LAMMPS 29Aug2024 - Intel

ウェブページ

https://www.lammps.org

バージョン

29Aug2024

ビルド環境

  • GCC 10.3.1 (gcc-toolset-10)
  • Intel oneAPI Compiler 2023.2.0
  • Intel MKL 2023.2.0
  • Intel MPI 2021.10.0
  • GSL 2.8

ビルドに必要なファイル

  • lammps-stable_29Aug2024.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=2024-Aug29
NAME=lammps-stable_29Aug2024
INSTALL_PREFIX=/apl/lammps/${VERSION}-intel

BASEDIR=/home/users/${USER}/Software/LAMMPS/${VERSION}
LAMMPS_TARBALL=${BASEDIR}/${NAME}.tar.gz

WORKDIR=/gwork/users/${USER}
LAMMPS_WORKDIR=${WORKDIR}/${NAME}

FFMPEG_BIN=/apl/ffmpeg/6.1/bin/ffmpeg
VMD_MOLFILE_INC=/home/users/${USER}/Software/VMD/1.9.4/vmd-1.9.4a57/plugins/include
GSL_ROOT=/apl/gsl/2.8

PARALLEL=12

#------------------------------------------------------------------
umask 0022
export LANG=C
ulimit -s unlimited

module -s purge

. ~/intel.2023.2.0/oneapi/compiler/latest/env/vars.sh

module -s load gcc-toolset/10
module -s load compiler-rt/2023.2.0
module -s load intelmpi/2021.10.0
module -s load mkl/2023.2.0
module -s load gsl/2.8

PYTHONEXE=/usr/bin/python3.6m
PYTHONINC=/usr/include/python3.6m

cd ${WORKDIR}
if [ -d ${NAME} ]; then
 mv ${NAME} lammps_erase
 rm -rf lammps_erase &
fi

tar zxf ${LAMMPS_TARBALL}

cd ${NAME}
sed -i -e "s/xHost/march=core-avx2/" cmake/CMakeLists.txt
mkdir build && cd build

cmake ../cmake \
 -DLAMMPS_MACHINE=rccs \
 -DENABLE_TESTING=on \
 -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
 -DCMAKE_C_COMPILER=icx \
 -DCMAKE_CXX_COMPILER=icpx \
 -DCMAKE_Fortran_COMPILER=ifx \
 -DCMAKE_MPI_C_COMPILER=mpiicx \
 -DCMAKE_MPI_CXX_COMPILER=mpicpx \
 -DCMAKE_MPI_Fortran_COMPILER=mpiifx \
 -DCMAKE_C_FLAGS_RELEASE="-O3 -DNDEBUG -march=core-avx2" \
 -DCMAKE_CXX_FLAGS_RELEASE="-O3 -DNDEBUG -march=core-avx2" \
 -DCMAKE_Fortran_FLAGS_RELEASE="-O3 -DNDEBUG -march=core-avx2" \
 -DPython_EXECUTABLE=${PYTHONEXE} \
 -DPython_INCLUDE_DIR=${PYTHONINC} \
 -DGSL_ROOT_DIR=${GSL_ROOT} \
 -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 \
 -DWITH_FFMPEG=on \
 -DFFMPEG_EXECUTABLE=${FFMPEG_BIN} \
 -DPKG_ADIOS=off \
 -DPKG_AMOEBA=on \
 -DPKG_ASPHERE=on \
 -DPKG_ATC=on \
 -DPKG_AWPMD=on \
 -DPKG_BOCS=on \
 -DPKG_BODY=on \
 -DPKG_BPM=on \
 -DPKG_BROWNIAN=on \
 -DPKG_CG-DNA=on \
 -DPKG_CG-SPICA=on \
 -DPKG_CLASS2=on \
 -DPKG_COLLOID=on \
 -DPKG_COLVARS=on \
 -DPKG_COMPRESS=on \
 -DPKG_CORESHELL=on \
 -DPKG_DIELECTRIC=on \
 -DPKG_DIFFRACTION=on \
 -DPKG_DIPOLE=on \
 -DPKG_DPD-BASIC=on \
 -DPKG_DPD-MESO=on \
 -DPKG_DPD-REACT=on \
 -DPKG_DPD-SMOOTH=on \
 -DPKG_DRUDE=on \
 -DPKG_EFF=on \
 -DPKG_ELECTRODE=on \
 -DPKG_EXTRA-COMMAND=on \
 -DPKG_EXTRA-COMPUTE=on \
 -DPKG_EXTRA-DUMP=on \
 -DPKG_EXTRA-FIX=on \
 -DPKG_EXTRA-MOLECULE=on \
 -DPKG_EXTRA-PAIR=on \
 -DPKG_FEP=on \
 -DPKG_GPU=off \
 -DPKG_GRANULAR=on \
 -DPKG_H5MD=on \
 -DPKG_INTEL=on \
 -DPKG_INTERLAYER=on \
 -DPKG_KIM=off \
 -DDOWNLOAD_KIM=off \
 -DPKG_KOKKOS=off \
 -DKokkos_ARCH_ZEN3=off \
 -DKokkos_ENABLE_OPENMP=off \
 -DPKG_KSPACE=on \
 -DPKG_LATBOLTZ=on \
 -DPKG_LEPTON=on \
 -DPKG_MACHDYN=on \
 -DDOWNLOAD_EIGEN3=on \
 -DPKG_MANIFOLD=on \
 -DPKG_MANYBODY=on \
 -DPKG_MC=on \
 -DPKG_MDI=off \
 -DDOWNLOAD_MDI=off \
 -DPKG_MEAM=on \
 -DPKG_MESONT=on \
 -DPKG_MGPT=on \
 -DPKG_MISC=on \
 -DPKG_ML-HDNNP=off \
 -DDOWNLOAD_N2P2=off \
 -DPKG_ML-IAP=off \
 -DMLIAP_ENABLE_PYTHON=off \
 -DPKG_ML-PACE=on \
 -DPKG_ML-POD=on \
 -DPKG_ML-QUIP=off \
 -DDOWNLOAD_QUIP=off \
 -DPKG_ML-RANN=on \
 -DPKG_ML-SNAP=on \
 -DPKG_ML-UF3=on \
 -DPKG_MOFFF=on \
 -DPKG_MOLECULE=on \
 -DPKG_MOLFILE=on \
 -DMOLFILE_INCLUDE_DIR=${VMD_MOLFILE_INC} \
 -DPKG_NETCDF=on \
 -DPKG_OPENMP=on \
 -DPKG_OPT=on \
 -DPKG_ORIENT=on \
 -DPKG_PERI=on \
 -DPKG_PHONON=on \
 -DPKG_PLUGIN=on \
 -DPKG_PLUMED=off \
 -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_RHEO=on \
 -DPKG_RIGID=on \
 -DPKG_SCAFACOS=off \
 -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
make install

cp -a ../examples ${INSTALL_PREFIX}

cd ${INSTALL_PREFIX}
for f in etc/profile.d/*; do
 if [ -f $f ]; then
   ln -s $f .
 fi
done

cd lib64
if [ -f liblammps_rccs.so ]; then
 ln -s liblammps_rccs.so liblammps.so
fi
if [ -f liblammps_rccs.so.0 ]; then
 ln -s liblammps_rccs.so.0 liblammps.so.0
fi

有効なパッケージ

AMOEBA ASPHERE ATC AWPMD BOCS BODY BPM BROWNIAN CG-DNA CG-SPICA CLASS2 
COLLOID COLVARS COMPRESS CORESHELL DIELECTRIC DIFFRACTION DIPOLE
DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH DRUDE EFF ELECTRODE EXTRA-COMMAND
EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX EXTRA-MOLECULE EXTRA-PAIR FEP GRANULAR
H5MD INTEL INTERLAYER KSPACE LATBOLTZ LEPTON MACHDYN MANIFOLD MANYBODY
MC MEAM MESONT MGPT MISC ML-PACE ML-POD ML-RANN ML-SNAP ML-UF3 MOFFF
MOLECULE MOLFILE NETCDF OPENMP OPT ORIENT PERI PHONON PLUGIN POEMS PTM
PYTHON QEQ QMMM QTB REACTION REAXFF REPLICA RHEO RIGID SHOCK SMTBQ SPH
SPIN SRD TALLY UEF VORONOI YAFF

テスト

テストログのコピーが /apl/lammps/2024-Aug29-intel/Testing 以下にあります。

The following tests FAILED:
        37 - SimpleCommands (SEGFAULT)
        39 - Groups (Failed)
        85 - PythonPyLammps (Failed)
       119 - MolPairStyle:coul_diel (Failed)
       126 - MolPairStyle:coul_shield (Failed)
       128 - MolPairStyle:coul_slater_long (Failed)
       253 - AtomicPairStyle:buck_coul_cut_qeq_point (Failed)
       254 - AtomicPairStyle:buck_coul_cut_qeq_shielded (Failed)
       271 - AtomicPairStyle:edip (Failed)
       277 - AtomicPairStyle:lepton_sphere (Failed)
       278 - AtomicPairStyle:lj_cut_sphere (Failed)
       279 - AtomicPairStyle:lj_expand_sphere (Failed)
       282 - AtomicPairStyle:meam_2nn (Failed)
       283 - AtomicPairStyle:meam_ms (Failed)
       285 - AtomicPairStyle:meam_spline (Failed)
       286 - AtomicPairStyle:meam_sw_spline (Failed)
       288 - AtomicPairStyle:pedone (Failed)
       290 - AtomicPairStyle:reaxff-acks2 (Failed)
       291 - AtomicPairStyle:reaxff-acks2_efield (Failed)
       292 - AtomicPairStyle:reaxff (Failed)
       293 - AtomicPairStyle:reaxff_lgvdw (Failed)
       294 - AtomicPairStyle:reaxff_noqeq (Failed)
       295 - AtomicPairStyle:reaxff_tabulate (Failed)
       296 - AtomicPairStyle:reaxff_tabulate_flag (Failed)
       315 - ManybodyPairStyle:drip (Failed)
       316 - ManybodyPairStyle:drip_real (Failed)
       317 - ManybodyPairStyle:edip_multi (Failed)
       321 - ManybodyPairStyle:ilp-graphene-hbn (Failed)
       322 - ManybodyPairStyle:ilp-graphene-hbn_notaper (Failed)
       325 - ManybodyPairStyle:kolmogorov_crespi_z (Failed)
       326 - ManybodyPairStyle:lcbop (Failed)
       336 - ManybodyPairStyle:pace_product (Failed)
       337 - ManybodyPairStyle:pace_recursive (Failed)
       342 - ManybodyPairStyle:rann (Failed)
       345 - ManybodyPairStyle:snap (Failed)
       353 - ManybodyPairStyle:tersoff (Failed)
       362 - ManybodyPairStyle:uf3 (Failed)
       369 - BondStyle:gaussian (SEGFAULT)
       372 - BondStyle:harmonic_restrain (Failed)
       373 - BondStyle:harmonic_shift (Failed)
       412 - KSpaceStyle:ewald_conp_charge (Failed)
       422 - KSpaceStyle:pppm_ad (Failed)
       423 - KSpaceStyle:pppm_cg (Failed)
       424 - KSpaceStyle:pppm_cg_ad (Failed)
       425 - KSpaceStyle:pppm_cg_tiled (Failed)
       434 - KSpaceStyle:pppm_disp_tip4p (Failed)
       442 - KSpaceStyle:pppm_tip4p (Failed)
       457 - FixTimestep:addtorque_const (Failed)
       464 - FixTimestep:deform_tri (Failed)
       470 - FixTimestep:efield_variable (Failed)
       471 - FixTimestep:heat (Failed)
       482 - FixTimestep:nph_sphere (Failed)
       484 - FixTimestep:npt_iso (Failed)
       486 - FixTimestep:npt_sphere_iso (Failed)
       495 - FixTimestep:nvt-psllod (Failed)
       496 - FixTimestep:nvt-sllod (Failed)
       514 - FixTimestep:rigid_npt_small (Failed)
       528 - FixTimestep:smd_couple (Failed)
       541 - FixTimestep:wall_lj1043_const (Failed)
       544 - FixTimestep:wall_morse_const (Failed)
       545 - FixTimestep:wall_region_harmonic_const (Failed)
       552 - DihedralStyle:cosine_squared_restricted (Failed)
       561 - DihedralStyle:quadratic (Failed)
       563 - DihedralStyle:table_cut_linear (Failed)
       564 - DihedralStyle:table_cut_spline (Failed)

メモ

View PDF