LAMMPS 29Sep21 Update 3 (intel MPI)
ウェブページ
https://www.lammps.org

バージョン
29Sep21 Update 3

ビルド環境Intel oneAPI Compiler Classic 2023.1.0
Intel MKL 2023.1.0
Intel MPI 2021.9.0

ビルドに必要なファイル
lammps-stable_29Sep2021_update3.tar.gz(一部ファイルは以下スクリプト中で取得)

ビルド手順#!/bin/sh
VERSION=29Sep21
NAME=lammps-stable_29Sep2021_update3
INSTALL_PREFIX=/apl/lammps/2021-Sep29-impi
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# load intel env (2023.1.0). ~/intel/oneapi/compiler/latest/env/vars.sh
module -s purge
module -s load intelmpi/2021.9.0
module -s load mkl/2023.1.0
export CC=mpiicc
export CXX=mpiicpc
export FC=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc
export MPIFC=mpiifort
PYTHONEXE=/usr/bin/python3.6m
PYTHONINC=/usr/include/python3.6m
PYTHONLIB=/usr/lib64/libpython3.6m.so
cd ${WORKDIR}
if [ -d ${NAME} ]; thenmv ${NAME} lammps_erase
rm -rf lammps_erase &fitar zxf ${LAMMPS_TARBALL}
cd ${NAME}
sed -i -e "s/xHost/march=core-avx2/" cmake/CMakeLists.txt
mkdir build && cd build# Disabled PKGs:# FFMPEG, ADIOS, MDI, VTK: noavail# MSCG: gsl too old# MESSAGE: ZeroMQ support not enabled# QUIP: failed to build# ML-HDNNP: failed to build# KIM: CDDL is imcompatible with GPL# LATTE: technical problem of cmake? (LAPACK and BLAS)# NETCDF: to avoid EVP_KDF_ctrl error# MPIIO: not maintained?
cmake ../cmake \-DLAMMPS_MACHINE=rccs \-DENABLE_TESTING=on \-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \-DCMAKE_C_COMPILER=mpiicc \-DCMAKE_CXX_COMPILER=mpiicpc \-DCMAKE_Fortran_COMPILER=mpiifort \-DCMAKE_MPI_C_COMPILER=mpiicc \-DCMAKE_MPI_CXX_COMPILER=mpiicpc \-DCMAKE_MPI_Fortran_COMPILER=mpiifort \-DPython_EXECUTABLE=${PYTHONEXE} \-DPython_INCLUDE_DIR=${PYTHONINC} \-DPython_LIBRARY=${PYTHONLIB} \-DLAMMPS_EXCEPTIONS=on \-DBUILD_SHARED_LIBS=on \-DBUILD_TOOLS=on \-DBUILD_MPI=on \-DBUILD_OMP=on \-DFFT=MKL \-DFFT_SINGLE=on \-DFFT_MKL_THREADS=on \-DWITH_JPEG=yes \-DWITH_PNG=yes \-DWITH_GZIP=yes \-DPKG_ASPHERE=on \-DPKG_ATC=on \-DPKG_AWPMD=on \-DPKG_BOCS=on \-DPKG_BODY=on \-DPKG_BROWNIAN=on \-DPKG_CG-DNA=on \-DPKG_CG-SDK=on \-DPKG_CLASS2=on \-DPKG_COLLOID=on \-DPKG_COLVARS=on \-DPKG_COMPRESS=on \-DPKG_CORESHELL=on \-DPKG_DIELECTRIC=on \-DPKG_DIFFRACTION=on \-DPKG_DIPOLE=on \-DPKG_DPD-BASIC=on \-DPKG_DPD-MESO=on \-DPKG_DPD-REACT=on \-DPKG_DPD-SMOOTH=on \-DPKG_DRUDE=on \-DPKG_EFF=on \-DPKG_EXTRA-COMPUTE=on \-DPKG_EXTRA-DUMP=on \-DPKG_EXTRA-FIX=on \-DPKG_EXTRA-MOLECULE=on \-DPKG_EXTRA-PAIR=on \-DPKG_FEP=on \-DPKG_GPU=off \-DPKG_GRANULAR=on \-DPKG_H5MD=on \-DPKG_INTEL=on \-DPKG_INTERLAYER=on \-DPKG_KIM=off \-DDOWNLOAD_KIM=no \-DPKG_KOKKOS=on \-DKokkos_ARCH_ZEN3=yes \-DKokkos_ENABLE_OPENMP=yes \-DPKG_KSPACE=on \-DPKG_LATBOLTZ=on \-DPKG_MACHDYN=on \-DDOWNLOAD_EIGEN3=on \-DPKG_MANIFOLD=on \-DPKG_MANYBODY=on \-DPKG_MC=on \-DPKG_MDI=off \-DPKG_MEAM=on \-DPKG_MESONT=on \-DPKG_MESSAGE=on \-DPKG_MGPT=on \-DPKG_MISC=on \-DPKG_ML-HDNNP=off \-DDOWNLOAD_N2P2=no \-DPKG_ML-IAP=off \-DPKG_ML-PACE=on \-DPKG_ML-QUIP=off \-DDOWNLOAD_QUIP=no \-DPKG_ML-RANN=on \-DPKG_ML-SNAP=on \-DPKG_MOFFF=on \-DPKG_MOLECULE=on \-DPKG_MOLFILE=on \-DMOLFILE_INCLUDE_DIR=${VMD_MOLFILE_INC} \-DPKG_MPIIO=off \-DPKG_MSCG=off \-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=yes \-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=yes \-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=yes \-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.0
fi

テスト結果
The following tests FAILED:
10 - AtomStyles (Failed)
32 - SimpleCommands (SEGFAULT)
88 - MolPairStyle:coul_diel (Failed)
94 - MolPairStyle:coul_shield (Failed)
117 - MolPairStyle:lj_charmm_coul_long_soft (Failed)
130 - MolPairStyle:lj_class2_soft (Failed)
139 - MolPairStyle:lj_cut_coul_long_soft (Failed)
145 - MolPairStyle:lj_cut_soft (Failed)
151 - MolPairStyle:lj_expand_coul_long (Failed)
164 - MolPairStyle:lj_sdk_coul_long (Failed)
165 - MolPairStyle:lj_sdk_coul_table (Failed)
169 - MolPairStyle:lj_switch3_coulgauss_long (Failed)
192 - MolPairStyle:tip4p_long_soft (Failed)
195 - MolPairStyle:wf_cut (Failed)203 - AtomicPairStyle:buck_coul_cut_qeq_point (Failed)
204 - AtomicPairStyle:buck_coul_cut_qeq_shielded (Failed)
221 - AtomicPairStyle:edip (Failed)
224 - AtomicPairStyle:hybrid-eam (Failed)
228 - AtomicPairStyle:meam (Failed)229 - AtomicPairStyle:meam_spline (Failed)
230 - AtomicPairStyle:meam_sw_spline (Failed)
233 - AtomicPairStyle:reaxff (Failed)234 - AtomicPairStyle:reaxff_lgvdw (Failed)
235 - AtomicPairStyle:reaxff_noqeq (Failed)236 - AtomicPairStyle:reaxff_tabulate (Failed)246 - ManybodyPairStyle:bop (Failed)
247 - ManybodyPairStyle:bop_save (Failed)
248 - ManybodyPairStyle:comb (Failed)
250 - ManybodyPairStyle:drip (Failed)
251 - ManybodyPairStyle:drip_real (Failed)
256 - ManybodyPairStyle:ilp-graphene-hbn (Failed)
257 - ManybodyPairStyle:ilp-graphene-hbn_notaper (Failed)258 - ManybodyPairStyle:kolmogorov_crespi_full (Failed)
261 - ManybodyPairStyle:lcbop (Failed)262 - ManybodyPairStyle:lebedeva_z (Failed)263 - ManybodyPairStyle:meam (Failed)269 - ManybodyPairStyle:nb3b_harmonic (Failed)270 - ManybodyPairStyle:pace_product (Failed)271 - ManybodyPairStyle:pace_recursive (Failed)272 - ManybodyPairStyle:polymorphic_sw (Failed)273 - ManybodyPairStyle:polymorphic_tersoff (Failed)281 - ManybodyPairStyle:tersoff (Failed)
286 - ManybodyPairStyle:tersoff_shift (Failed)
287 - ManybodyPairStyle:tersoff_table (Failed)295 - BondStyle:gaussian (Failed)
312 - AngleStyle:cosine_delta (Failed)314 - AngleStyle:cosine_shift (Failed)336 - KSpaceStyle:ewald_tri (Failed)338 - KSpaceStyle:pppm_ad (Failed)339 - KSpaceStyle:pppm_cg (Failed)341 - KSpaceStyle:pppm_cg_tiled (Failed)
347 - KSpaceStyle:pppm_disp_tip4p (Failed)354 - KSpaceStyle:pppm_tip4p (Failed)359 - KSpaceStyle:scafacos_direct (Failed)360 - KSpaceStyle:scafacos_ewald (Failed)361 - KSpaceStyle:scafacos_fmm (Failed)362 - KSpaceStyle:scafacos_fmm_tuned (Failed)363 - KSpaceStyle:scafacos_p2nfft (Failed)364 - FixTimestep:adapt_coul (Failed)
367 - FixTimestep:addforce_const (Failed)368 - FixTimestep:addforce_variable (Failed)369 - FixTimestep:addtorque_const (Failed)372 - FixTimestep:aveforce_variable (Failed)374 - FixTimestep:drag (Failed)378 - FixTimestep:heat (Failed)381 - FixTimestep:momentum (Failed)383 - FixTimestep:nph (Failed)384 - FixTimestep:nph_sphere (Failed)386 - FixTimestep:npt_iso (Failed)
387 - FixTimestep:npt_sphere_aniso (Failed)388 - FixTimestep:npt_sphere_iso (Failed)389 - FixTimestep:npt_sphere_tri (Failed)
397 - FixTimestep:nvt (Failed)399 - FixTimestep:oneway (Failed)
412 - FixTimestep:rigid_npt_small (Failed)424 - FixTimestep:shake_angle (Failed)426 - FixTimestep:smd_couple (Failed)429 - FixTimestep:spring_couple (Failed)
430 - FixTimestep:spring_rg (Failed)432 - FixTimestep:spring_tether (Failed)433 - FixTimestep:temp_berendsen (Failed)
434 - FixTimestep:temp_csld (Failed)
435 - FixTimestep:temp_csvr (Failed)
436 - FixTimestep:temp_rescale (Failed)455 - DihedralStyle:table_cut_linear (Failed)
457 - DihedralStyle:table_linear (Failed)458 - DihedralStyle:table_spline (Failed)
466 - ImproperStyle:harmonic (Failed)468 - ImproperStyle:inversion_harmonic (Failed)メモ
Update が適用されているため、以前にビルドしたものとはコードレベルで違います。
2022-Jun23 のメモをご確認ください。内容はほぼ共通です。