remove .txt doc sources

"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

Build LAMMPS :h2

LAMMPS can be built as an executable or library from source code via

either traditional makefiles (which may require manual editing)

for use with GNU make or gmake, or a build environment generated by CMake

(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an

alternative you can download a package with pre-built executables

as described on the "Install"_Install.html doc page.

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"Build LAMMPS with CMake"_Build_cmake.html

"Build LAMMPS with make"_Build_make.html

"Link LAMMPS as a library to another code"_Build_link.html

"Basic build options"_Build_basics.html

"Optional build settings"_Build_settings.html

"Include packages in build"_Build_package.html

"Packages with extra build options"_Build_extras.html

"Notes for building LAMMPS on Windows"_Build_windows.html

"Development build options (CMake only)"_Build_development.html  :all(b)

If you have problems building LAMMPS, it is often due to software

issues on your local machine.  If you can, find a local expert to

help.  If you're still stuck, send an email to the "LAMMPS mail

list"_http://lammps.sandia.gov/mail.html.

"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

Basic build options :h3

The following topics are covered on this page, for building both with

CMake and make:

"Serial vs parallel build"_#serial

"Choice of compiler and compile/link options"_#compile

"Build LAMMPS as an executable or a library"_#exe

"Build the LAMMPS documentation"_#doc

"Install LAMMPS after a build"_#install :ul

:line

Serial vs parallel build :h4,link(serial)

LAMMPS can be built to run in parallel using the ubiquitous "MPI

(message-passing

interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface

library.  Or it can built to run on a single processor (serial)

without MPI.  It can also be built with support for OpenMP threading

(see more discussion below).

[CMake variables]:

-D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no

-D BUILD_OMP=value        # yes or no (default)

-D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc

                          # no default value :pre

The executable created by CMake (after running make) is lmp_name.  If

the LAMMPS_MACHINE variable is not specified, the executable is just

lmp.  Using BUILD_MPI=no will produce a serial executable.

[Traditional make]:

cd lammps/src

make mpi                # parallel build, produces lmp_mpi using Makefile.mpi

make serial             # serial build, produces lmp_serial using Makefile/serial

make mybox :pre         # uses Makefile.mybox to produce lmp_mybox :pre

Serial build (see src/MAKE/Makefile.serial):

MPI_INC =       -I../STUBS

MPI_PATH =      -L../STUBS

MPI_LIB =       -lmpi_stubs :pre

For a parallel build, if MPI is installed on your system in the usual

place (e.g. under /usr/local), you do not need to specify the 3

variables MPI_INC, MPI_PATH, MPI_LIB.  The MPI wrapper on the compiler

(e.g. mpicxx, mpiCC) knows where to find the needed include and

library files.  Failing this, these 3 variables can be used to specify

where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)

are found, and the name of the library files (MPI_LIB).

For a serial build, you need to specify the 3 variables, as shown

above.

For a serial LAMMPS build, use the dummy MPI library provided in

src/STUBS.  You also need to build the STUBS library for your platform

before making LAMMPS itself.  A "make serial" build does this for.

Otherwise, type "make mpi-stubs" from the src directory, or "make"

from the src/STUBS dir.  If the build fails, you will need to edit the

STUBS/Makefile for your platform.

The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()

that calls gettimeofday() .  If your system doesn't support

gettimeofday() , you'll need to insert code to call another timer.

Note that the ANSI-standard function clock() rolls over after an hour

or so, and is therefore insufficient for timing long LAMMPS

simulations.

[CMake and make info]:

If you are installing MPI yourself, we recommend MPICH2 from Argonne

National Laboratory or OpenMPI.  MPICH can be downloaded from the

"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/.

OpenMPI can be downloaded from the "OpenMPI

site"_http://www.open-mpi.org.  Other MPI packages should also work.

If you are running on a large parallel machine, your system admins or

the vendor should have already installed a version of MPI, which is

likely to be faster than a self-installed MPICH or OpenMPI, so find

out how to build and link with it.

The majority of OpenMP (threading) support in LAMMPS is provided by

the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for

details. The USER-INTEL package also provides OpenMP support (it is

compatible with USER-OMP) and adds vectorization support when compiled

with the Intel compilers on top of that. Also, the KOKKOS package can

be compiled for using OpenMP threading.

However, there are a few commands in LAMMPS that have native OpenMP

support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and

USER-DPD packages.  In addition some packages support OpenMP threading

indirectly through the libraries they interface to: e.g. LATTE and

USER-COLVARS.  See the "Packages details"_Packages_details.html doc

page for more info on these packages and the doc pages for their

respective commands for OpenMP threading info.

For CMake, if you use BUILD_OMP=yes, you can use these packages and

turn on their native OpenMP support and turn on their native OpenMP

support at run time, by setting the OMP_NUM_THREADS environment

variable before you launch LAMMPS.

For building via conventional make, the CCFLAGS and LINKFLAGS

variables in Makefile.machine need to include the compiler flag that

enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel

compilers it is -qopenmp.  If you are using a different compiler,

please refer to its documentation.

[OpenMP Compiler compatibility info]: :link(default-none-issues)

Some compilers do not fully support the 'default(none)' directive

and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0

semantics, which are incompatible with the OpenMP 3.1 directives used

in LAMMPS (for maximal compatibility with compiler versions in use).

In those case, all 'default(none)' directives (which aid in detecting

incorrect and unwanted sharing) can be replaced with 'default(shared)'

while dropping all 'shared()' directives. The script

'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate

this conversion.

:line

Choice of compiler and compile/link options :h4,link(compile)

The choice of compiler and compiler flags can be important for

performance.  Vendor compilers can produce faster code than

open-source compilers like GNU.  On boxes with Intel CPUs, we suggest

trying the "Intel C++ compiler"_intel.

:link(intel,https://software.intel.com/en-us/intel-compilers)

On parallel clusters or supercomputers which use "modules" for their

compile/link environments, you can often access different compilers by

simply loading the appropriate module before building LAMMPS.

[CMake variables]:

-D CMAKE_CXX_COMPILER=name            # name of C++ compiler

-D CMAKE_C_COMPILER=name              # name of C compiler

-D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre

-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler

-D CMAKE_C_FLAGS=string               # flags to use with C compiler

-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre

By default CMake will use a compiler it finds and it will add

optimization flags appropriate to that compiler and any "accelerator

packages"_Speed_packages.html you have included in the build.

You can tell CMake to look for a specific compiler with these variable

settings.  Likewise you can specify the FLAGS variables if you want to

experiment with alternate optimization flags.  You should specify all

3 compilers, so that the small number of LAMMPS source files written

in C or Fortran are built with a compiler consistent with the one used

for all the C++ files:

Building with GNU Compilers:

cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran

Building with Intel Compilers:

cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort

Building with LLVM/Clang Compilers:

cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre

NOTE: When the cmake command completes, it prints info to the screen

as to which compilers it is using, and what flags will be used in the

compilation.  Note that if the top-level compiler is mpicxx, it is

simply a wrapper on a real compiler.  The underlying compiler info is

what will be listed in the CMake output.  You should check to insure

you are using the compiler and optimization flags are the ones you

want.

[Makefile.machine settings]:

Parallel build (see src/MAKE/Makefile.mpi):

CC =            mpicxx

CCFLAGS =       -g -O3

LINK =          mpicxx

LINKFLAGS =     -g -O :pre

Serial build (see src/MAKE/Makefile.serial):

CC =            g++

CCFLAGS =       -g -O3

LINK =          g++

LINKFLAGS =     -g -O :pre

The "compiler/linker settings" section of a Makefile.machine lists

compiler and linker settings for your C++ compiler, including

optimization flags.  You should always use mpicxx or mpiCC for

a parallel build, since these compiler wrappers will include

a variety of settings appropriate for your MPI installation.

NOTE: If you build LAMMPS with any "accelerator

packages"_Speed_packages.html included, they have specific

optimization flags that are either required or recommended for optimal

performance.  You need to include these in the CCFLAGS and LINKFLAGS

settings above.  For details, see the individual package doc pages

listed on the "Speed packages"_Speed_packages.html doc page.  Or

examine these files in the src/MAKE/OPTIONS directory.  They

correspond to each of the 5 accelerator packages and their hardware

variants:

Makefile.opt                   # OPT package

Makefile.omp                   # USER-OMP package

Makefile.intel_cpu             # USER-INTEL package for CPUs

Makefile.intel_coprocessor     # USER-INTEL package for KNLs

Makefile.gpu                   # GPU package

Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs

Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)

Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP) :pre

:line

Build LAMMPS as an executable or a library :h4,link(exe)

LAMMPS can be built as either an executable or as a static or shared

library.  The LAMMPS library can be called from another application or

a scripting language.  See the "Howto couple"_Howto_couple.html doc

page for more info on coupling LAMMPS to other codes.  See the

"Python"_Python_head.html doc page for more info on wrapping and

running LAMMPS from Python via its library interface.

[CMake variables]:

-D BUILD_EXE=value           # yes (default) or no

-D BUILD_LIB=value           # yes or no (default)

-D BUILD_SHARED_LIBS=value   # yes or no (default)

-D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc

                             # no default value :pre

Setting BUILD_EXE=no will not produce an executable.  Setting

BUILD_LIB=yes will produce a static library named liblammps.a.

Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a

shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated

libraries will be named liblammps_name.a or liblammps_name.so instead.

[Traditional make]:

cd lammps/src

make machine               # build LAMMPS executable lmp_machine

make mode=lib machine      # build LAMMPS static lib liblammps_machine.a

make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so :pre

The two library builds also create generic soft links, named

liblammps.a and liblammps.so, which point to the liblammps_machine

files.

[CMake and make info]:

Note that for a shared library to be usable by a calling program, all

the auxiliary libraries it depends on must also exist as shared

libraries.  This will be the case for libraries included with LAMMPS,

such as the dummy MPI library in src/STUBS or any package libraries in

the lib/packages directory, since they are always built as shared

libraries using the -fPIC switch.  However, if a library like MPI or

FFTW does not exist as a shared library, the shared library build will

generate an error.  This means you will need to install a shared

library version of the auxiliary library.  The build instructions for

the library should tell you how to do this.

As an example, here is how to build and install the "MPICH

library"_mpich, a popular open-source version of MPI, distributed by

Argonne National Lab, as a shared library in the default

/usr/local/lib location:

:link(mpich,http://www-unix.mcs.anl.gov/mpi)

./configure --enable-shared

make

make install :pre

You may need to use "sudo make install" in place of the last line if

you do not have write privileges for /usr/local/lib.  The end result

should be the file /usr/local/lib/libmpich.so.

:line

Build the LAMMPS documentation :h4,link(doc)

[CMake variable]:

-D BUILD_DOC=value       # yes or no (default) :pre

This will create the HTML doc pages within the CMake build directory.

The reason to do this is if you want to "install" LAMMPS on a system

after the CMake build via "make install", and include the doc pages in

the install.

[Traditional make]:

cd lammps/doc

make html       # html doc pages

make pdf        # single Manual.pdf file :pre

This will create a lammps/doc/html dir with the HTML doc pages so that

you can browse them locally on your system.  Type "make" from the

lammps/doc dir to see other options.

NOTE: You can also download a tarball of the documentation for the

current LAMMPS version (HTML and PDF files), from the website

"download page"_http://lammps.sandia.gov/download.html.

:line

Build LAMMPS tools :h4,link(tools)

Some tools described in "Auxiliary tools"_Tools.html can be built directly

using CMake or Make.

[CMake variable]:

-D BUILD_TOOLS=value       # yes or no (default) :pre

The generated binaries will also become part of the LAMMPS installation (see below)

[Traditional make]:

cd lammps/tools

make all              # build all binaries of tools

make binary2txt       # build only binary2txt tool

make chain            # build only chain tool

make micelle2d        # build only micelle2d tool

make thermo_extract   # build only thermo_extract tool

:pre

:line

Install LAMMPS after a build :h4,link(install)

After building LAMMPS, you may wish to copy the LAMMPS executable of

library, along with other LAMMPS files (library header, doc files) to

a globally visible place on your system, for others to access.  Note

that you may need super-user privileges (e.g. sudo) if the directory

you want to copy files to is protected.

[CMake variable]:

cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake

make                        # perform make after CMake command

make install                # perform the installation into prefix :pre

[Traditional make]:

There is no "install" option in the src/Makefile for LAMMPS.  If you

wish to do this you will need to first build LAMMPS, then manually

copy the desired LAMMPS files to the appropriate system directories.

"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

Development build options (CMake only) :h3

The CMake build of LAMMPS has a few extra options which are useful during

development,  testing or debugging.

:line

Verify compilation flags :h4,link(compilation)

Sometimes it is necessary to verify the complete sequence of compilation flags

generated by the CMake build. To enable a more verbose output during

compilation you can use the following option.

-D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes :pre

Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:

make VERBOSE=1 :pre

:line

Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)

Compilers such as GCC and Clang support generating binaries which use different

sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,

code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the

language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.

The following settings allow you enable these features if your compiler supports

it. Please note that they come with a performance hit. However, they are

usually faster than using tools like Valgrind.

-D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes

-D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes

-D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes

:pre

:line

Code Coverage and Testing :h4,link(testing)

We do extensive regression testing of the LAMMPS code base on a continuous

basis. Some of the logic to do this has been added to the CMake build so

developers can run the tests directly on their workstation.

NOTE: this is incomplete and only represents a small subset of tests that we run

-D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes

-D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)

-D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag

:pre

If you enable testing in the CMake build it will create an additional target called "test". You can run them with:

make test

:pre

The test cases used come from the lammps-testing repository. They are

derivatives of the examples folder with some modifications to make the run

faster.

You can also collect code coverage metrics while running the tests by enabling

coverage support during building.

-D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes :pre

This will also add the following targets to generate coverage reports after running the LAMMPS executable:

make test               # run tests first!

make gen_coverage_html  # generate coverage report in HTML format

make gen_coverage_xml   # generate coverage report in XML format

:pre

These reports require GCOVR to be installed. The easiest way to do this to install it via pip:

pip install git+https://github.com/gcovr/gcovr.git :pre

:pre