Linux non-root user installation lamps

#Install lamps-7Aug19 (version: 2019-08-07)

For convenience, I created a folder /home/hsiung/software/lammps. All files are downloaded and installed in this folder.

cat /etc/redhat-release

Use the cat command to check the version: CentOS Linux release 7.9.2009 (Core)

1. Download and install openmpi (mpich can also be used, see the installation process of lamps-10Aug15 below for details)

openmpi official website https://www.open-mpi.org/software/ompi/v4.1/

Here I downloaded openmpi-4.1.1.tar.gz and uploaded it to the folder

#Decompress
   tar -zxvf openmpi-4.1.1.tar.gz
   
   cd openmpi-4.1.1

#Create a folder to use as the installation location of openmpi

   mkdir openmpi411
   
   ./configure --prefix=/home/hsiung/software/lammps/openmpi411

? make

   make install

#If no error is reported, the installation is basically successful. Then add environment variables.

   vim ~/.bashrc

   export PATH=/home/hsiung/software/lammps/openmpi411/bin:$PATH
   export LD_LIBRARY_PATH=/home/hsiung/software/lammps/openmpi411/lib/:$LD_LIBRARY_PATH

   source ~/.bashrc

2. Download and install fftw

fftw official website https://www.fftw.org/download.html

Here I downloaded fftw-3.3.10.tar.gz and uploaded it to the folder

#Decompress
   tar -zxvf fftw-3.3.10.tar.gz
   
   cd fftw-3.3.10

#Create a folder to use as the installation location of fftw3310

   mkdir fftw3310
   
   ./configure --prefix=/home/hsiung/software/lammps/fftw3310

? make

   make install

#If no error is reported, the installation is basically successful. Then add environment variables.

   vim ~/.bashrc

   export PATH=/home/hsiung/software/lammps/fftw3310/bin:$PATH
   export LD_LIBRARY_PATH=/home/hsiung/software/lammps/fftw3310/lib:$LD_LIBRARY_PATH

   source ~/.bashrc

3. Lammps software package download

lammps official website https://download.lammps.org/tars/index.html

Download the lammps-7Aug2019.tar.gz installation package and upload it to the folder

#Decompress
   tar -zxvf lammps-7Aug2019.tar.gz
   
   cd /home/hsiung/software/lammps/lammps-7Aug19/src/MAKE

#Modify the Makefile.mpi file

# MPI library
# see discussion in Section 2.2 (step 5) of manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library

MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/home/hsiun/software/lammps/openmpi411/include
MPI_PATH = -L/home/hsiung/software/lammps/openmpi411/lib
MPI_LIB = -lmpi

#FFT library
# see discussion in Section 2.2 (step 6) of manual
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library

FFT_INC = -DFFT_FFTW3 -I/home/hsiung/software/lammps/fftw3310/include
FFT_PATH = -L/home/hsiung/software/lammps/fftw3310/lib
FFT_LIB = -lfftw3

#Then enter the src directory:
   cd..
   make yes-all
   make no-lib
   make mpi

Error reporting

#If no error is reported here, an lmp_mpi file will be generated.
     ls -ali lmp_mpi
     697286107 -rwxrwxr-x. 1 hsiung hsiung 104631768 Nov 2 08:45 lmp_mpi
#If an error is reported here
     make[1]: *** [Makefile:89: ../lmp_mpi] Error 1
     make[1]: Leaving directory '/home/hsiung/software/lammps/lammps-7Aug19/src/Obj_mpi'
     make: *** [Makefile:212: mpi] Error 2
   #Clear old compiled files
       make clean-all
   #Check whether the Makefile.mpi file has been modified improperly
       make mpi

#Add environment variables
   vim ~/.bashrc

   export PATH=/home/hsiung/software/lammps/lammps-7Aug19/src:$PATH

   source ~/.bashrc

#test
     cd /home/hsiung/software/lammps/lammps-7Aug19/examples
  #For example, enter melt
     cd /home/hsiung/software/lammps33/lammps-7Aug19/examples/melt
     mpirun -np 1 lmp_mpi < in.melt

#File deletion (because the disk capacity is limited, tar.gz and decompressed files can be deleted according to your own needs)

rm-rf lammps-7Aug2019.tar.gz lammps-7Aug2019 fftw-3.3.10.tar.gz fftw-3.3.10 openmpi-4.1.1.tar.gz openmpi-4.1.1

#Install lamps-10Aug15 (version: 2015-08-10)

%%%Because I need to use a package developed by others, I found that I kept getting errors after installing version 19, so I checked the date of the package developed by the author, so I tried to install the version of lamps corresponding to the date.

1. Download and install mpich (openmpi is not used here because the lamps-10Aug15 manual (/doc/Manual.pdf is included in the decompressed package) mentioned that it may be incompatible, so I chose to install mpich)

mpich official website https://www.mpich.org/static/downloads/

Here I downloaded mpich-3.2.1.tar.gz and uploaded it to the folder

 #Decompress
    tar -zxvf mpich-3.2.1.tar.gz
   
    cd mpich-3.2.1.tar.gz

 #Create a folder to use as the installation location of mpich

    mkdir mpich321
   
    ./configure --prefix=/home/hsiung/software/lammps/mpich321

? make

    make install

#If no error is reported, the installation is basically successful. Then add environment variables.

 vim ~/.bashrc

   export MPI=/home/hsiung/software/lammps/mpich321
   export PATH=$MPI/bin:$PATH
   export LD_LIBRARY_PATH=$MPI/lib:$LD_LIBRARY_PATH
   export MANPATH=$MANPATH:$MPI/share/man
   export INFOPATH=$INFOPATH:$MPI/share/man
   export INCLUDE=$MPI/include:$INCLUDE

   source ~/.bashrc

2. Download and install fftw (see the lamps-7Aug19 installation process above for details)

3. Lammps software package download

(For details, please see the installation process of lamps-7Aug19 above)

#Modify the Makefile.mpi file

#LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual

LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 ###Old versions are not complete here, and may appear during compilation’Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS for your LAMMPS makefile’

MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/home/hsiung/software/lammps/mpich321/include
MPI_PATH = -L/home/hsiung/software/lammps/mpich321/include
MPI_LIB = -lmpi

FFT_INC = -DFFT_FFTW3 -I/home/hsiung/software/lammps/fftw3310/include
FFT_PATH = -L/home/hsiung/software/lammps/fftw3310/lib
FFT_LIB = -lfftw3

#Then enter the src directory:

cd /home/hsiung/software/lammps/lammps-10Aug15/src
 
make yes-ASPHERE yes-BODY yes-CLASS2 yes-COLLOID yes-COMPRESS yes-CORESHELL yes-DIPOLE yes-GRANULAR yes-KSPACE yes-MANYBODY yes-MC yes-MISC yes-MOLECULE yes-MPIIO yes-OPT yes-PERI yes -QEQ yes-REPLICA yes-RIGID yes-SHOCK yes-SNAP yes-SPIN yes-SRD

#Compile poems library

cd /home/hsiung/software/lammps/lammps-10Aug15/lib/poems
rm*.o
make -f Makefile.g++
cd /home/hsiung/software/lammps/lammps-10Aug15/src
make yes-poems

#Compile mean library

cd /home/hsiung/software/lammps/lammps-10Aug15/lib/mean
rm*.o
make -f Makefile.gfortran
cp Makefile.lammps.gfortran Makefile.lammps
cd /home/hsiung/software/lammps/lammps-10Aug15/src
make yes-meam

#Compile reax library

cd /home/hsiung/software/lammps/lammps-10Aug15/lib/reax
rm*.o
make -f Makefile.gfortran
cp Makefile.lammps.gfortran Makefile.lammps
cd /home/hsiung/software/lammps/lammps-10Aug15/src
make yes-reax

#Compile user library

cd /home/hsiung/software/lammps/lammps-10Aug15/src
 
make yes-USER-BOCS yes-USER-CGDNA yes-USER-CGSDK yes-USER-DIFFRACTION yes-USER-DPD yes-USER-DRUDE yes-USER-EFF yes-USER-FEP yes-USER-INTEL yes-USER- LB yes-USER-MANIFOLD yes-USER-MEAMC yes-USER-MESO yes-USER-MGPT yes-USER-MISC yes-USER-MOFFF yes-USER-MOLFILE yes-USER-OMP yes-USER-PHONON yes-USER- PTM yes-USER-QTB yes-USER-REAXC yes-USER-SMTBQ yes-USER-SDPD yes-USER-SPH yes-USER-TALLY yes-USER-UEF

make mpi

#For the following steps, refer to the lamps-7Aug19 installation process.

Study notes (if there is any infringement, it will be deleted if contacted)

Reference materials

http://t.csdnimg.cn/rw5TE

http://t.csdnimg.cn/kUs5C

Does anyone know how to install lamps? Can you teach me? – yellow fish’s answer – Zhihu
https://www.zhihu.com/question/378572817/answer/2847696158

Does anyone know how to install lamps? Can you teach me? – Answer from Gentai Technology – Zhihu
https://www.zhihu.com/question/378572817/answer/2278958243

#Install lamps-7Aug19 (version: 2019-08-07)

1. Download and install openmpi (mpich can also be used, see the installation process of lamps-10Aug15 below for details) openmpi official website https://www.open-mpi.org/software/ompi/v4.1/

2. Download and install fftw fftw official website https://www.fftw.org/download.html

3. Lammps software package download

#Install lamps-10Aug15 (version: 2015-08-10)

1. Download and install mpich (openmpi is not used here because the lamps-10Aug15 manual (/doc/Manual.pdf is included in the decompressed package) mentioned that it may be incompatible, so I chose to install mpich) mpich official website https://www.mpich.org/static/downloads/

2. Download and install fftw (see the lamps-7Aug19 installation process above for details)

3. Lammps software package download

Reference materials

1. Download and install openmpi (mpich can also be used, see the installation process of lamps-10Aug15 below for details)

openmpi official website https://www.open-mpi.org/software/ompi/v4.1/

2. Download and install fftw

fftw official website https://www.fftw.org/download.html

1. Download and install mpich (openmpi is not used here because the lamps-10Aug15 manual (/doc/Manual.pdf is included in the decompressed package) mentioned that it may be incompatible, so I chose to install mpich)

mpich official website https://www.mpich.org/static/downloads/