cmake

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Building LAMMPS using CMAKE with OpenMPI on Rocky Linux 8

What is LAMMPS (briefly)?

LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. More Information on the software, do take a look at https://www.lammps.org/

Where to Download?

You can download the latest stable from Download LAMMPS

Step 1: Ensure Prerequisites are present

Step 2: Download and build LAMMPS

For more information, do take a look at https://docs.lammps.org/Install_tarball.html

$ tar -zxvf lammps-stable.tar.gz
$ cd lammps-2Aug203
$ mkdir build
$ touch setup.sh
$ vim setup.sh

Inside the setup.sh

cmake   -C ../cmake/presets/most.cmake ../cmake             \
        -D CMAKE_INSTALL_PREFIX=/usr/local/lammps-2Aug2023  \
        -D BUILD_MPI=on                                     \
        -D BUILD_SHARED_LIBS=yes                            \
        -D FFT=FFTW3                                        \
        -D FFTW3_INCLUDE_DIRS=${FFTW_INC}                   \
        -D FFTW3_LIBRARIES=${FFTW_LIB}/libfftw3_mpi.a

Notes:
The -C ../cmake/presets/most.cmake command adds the packages that don’t need extra libraries.

Make and Compile……

$ make -j 16 
$ make install

References:

  1. Compiling LAMMPS and using it with Python
  2. Building LAMMPS using CMake
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Compiling cmake-3.21.3 on Rocky Linux 8.5

If you are compiling the cmake-3.21.3 on Rocky Linux 8.5, and encounter the issues

-- Could NOT find OpenSSL, try to set the path to OpenSSL root folder in the system variable OPENSSL_ROOT_DIR (missing: OPENSSL_CRYPTO_LIBRARY OPENSSL_INCLUDE_DIR)

The problem is easy to resolve, you just need to install the openssl and openssl-devel libraries

# dnf install openssl openssl-devel

You should be able to bootrap easily.

Alternatively, instead of using ./boostrap, you can use the traditional configure command

#./configure --prefix=/usr/local/cmake-3.21.3
# make
# make install
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The C++ compiler does not support C++11 during bootstrap for cmake

What is CMAKE?

CMake is an open-source, cross-platform family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice. 

You can download the latest cmake from https://cmake.org/download/

Prerequisites that I use

  • gnu-6.5
  • m4-1.4.18
  • gmp-6.1.0
  • mpfr-3.1.4
  • mpc-1.0.3
  • isl-0.18
  • gsl-2.1

Step 1: You can use the bootstrap which will default the cmake to default location ie /usr/local/. If you are using bootstrap,

# tar -zxvf cmake-3.21.3.tar.gz
# cd cmake-3.21.3 
# ./bootstrap 
# make 
# make install

Errors encountered

CMake 3.21.3, Copyright 2000-2021 Kitware, Inc. and Contributors
Found GNU toolchain
C compiler on this system is: gcc
C++ compiler on this system is: g++  -std=gnu++1y
Makefile processor on this system is: gmake
g++ has setenv
g++ has unsetenv
g++ does not have environ in stdlib.h
g++ has stl wstring
g++ has <ext/stdio_filebuf.h>
---------------------------------------------
gmake: Warning: File `Makefile' has modification time 0.15 s in the future
gmake: `cmake' is up to date.
gmake: warning:  Clock skew detected.  Your build may be incomplete.
loading initial cache file /myhome/melvin/Downloads/cmake-3.21.3/Bootstrap.cmk/InitialCacheFlags.cmake
CMake Error at CMakeLists.txt:107 (message):
  The C++ compiler does not support C++11 (e.g.  std::unique_ptr).


-- Configuring incomplete, errors occurred!
See also "/myhome/melvin/Downloads/cmake-3.21.3/CMakeFiles/CMakeOutput.log".
See also "/myhome/melvin/Downloads/cmake-3.21.3/CMakeFiles/CMakeError.log".

Resolutions:

Step 1: You may want to export this before compiling

export CXXFLAGS="-O3"

Step 2: You might want to move to an unmounted directory like /root and try compiling again with root access.

Alternatively, instead of using ./boostrap, you can use the traditional configure command

#./configure --prefix=/usr/local/cmake-3.21.3
# make
# make install

References:

  1. The C++ compiler does not support C++11 (e.g. std::unique_ptr). building OpenWRT
  2. c++11 std::unique_ptr error cmake 3.11.3 bootstrap