Compiling LAMMPS

This note intends to the struggling work to deploy LAMMPS on some Linux clusters

• Compiling LAMMPS
• Preparation
  • 1. Prerequisite
  • 2. Download
  • 3. Packages
• I. Compiling with GCC + OMPI
  • USC1_Eagle - Centos 6.5 cluster with InfiniBand
  • Module file
  • USC2_Tachyon - Centos 6.9 cluster with InfiniBand
  • use OMPI_5
  • use OMPI_3
  • Module file
  • CAN2_GPU - Centos 7 cluster with GPU
  • CAN3_GPU - Ubuntu 20 with GPU
• GCC + OpenSHMEM
• Compile with openMPI4.0.1-gcc7.4.0 on CAN
• MVAPICH-GCC
  • USC2
• Compile with IMPI-2019xe + MKL
  • USC1_Eagle - Centos 6.5 cluster with InfiniBand
• Compiling with LLVM + OMPI
  • USC2_Tachyon - Centos 6.9 cluster with InfiniBand
• Compile with Conda

Preparation

1. Prerequisite

• Compiler: Intel, GCC, Clang,...
• MPI implementation: OMPI, IMPI, MPICH,...
• Libraries depend on which packages will be installed: FFTW, intel MKL,...
• Newer LAMMPS may be no longer compatible with an old openMPI, as well FFTW/MKL, so these libs need to be updated too.
• OpenMPI may the fastest
• There is no longer USER_ packages from Jul-2021
• Need CMAKE, newer is better (a newer Cmake version may reduce the probability of error during compiling). Basic cmake:

cmake -D OPTION_A=VALUE_A -D OPTION_B=VALUE_B ...     ../cmake make

• Module environment

module load <module_name>
module display <module_name>

• Only one installation for eagle/lion/leopard/cheetah, but need to load different OpenMPI for each cluster. Also need to load Conda to overwrite the default python of the system (different Ver. of python may cause runtime error)

2. Download

LAMMPS site Souce code

### download tar file
tar -xvf lammps-stable_7Aug2019
cd lammps-stable_7Aug2019
mkdir build && cd build

### or download use Git:
git clone --branch patch_20Nov2019 https://github.com/lammps/lammps.git lammps_patch_20Nov2019
cd lammps_patch_20Nov2019
git checkout patch_20Nov2019

git clone https://github.com/lammps/lammps.git    lammps_dev
cd lammps_dev
git pull origin develop

3. Packages

Note

• include these OPTIONS in Cmake command, to build package-lib automatically:
• python > 3.7.12 require to update GCC-conda=11: conda install -c conda-forge gcc=11 gxx=11. But don't use this to void requiring higher GLIBC. Also, zlib=1.2.12 require GLIBC=2.14.
• To void hidden libs by conda, need to downgrade libs versions in conda < libs in linux system. So that to void these errors, use conda install -c conda-forge libgcc-ng=7 zlib=1.2.8 python=3.7.12
• Do not use GCC-11 to avoid error: Dwarf Error: found dwarf version '5', use: export CFLAGS='-gdwarf-4 -gstrict-dwarf' not solve this error
• install openBLAS for LAPACK and BLAS, so need load GSL
• use static link for openBLAS, so need to export it and set cmake var

1.UFM potential

cd lammps-folder/src/
git clone https://github.com/plrodolfo/FluidFreeEnergyforLAMMPS.git USER-FFE
copy new pair_ufm into /src
copy new pair_eam.cpp & pair_eam.h into /src and delete corresponding files in /src/MANYBODY

2.POEMS, OPT

-D PKG_OPT=yes

3.MSCG

-D PKG_MSCG=yes -D DOWNLOAD_MSCG=yes

5.VORONOI

-D PKG_VORONOI=yes -D DOWNLOAD_VORO=yes

6.KSPACE

• if use MKL for FFT, then need MKL library

-D FFT=MKL  \
-D MKL_INCLUDE_DIRS=/uhome/p001cao/local/intel/xe2019/compilers_and_libraries_2019.5.281/linux/mkl/include  \
-D MKL_LIBRARY=/uhome/p001cao/local/intel/xe2019/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64  \

• if FTWW3, then dont need MKL_LIBRARY

-D FFT=FFTW3
-D FFTW3_INCLUDE_DIRS=/uhome/p001cao/local/fftw/3.3.8-openmpi4.0.1-Intel2019xe-double/include \
-D FFTW3_LIBRARY=/uhome/p001cao/local/fftw/3.3.8-openmpi4.0.1-Intel2019xe-double/lib \

• or use FFTW3 from intel_mkl: (not support long-double precision)

-D FFT=FFTW3
-D FFTW3_INCLUDE_DIRS=/uhome/p001cao/local/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mkl/include/fftw

7.**LAPACK & BLAS*

• These packages LAPACK & BLAS: MSCG, ATC, AWPMD, ML-QUIP, LATTE, PLUMED (can self build its libs)
• Use "intel/mkl" package, then LAPACK & BLAS will be found automatically

module load intel/mkl
module load tooldev/gsl-2.6

• Use external LAPACK & BLAS

  export myLAPACK=/uhome/p001cao/app/lapack-3.10/liblapack.a
  export myBLAS=/uhome/p001cao/app/lapack-3.10/libblas.a

  -DLAPACK_LIBRARIES=${myLAPACK} -DBLAS_LIBRARIES=${myBLAS}

8.OpenMP

-D PKG_USER-OMP=yes -D BUILD_OMP=yes -D PKG_USER-INTEL=no

9.make no packages

-D PKG_GPU=no -D PKG_KIM=no -D PKG_LATTE=no -D PKG_MSCG=no -D PKG_KOKKOS=no \
-D PKG_USER-ADIOS=no -D PKG_USER-NETCDF=no -D PKG_USER-OMP=no -D PKG_USER-INTEL=no \
-D PKG_USER-QUIP=no -D PKG_USER-SCAFACOS=no -D PKG_USER-QMMM=no -D PKG_USER-VTK=no \
-D PKG_USER-H5MD=no \

10.KOKKOS For multicore CPUs using OpenMP, set these 2 variables.

-DKokkos_ARCH_WSM=yes                 # HOSTARCH = HOST from list above
-DKokkos_ENABLE_OPENMP=yes
-DBUILD_OMP=yes

11.PLUMED

• pre-compile Plumed separately:

module load plumed

-D PKG_PLUMED=yes -D DOWNLOAD_PLUMED=no -D PLUMED_MODE=static

• self-build PLUMED:
• We will need GSL to link LAPACK, BLAS (require MKL)

• Cmake setting

  -D PKG_PLUMED=yes -D DOWNLOAD_PLUMED=yes -D PLUMED_MODE=static
  

• Can Configure Plumed to use Internal LAPACK&BLAS: (no need install BLAS&LAPACK or MKL+GSL). Edit file: ../cmake/Modules/Packages/PLUMED.cmake, Comment out these lines:

    # find_package(LAPACK REQUIRED)
    # find_package(BLAS REQUIRED)
    # find_package(GSL REQUIRED)
    # list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
  

• Edit file: ../cmake/Modules/Packages/PLUMED.cmake

  ###change lines:
      # URL http...... (line 65)
      # URL_MD5
  ### into:
        GIT_REPOSITORY https://github.com/plumed/plumed2.git
        GIT_TAG master                            # hack-the-tree   v2.6.2   v2.7b
  
        CONFIGURE_COMMAND <SOURCE_DIR>/configure  ....   ...
                    --enable-modules=all --enable-asmjit --disable-external-blas --disable-external-lapack
        ...
  ### add this command after line 76 (inside ExternalProject_Add(...)):
        UPDATE_COMMAND ""
  

• New udate from LAMMPS: LAPACK & BLAS now can be compiled internally in LAMMPS with option -DUSE_INTERNAL_LINALG=yes. So new setting in file: ../cmake/Modules/Packages/PLUMED.cmake should be

shell find_package(LAPACK REQUIRED) find_package(BLAS REQUIRED) find_package(GSL REQUIRED) list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)

```shell
###change lines:
    # URL http...... (line 65)
    # URL_MD5
### into:
      GIT_REPOSITORY https://github.com/plumed/plumed2.git
      GIT_TAG master                            # hack-the-tree   v2.6.2   v2.7b

      CONFIGURE_COMMAND <SOURCE_DIR>/configure  ....   ...
                  --enable-modules=all --enable-asmjit
      ...
### add this command after line 76 (inside ExternalProject_Add(...)):
      UPDATE_COMMAND ""
```

```sh
module load tooldev/gsl-2.7

-DPKG_PLUMED=yes -DUSE_INTERNAL_LINALG=yes  \
```

12.[ML_QUIP] (source code) compile QUIP the minimum requirements are:

• A working Fortran compiler. QUIP is tested with gfortran 4.4 and later, and ifort 11.1
• Linear algebra libraries BLAS and LAPACK. QUIP is tested with reference versions libblas-dev and liblapack-dev on Ubuntu 12.04, and mkl 11.1 with ifort.
• modify ML-QUIP.cmake : add this command after line 76 (inside ExternalProject_Add(...)):

    GIT_REPOSITORY "https://github.com/libAtoms/QUIP/"
    GIT_TAG          5989901       #   origin/public
    ...
    UPDATE_COMMAND ""

13.MLIAP

• require python >3.6

14.MACHDYN

• require Eigen

-D MACHDYN=yes -D DOWNLOAD_EIGEN3=yes

open file: ../cmake/Modules/Packages/USER-SMD.cmake

### change:
    URL http...... (line 12)
    URL_MD5
### into:
    GIT_REPOSITORY https://github.com/eigenteam/eigen-git-mirror.git
    GIT_TAG  3.3.7

14.MOLFILE package

• to dump PDB file, need install VMD-plugins
• compatible with VMD 1.9 and 1.9.1
• Compile VMD
• compile plugins (just this is need for Lammps) see this

tar zxvf vmd-1.9.src.tar.gz
cd plugins
make LINUXPPC64
export PLUGINDIR=/uhome/p001cao/local/wSourceCode/vmd/vmd-1.9/plugins
make distrib

• compile VMD

cd vmd-1.9.4a51
module load compiler/gcc-10.3
export VMDINSTALLDIR=/uhome/p001cao/app/vmd
./configure LINUXPPC64 OPENGL SILENT PTHREADS
cd src
make

• path in lib/molfile/Make.lammps: molfile_SYSPATH =-L/uhome/p001cao/local/wSourceCode/vmd/vmd-1.9/plugins/LINUXPPC64/molfile

export =/uhome/p001cao/local/wSourceCode/vmd/vmd-1.9/plugins/include

-D MOLFILE_INCLUDE_DIR=${PlugIncDIR}
-D PKG_MOLFILE=yes

15.PYTHON (use 1 of following ways)

Note: new numpy require higher GLIBC

• use module load → do not need setting in Cmake (but this may intefere some libs: openmpi,lapack,blas,... - should not use)

module load conda/py37Lammps

• use Python_ROOT_DIR (same as module load): → will encounter the error: Anaconda environments prevent CMake from generating a safe runtime search path → cannot be solved so far.

export pyROOT=/uhome/p001cao/app/miniconda3/envs/py37Lammps
-DPython_ROOT_DIR=${pyROOT}   # this setting must be put on the head of cmake

• use Python_EXECUTABLE # (Python_EXECUTABLE depend on cmake's version) (but this case still use system Python while compiling, so cannot use on multi-OS with different Versions )

export pyEXE=/uhome/p001cao/app/miniconda3/envs/py37Lammps/bin/python
export pyINC=/uhome/p001cao/app/miniconda3/envs/py37Lammps/include/python3.7m
export pyLIB=/uhome/p001cao/app/miniconda3/envs/py37Lammps/lib/libpython3.7m.a

-DPython_EXECUTABLE=${pyEXE} -DPython_INCLUDE_DIR=${pyINC} -DPython_LIBRARY=${pyLIB}

I. Compiling with GCC + OMPI

Note

• must export compilers to to avoid miss matching compilers

export PATH=/uhome/p001cao/app/openmpi/4.1.1-gcc11.2-noUCX-eagle/bin:$PATH
export CC=mpicc  export CXX=mpic++  export FORTRAN=mpifort
## can use: -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_Fortran_COMPILER=mpif90 \

• "GCC + gold linker" is good now

module load tooldev/binutils-2.36

-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt"

• use MKL

module load intel/mkl-xe19u5
source mklvars.sh intel64
module load tooldev/gsl-2.6

-DFFT=MKL

• use external BLAS&LAPACK instead of MKL

module load tooldev/gsl-2.6
export myLAPACK=/uhome/p001cao/app/lapack-3.10/liblapack.a
export myBLAS=/uhome/p001cao/app/lapack-3.10/libblas.a

-DBLAS_LIBRARIES=${myBLAS} -DLAPACK_LIBRARIES=${myLAPACK}

• use FFTW instead of MKL

module load fftw/fftw3.3.8-ompi4.1-gcc11.2

-DFFT=FFTW3

• consider linkers

module load llvm/llvm-gcc10-lld                    ## to use lld
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=lld -lrt" \
module load tooldev/binutils-2.35                ## gold
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \

USC1_Eagle - Centos 6.5 cluster with InfiniBand

Note

• use different openmpi for Eagle vs Lion
• Note: python>3.7.9 require GLIBC new conda install python=3.7.5 pandas=1.0 numpy=1.19
• Use GCC-11 need also update GCC-conda = 11 conda install -c conda-forge libstdcxx-ng=11 libgcc-ng=11 libgfortran-ng=11
• install GSL, required by SCAFACOS package

cd lammps_master
mkdir build   &&   cd build

## module load tooldev/gsl-2.6
module load tooldev/binutils-2.36         ## gold
module load tooldev/cmake-3.21
module load fftw/fftw3.3.10-ompi5.0-gcc11.2
module load mpi/ompi5.0.0-gcc11.2

export PATH=/uhome/p001cao/app/openmpi/5.0.0-gcc11.2-eagle/bin:$PATH
export CC=mpicc  export CXX=mpic++  export FC=mpifort  export F90=mpif90
## MOLFILE_plugins/ python 3/ LAPACK&BLAS
export PlugIncDIR=/uhome/p001cao/local/wSourceCode/vmd/vmd-1.9/plugins/include
export pyROOT=/uhome/p001cao/app/miniconda3/envs/py37Lammps

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DPython_ROOT_DIR=${pyROOT} -DMOLFILE_INCLUDE_DIR=${PlugIncDIR} \
-DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi -DPKG_OPENMP=yes \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=yes \
-DPKG_INTEL=no -DPKG_GPU=no -DPKG_KOKKOS=no \
-DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_VTK=no -DPKG_ML-PACE=no \
-DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_KIM=no -DPKG_H5MD=no \
-DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes -DDOWNLOAD_SCAFACOS=no -DPKG_SCAFACOS=no \
-DPKG_MESONT=no -DPKG_ML-QUIP=no \
-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DFFT=FFTW3 \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_Fortran_COMPILER=mpif90 \
-DCMAKE_INSTALL_PREFIX=/uhome/p001cao/app/lammps/gccOMPI5-dev

make -j 20
## test:  mpirun -np 2 lmp_mpi
make install

Module file

### Module file
module load conda/py37Lammps
module load fftw/fftw3.3.10-ompi5.0-gcc11.2
## for Tcl script use only
set     topdir          /uhome/p001cao/app/lammps/gccOMPI5-29Sep21

prepend-path    PATH                    $topdir/bin
prepend-path    LD_LIBRARY_PATH         $topdir/lib64
prepend-path    INCLUDE                 $topdir/include/lammps

prepend-path    PATH  /uhome/p001cao/local/wSourceCode/vmd/vmd-1.9/plugins/LINUXPPC64/molfile

USC2_Tachyon - Centos 6.9 cluster with InfiniBand

git pull origin develop

module load tooldev/binutils-2.37                ## gold
module load tooldev/cmake-3.20.3
module load fftw/fftw3.3.10-ompi4.1.3-gcc10.3
module load mpi/ompi4.1.3-gcc10.3

export PATH=$PATH:/home1/p001cao/app/openmpi/4.1.3-gcc10.3/bin
export CC=mpicc  export CXX=mpic++  export FC=mpifort  export F90=mpif90
export CFLAGS='-gdwarf-4 -gstrict-dwarf'
### python (require py3) & BLAS+LAPACK
export pyROOT=/home1/p001cao/app/miniconda3/envs/py37Lammps

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DPython_ROOT_DIR=${pyROOT} \
-DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi -DPKG_OPENMP=yes \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=no \
-DPKG_INTEL=no -DPKG_GPU=no -DPKG_KOKKOS=no \
-DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_VTK=no -DPKG_H5MD=no \
-DPKG_MESONT=no -DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_KIM=no -DPKG_SCAFACOS=no \
-DPKG_ML-PACE=yes -DPKG_ML-QUIP=no -DPKG_ML-HDNNP=no -DPKG_MDI=no \
-DPKG_PLUMED=yes \
-DFFT=FFTW3 \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/gccOMPI4-dev

make -j 16 && make install

### no need download option
-DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes -DDOWNLOAD_PLUMED=yes -DDOWNLOAD_QUIP=yes\

use OMPI_5

module load tooldev/binutils-2.37                ## gold
module load tooldev/cmake-3.20.3
module load fftw/fftw3.3.10-ompi5.0-gcc11.2
module load mpi/ompi5.0.0-gcc10.3

export pyROOT=/home1/p001cao/app/miniconda3/envs/py37Lammps

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DPython_ROOT_DIR=${pyROOT} \
-DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi -DPKG_OPENMP=yes \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=no \
-DPKG_INTEL=no -DPKG_GPU=no -DPKG_KOKKOS=no \
-DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_VTK=no -DPKG_ML-PACE=no \
-DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_KIM=no -DPKG_H5MD=no \
-DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes -DDOWNLOAD_SCAFACOS=no -DPKG_SCAFACOS=no \
-DPKG_MESONT=no -DPKG_ML-QUIP=yes -DDOWNLOAD_QUIP=yes \
-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DFFT=FFTW3 \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/gccOMPI5-dev

use OMPI_3

• This does not work, due to OMPI3 error

module load tooldev/binutils-2.37                ## gold
module load cmake/3.16.2
module load fftw/3.3.8/gcc-7.4.0/ompi-3.1.4/double
module load mpi/gcc-7.4.0/ompi/3.1.4

export pyROOT=/home1/p001cao/app/miniconda3/envs/py37Lammps

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DPython_ROOT_DIR=${pyROOT} \
-DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi -DPKG_OPENMP=yes \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=yes \
-DPKG_INTEL=no -DPKG_GPU=no -DPKG_KOKKOS=no \
-DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_VTK=no -DPKG_ML-PACE=no \
-DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_KIM=no -DPKG_H5MD=no \
-DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes -DDOWNLOAD_SCAFACOS=no -DPKG_SCAFACOS=no \
-DPKG_MESONT=no -DPKG_ML-QUIP=no \
-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DFFT=FFTW3 \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/gccOMPI3-dev

## use Internal LAPACK&BLAS, then no need (GSL & MKL): open file: ../cmake/Modules/Packages/USER_PLUMED.cmake comment out line 9→12: find LAPACK, BLAS, GSL (Plumed build itself, no need GSL anymore) → then, do not need these: module load tooldev/gsl-2.6 module load intel/mkl-xe19u5 source mklvars.sh intel64 -DFFT=MKL ## must set before Plumed ## or use openBLAS (bad performance) module load tooldev/gsl-2.6 export myBLAS=/home1/p001cao/app/tooldev/openBLAS-0.3.19/lib64/libopenblas.a -DBLAS_LIBRARIES=\({myBLAS} -DLAPACK_LIBRARIES=\)

## load plumed separately (bad alloc) module load plumed2/2.7htt-gcc -DPKG_USER-PLUMED=yes -DDOWNLOAD_PLUMED=no -DPLUMED_MODE=shared \

##openKim: must create module file for openKim to add its PKG's path

Module file

module load tooldev/gsl-2.6
module load conda/py37Lammps
module load fftw/fftw3.3.10-ompi5.0-gcc11.2

## for Tcl script use only
set     topdir          /home1/p001cao/app/lammps/gccOMPI5-dev

prepend-path    PATH                    $topdir/bin
prepend-path    LD_LIBRARY_PATH         $topdir/lib64
prepend-path    INCLUDE                 $topdir/include/lammps

CAN2_GPU - Centos 7 cluster with GPU

• See GPU package

## cuda
export CUDA_PATH=/home/thang/app/cuda-10.2
export bin2c=/home/thang/app/cuda-10.2/bin/bin2c

-DPKG_GPU=yes -DGPU_API=cuda -DGPU_ARCH=sm_61 -DBIN2C=${bin2c} -DGPU_PREC=double \

• for Pascal architect of GPU, use ARCH=sm_60/sm_61

module load mpi/ompi4.1-gcc7.4-cuda      ## cuda-10 only support to gcc-8
module load cmake-3.20.3
module load fftw/fftw3.3.8-ompi4.1-gcc7.4

export PATH=$PATH:/home/thang/app/openmpi/4.1.1-gcc7.4-cuda/bin
export CC=mpicc  export CXX=mpic++  export FC=mpifort  export F90=mpif90
## python (require py3)
export pyROOT=/home/thang/app/miniconda3/envs/py37Lammps
## cuda
export CUDA_PATH=/home/thang/app/cuda-10.2
export bin2c=/home/thang/app/cuda-10.2/bin/bin2c

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DPython_ROOT_DIR=${pyROOT} \
-DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi -DPKG_OPENMP=yes \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=no \
-DPKG_INTEL=no -DPKG_KOKKOS=no \
-DPKG_GPU=yes -DGPU_API=cuda -DGPU_ARCH=sm_61 -DBIN2C=${bin2c} -DGPU_PREC=double \
-DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_VTK=no -DPKG_ML-PACE=no \
-DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_KIM=no -DPKG_H5MD=no \
-DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes -DDOWNLOAD_SCAFACOS=no -DPKG_SCAFACOS=no \
-DPKG_MESONT=no -DPKG_ML-QUIP=no \
-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DFFT=FFTW3 \
-DCMAKE_INSTALL_PREFIX=/home/thang/app/lammps/gccOMPI-dev

CAN3_GPU - Ubuntu 20 with GPU

• python and fftw are availabe by command

sudo apt-get install -y fftw-dev

module load ompi/4.1.0-gcc7.5-cuda10.2      ## cuda-10 only support to gcc-8
module load cmake-3.18.3

export PATH=$PATH:/opt/app/openmpi/4.1.0-gcc7.5-cuda10.2/bin
export CC=mpicc  export CXX=mpic++  export FC=mpifort  export F90=mpif90
## cuda (python is availabe on Ubuntu)
export CUDA_PATH=/usr/local/cuda-11.0
export bin2c=/usr/local/cuda-11.0/bin/bin2c

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DPython_ROOT_DIR=${pyROOT} \
-DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi -DPKG_OPENMP=yes \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_SHARED_LIBS=no \
-DPKG_INTEL=no -DPKG_KOKKOS=no \
-DPKG_GPU=yes -DGPU_API=cuda -DGPU_ARCH=sm_61 -DBIN2C=${bin2c} -DGPU_PREC=double \
-DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_VTK=no -DPKG_ML-PACE=no \
-DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_KIM=no -DPKG_H5MD=no \
-DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes -DDOWNLOAD_SCAFACOS=no -DPKG_SCAFACOS=no \
-DPKG_MESONT=no -DPKG_ML-QUIP=yes -DDOWNLOAD_QUIP=yes -DPKG_ML-IAP=no \
-DPKG_PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DFFT=FFTW3 \
-DCMAKE_INSTALL_PREFIX=/opt/app/lammps/master-gpu

make -j 24 && sudo make install

#######################################

KOKKOS (USC 2) - 05May20 (error tbb_malloc  --> change TBB folder in file TBB.cmake)

-DBUILD_OMP=yes -DKokkos_ARCH_WSM=yes -DKokkos_ENABLE_OPENMP=yes  \
-DLMP_KOKKOS_USE_ATOMICS=yes -DKokkos_ENABLE_HWLOC=yes \

### TBB lib

set     topdir          /home1/p001cao/local/wSourceCode/Tooldev/oneTBB-2020.2
setenv          TBBROOT                 $topdir/bin
prepend-path    INCLUDE          $topdir/include
prepend-path    LD_LIBRARY_PATH         $topdir/build/linux_intel64_gcc_cc9.2.0_libc2.12_kernel2.6.32_release


###-- edit /cmake/Modules/FindTBB_MALLOC.cmake

find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb.h PATHS $ENV{TBBROOT}/include/tbb)
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
$ENV{TBBROOT}/build/linux_intel64_gcc_cc9.2.0_libc2.12_kernel2.6.32_release)


https://github.com/kokkos/kokkos/blob/master/BUILD.md
###-- must use
https://stackoverflow.com/questions/52018092/how-to-set-rpath-and-runpath-with-gcc-ld##52020177
export myGCC=/home1/p001cao/app/compiler/gcc-9.2.0
-DCMAKE_CXX_LINK_FLAGS="-L${myGCC}/lib64 -Wl,-rpath,${myGCC}/lib64" \

module load mpi/ompi4.0.3-gcc9.2.0
module load tooldev/gsl-2.6
module load tooldev/cmake-3.17.2

module load tooldev/binutils-2.32
module load tooldev/tbb-2020.2
 export TBB_MALLOC_LIBRARY
 export TBB_MALLOC_INCLUDE_DIR
cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DBUILD_MPI=yes -DLAMMPS_MACHINE=mpi \
-DBUILD_OMP=yes -DKokkos_ARCH_WSM=yes -DKokkos_ENABLE_OPENMP=yes  \
-DBUILD_SHARED_LIBS=yes -DLAMMPS_EXCEPTIONS=yes \
-DPKG_GPU=no -DPKG_LATTE=no -DPKG_KIM=no -DPKG_MSCG=no -DPKG_USER-INTEL=no\
-DDOWNLOAD_VORO=yes -DDOWNLOAD_EIGEN3=yes \
-DPKG_USER-ADIOS=no -DPKG_USER-NETCDF=no -DPKG_USER-QUIP=no -DPKG_USER-SCAFACOS=no \
-DPKG_USER-QMMM=no -DPKG_USER-VTK=no -DPKG_USER-H5MD=no \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/05May20-gcc

GCC + OpenSHMEM

module load mpi/ompi4.1.0-gcc10.2
module load tooldev/binutils-2.35                ## gold
module load tooldev/cmake-3.18.0
module load fftw/fftw3.3.8-ompi4.1-gcc10.2

export PATH=$PATH:/home1/p001cao/app/openmpi/4.1.0-gcc10.2/bin
export CC=shmemcc
export CXX=shmemc++
export FORTRAN=shmemfort
cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi \
-DPKG_USER-OMP=yes -DPKG_USER-INTEL=no -DPKG_GPU=no -DPKG_KOKKOS=no \
-DPKG_USER-SMD=yes -DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes \
-DPKG_KIM=no -DDOWNLOAD_KIM=no -DPKG_LATTE=no -DPKG_MSCG=no -DPKG_USER-ATC=no -DPKG_USER-MESONT=no  \
-DPKG_USER-ADIOS=no -DPKG_USER-NETCDF=no -DPKG_USER-QUIP=no -DPKG_USER-SCAFACOS=no \
-DPKG_USER-VTK=no -DPKG_USER-H5MD=no \
-DFFT=FFTW3 \
-DPKG_USER-PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_Fortran_COMPILER=mpifort \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/gccSHMEM-master

Compile with openMPI4.0.1-gcc7.4.0 on CAN

module load mpi/openmpi4.0.2-gcc7.4.0
module load cmake-3.12

-D PKG_USER-ATC=no -D PKG_VORONOI=no -D PKG_USER-SMD=no -D PKG_USER-PLUMED=no

cmake  -C ../cmake/presets/all_on.cmake \
-D CMAKE_INSTALL_PREFIX=/home/thang/app/lammps/20Nov19 \
-D BUILD_MPI=yes -D LAMMPS_MACHINE=mpi \
-D BUILD_LIB=yes -D BUILD_SHARED_LIBS=yes -D LAMMPS_EXCEPTIONS=yes \
-D PKG_GPU=no -D PKG_KIM=no -D PKG_LATTE=no -D PKG_MSCG=no -D PKG_KOKKOS=no \
-D PKG_USER-ATC=no -D PKG_VORONOI=no -D PKG_USER-SMD=no \
-D BUILD_OMP=yes -D PKG_USER-OMP=yes -D PKG_USER-INTEL=no \
-D PKG_USER-ADIOS=no -D PKG_USER-NETCDF=no -D PKG_USER-QUIP=no -D PKG_USER-SCAFACOS=no \
-D PKG_USER-QMMM=no -D PKG_USER-VTK=no -D PKG_USER-H5MD=no \
-D PKG_USER-PLUMED=no -D DOWNLOAD_PLUMED=no -D PLUMED_MODE=shared \
-D CMAKE_C_COMPILER=mpicc  -D CMAKE_CXX_COMPILER=mpic++ -D CMAKE_Fortran_COMPILER=mpifort \
../cmake

MVAPICH-GCC

module load mpi/mvapich2-2.3.2-gcc9.2.0 module load plumed2/2.7htt-mvapich module load conda/py37mvapichSupp

Configure

cmake ../cmake -DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-C ../cmake/presets/all_on.cmake \
-DBUILD_MPI=yes -DLAMMPS_MACHINE=mpi \
-DBUILD_OMP=yes -DPKG_USER-OMP=yes -DPKG_USER-INTEL=no \
-DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes -DLAMMPS_EXCEPTIONS=yes \
-DPKG_GPU=no -DPKG_LATTE=no -DPKG_KOKKOS=no -DPKG_KIM=no -DPKG_MSCG=no \
-DDOWNLOAD_VORO=yes -DDOWNLOAD_EIGEN3=yes \
-DPKG_USER-ADIOS=no -DPKG_USER-NETCDF=no -DPKG_USER-QUIP=no -DPKG_USER-SCAFACOS=no \
-DPKG_USER-QMMM=no -DPKG_USER-VTK=no -DPKG_USER-H5MD=no \
-DPKG_USER-PLUMED=yes -DDOWNLOAD_PLUMED=no -DPLUMED_MODE=shared \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_Fortran_COMPILER=mpifort \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/19Mar20-mva

https://github.com/lammps/lammps/blob/master/lib/message/cslib/src/STUBS_ZMQ/zmq.h

A. Compile Lammps19 with openMPI-4.0.2, Intel2019xe and MKL (w/wt FFTW-3.3.8) (USC) II: Load modules module load mpi/ompi4.0.2-Intel2019xe-noIB module load intel/mkl-2019xe module load gcc/gcc-7.4.0 module load plumed2/2.6htt module load cmake-3.15.1 III: Compiling LAMMPS

• if occur error not found compiler, use this command to find path

find / -name icpc find / -name ifort

find / -name icc

iii. Compile lammps cd lammps-folder mkdir build cd build

Step1: configuration

Note: write CMAKE command below on single line

cmake  -C ../cmake/presets/all_on.cmake \
-D CMAKE_INSTALL_PREFIX=/uhome/p001cao/local/lammps/20Nov19 \
-D BUILD_MPI=yes -D LAMMPS_MACHINE=mpi \
-D BUILD_LIB=yes -D BUILD_SHARED_LIBS=yes -D LAMMPS_EXCEPTIONS=yes \
-D PKG_GPU=no -D PKG_KIM=no -D PKG_LATTE=no -D PKG_MSCG=no -D PKG_KOKKOS=no \
-D DOWNLOAD_VORO=yes -D DOWNLOAD_EIGEN3=yes \
-D BUILD_OMP=yes -D PKG_USER-OMP=yes -D PKG_USER-INTEL=no \
-D PKG_USER-ADIOS=no -D PKG_USER-NETCDF=no -D PKG_USER-QUIP=no -D PKG_USER-SCAFACOS=no \
-D PKG_USER-QMMM=no -D PKG_USER-VTK=no -D PKG_USER-H5MD=no \
-D PKG_USER-PLUMED=yes -D DOWNLOAD_PLUMED=no -D PLUMED_MODE=shared \
-D FFT=MKL \
-D MKL_LIBRARY=/uhome/p001cao/local/intel/xe2019/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 \
-D CMAKE_C_COMPILER=mpicc  -D CMAKE_CXX_COMPILER=mpic++ -D CMAKE_Fortran_COMPILER=mpifort \
../cmake

Step 2: compile ( in /build) make -j 8 test: mpirun -np 2 lmp_mpi LAMMPS (19 Jul 2019) Total wall time: 0:00:21

step 3: copy file make install

Step 4: create module file create file "7Aug19"

## for Tcl script use only
set     topdir          /uhome/p001cao/local/lammps/7Aug19
set     version         7Aug19

module load  mpi/openMPI/4.0.2-Intel2018xe
module load  fftw/3.3.8/openmpi4.0.2-intel2018xe-double
module load  conda2-2019
module load  plumed2/2.6.0


setenv          LAMMPS                  $topdir

prepend-path    PATH                                    $topdir/bin
prepend-path    LD_LIBRARY_PATH         $topdir/lib64
prepend-path    INCLUDE                            $topdir/include/lammps

save it in: /uhome/p001cao/local/share/lmodfiles/lammps Ref: https://lammps.sandia.gov/doc/Build_basics.html

USC2

Note: Kokkos may require TBB lib → might only Intel can work

## Download specific TAG: git clone --branch <tag_name> <repo_url>
git clone --branch stable_3Mar2020 https://github.com/lammps/lammps.git lammps_stable_3Mar2020
cd lammps_stable_3Mar2020
mkdir build
cd build
###--- module load mpi/ompi4.0.3-intel19u5 module load intel/mkl-xe19u5 module load plumed2/2.7htt module load tooldev/cmake-3.17.2

Configure

cmake ../cmake -C ../cmake/presets/all_on.cmake \ -DBUILD_MPI=yes -DLAMMPS_MACHINE=mpi \ -DBUILD_OMP=yes -DKokkos_ARCH_WSM=yes -DKokkos_ENABLE_OPENMP=yes \ -DBUILD_SHARED_LIBS=yes -DLAMMPS_EXCEPTIONS=yes \ -DPKG_GPU=no -DPKG_LATTE=no -DPKG_KIM=no -DPKG_MSCG=no -DPKG_USER-INTEL=no\ -DDOWNLOAD_VORO=yes -DDOWNLOAD_EIGEN3=yes \ -DPKG_USER-ADIOS=no -DPKG_USER-NETCDF=no -DPKG_USER-QUIP=no -DPKG_USER-SCAFACOS=no \ -DPKG_USER-QMMM=no -DPKG_USER-VTK=no -DPKG_USER-H5MD=no \ -DPKG_USER-PLUMED=yes -DDOWNLOAD_PLUMED=no -DPLUMED_MODE=shared \ -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ \ -DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/05May20

Compile with IMPI-2019xe + MKL

Note: use intelMPI can run all both centos7 & centos6

USC1_Eagle - Centos 6.5 cluster with InfiniBand

Load modules

module load intel/compiler-xe19u5
module load mpi/impi-xe19u5
module load intel/mkl-xe19u5
module load plumed2/2.6httIMPI
module load conda/py37
module load cmake-3.15.1

configuration
cd lammps-folder
mkdir build
cd build
cmake  -C ../cmake/presets/all_on.cmake \
-D CMAKE_INSTALL_PREFIX=/uhome/p001cao/app/lammps/20Nov19impi \
-D BUILD_MPI=yes -D LAMMPS_MACHINE=mpi \
-D BUILD_LIB=yes -D BUILD_SHARED_LIBS=yes -D LAMMPS_EXCEPTIONS=yes \
-D PKG_GPU=no -D PKG_KIM=no -D PKG_LATTE=no -D PKG_MSCG=no -D PKG_KOKKOS=no \
-D DOWNLOAD_VORO=yes -D DOWNLOAD_EIGEN3=yes \
-D BUILD_OMP=yes -D PKG_USER-OMP=yes -D PKG_USER-INTEL=no \
-D PKG_USER-ADIOS=no -D PKG_USER-NETCDF=no -D PKG_USER-QUIP=no -D PKG_USER-SCAFACOS=no \
-D PKG_USER-QMMM=no -D PKG_USER-VTK=no -D PKG_USER-H5MD=no \
-D PKG_USER-PLUMED=yes -D DOWNLOAD_PLUMED=no -D PLUMED_MODE=shared \
-D FFT=MKL \
-D MKL_LIBRARY=/uhome/p001cao/app/intel/xe19u5/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin \
-D CMAKE_C_COMPILER=mpiicc -D CMAKE_CXX_COMPILER=mpiicpc -D CMAKE_Fortran_COMPILER=mpiifort \
../cmake

make -j 8
test:  mpirun -np 2 ./lmp_mpi
make install

Step 4: create module file create file "7Aug19-Impi"

module load intel/2019xe module load mpi/impi-2019xe module load plumed2/2.6.0-Impi module load conda2-2019 setenv LAMMPS $topdir

prepend-path PATH $topdir/bin prepend-path LD_LIBRARY_PATH $topdir/lib64 prepend-path INCLUDE $topdir/include/lammps

### 2. USC 2

```shell
module load compiler/gcc-10.2              # must load before impi
module load intel/compiler-xe19u5           # intel include lld linker  require GLIBC 2.15
module load intel/mkl-xe19u5
module load intel/impi-xe19u5
source mpivars.sh release
module load tooldev/cmake-3.18.0
module load tooldev/gsl-2.6
module load tooldev/binutils-2.32                # gold

export PATH=$PATH:/home1/p001cao/app/intel/xe19u5/compilers_and_libraries_2019.5.281/linux/bin
export CC=mpiicc
export CXX=mpiicpc
export FORTRAN=mpiifort

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=gold -lrt" \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi \
-DPKG_USER-OMP=yes -DPKG_USER-INTEL=yes -DPKG_GPU=no -DPKG_KOKKOS=no \
-DPKG_USER-SMD=yes -DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes \
-DPKG_KIM=no -DDOWNLOAD_KIM=no -DPKG_LATTE=no -DPKG_MSCG=no -DPKG_USER-ATC=no \
-DPKG_USER-ADIOS=no -DPKG_USER-NETCDF=no -DPKG_USER-QUIP=no -DPKG_USER-SCAFACOS=no \
-DPKG_USER-VTK=no -DPKG_USER-H5MD=no \
-DFFT=MKL \
-DPKG_USER-PLUMED=yes -DDOWNLOAD_PLUMED=yes\
-DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc -DCMAKE_Fortran_COMPILER=mpiifort \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/app/lammps/impi-master
#-- NOTE: Kokkos require TBB lib
module load intel/tbb-xe20u2
##-- edit /cmake/Modules/FindTBB_MALLOC.cmake
find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb.h PATHS $ENV{TBBROOT}/include/tbb)
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.8)
##--
-DCMAKE_EXE_LINKER_FLAGS="-fuse-ld=lld -lrt" \
source compilervars.sh intel64
source mklvars.sh intel64

Compiling with LLVM + OMPI

USC2_Tachyon - Centos 6.9 cluster with InfiniBand

Note

• To void libs hidden by conda-lib, set absolute path for dynamic libs (*.so). See compile LLVM for more information
• if the error relates to conda (require new GLIBC),
  • relate to zlib, install lower version conda install -c conda-forge zlib=1.2.11
  • relate to libstdc++, use export LD_LIBRARY_PATH=path/to/new/lib:$LD_LIBRARY_PATH
• if the error relates to `openmpi/mca_pmix_pmix3x.so: undefined symbol:' → delete isntall folder and reinstall

Info

• can use export CFLAGS, export CXXFLAGS. This same as -DCMAKE_CXX_LINK_FLAGS (CPPFLAG means both)
• LDFLAGS same as CMAKE_EXE_LINKER_FLAGS
• Some packages, such as QUIP, LATTE, PLUMED... requires LAPACK (and BLAS), which may not available on some systems. Then, use -DUSE_INTERNAL_LINALG=yes to install them, internally. With this option, we don't need to compile LAPACK & BLAS in PLUMED, so this make a simplified setting for PLUMED. Note to load moduletooldev/gsl-2.7for automatically findLAPACK & BLAS`.
• LEPTON_ENABLE_JIT requires 'sys/auxv.h' that is only available on newer GLIBC. So disable it.

cd /home1/p001cao/0SourceCode/lammps_dev
git pull origin develop
rm -rf build_LLVM && mkdir build_LLVM && cd build_LLVM

module load tooldev/cmake-3.27
module load tooldev/binutils-2.40
module load tooldev/gsl-2.7
module load mpi/fftw3.3.10-ompi4.1.x-clang17
module load mpi/ompi4.1.x-clang17-ucx1.15

OPENMPI=/home1/p001cao/app/mpi/openmpi4.1.x-clang17-ucx1.15
export PATH=${OPENMPI}/bin:$PATH
export CC=mpicc CXX=mpic++ FC=mpifort
export LDFLAGS="-fuse-ld=lld -lrt"
## python (require py3), BLAS+LAPACK
export LD_LIBRARY_PATH=/home1/p001cao/app/compiler/gcc-11/lib64:$LD_LIBRARY_PATH   # to avoid using libstdc++.so in conda
myBLAS=/home1/p001cao/app/tooldev/openBLAS0.3.23-clang17/lib64/libopenblas.so
myPREFIX=/home1/p001cao/app/lammps/llvmOMPI4-dev

cmake ../cmake -C ../cmake/presets/all_on.cmake \
  -DBUILD_MPI=yes -DBUILD_OMP=yes -DPKG_OPENMP=yes \
  -DLAMMPS_MACHINE=mpi -DBUILD_SHARED_LIBS=yes \
  -DPKG_GPU=no -DPKG_KOKKOS=no -DPKG_INTEL=no -DPKG_MDI=no \
  -DPKG_SCAFACOS=no -DPKG_ADIOS=no -DPKG_NETCDF=no -DPKG_VTK=no -DPKG_H5MD=no \
  -DPKG_MESONT=no -DPKG_LATTE=no -DPKG_MSCG=no -DPKG_ATC=no -DPKG_KIM=no \
  -DPKG_LEPTON=yes -DLEPTON_ENABLE_JIT=no \
  -DPKG_ML-QUIP=no -DPKG_ML-PACE=no -DPKG_ML-HDNNP=no \
  -DPKG_PLUMED=yes -DUSE_INTERNAL_LINALG=yes  \
  -DFFT=FFTW3 -DBLAS_LIBRARIES=${myBLAS} -DLAPACK_LIBRARIES=${myBLAS} \
  -DCMAKE_INSTALL_PREFIX=${myPREFIX}

make -j 16 && make install

with python

export pyROOT=/home1/p001cao/app/miniconda3/envs/py39link_lammps
export myZLIB=/home1/p001cao/app/tooldev/zlib-1.2.12               # avoid zlib hidden by conda

-DPython_ROOT_DIR=${pyROOT} \
-DZLIB_INCLUDE_DIR=${myZLIB}/include -DZLIB_LIBRARY=${myZLIB}/lib/libz.so.1.2.12 \

Compile with Conda

This way may eliminate some work on installing dependencies

See this link