complete using tab/tabs directives in Build_settings
This commit is contained in:
Axel Kohlmeyer
@ -341,37 +341,34 @@ If this option is enabled, large files can be read or written with
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gzip compression by several LAMMPS commands, including
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:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
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CMake build
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^^^^^^^^^^^
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.. tabs::
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.. code-block:: bash
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.. tab:: CMake build
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-D WITH_GZIP=value # yes or no
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# default is yes if CMake can find gzip, else no
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-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
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.. code-block:: bash
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Traditional make
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^^^^^^^^^^^^^^^^
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-D WITH_GZIP=value # yes or no
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# default is yes if CMake can find gzip, else no
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-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
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.. code-block:: make
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.. tab:: Traditional make
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LMP_INC = -DLAMMPS_GZIP
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.. code-block:: make
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CMake and make info
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^^^^^^^^^^^^^^^^^^^
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LMP_INC = -DLAMMPS_GZIP
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This option requires that your machine supports the "popen()" function
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in the standard runtime library and that a gzip executable can be
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This option requires that your operating system fully supports the "popen()"
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function in the standard runtime library and that a ``gzip`` executable can be
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found by LAMMPS during a run.
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.. note::
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On some clusters with high-speed networks, using the fork()
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library call (required by popen()) can interfere with the fast
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communication library and lead to simulations using compressed output
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or input to hang or crash. For selected operations, compressed file
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I/O is also available using a compression library instead, which is
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what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
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On some clusters with high-speed networks, using the "fork()" library
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call (required by "popen()") can interfere with the fast communication
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library and lead to simulations using compressed output or input to
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hang or crash. For selected operations, compressed file I/O is also
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available using a compression library instead, which is what the
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:ref:`COMPRESS package <PKG-COMPRESS>` enables.
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----------
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@ -380,65 +377,66 @@ found by LAMMPS during a run.
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Memory allocation alignment
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---------------------------------------
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This setting enables the use of the posix_memalign() call instead of
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malloc() when LAMMPS allocates large chunks or memory. This can make
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vector instructions on CPUs more efficient, if dynamically allocated
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memory is aligned on larger-than-default byte boundaries.
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On most current systems, the malloc() implementation returns
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This setting enables the use of the "posix_memalign()" call instead of
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"malloc()" when LAMMPS allocates large chunks or memory. Vector
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instructions on CPUs may become more efficient, if dynamically allocated
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memory is aligned on larger-than-default byte boundaries. On most
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current operating systems, the "malloc()" implementation returns
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pointers that are aligned to 16-byte boundaries. Using SSE vector
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instructions efficiently, however, requires memory blocks being
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aligned on 64-byte boundaries.
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instructions efficiently, however, requires memory blocks being aligned
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on 64-byte boundaries.
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CMake build
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^^^^^^^^^^^
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.. tabs::
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.. code-block:: bash
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.. tab:: CMake build
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-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
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.. code-block:: bash
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Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using posix_memalign()
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and revert to using the malloc() C-library function instead. When
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compiling LAMMPS for Windows systems, malloc() will always be used
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and this setting ignored.
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-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
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Traditional make
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^^^^^^^^^^^^^^^^
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Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
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"posix_memalign()" and revert to using the "malloc()" C-library
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function instead. When compiling LAMMPS for Windows systems,
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"malloc()" will always be used and this setting is ignored.
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.. code-block:: make
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.. tab:: Traditional make
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LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
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.. code-block:: make
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Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory allocated
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with the malloc() function call instead. ``-DLAMMPS_MEMALIGN`` **cannot**
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be used on Windows, as it does use different function calls for
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allocating aligned memory, that are not compatible with how LAMMPS
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manages its dynamical memory.
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LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
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Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
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allocated with the "malloc()" function call
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instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
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Windows different function calls with different semantics for
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allocating aligned memory, that are not compatible with how LAMMPS
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manages its dynamical memory.
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----------
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.. _longlong:
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Workaround for long long integers
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------------------------------------------------
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---------------------------------
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If your system or MPI version does not recognize "long long" data
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types, the following setting will be needed. It converts "long long"
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to a "long" data type, which should be the desired 8-byte integer on
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those systems:
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CMake build
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^^^^^^^^^^^
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.. tabs::
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.. code-block:: bash
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.. tab:: CMake build
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-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
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.. code-block:: bash
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Traditional make
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^^^^^^^^^^^^^^^^
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-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
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.. code-block:: make
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.. tab:: Traditional make
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LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
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.. code-block:: make
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LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
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----------
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@ -453,19 +451,19 @@ Instead, the call stack is unwound and control returns to the caller,
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e.g. to Python. Of course, the calling code has to be set up to
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*catch* exceptions thrown from within LAMMPS.
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CMake build
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^^^^^^^^^^^
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.. tabs::
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.. code-block:: bash
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.. tab:: CMake build
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-D LAMMPS_EXCEPTIONS=value # yes or no (default)
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.. code-block:: bash
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Traditional make
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^^^^^^^^^^^^^^^^
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-D LAMMPS_EXCEPTIONS=value # yes or no (default)
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.. code-block:: make
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.. tab:: Traditional make
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LMP_INC = -DLAMMPS_EXCEPTIONS
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.. code-block:: make
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LMP_INC = -DLAMMPS_EXCEPTIONS
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.. note::
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