forked from lijiext/lammps
more typesetting updates
This commit is contained in:
Axel Kohlmeyer
parent
a915397668
commit
44a54324c1
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@ -7,8 +7,13 @@ in addition to:
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.. code-block:: bash
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-D PKG_NAME=yes # CMake
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make yes-name # make
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$ cmake -D PKG_NAME=yes
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or
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.. code-block:: bash
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$ make yes-name
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as described on the :doc:`Build\_package <Build_package>` doc page.
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@ -20,18 +25,35 @@ You may need to tell LAMMPS where it is found on your system.
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This is the list of packages that may require additional steps.
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+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
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| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
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+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
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| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
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+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
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| :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-MOLFILE <user-molfile>` |
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+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
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| :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>` |
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+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
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| :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | |
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+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
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.. table_from_list::
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:columns: 6
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* :ref:`COMPRESS <compress>`
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* :ref:`GPU <gpu>`
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* :ref:`KIM <kim>`
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* :ref:`KOKKOS <kokkos>`
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* :ref:`LATTE <latte>`
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* :ref:`MESSAGE <message>`
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* :ref:`MSCG <mscg>`
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* :ref:`OPT <opt>`
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* :ref:`POEMS <poems>`
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* :ref:`PYTHON <python>`
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* :ref:`VORONOI <voronoi>`
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* :ref:`USER-ADIOS <user-adios>`
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* :ref:`USER-ATC <user-atc>`
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* :ref:`USER-AWPMD <user-awpmd>`
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* :ref:`USER-COLVARS <user-colvars>`
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* :ref:`USER-H5MD <user-h5md>`
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* :ref:`USER-INTEL <user-intel>`
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* :ref:`USER-MOLFILE <user-molfile>`
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* :ref:`USER-NETCDF <user-netcdf>`
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* :ref:`USER-PLUMED <user-plumed>`
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* :ref:`USER-OMP <user-omp>`
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* :ref:`USER-QMMM <user-qmmm>`
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* :ref:`USER-QUIP <user-quip>`
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* :ref:`USER-SCAFACOS <user-scafacos>`
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* :ref:`USER-SMD <user-smd>`
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* :ref:`USER-VTK <user-vtk>`
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----------
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@ -127,10 +149,10 @@ script with the specified args:
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.. code-block:: bash
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make lib-gpu # print help message
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make lib-gpu args="-b" # build GPU library with default Makefile.linux
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make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
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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
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$ make lib-gpu # print help message
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$ make lib-gpu args="-b" # build GPU library with default Makefile.linux
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$ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
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$ 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
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Note that this procedure starts with a Makefile.machine in lib/gpu, as
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specified by the "-m" switch. For your convenience, machine makefiles
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@ -181,7 +203,8 @@ use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
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command, you also need to have libcurl installed with the matching
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development headers and the curl-config tool.
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See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
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See the `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
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web page to
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learn how to install a pre-build binary of the OpenKIM Repository of Models.
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See the list of all KIM models here: https://openkim.org/browse/models
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@ -231,13 +254,13 @@ invoke the lib/kim/Install.py script with the specified args.
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.. code-block:: bash
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make lib-kim # print help message
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make lib-kim args="-b " # (re-)install KIM API lib with only example models
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make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
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make lib-kim args="-b -a everything" # install KIM API lib with all models
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make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
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make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
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make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
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$ make lib-kim # print help message
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$ make lib-kim args="-b " # (re-)install KIM API lib with only example models
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$ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
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$ make lib-kim args="-b -a everything" # install KIM API lib with all models
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$ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
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$ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
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$ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
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Settings for OpenKIM web queries discussed above need to be applied by adding
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them to the LMP\_INC variable through editing the Makefile.machine you are
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@ -410,10 +433,10 @@ args:
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.. code-block:: bash
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make lib-latte # print help message
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make lib-latte args="-b" # download and build in lib/latte/LATTE-master
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make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
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make lib-latte args="-b -m gfortran" # download and build in lib/latte and
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$ make lib-latte # print help message
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$ make lib-latte args="-b" # download and build in lib/latte/LATTE-master
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$ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
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$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
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# copy Makefile.lammps.gfortran to Makefile.lammps
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Note that 3 symbolic (soft) links, "includelink" and "liblink" and
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@ -455,9 +478,9 @@ simply invoke the lib/message/Install.py script with the specified args:
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.. code-block:: bash
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make lib-message # print help message
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make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
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make lib-message args="-s" # build as serial lib with no ZMQ support
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$ make lib-message # print help message
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$ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
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$ make lib-message args="-s" # build as serial lib with no ZMQ support
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The build should produce two files: lib/message/cslib/src/libmessage.a
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and lib/message/Makefile.lammps. The latter is copied from an
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@ -505,12 +528,12 @@ invoke the lib/mscg/Install.py script with the specified args:
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.. code-block:: bash
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make lib-mscg # print help message
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make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
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$ make lib-mscg # print help message
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$ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
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# with the settings compatible with "make serial"
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make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
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$ make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
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# with the settings compatible with "make mpi"
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make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
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$ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
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Note that 2 symbolic (soft) links, "includelink" and "liblink", will
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be created in lib/mscg to point to the MS-CG src/installation dir.
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@ -561,10 +584,10 @@ lib/poems/Install.py script with the specified args:
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.. code-block:: bash
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make lib-poems # print help message
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make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
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make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
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make lib-poems args="-m icc" # build with Intel icc compiler
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$ make lib-poems # print help message
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$ make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
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$ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
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$ make lib-poems args="-m icc" # build with Intel icc compiler
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The build should produce two files: lib/poems/libpoems.a and
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lib/poems/Makefile.lammps. The latter is copied from an existing
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@ -651,10 +674,10 @@ args:
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.. code-block:: bash
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make lib-voronoi # print help message
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make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
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make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
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make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
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$ make lib-voronoi # print help message
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$ make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
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$ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
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$ 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
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Note that 2 symbolic (soft) links, "includelink" and "liblink", are
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created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
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@ -692,14 +715,14 @@ Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software
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.. code-block:: bash
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make yes-user-adios
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$ make yes-user-adios
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otherwise, set ADIOS2\_DIR environment variable when turning on the package:
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.. code-block:: bash
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ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
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$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
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----------
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@ -728,10 +751,10 @@ lib/atc/Install.py script with the specified args:
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.. code-block:: bash
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make lib-atc # print help message
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make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
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make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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make lib-atc args="-m icc" # build with Intel icc compiler
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$ make lib-atc # print help message
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$ make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
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$ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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$ make lib-atc args="-m icc" # build with Intel icc compiler
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The build should produce two files: lib/atc/libatc.a and
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lib/atc/Makefile.lammps. The latter is copied from an existing
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@ -750,10 +773,10 @@ lib/linalg with a command like these:
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.. code-block:: bash
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make lib-linalg # print help message
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make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
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make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
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make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
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$ make lib-linalg # print help message
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$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
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$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
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$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
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----------
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@ -779,10 +802,10 @@ lib/awpmd/Install.py script with the specified args:
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.. code-block:: bash
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make lib-awpmd # print help message
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make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
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make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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make lib-awpmd args="-m icc" # build with Intel icc compiler
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$ make lib-awpmd # print help message
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$ make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
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$ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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$ make lib-awpmd args="-m icc" # build with Intel icc compiler
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The build should produce two files: lib/awpmd/libawpmd.a and
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lib/awpmd/Makefile.lammps. The latter is copied from an existing
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@ -801,10 +824,10 @@ library in lib/linalg with a command like these:
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.. code-block:: bash
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make lib-linalg # print help message
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make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
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make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
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make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
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$ make lib-linalg # print help message
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$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
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$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
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$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
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----------
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@ -853,10 +876,10 @@ the specified args:
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.. code-block:: bash
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make lib-colvars # print help message
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make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
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make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
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$ make lib-colvars # print help message
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$ make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
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$ make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
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The "machine" argument of the "-m" flag is used to find a Makefile.machine to
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use as build recipe. If it does not already exist in lib/colvars, it will be
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@ -867,8 +890,8 @@ Optional flags may be specified as environment variables:
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.. code-block:: bash
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COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
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COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
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$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
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$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
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The build should produce two files: the library lib/colvars/libcolvars.a
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(which also includes Lepton objects if enabled) and the specification file
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@ -968,10 +991,10 @@ from the src folder through the following make args:
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.. code-block:: bash
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make lib-plumed # print help message
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make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
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make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
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make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
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$ make lib-plumed # print help message
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$ make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
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$ make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
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$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
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# /usr/local and use shared linkage mode
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Note that 2 symbolic (soft) links, "includelink" and "liblink" are
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@ -984,8 +1007,8 @@ package and compile LAMMPS in the usual manner:
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.. code-block:: bash
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make yes-user-plumed
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make machine
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$ make yes-user-plumed
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$ make machine
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Once this compilation completes you should be able to run LAMMPS in the
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usual way. For shared linkage mode, libplumed.so must be found by the
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@ -1035,8 +1058,8 @@ lib/h5md/Install.py script with the specified args:
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.. code-block:: bash
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make lib-h5md # print help message
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make lib-h5md args="-m h5cc" # build with h5cc compiler
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$ make lib-h5md # print help message
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$ make lib-h5md args="-m h5cc" # build with h5cc compiler
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The build should produce two files: lib/h5md/libch5md.a and
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lib/h5md/Makefile.lammps. The latter is copied from an existing
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@ -1264,10 +1287,10 @@ lib/qmmm/Install.py script with the specified args:
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.. code-block:: bash
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make lib-qmmm # print help message
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make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
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make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
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make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
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$ make lib-qmmm # print help message
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$ make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
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$ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
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$ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
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The build should produce two files: lib/qmmm/libqmmm.a and
|
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lib/qmmm/Makefile.lammps. The latter is copied from an existing
|
||||
|
|
@ -1402,9 +1425,9 @@ 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
|
||||
$ 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
|
||||
|
|
|
|||
|
|
@ -19,9 +19,9 @@ sub-directories and optionally 2 PDF files and 2 e-book format files:
|
|||
If you downloaded LAMMPS as a tarball from the web site, all these
|
||||
directories and files should be included.
|
||||
|
||||
If you downloaded LAMMPS from the public git repository, then
|
||||
the HTML and PDF files are not included. Instead you need to create
|
||||
them, in one of two ways:
|
||||
If you downloaded LAMMPS from the public git repository, then the HTML
|
||||
and PDF files are not included. Instead you need to create them, in one
|
||||
of two ways:
|
||||
|
||||
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
|
||||
site. Just type "make fetch". This should download a html\_www
|
||||
|
|
@ -41,10 +41,10 @@ b. You can build the HTML and PDF files yourself, by typing "make html"
|
|||
be able to view the math offline, some extra data and javascript code
|
||||
needs to be downloaded and the HTML generation needs to be changed to
|
||||
reference them. When typing "make html-offline" this is done
|
||||
automatically. Same as for the sphinx tool, this download is
|
||||
required only once. After that also the processing of the
|
||||
documentation can be done without internet access. To generate the
|
||||
PDF version of the manual, additionally the PDFLaTeX software and
|
||||
automatically. Same as for the sphinx tool and its extensions, this
|
||||
download is required only once. After that also the processing of
|
||||
the documentation can be done without internet access. To generate
|
||||
the PDF version of the manual, additionally the PDFLaTeX software and
|
||||
several LaTeX packages are required.
|
||||
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -1,25 +1,25 @@
|
|||
Basics of running LAMMPS
|
||||
========================
|
||||
|
||||
LAMMPS is run from the command line, reading commands from a
|
||||
file via the -in command line flag, or from standard input.
|
||||
LAMMPS is run from the command line, reading commands from a file via
|
||||
the -in command line flag, or from standard input.
|
||||
Using the "-in in.file" variant is recommended:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: bash
|
||||
|
||||
lmp_serial < in.file
|
||||
lmp_serial -in in.file
|
||||
/path/to/lammps/src/lmp_serial < in.file
|
||||
mpirun -np 4 lmp_mpi -in in.file
|
||||
mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file
|
||||
mpirun -np 6 /usr/local/bin/lmp -in in.file
|
||||
$ lmp_serial -in in.file
|
||||
$ lmp_serial < in.file
|
||||
$ /path/to/lammps/src/lmp_serial -i in.file
|
||||
$ mpirun -np 4 lmp_mpi -in in.file
|
||||
$ mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file
|
||||
$ mpirun -np 6 /usr/local/bin/lmp -in in.file
|
||||
|
||||
You normally run the LAMMPS command in the directory where your
|
||||
input script is located. That is also where output files are
|
||||
produced by default, unless you provide specific other paths in
|
||||
your input script or on the command line. As in some of the
|
||||
examples above, the LAMMPS executable itself can be placed elsewhere.
|
||||
You normally run the LAMMPS command in the directory where your input
|
||||
script is located. That is also where output files are produced by
|
||||
default, unless you provide specific other paths in your input script or
|
||||
on the command line. As in some of the examples above, the LAMMPS
|
||||
executable itself can be placed elsewhere.
|
||||
|
||||
.. note::
|
||||
|
||||
|
|
@ -27,7 +27,8 @@ examples above, the LAMMPS executable itself can be placed elsewhere.
|
|||
in parallel with mpirun; for those systems the -in form is required.
|
||||
|
||||
As LAMMPS runs it prints info to the screen and a logfile named
|
||||
log.lammps. More info about output is given on the :doc:`Run output <Run_output>` doc page.
|
||||
*log.lammps*\ . More info about output is given on the
|
||||
:doc:`Run output <Run_output>` doc page.
|
||||
|
||||
If LAMMPS encounters errors in the input script or while running a
|
||||
simulation it will print an ERROR message and stop or a WARNING
|
||||
|
|
@ -35,26 +36,27 @@ message and continue. See the :doc:`Errors <Errors>` doc page for a
|
|||
discussion of the various kinds of errors LAMMPS can or can't detect,
|
||||
a list of all ERROR and WARNING messages, and what to do about them.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
LAMMPS can run the same problem on any number of processors, including
|
||||
a single processor. In theory you should get identical answers on any
|
||||
LAMMPS can run the same problem on any number of processors, including a
|
||||
single processor. In theory you should get identical answers on any
|
||||
number of processors and on any machine. In practice, numerical
|
||||
round-off can cause slight differences and eventual divergence of
|
||||
molecular dynamics phase space trajectories. See the :doc:`Errors common <Errors_common>` doc page for discussion of this.
|
||||
round-off due to using floating-point math can cause slight differences
|
||||
and an eventual divergence of molecular dynamics trajectories. See the
|
||||
:doc:`Errors common <Errors_common>` doc page for discussion of this.
|
||||
|
||||
LAMMPS can run as large a problem as will fit in the physical memory
|
||||
of one or more processors. If you run out of memory, you must run on
|
||||
more processors or define a smaller problem.
|
||||
LAMMPS can run as large a problem as will fit in the physical memory of
|
||||
one or more processors. If you run out of memory, you must run on more
|
||||
processors or define a smaller problem. The amount of memory needed and
|
||||
how well it can be distributed across processors may vary based
|
||||
on the models and settings and commands used.
|
||||
|
||||
If you run LAMMPS in parallel via mpirun, you should be aware of the
|
||||
:doc:`processors <processors>` command which controls how MPI tasks are
|
||||
mapped to the simulation box, as well as mpirun options that control
|
||||
how MPI tasks are assigned to physical cores of the node(s) of the
|
||||
machine you are running on. These settings can improve performance,
|
||||
though the defaults are often adequate.
|
||||
:doc:`processors <processors>` command, which controls how MPI tasks are
|
||||
mapped to the simulation box, as well as mpirun options that control how
|
||||
MPI tasks are assigned to physical cores of the node(s) of the machine
|
||||
you are running on. These settings can improve performance, though the
|
||||
defaults are often adequate.
|
||||
|
||||
For example, it is often important to bind MPI tasks (processes) to
|
||||
physical cores (processor affinity), so that the operating system does
|
||||
|
|
@ -67,10 +69,10 @@ can set the number of threads per MPI task via the environment
|
|||
variable OMP\_NUM\_THREADS, before you launch LAMMPS:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: bash
|
||||
|
||||
export OMP_NUM_THREADS=2 # bash
|
||||
setenv OMP_NUM_THREADS 2 # csh or tcsh
|
||||
$ export OMP_NUM_THREADS=2 # bash
|
||||
$ setenv OMP_NUM_THREADS 2 # csh or tcsh
|
||||
|
||||
This can also be done via the :doc:`package <package>` command or via
|
||||
the :doc:`-pk command-line switch <Run_options>` which invokes the
|
||||
|
|
|
|||
|
|
@ -26,10 +26,10 @@ letter abbreviation can be used:
|
|||
For example, the lmp\_mpi executable might be launched as follows:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
|
||||
mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy
|
||||
$ mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
|
||||
$ mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -438,7 +438,7 @@ is the same operation as if the following 2-line input script were
|
|||
run:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
read_restart restartfile [remap]
|
||||
write_data datafile keyword value ...
|
||||
|
|
@ -483,7 +483,7 @@ is the same operation as if the following 2-line input script were
|
|||
run:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
read_restart restartfile [remap]
|
||||
write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
|
||||
|
|
@ -506,8 +506,7 @@ dump file to still be produced.
|
|||
|
||||
The syntax following restartfile (or remap), namely
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
group-ID dumpstyle dumpfile arg1 arg2 ...
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue