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lammps/doc/src/Build_extras.rst

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Packages with extra build options
=================================
When building with some packages, additional steps may be required,
in addition to:
.. code-block:: bash
$ cmake -D PKG_NAME=yes
or
.. code-block:: bash
$ make yes-name
as described on the :doc:`Build_package <Build_package>` doc page.
For a CMake build there may be additional optional or required
variables to set. For a build with make, a provided library under the
lammps/lib directory may need to be built first. Or an external
library may need to exist on your system or be downloaded and built.
You may need to tell LAMMPS where it is found on your system.
This is the list of packages that may require additional steps.
.. table_from_list::
:columns: 6
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MESSAGE <message>`
* :ref:`MSCG <mscg>`
* :ref:`OPT <opt>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`VORONOI <voronoi>`
* :ref:`USER-ADIOS <user-adios>`
* :ref:`USER-ATC <user-atc>`
* :ref:`USER-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
* :ref:`USER-QUIP <user-quip>`
* :ref:`USER-SCAFACOS <user-scafacos>`
* :ref:`USER-SMD <user-smd>`
* :ref:`USER-VTK <user-vtk>`
----------
.. _compress:
COMPRESS package
----------------
To build with this package you must have the zlib compression library
available on your system.
CMake build
^^^^^^^^^^^
If CMake cannot find the library, you can set these variables:
.. code-block:: bash
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
Traditional make
^^^^^^^^^^^^^^^^
If make cannot find the library, you can edit the file
``lib/compress/Makefile.lammps`` to specify the paths and library
name.
----------
.. _gpu:
GPU package
---------------------
To build with this package, you must choose options for precision and
which GPU hardware to build for. The GPU package currently supports
three different types of backends: OpenCL, CUDA and HIP.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D GPU_API=value # value = opencl (default) or cuda or hip
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_30
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_30' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# value = yes (default) or no
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
* sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
* sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
* sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
* sm_50 or sm_52 for Maxwell (supported since CUDA 6)
* sm_60 or sm_61 for Pascal (supported since CUDA 8)
* sm_70 for Volta (supported since CUDA 9)
* sm_75 for Turing (supported since CUDA 10)
A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
CMake can detect which version of the CUDA toolkit is used and thus can
include support for **all** major GPU architectures supported by this toolkit.
Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
.. code:: bash
# AMDGPU target
export HIP_PLATFORM=hcc
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash
# CUDA target
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export CUDA_PATH=/usr/local/cuda
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
make -j 4
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
You can do this manually if you prefer; follow the instructions in
``lib/gpu/README``. Note that the GPU library uses MPI calls, so you must
use the same MPI library (or the STUBS library) settings as the main
LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ ,
``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever
Makefile you use.
You can also build the library in one step from the ``lammps/src`` dir,
using a command like these, which simply invoke the ``lib/gpu/Install.py``
script with the specified args:
.. code-block:: bash
$ make lib-gpu # print help message
$ make lib-gpu args="-b" # build GPU library with default Makefile.linux
$ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
$ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
Note that this procedure starts with a Makefile.machine in lib/gpu, as
specified by the "-m" switch. For your convenience, machine makefiles
for "mpi" and "serial" are provided, which have the same settings as
the corresponding machine makefiles in the main LAMMPS source
folder. In addition you can alter 4 important settings in the
Makefile.machine you start from via the corresponding -c, -a, -p, -e
switches (as in the examples above), and also save a copy of the new
Makefile if desired:
* ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system
* ``CUDA_ARCH`` = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
* ``CUDA_PRECISION`` = precision (double, mixed, single)
* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
The file Makefile.linux_multi is set up to include support for multiple
GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler.
If the library build is successful, 3 files should be created:
``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS
to link with CUDA libraries. If the settings in ``Makefile.lammps`` for
your machine are not correct, the LAMMPS build will fail, and
``lib/gpu/Makefile.lammps`` may need to be edited.
.. note::
If you re-build the GPU library in ``lib/gpu``, you should always
un-install the GPU package in ``lammps/src``, then re-install it and
re-build LAMMPS. This is because the compilation of files in the GPU
package uses the library settings from the ``lib/gpu/Makefile.machine``
used to build the GPU library.
----------
.. _kim:
KIM package
---------------------
To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS.
If you would like to use the :doc:`kim_query <kim_commands>`
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
If you would like to use the :doc:`kim_property <kim_commands>`
command, you need to build LAMMPS with the Python 3.6 or later package
installed. See the :doc:`Python <python>` doc page for more info on building
LAMMPS with the version of Python on your system.
After successfully building LAMMPS with Python, you need to
install the kim-property Python package, which can be easily done using
*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
``conda install kim-property`` if LAMMPS is built in Conda. More detailed
information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
In addition to installing the KIM API, it is also necessary to install the
library of KIM models (interatomic potentials).
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models
(Also note that when downloading and installing from source
the KIM API library with all its models, may take a long time (tens of
minutes to hours) to build. Of course you only need to do that once.)
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes
If ``DOWNLOAD_KIM`` is set, the KIM library will be downloaded and built
inside the CMake build directory. If the KIM library is already on
your system (in a location CMake cannot find it), set the ``PKG_CONFIG_PATH``
environment variable so that libkim-api can be found.
*For using OpenKIM web queries in LAMMPS*\ :
If the ``LMP_DEBUG_CURL`` environment variable is set, the libcurl verbose
mode will be on, and any libcurl calls within the KIM web query display a
lot of information about libcurl operations. You hardly ever want this
set in production use, you will almost always want this when you debug or
report problems.
The libcurl performs peer SSL certificate verification by default. This
verification is done using a CA certificate store that the SSL library can
use to make sure the peer's server certificate is valid. If SSL reports an
error ("certificate verify failed") during the handshake and thus refuses
further communication with that server, you can set ``LMP_NO_SSL_CHECK``\ .
If ``LMP_NO_SSL_CHECK`` is set, libcurl does not verify the peer and connection
succeeds regardless of the names in the certificate. This option is insecure.
As an alternative, you can specify your own CA cert path by setting the
environment variable ``CURL_CA_BUNDLE`` to the path of your choice. A call
to the KIM web query would get this value from the environmental variable.
Traditional make
^^^^^^^^^^^^^^^^
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``\ . You can also do it in one
step from the lammps/src dir, using a command like these, which simply
invoke the ``lib/kim/Install.py`` script with the specified args.
.. code-block:: bash
$ make lib-kim # print help message
$ make lib-kim args="-b " # (re-)install KIM API lib with only example models
$ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
$ make lib-kim args="-b -a everything" # install KIM API lib with all models
$ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
$ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
$ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
Settings for OpenKIM web queries discussed above need to be applied by adding
them to the ``LMP_INC`` variable through editing the ``Makefile.machine`` you are
using. For example:
.. code-block:: make
LMP_INC = -DLMP_NO_SSL_CHECK
----------
.. _kokkos:
KOKKOS package
--------------
Using the KOKKOS package requires choosing several settings. You have
to select whether you want to compile with parallelization on the host
and whether you want to include offloading of calculations to a device
(e.g. a GPU). The default setting is to have no host parallelization
and no device offloading. In addition, you can select the hardware
architecture to select the instruction set. Since most hardware is
backward compatible, you may choose settings for an older architecture
to have an executable that will run on this and newer architectures.
.. note::
If you run Kokkos on a different GPU architecture than what LAMMPS
was compiled with, there will be a delay during device initialization
while the just-in-time compiler is recompiling all GPU kernels for
the new hardware. This is, however, only supported for GPUs of the
**same** major hardware version and different minor hardware versions,
e.g. 5.0 and 5.2 but not 5.2 and 6.0. LAMMPS will abort with an
error message indicating a mismatch, if that happens.
The settings discussed below have been tested with LAMMPS and are
confirmed to work. Kokkos is an active project with ongoing improvements
and projects working on including support for additional architectures.
More information on Kokkos can be found on the
`Kokkos GitHub project <https://github.com/kokkos>`_.
Available Architecture settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are the possible choices for the Kokkos architecture ID. They must
be specified in uppercase.
.. list-table::
:header-rows: 0
:widths: auto
* - **Arch-ID**
- **HOST or GPU**
- **Description**
* - AMDAVX
- HOST
- AMD 64-bit x86 CPU (AVX 1)
* - EPYC
- HOST
- AMD EPYC Zen class CPU (AVX 2)
* - ARMV80
- HOST
- ARMv8.0 Compatible CPU
* - ARMV81
- HOST
- ARMv8.1 Compatible CPU
* - ARMV8_THUNDERX
- HOST
- ARMv8 Cavium ThunderX CPU
* - ARMV8_THUNDERX2
- HOST
- ARMv8 Cavium ThunderX2 CPU
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
* - SNB
- HOST
- Intel Sandy/Ivy Bridge CPU (AVX 1)
* - HSW
- HOST
- Intel Haswell CPU (AVX 2)
* - BDW
- HOST
- Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
* - SKX
- HOST
- Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
* - KNC
- HOST
- Intel Knights Corner Xeon Phi
* - KNL
- HOST
- Intel Knights Landing Xeon Phi
* - BGQ
- HOST
- IBM Blue Gene/Q CPU
* - POWER7
- HOST
- IBM POWER7 CPU
* - POWER8
- HOST
- IBM POWER8 CPU
* - POWER9
- HOST
- IBM POWER9 CPU
* - KEPLER30
- GPU
- NVIDIA Kepler generation CC 3.0 GPU
* - KEPLER32
- GPU
- NVIDIA Kepler generation CC 3.2 GPU
* - KEPLER35
- GPU
- NVIDIA Kepler generation CC 3.5 GPU
* - KEPLER37
- GPU
- NVIDIA Kepler generation CC 3.7 GPU
* - MAXWELL50
- GPU
- NVIDIA Maxwell generation CC 5.0 GPU
* - MAXWELL52
- GPU
- NVIDIA Maxwell generation CC 5.2 GPU
* - MAXWELL53
- GPU
- NVIDIA Maxwell generation CC 5.3 GPU
* - PASCAL60
- GPU
- NVIDIA Pascal generation CC 6.0 GPU
* - PASCAL61
- GPU
- NVIDIA Pascal generation CC 6.1 GPU
* - VOLTA70
- GPU
- NVIDIA Volta generation CC 7.0 GPU
* - VOLTA72
- GPU
- NVIDIA Volta generation CC 7.2 GPU
* - TURING75
- GPU
- NVIDIA Turing generation CC 7.5 GPU
* - VEGA900
- GPU
- AMD GPU MI25 GFX900
* - VEGA906
- GPU
- AMD GPU MI50/MI60 GFX906
Basic CMake build settings:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
For multicore CPUs using OpenMP, set these 2 variables.
.. code-block:: bash
-D Kokkos_ARCH_HOSTARCH=yes # HOSTARCH = HOST from list above
-D Kokkos_ENABLE_OPENMP=yes
-D BUILD_OMP=yes
Please note that enabling OpenMP for KOKKOS requires that OpenMP is
also :ref:`enabled for the rest of LAMMPS <serial>`.
For Intel KNLs using OpenMP, set these variables:
.. code-block:: bash
-D Kokkos_ARCH_KNL=yes
-D Kokkos_ENABLE_OPENMP=yes
For NVIDIA GPUs using CUDA, set these variables:
.. code-block:: bash
-D Kokkos_ARCH_HOSTARCH=yes # HOSTARCH = HOST from list above
-D Kokkos_ARCH_GPUARCH=yes # GPUARCH = GPU from list above
-D Kokkos_ENABLE_CUDA=yes
-D Kokkos_ENABLE_OPENMP=yes
-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
This will also enable executing FFTs on the GPU, either via the internal
KISSFFT library, or - by preference - with the cuFFT library bundled
with the CUDA toolkit, depending on whether CMake can identify its
location. The *wrapper* value for ``CMAKE_CXX_COMPILER`` variable is
the path to the CUDA nvcc compiler wrapper provided in the Kokkos
library: ``lib/kokkos/bin/nvcc_wrapper``\ . The setting should include
the full path name to the wrapper, e.g.
.. code-block:: bash
-D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
To simplify the compilation, three preset files are included in the
``cmake/presets`` folder, ``kokkos-serial.cmake``, ``kokkos-openmp.cmake``,
and ``kokkos-cuda.cmake``. They will enable the KOKKOS package and
enable some hardware choice. So to compile with OpenMP host parallelization,
CUDA device parallelization (for GPUs with CC 5.0 and up) with some
common packages enabled, you can do the following:
.. code-block:: bash
mkdir build-kokkos-cuda
cd build-kokkos-cuda
cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake --build .
Basic traditional make settings:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Choose which hardware to support in ``Makefile.machine`` via
``KOKKOS_DEVICES`` and ``KOKKOS_ARCH`` settings. See the
``src/MAKE/OPTIONS/Makefile.kokkos*`` files for examples.
For multicore CPUs using OpenMP:
.. code-block:: make
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = HOSTARCH # HOSTARCH = HOST from list above
For Intel KNLs using OpenMP:
.. code-block:: make
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = KNL
For NVIDIA GPUs using CUDA:
.. code-block:: make
KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU
KOKKOS_CUDA_OPTIONS = "enable_lambda"
# GPUARCH = GPU from list above
FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional)
FFT_LIB = -lcufft # link to cuFFT library
For GPUs, you also need the following lines in your ``Makefile.machine``
before the CC line is defined. They tell ``mpicxx`` to use an ``nvcc``
compiler wrapper, which will use ``nvcc`` for compiling CUDA files and a
C++ compiler for non-Kokkos, non-CUDA files.
.. code-block:: make
# For OpenMPI
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
CC = mpicxx
.. code-block:: make
# For MPICH and derivatives
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
CC = mpicxx -cxx=$(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
Advanced KOKKOS compilation settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are other allowed options when building with the KOKKOS package
that can improve performance or assist in debugging or profiling. Below
are some examples that may be useful in combination with LAMMPS. For
the full list (which keeps changing as the Kokkos package itself evolves),
please consult the Kokkos library documentation.
As alternative to using multi-threading via OpenMP
(``-DKokkos_ENABLE_OPENMP=on`` or ``KOKKOS_DEVICES=OpenMP``) it is also
possible to use Posix threads directly (``-DKokkos_ENABLE_PTHREAD=on``
or ``KOKKOS_DEVICES=Pthread``). While binding of threads to individual
or groups of CPU cores is managed in OpenMP with environment variables,
you need assistance from either the "hwloc" or "libnuma" library for the
Pthread thread parallelization option. To enable use with CMake:
``-DKokkos_ENABLE_HWLOC=on`` or ``-DKokkos_ENABLE_LIBNUMA=on``; and with
conventional make: ``KOKKOS_USE_TPLS=hwloc`` or
``KOKKOS_USE_TPLS=libnuma``.
The CMake option ``-DKokkos_ENABLE_LIBRT=on`` or the makefile setting
``KOKKOS_USE_TPLS=librt`` enables the use of a more accurate timer
mechanism on many Unix-like platforms for internal profiling.
The CMake option ``-DKokkos_ENABLE_DEBUG=on`` or the makefile setting
``KOKKOS_DEBUG=yes`` enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures. As to be expected, enabling
this option will negatively impact the performance and thus is only
recommended when developing a Kokkos-enabled style in LAMMPS.
The CMake option ``-DKokkos_ENABLE_CUDA_UVM=on`` or the makefile
setting ``KOKKOS_CUDA_OPTIONS=enable_lambda,force_uvm`` enables the
use of CUDA "Unified Virtual Memory" (UVM) in Kokkos. UVM allows to
transparently use RAM on the host to supplement the memory used on the
GPU (with some performance penalty) and thus enables running larger
problems that would otherwise not fit into the RAM on the GPU.
Please note, that the LAMMPS KOKKOS package must **always** be compiled
with the *enable_lambda* option when using GPUs. The CMake configuration
will thus always enable it.
----------
.. _latte:
LATTE package
-------------------------
To build with this package, you must download and build the LATTE
library.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded and
built inside the CMake build directory. If the LATTE library is
already on your system (in a location CMake cannot find it),
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file,
not the directory the library file is in.
Traditional make
^^^^^^^^^^^^^^^^
You can download and build the LATTE library manually if you prefer;
follow the instructions in ``lib/latte/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invokes the ``lib/latte/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-latte # print help message
$ make lib-latte args="-b" # download and build in lib/latte/LATTE-master
$ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, ``includelink`` and ``liblink`` and
``filelink.o``, are created in ``lib/latte`` to point to required
folders and files in the LATTE home directory. When LAMMPS itself is
built it will use these links. You should also check that the
``Makefile.lammps`` file you create is appropriate for the compiler you
use on your system to build LATTE.
----------
.. _message:
MESSAGE package
-----------------------------
This package can optionally include support for messaging via sockets,
using the open-source `ZeroMQ library <http://zeromq.org>`_, which must
be installed on your system.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
-D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location)
-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the CSlib library in
``lib/message``\ . You can build the CSlib library manually if you prefer;
follow the instructions in ``lib/message/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/message/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-message # print help message
$ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
$ make lib-message args="-s" # build as serial lib with no ZMQ support
The build should produce two files: ``lib/message/cslib/src/libmessage.a``
and ``lib/message/Makefile.lammps``. The latter is copied from an
existing ``Makefile.lammps.*`` and has settings to link with the ZeroMQ
library if requested in the build.
----------
.. _mscg:
MSCG package
-----------------------
To build with this package, you must download and build the MS-CG
library. Building the MS-CG library requires that the GSL
(GNU Scientific Library) headers and libraries are installed on your
machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for
more details.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location)
If ``DOWNLOAD_MSCG`` is set, the MSCG library will be downloaded and built
inside the CMake build directory. If the MSCG library is already on
your system (in a location CMake cannot find it), ``MSCG_LIBRARY`` is the
filename (plus path) of the MSCG library file, not the directory the
library file is in. ``MSCG_INCLUDE_DIR`` is the directory the MSCG
include file is in.
Traditional make
^^^^^^^^^^^^^^^^
You can download and build the MS-CG library manually if you prefer;
follow the instructions in ``lib/mscg/README``\ . You can also do it in one
step from the ``lammps/src`` dir, using a command like these, which simply
invoke the ``lib/mscg/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-mscg # print help message
$ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial"
$ make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi"
$ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
Note that 2 symbolic (soft) links, "includelink" and "liblink", will
be created in ``lib/mscg`` to point to the MS-CG ``src/installation``
dir. When LAMMPS is built in src it will use these links. You should
not need to edit the ``lib/mscg/Makefile.lammps`` file.
----------
.. _opt:
OPT package
---------------------
CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_OPT=yes``
Traditional make
^^^^^^^^^^^^^^^^
The compile flag ``-restrict`` must be used to build LAMMPS with the OPT
package when using Intel compilers. It should be added to the CCFLAGS
line of your ``Makefile.machine``. See
``src/MAKE/OPTIONS/Makefile.opt`` for an example.
----------
.. _poems:
POEMS package
-------------------------
CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_OPT=yes``
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the POEMS library in ``lib/poems``\ .
You can do this manually if you prefer; follow the instructions in
``lib/poems/README``\ . You can also do it in one step from the ``lammps/src``
dir, using a command like these, which simply invoke the
``lib/poems/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-poems # print help message
$ make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
$ make lib-poems args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/poems/libpoems.a`` and
``lib/poems/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
POEMS library (though typically the settings are just blank). If
necessary, you can edit/create a new ``lib/poems/Makefile.machine`` file
for your system, which should define an ``EXTRAMAKE`` variable to specify
a corresponding ``Makefile.lammps.machine`` file.
----------
.. _python:
PYTHON package
---------------------------
Building with the PYTHON package requires you have a Python shared
library available on your system, which needs to be a Python 2.7
version or a Python 3.x version. See ``lib/python/README`` for more
details.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D PYTHON_EXECUTABLE=path # path to Python executable to use
Without this setting, CMake will guess the default Python on your
system. To use a different Python version, you can either create a
virtualenv, activate it and then run cmake. Or you can set the
PYTHON_EXECUTABLE variable to specify which Python interpreter should
be used. Note note that you will also need to have the development
headers installed for this version, e.g. python2-devel.
Traditional make
^^^^^^^^^^^^^^^^
The build uses the ``lib/python/Makefile.lammps`` file in the compile/link
process to find Python. You should only need to create a new
``Makefile.lammps.*`` file (and copy it to ``Makefile.lammps``) if
the LAMMPS build fails.
----------
.. _voronoi:
VORONOI package
-----------------------------
To build with this package, you must download and build the `Voro++ library <voro-home_>`_.
.. _voro-home: http://math.lbl.gov/voro++
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location)
If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded and
built inside the CMake build directory. If the Voro++ library is
already on your system (in a location CMake cannot find it),
``VORO_LIBRARY`` is the filename (plus path) of the Voro++ library file,
not the directory the library file is in. ``VORO_INCLUDE_DIR`` is the
directory the Voro++ include file is in.
Traditional make
^^^^^^^^^^^^^^^^
You can download and build the Voro++ library manually if you prefer;
follow the instructions in ``lib/voronoi/README``. You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/voronoi/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-voronoi # print help message
$ make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
$ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
$ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
created in lib/voronoi to point to the Voro++ source dir. When LAMMPS
builds in ``src`` it will use these links. You should not need to edit
the ``lib/voronoi/Makefile.lammps`` file.
----------
.. _user-adios:
USER-ADIOS package
-----------------------------------
The USER-ADIOS package requires the `ADIOS I/O library
<https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
sure that you have ADIOS built either with or without MPI to match if
you build LAMMPS with or without MPI. ADIOS compilation settings for
LAMMPS are automatically detected, if the PATH and LD_LIBRARY_PATH
environment variables have been updated for the local ADIOS installation
and the instructions below are followed for the respective build
systems.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes
Traditional make
^^^^^^^^^^^^^^^^
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x
software is installed in PATH, there is nothing else to do:
.. code-block:: bash
$ make yes-user-adios
otherwise, set ADIOS2_DIR environment variable when turning on the package:
.. code-block:: bash
$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
----------
.. _user-atc:
USER-ATC package
-------------------------------
The USER-ATC package requires the MANYBODY package also be installed.
CMake build
^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-ATC=yes"
and "-D PKG_MANYBODY=yes".
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the ATC library in ``lib/atc``.
You can do this manually if you prefer; follow the instructions in
``lib/atc/README``. You can also do it in one step from the
``lammps/src`` dir, using a command like these, which simply invoke the
``lib/atc/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-atc # print help message
$ make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-atc args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
ATC library. If necessary, you can edit/create a new
``lib/atc/Makefile.machine`` file for your system, which should define
an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
Note that the Makefile.lammps file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/atc/README`` these
can either exist on your system, or you can use the files provided in
``lib/linalg``. In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
----------
.. _user-awpmd:
USER-AWPMD package
------------------
CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the AWPMD library in ``lib/awpmd``.
You can do this manually if you prefer; follow the instructions in
``lib/awpmd/README``. You can also do it in one step from the ``lammps/src``
dir, using a command like these, which simply invoke the
``lib/awpmd/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-awpmd # print help message
$ make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-awpmd args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
AWPMD library. If necessary, you can edit/create a new
``lib/awpmd/Makefile.machine`` file for your system, which should define
an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
Note that the ``Makefile.lammps`` file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/awpmd/README``
these can either exist on your system, or you can use the files
provided in ``lib/linalg``. In the latter case you also need to build the
library in ``lib/linalg`` with a command like these:
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
----------
.. _user-colvars:
USER-COLVARS package
---------------------------------------
This package includes into the LAMMPS distribution the Colvars library, which
can be built for the most part with all major versions of the C++ language.
CMake build
^^^^^^^^^^^
This is the recommended build recipe: no additional settings are normally
needed besides ``-D PKG_USER-COLVARS=yes``.
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, one must build the Colvars library in lib/colvars.
This can be done manually in the same folder by using or adapting one of
the provided Makefiles: for example, ``Makefile.g++`` for the GNU C++
compiler. C++11 compatibility may need to be enabled for some older
compilers (as is done in the example makefile).
In general, it is safer to use build setting consistent with the rest of
LAMMPS. This is best carried out from the LAMMPS src directory using a
command like these, which simply invoke the ``lib/colvars/Install.py`` script with
the specified args:
.. code-block:: bash
$ make lib-colvars # print help message
$ make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
The "machine" argument of the "-m" flag is used to find a Makefile.machine to
use as build recipe. If it does not already exist in ``lib/colvars``, it will be
auto-generated by using compiler flags consistent with those parsed from the
core LAMMPS makefiles.
Optional flags may be specified as environment variables:
.. code-block:: bash
$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
The build should produce two files: the library ``lib/colvars/libcolvars.a``
(which also includes Lepton objects if enabled) and the specification file
``lib/colvars/Makefile.lammps``. The latter is auto-generated, and normally does
not need to be edited.
----------
.. _user-plumed:
USER-PLUMED package
-------------------------------------
.. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
Before building LAMMPS with this package, you must first build PLUMED.
PLUMED can be built as part of the LAMMPS build or installed separately
from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
The USER-PLUMED package has been tested to work with Plumed versions
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
with a different version of the Plumed kernel.
PLUMED can be linked into MD codes in three different modes: static,
shared, and runtime. With the "static" mode, all the code that PLUMED
requires is linked statically into LAMMPS. LAMMPS is then fully
independent from the PLUMED installation, but you have to rebuild/relink
it in order to update the PLUMED code inside it. With the "shared"
linkage mode, LAMMPS is linked to a shared library that contains the
PLUMED code. This library should preferably be installed in a globally
accessible location. When PLUMED is linked in this way the same library
can be used by multiple MD packages. Furthermore, the PLUMED library
LAMMPS uses can be updated without the need for a recompile of LAMMPS
for as long as the shared PLUMED library is ABI-compatible.
The third linkage mode is "runtime" which allows the user to specify
which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
environment variable. This variable should point to the location of the
libplumedKernel.so dynamical shared object, which is then loaded at
runtime. This mode of linking is particularly convenient for doing
PLUMED development and comparing multiple PLUMED versions as these sorts
of comparisons can be done without recompiling the hosting MD code. All
three linkage modes are supported by LAMMPS on selected operating
systems (e.g. Linux) and using either CMake or traditional make
build. The "static" mode should be the most portable, while the
"runtime" mode support in LAMMPS makes the most assumptions about
operating system and compiler environment. If one mode does not work,
try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the
LAMMPS build.
CMake build
^^^^^^^^^^^
When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
command you must ensure that GSL is installed in locations that are
specified in your environment. There are then two additional variables
that control the manner in which PLUMED is obtained and linked into
LAMMPS.
.. code-block:: bash
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
downloaded (the version of PLUMED that will be downloaded is hard-coded
to a vetted version of PLUMED, usually a recent stable release version)
and built inside the CMake build directory. If ``DOWNLOAD_PLUMED`` is
set to "no" (the default), CMake will try to detect and link to an
installed version of PLUMED. For this to work, the PLUMED library has
to be installed into a location where the ``pkg-config`` tool can find
it or the PKG_CONFIG_PATH environment variable has to be set up
accordingly. PLUMED should be installed in such a location if you
compile it using the default make; make install commands.
The ``PLUMED_MODE`` setting determines the linkage mode for the PLUMED
library. The allowed values for this flag are "static" (default),
"shared", or "runtime". For a discussion of PLUMED linkage modes,
please see above. When ``DOWNLOAD_PLUMED`` is enabled the static
linkage mode is recommended.
Traditional make
^^^^^^^^^^^^^^^^
PLUMED needs to be installed before the USER-PLUMED package is installed
so that LAMMPS can find the right settings when compiling and linking
the LAMMPS executable. You can either download and build PLUMED inside
the LAMMPS plumed library folder or use a previously installed PLUMED
library and point LAMMPS to its location. You also have to choose the
linkage mode: "static" (default), "shared" or "runtime". For a
discussion of PLUMED linkage modes, please see above.
Download/compilation/configuration of the plumed library can be done
from the src folder through the following make args:
.. code-block:: bash
$ make lib-plumed # print help message
$ make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
$ make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink`` are
created in lib/plumed that point to the location of the PLUMED build to
use. A new file ``lib/plumed/Makefile.lammps`` is also created with settings
suitable for LAMMPS to compile and link PLUMED using the desired linkage
mode. After this step is completed, you can install the USER-PLUMED
package and compile LAMMPS in the usual manner:
.. code-block:: bash
$ make yes-user-plumed
$ make machine
Once this compilation completes you should be able to run LAMMPS in the
usual way. For shared linkage mode, libplumed.so must be found by the
LAMMPS executable, which on many operating systems means, you have to
set the LD_LIBRARY_PATH environment variable accordingly.
Support for the different linkage modes in LAMMPS varies for different
operating systems, using the static linkage is expected to be the most
portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if the
USER-PLUMED package with "make yes-user-plumed" to update the required
makefile settings with the changes in the lib/plumed folder.
----------
.. _user-h5md:
USER-H5MD package
---------------------------------
To build with this package you must have the HDF5 software package
installed on your system, which should include the h5cc compiler and
the HDF5 library.
CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it is
installed. Use the ccmake (terminal window) or cmake-gui (graphical)
tools to see these options and set them interactively from their user
interfaces.
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the CH5MD library in
``lib/h5md``. You can do this manually if you prefer; follow the
instructions in ``lib/h5md/README``. You can also do it in one step
from the ``lammps/src`` dir, using a command like these, which simply
invoke the ``lib/h5md/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-h5md # print help message
$ make lib-h5md args="-m h5cc" # build with h5cc compiler
The build should produce two files: ``lib/h5md/libch5md.a`` and
``lib/h5md/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
system HDF5 library. If necessary, you can edit/create a new
``lib/h5md/Makefile.machine`` file for your system, which should define
an EXTRAMAKE variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
----------
.. _user-intel:
USER-INTEL package
-----------------------------------
To build with this package, you must choose which hardware you want to
build for, either x86 CPUs or Intel KNLs in offload mode. You should
also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
used in tandem with the USER-INTEL package to good effect, as explained
on the :doc:`Speed intel <Speed_intel>` doc page.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D INTEL_ARCH=value # value = cpu (default) or knl
-D INTEL_LRT_MODE=value # value = threads, none, or c++11
In Long-range thread mode (LRT) a modified verlet style is used, that
operates the Kspace calculation in a separate thread concurrently to
other calculations. This has to be enabled in the :doc:`package intel <package>`
command at runtime. With the setting "threads" it used the pthreads
library, while c++11 will use the built-in thread support of C++11
compilers. The option "none" skips compilation of this feature. The
default is to use "threads" if pthreads is available and otherwise "none".
Best performance is achieved with Intel hardware, Intel compilers, as well as
the Intel TBB and MKL libraries. However, the code also compiles, links, and
runs with other compilers and without TBB and MKL.
Traditional make
^^^^^^^^^^^^^^^^
Choose which hardware to compile for in Makefile.machine via the
following settings. See ``src/MAKE/OPTIONS/Makefile.intel_cpu*`` and
``Makefile.knl`` files for examples. and ``src/USER-INTEL/README`` for
additional information.
For CPUs:
.. code-block:: make
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
For KNLs:
.. code-block:: make
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
----------
.. _user-mesont:
USER-MESONT package
-------------------------
This package includes a library written in Fortran 90 in the
``lib/mesont`` folder, so a working Fortran 90 compiler is required to
compile it. Also, the files with the force field data for running the
bundled examples are not included in the source distribution. Instead
they will be downloaded the first time this package is installed.
**CMake build**\ :
No additional settings are needed besides ``-D PKG_USER-MESONT=yes``
**Traditional make**\ :
Before building LAMMPS, you must build the *mesont* library in ``lib/mesont``\ .
You can also do it in one step from the ``lammps/src`` dir, using a command like
these, which simply invoke the ``lib/mesont/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-mesont # print help message
$ make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-mesont args="-m ifort" # build with Intel icc compiler
The build should produce two files: ``lib/mesont/libmesont.a`` and
``lib/mesont/Makefile.lammps``\ . The latter is copied from an existing
``Makefile.lammps.\*`` and has settings needed to build LAMMPS with the
*mesont* library (though typically the settings contain only the Fortran
runtime library). If necessary, you can edit/create a new
``lib/mesont/Makefile.machine`` file for your system, which should
define an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.machine`` file.
----------
.. _user-molfile:
USER-MOLFILE package
---------------------------------------
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed
-D PKG_USER-MOLFILE=yes
Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
the molfile plugin header files. These should match the ABI of the
plugin files used, and thus one typically sets them to include
folder of the local VMD installation in use. LAMMPS ships with a
couple of default header files that correspond to a popular VMD
version, usually the latest release.
Traditional make
^^^^^^^^^^^^^^^^
The ``lib/molfile/Makefile.lammps`` file has a setting for a dynamic
loading library libdl.a that is typically present on all systems. It
is required for LAMMPS to link with this package. If the setting is
not valid for your system, you will need to edit the Makefile.lammps
file. See ``lib/molfile/README`` and ``lib/molfile/Makefile.lammps`` for
details. It is also possible to configure a different folder with
the VMD molfile plugin header files. LAMMPS ships with a couple of
default headers, but these are not compatible with all VMD versions,
so it is often best to change this setting to the location of the
same include files of the local VMD installation in use.
----------
.. _user-netcdf:
USER-NETCDF package
-------------------------------------
To build with this package you must have the NetCDF library installed
on your system.
CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
This should auto-detect the NETCDF library if it is installed on your
system at standard locations. Several advanced CMake NETCDF options
exist if you need to specify where it was installed. Use the ``ccmake``
(terminal window) or ``cmake-gui`` (graphical) tools to see these
options and set them interactively from their user interfaces.
Traditional make
^^^^^^^^^^^^^^^^
The ``lib/netcdf/Makefile.lammps`` file has settings for NetCDF include
and library files which LAMMPS needs to build with this package. If
the settings are not valid for your system, you will need to edit the
``Makefile.lammps`` file. See ``lib/netcdf/README`` for details.
----------
.. _user-omp:
USER-OMP package
-------------------------------
CMake build
^^^^^^^^^^^
No additional settings are required besides ``-D PKG_USER-OMP=yes``. If
CMake detects OpenMP support, the USER-OMP code will be compiled with
multi-threading support enabled, otherwise as optimized serial code.
Traditional make
^^^^^^^^^^^^^^^^
To enable multi-threading support in the USER-OMP package (and other
styles supporting OpenMP) the following compile and link flags must be
added to your Makefile.machine file. See
``src/MAKE/OPTIONS/Makefile.omp`` for an example.
.. parsed-literal::
CCFLAGS: -fopenmp # for GNU and Clang Compilers
CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux
LINKFLAGS: -fopenmp # for GNU and Clang Compilers
LINKFLAGS: -qopenmp # for Intel compilers on Linux
For other platforms and compilers, please consult the documentation
about OpenMP support for your compiler.
----------
.. _user-qmmm:
USER-QMMM package
---------------------------------
For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix
qmmm <fix_qmmm>` included can be built, but will not be able to do a
QM/MM simulation on as such. You must also build a QM code - currently
only Quantum ESPRESSO (QE) is supported - and create a new executable
which links LAMMPS and the QM code together. Details are given in the
``lib/qmmm/README`` file. It is also recommended to read the
instructions for :doc:`linking with LAMMPS as a library <Build_link>`
for background information. This requires compatible Quantum Espresso
and LAMMPS versions. The current interface and makefiles have last been
verified to work in February 2020 with Quantum Espresso versions 6.3 to
6.5.
CMake build
^^^^^^^^^^^
When using CMake, building a LAMMPS library is required and it is
recommended to build a shared library, since any libraries built from
the sources in the *lib* folder (including the essential libqmmm.a)
are not included in the static LAMMPS library and (currently) not
installed, while their code is included in the shared LAMMPS library.
Thus a typical command line to configure building LAMMPS for USER-QMMM
would be:
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
-D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
After completing the LAMMPS build and also configuring and compiling
Quantum ESPRESSO with external library support (via "make couple"),
go back to the ``lib/qmmm` folder and follow the instructions on the
README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the ``lib/qmmm`` folder. You need to make certain, that
Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the QMMM library in ``lib/qmmm``.
You can do this manually if you prefer; follow the first two steps
explained in ``lib/qmmm/README``. You can also do it in one step from
the ``lammps/src`` dir, using a command like these, which simply invoke
the ``lib/qmmm/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-qmmm # print help message
$ make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
$ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
$ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
The build should produce two files: ``lib/qmmm/libqmmm.a`` and
``lib/qmmm/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
QMMM library (though typically the settings are just blank). If
necessary, you can edit/create a new ``lib/qmmm/Makefile.<machine>`` file
for your system, which should define an ``EXTRAMAKE`` variable to
specify a corresponding ``Makefile.lammps.<machine>`` file.
You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support (via "make couple"), go back to
the ``lib/qmmm`` folder and follow the instructions in the README file to
build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the
lib/qmmm folder.
----------
.. _user-quip:
USER-QUIP package
---------------------------------
To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need
to be downloaded and configured. See step 1 and step 1.1 in the
``lib/quip/README`` file for details on how to do this.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
CMake will not download and build the QUIP library. But once you have
done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
work. Set QUIP_LIBRARY if CMake cannot find the QUIP library.
Traditional make
^^^^^^^^^^^^^^^^
The download/build procedure for the QUIP library, described in
``lib/quip/README`` file requires setting two environment variables,
QUIP_ROOT and QUIP_ARCH. These are accessed by the
lib/quip/Makefile.lammps file which is used when you compile and link
LAMMPS with this package. You should only need to edit
``Makefile.lammps`` if the LAMMPS build can not use its settings to
successfully build on your system.
----------
.. _user-scafacos:
USER-SCAFACOS package
-----------------------------------------
To build with this package, you must download and build the `ScaFaCoS
Coulomb solver library <scafacos-home_>`_
.. _scafacos-home: http://www.scafacos.de
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location)
If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded
and built inside the CMake build directory. If the ScaFaCoS library
is already on your system (in a location CMake cannot find it),
SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR
is the directory the ScaFaCoS include file is in.
Traditional make
^^^^^^^^^^^^^^^^
You can download and build the ScaFaCoS library manually if you
prefer; follow the instructions in ``lib/scafacos/README``. You can also
do it in one step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/scafacos/Install.py`` script with the
specified args:
make lib-scafacos # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the ``lib/scafacos/Makefile.lammps`` file.
----------
.. _user-smd:
USER-SMD package
-------------------------------
To build with this package, you must download the Eigen3 library.
Eigen3 is a template library, so you do not need to build it.
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be downloaded and
inside the CMake build directory. If the Eigen3 library is already on
your system (in a location CMake cannot find it), ``EIGEN3_INCLUDE_DIR``
is the directory the Eigen3++ include file is in.
Traditional make
^^^^^^^^^^^^^^^^
You can download the Eigen3 library manually if you prefer; follow the
instructions in ``lib/smd/README``. You can also do it in one step from
the ``lammps/src`` dir, using a command like these, which simply invoke
the ``lib/smd/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-smd # print help message
$ make lib-smd args="-b" # download to lib/smd/eigen3
$ make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
Note that a symbolic (soft) link named ``includelink`` is created in
``lib/smd`` to point to the Eigen dir. When LAMMPS builds it will use
this link. You should not need to edit the ``lib/smd/Makefile.lammps``
file.
----------
.. _user-vtk:
USER-VTK package
-------------------------------
To build with this package you must have the VTK library installed on
your system.
CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist if
you need to specify where it was installed. Use the ``ccmake`` (terminal
window) or ``cmake-gui`` (graphical) tools to see these options and set
them interactively from their user interfaces.
Traditional make
^^^^^^^^^^^^^^^^
The ``lib/vtk/Makefile.lammps`` file has settings for accessing VTK files
and its library, which LAMMPS needs to build with this package. If
the settings are not valid for your system, check if one of the other
``lib/vtk/Makefile.lammps.*`` files is compatible and copy it to
Makefile.lammps. If none of the provided files work, you will need to
edit the ``Makefile.lammps`` file. See ``lib/vtk/README`` for details.
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