul_table (Failed)
213 - MolPairStyle:lj_switch3_coulgauss_long (Failed)
237 - MolPairStyle:tip4p_long_soft (Failed)
240 - MolPairStyle:wf_cut (Failed)249 - AtomicPairStyle:buck_coul_cut_qeq_point (Failed)
250 - AtomicPairStyle:buck_coul_cut_qeq_shielded (Failed)267 - AtomicPairStyle:edip (Failed)273 - AtomicPairStyle:lepton_sphere (Failed)274 - AtomicPairStyle:lj_cut_sphere (Failed)
275 - AtomicPairStyle:lj_expand_sphere (Failed)
277 - AtomicPairStyle:meam (Failed)
280 - AtomicPairStyle:meam_spline (Failed)281 - AtomicPairStyle:meam_sw_spline (Failed)284 - AtomicPairStyle:reaxff-acks2 (Failed)285 - AtomicPairStyle:reaxff-acks2_efield (Failed)
286 - AtomicPairStyle:reaxff (Failed)
287 - AtomicPairStyle:reaxff_lgvdw (Failed)288 - AtomicPairStyle:reaxff_noqeq (Failed)289 - AtomicPairStyle:reaxff_tabulate (Failed)
290 - AtomicPairStyle:reaxff_tabulate_flag (Failed)
307 - ManybodyPairStyle:comb (Failed)
315 - ManybodyPairStyle:ilp-graphene-hbn (Failed)
316 - ManybodyPairStyle:ilp-graphene-hbn_notaper (Failed)
320 - ManybodyPairStyle:lcbop (Failed)329 - ManybodyPairStyle:pace_product (Failed)
330 - ManybodyPairStyle:pace_recursive (Failed)345 - ManybodyPairStyle:tersoff (Failed)
350 - ManybodyPairStyle:tersoff_shift (Failed)360 - BondStyle:gaussian (Subprocess aborted)363 - BondStyle:harmonic_restrain (Failed)399 - KSpaceStyle:ewald_conp_charge (Failed)409 - KSpaceStyle:pppm_ad (Failed)
410 - KSpaceStyle:pppm_cg (Failed)
412 - KSpaceStyle:pppm_cg_tiled (Failed)421 - KSpaceStyle:pppm_disp_tip4p (Failed)429 - KSpaceStyle:pppm_tip4p (Failed)
434 - KSpaceStyle:scafacos_direct (Failed)
435 - KSpaceStyle:scafacos_ewald (Failed)
436 - KSpaceStyle:scafacos_fmm (Failed)
437 - KSpaceStyle:scafacos_fmm_tuned (Failed)
438 - KSpaceStyle:scafacos_p2nfft (Failed)442 - FixTimestep:addforce_const (Failed)444 - FixTimestep:addtorque_const (Failed)451 - FixTimestep:deform_tri (Failed)468 - FixTimestep:nph (Failed)469 - FixTimestep:nph_sphere (Failed)471 - FixTimestep:npt_iso (Failed)472 - FixTimestep:npt_sphere_aniso (Failed)473 - FixTimestep:npt_sphere_iso (Failed)482 - FixTimestep:nvt-psllod (Failed)483 - FixTimestep:nvt-sllod (Failed)
501 - FixTimestep:rigid_npt_small (Failed)
515 - FixTimestep:smd_couple (Failed)523 - FixTimestep:temp_csld (Failed)531 - FixTimestep:wall_morse_const (Failed)533 - FixTimestep:wall_table_linear (Failed)534 - FixTimestep:wall_table_spline (Failed)549 - DihedralStyle:table_cut_linear (Failed)551 - DihedralStyle:table_linear (Failed)552 - DihedralStyle:table_spline (Failed)562 - ImproperStyle:inversion_harmonic (Failed)

Notes
If your calculation can be accelerated by "intel" package, this version might be better thanGCC version. Pleaseconsider to use GCC version if your calculation can't be accelerated by "intel" package.
In case you employ "intel" package, please disable libhcoll.
You don't need to mind this if you use module to set up lammps environment. I_MPI_COLL_EXTERNAL=no isdefined in the module file (lammps/2023-Aug2-intel).
Accelration of "intel" package does not work for Intel Classic Compilers if "-xHost" is specified. In the above
procedure, we manually replaced the optimization option.

In case of new oneAPI compilers (icx, icpx, ifx), "-xHost" works well. However, the performance is bit worse
than classic compilers + "-march=core-avx2". (in case of rhodo test)
There seem to be some problems for oneAPI compilers (icx, icpx, ifx).
Scafacos of this lammps version doesn't support new compilers. (failed to build)
There is some performance issue of "intel" package as described above.
Open MPI also works fine. Segmentation fault of SimpleCommands disappears and the results of other tests arealmost the same as those of Intel MPI version. However, computation performance of Open MPI version is bitunstable than Intel MPI.