2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>processors command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>processors Px Py Pz keyword args ...
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</PRE>
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<UL><LI>Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>grid</I> or <I>map</I> or <I>part</I> or <I>file</I>
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<PRE> <I>grid</I> arg = gstyle params ...
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gstyle = <I>onelevel</I> or <I>twolevel</I> or <I>numa</I> or <I>custom</I>
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onelevel params = none
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twolevel params = Nc Cx Cy Cz
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Nc = number of cores per node
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Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
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numa params = none
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custom params = infile
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infile = file containing grid layout
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<I>map</I> arg = <I>cart</I> or <I>cart/reorder</I> or <I>xyz</I> or <I>xzy</I> or <I>yxz</I> or <I>yzx</I> or <I>zxy</I> or <I>zyx</I>
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cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
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cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
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xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
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<I>numa</I> arg = none
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<I>part</I> args = Psend Precv cstyle
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Psend = partition # (1 to Np) which will send its processor layout
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Precv = partition # (1 to Np) which will recv the processor layout
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cstyle = <I>multiple</I>
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<I>multiple</I> = Psend grid will be multiple of Precv grid in each dimension
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<I>file</I> arg = outfile
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outfile = name of file to write 3d grid of processors to
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>processors * * 5
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processors 2 4 4
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processors * * 8 map xyz
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processors * * * grid numa
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processors * * * grid twolevel 4 * * 1
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processors 4 8 16 grid custom myfile
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processors * * * part 1 2 multiple
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Specify how processors are mapped as a 3d logical grid to the global
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simulation box. This involves 2 steps. First if there are P
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processors it means choosing a factorization P = Px by Py by Pz so
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that there are Px processors in the x dimension, and similarly for the
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y and z dimensions. Second, the P processors are mapped to the
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logical 3d grid. The arguments to this command control each of these
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2 steps.
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</P>
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<P>The Px, Py, Pz parameters affect the factorization. Any of the 3
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parameters can be specified with an asterisk "*", which means LAMMPS
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will choose the number of processors in that dimension of the grid.
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It will do this based on the size and shape of the global simulation
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box so as to minimize the surface-to-volume ratio of each processor's
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sub-domain.
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</P>
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<P>Since LAMMPS does not load-balance by changing the grid of 3d
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processors on-the-fly, choosing explicit values for Px or Py or Pz can
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be used to override the LAMMPS default if it is known to be
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sub-optimal for a particular problem. E.g. a problem where the extent
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of atoms will change dramatically in a particular dimension over the
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course of the simulation.
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</P>
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<P>The product of Px, Py, Pz must equal P, the total # of processors
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LAMMPS is running on. For a <A HREF = "dimension.html">2d simulation</A>, Pz must
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equal 1.
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</P>
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<P>Note that if you run on a prime number of processors P, then a grid
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such as 1 x P x 1 will be required, which may incur extra
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communication costs due to the high surface area of each processor's
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sub-domain.
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</P>
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<P>Also note that if multiple partitions are being used then P is the
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number of processors in this partition; see <A HREF = "Section_start.html#start_6">this
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section</A> for an explanation of the
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-partition command-line switch. Also note that you can prefix the
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processors command with the <A HREF = "partition.html">partition</A> command to
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easily specify different Px,Py,Pz values for different partitions.
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</P>
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<P>You can use the <A HREF = "partition.html">partition</A> command to specify
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different processor grids for different partitions, e.g.
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</P>
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<PRE>partition yes 1 processors 4 4 4
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partition yes 2 processors 2 3 2
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</PRE>
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<HR>
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2011-12-14 01:51:57 +08:00
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<P>The <I>grid</I> keyword affects the factorization of P into Px,Py,Pz and it
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can also affect how the P processor IDs are mapped to the 3d grid of
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processors.
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</P>
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<P>The <I>onelevel</I> style creates a 3d grid that is compatible with the
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Px,Py,Pz settings, and which minimizes the surface-to-volume ratio of
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each processor's sub-domain, as described above. The mapping of
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processors to the grid is determined by the <I>map</I> keyword setting.
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</P>
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<P>The <I>twolevel</I> style can be used on machines with multicore nodes to
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minimize off-node communication. It insures that contiguous
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sub-sections of the 3d grid are assigned to all the cores of a node.
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For example if <I>Nc</I> is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of
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the 3d grid will correspond to the cores of each node. This affects
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both the factorization and mapping steps.
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</P>
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<P>The <I>Cx</I>, <I>Cy</I>, <I>Cz</I> settings are similar to the <I>Px</I>, <I>Py</I>, <I>Pz</I>
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settings, only their product should equal <I>Nc</I>. Any of the 3
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parameters can be specified with an asterisk "*", which means LAMMPS
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will choose the number of cores in that dimension of the node's
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sub-grid. As with Px,Py,Pz, it will do this based on the size and
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shape of the global simulation box so as to minimize the
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surface-to-volume ratio of each processor's sub-domain.
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</P>
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<P>IMPORTANT NOTE: For the <I>twolevel</I> style to work correctly, it
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assumes the MPI ranks of processors LAMMPS is running on are ordered
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by core and then by node. E.g. if you are running on 2 quad-core
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nodes, for a total of 8 processors, then it assumes processors 0,1,2,3
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are on node 1, and processors 4,5,6,7 are on node 2. This is the
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default rank ordering for most MPI implementations, but some MPIs
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provide options for this ordering, e.g. via environment variable
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settings.
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</P>
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<P>The <I>numa</I> style operates similar to the <I>twolevel</I> keyword except
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that it auto-detects which cores are running on which nodes.
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Currently, it does this in only 2 levels, but it may be extended in
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the future to account for socket topology and other non-uniform memory
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access (NUMA) costs. It also uses a different algorithm than the
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<I>twolevel</I> keyword for doing the two-level factorization of the
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simulation box into a 3d processor grid to minimize off-node
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communication, and it does its own MPI-based mapping of nodes and
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cores to the logical 3d grid. Thus it may produce a different layout
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of the processors than the <I>twolevel</I> options.
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</P>
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<P>The <I>numa</I> style will give an error if the number of MPI processes is
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not divisible by the number of cores used per node, or any of the Px
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or Py of Pz values is greater than 1.
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</P>
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<P>IMPORTANT NOTE: Unlike the <I>twolevel</I> style, the <I>numa</I> style does not
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require any particular ordering of MPI ranks i norder to work
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correctly. This is because it auto-detects which processes are
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running on which nodes.
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</P>
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<P>The <I>custom</I> style uses the file <I>infile</I> to define both the 3d
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factorization and the mapping of processors to the grid.
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</P>
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<P>The file should have the following format. Any number of initial
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blank or comment lines (starting with a "#" character) can be present.
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The first non-blank, non-comment line should have
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3 values:
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</P>
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<PRE>Px Py Py
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</PRE>
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<P>These must be compatible with the total number of processors
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and the Px, Py, Pz settings of the processors commmand.
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</P>
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<P>This line should be immediately followed by
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P = Px*Py*Pz lines of the form:
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</P>
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<PRE>ID I J K
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</PRE>
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<P>where ID is a processor ID (from 0 to P-1) and I,J,K are the
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processors location in the 3d grid. I must be a number from 1 to Px
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(inclusive) and similarly for J and K. The P lines can be listed in
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any order, but no processor ID should appear more than once.
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</P>
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<HR>
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<P>The <I>map</I> keyword affects how the P processor IDs (from 0 to P-1) are
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mapped to the 3d grid of processors. It is only used by the
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<I>onelevel</I> and <I>twolevel</I> grid settings.
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</P>
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<P>The <I>cart</I> style uses the family of MPI Cartesian functions to perform
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the mapping, namely MPI_Cart_create(), MPI_Cart_get(),
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MPI_Cart_shift(), and MPI_Cart_rank(). It invokes the
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MPI_Cart_create() function with its reorder flag = 0, so that MPI is
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not free to reorder the processors.
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</P>
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<P>The <I>cart/reorder</I> style does the same thing as the <I>cart</I> style
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except it sets the reorder flag to 1, so that MPI can reorder
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processors if it desires.
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</P>
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<P>The <I>xyz</I>, <I>xzy</I>, <I>yxz</I>, <I>yzx</I>, <I>zxy</I>, and <I>zyx</I> styles are all
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similar. If the style is IJK, then it maps the P processors to the
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grid so that the processor ID in the I direction varies fastest, the
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processor ID in the J direction varies next fastest, and the processor
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ID in the K direction varies slowest. For example, if you select
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style <I>xyz</I> and you have a 2x2x2 grid of 8 processors, the assignments
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of the 8 octants of the simulation domain will be:
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</P>
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<PRE>proc 0 = lo x, lo y, lo z octant
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proc 1 = hi x, lo y, lo z octant
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proc 2 = lo x, hi y, lo z octant
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proc 3 = hi x, hi y, lo z octant
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proc 4 = lo x, lo y, hi z octant
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proc 5 = hi x, lo y, hi z octant
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proc 6 = lo x, hi y, hi z octant
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proc 7 = hi x, hi y, hi z octant
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</PRE>
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<P>Note that, in principle, an MPI implementation on a particular machine
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should be aware of both the machine's network topology and the
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specific subset of processors and nodes that were assigned to your
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simulation. Thus its MPI_Cart calls can optimize the assignment of
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MPI processes to the 3d grid to minimize communication costs. In
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practice, however, few if any MPI implementations actually do this.
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So it is likely that the <I>cart</I> and <I>cart/reorder</I> styles simply give
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the same result as one of the IJK styles.
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</P>
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<P>Also note, that for the <I>twolevel</I> grid style, the <I>map</I> setting is
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used to first map the nodes to the 3d grid, then again to the cores
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within each node. For the latter step, the <I>cart</I> and <I>cart/reorder</I>
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styles are not supported, so an <I>xyz</I> style is used in their place.
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</P>
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<HR>
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2011-12-13 23:58:47 +08:00
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<P>The <I>part</I> keyword affects the factorization of P into Px,Py,Pz.
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</P>
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<P>It can be useful when running in multi-partition mode, e.g. with the
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<A HREF = "run_style.html">run_style verlet/split</A> command. It specifies a
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dependency bewteen a sending partition <I>Psend</I> and a receiving
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partition <I>Precv</I> which is enforced when each is setting up their own
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mapping of their processors to the simulation box. Each of <I>Psend</I>
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and <I>Precv</I> must be integers from 1 to Np, where Np is the number of
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partitions you have defined via the <A HREF = "Section_start.html#start_6">-partition command-line
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switch</A>.
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</P>
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<P>A "dependency" means that the sending partition will create its 3d
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logical grid as Px by Py by Pz and after it has done this, it will
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send the Px,Py,Pz values to the receiving partition. The receiving
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partition will wait to receive these values before creating its own 3d
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logical grid and will use the sender's Px,Py,Pz values as a
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constraint. The nature of the constraint is determined by the
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<I>cstyle</I> argument.
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</P>
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<P>For a <I>cstyle</I> of <I>multiple</I>, each dimension of the sender's processor
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grid is required to be an integer multiple of the corresponding
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dimension in the receiver's processor grid. This is a requirement of
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the <A HREF = "run_style.html">run_style verlet/split</A> command.
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</P>
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<P>For example, assume the sending partition creates a 4x6x10 grid = 240
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processor grid. If the receiving partition is running on 80
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processors, it could create a 4x2x10 grid, but it will not create a
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2x4x10 grid, since in the y-dimension, 6 is not an integer multiple of
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4.
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</P>
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<P>IMPORTANT NOTE: If you use the <A HREF = "partition.html">partition</A> command to
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invoke different "processsors" commands on different partitions, and
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you also use the <I>part</I> keyword, then you must insure that both the
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sending and receiving partitions invoke the "processors" command that
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connects the 2 partitions via the <I>part</I> keyword. LAMMPS cannot
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easily check for this, but your simulation will likely hang in its
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setup phase if this error has been made.
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</P>
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2011-12-08 08:00:59 +08:00
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<HR>
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2011-12-14 02:30:06 +08:00
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<P>The <I>file</I> keyword writes the mapping of the factorization of P
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2011-12-13 23:58:47 +08:00
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processors and their mapping to the 3d grid to the specified file
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2011-12-14 02:30:06 +08:00
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<I>outfile</I>. This is useful to check that you assigned physical
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2011-12-13 23:58:47 +08:00
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processors in the manner you desired, which can be tricky to figure
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2011-12-14 02:30:06 +08:00
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out, especially when running on multiple partitions or on, a multicore
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2011-12-13 23:58:47 +08:00
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machine or when the processor ranks were reordered by use of the
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<A HREF = "Section_start.html#start_6">-reorder command-line switch</A> or due to
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use of MPI-specific launch options such as a config file.
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</P>
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<P>If you have multiple partitions you should insure that each one writes
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to a different file, e.g. using a <A HREF = "variable.html">world-style variable</A>
|
2011-12-14 01:51:57 +08:00
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|
for the filename. The file has a self-explanatory header, followed by
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one-line per processor in this format:
|
2011-12-13 23:58:47 +08:00
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</P>
|
2011-12-14 02:30:06 +08:00
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<P>world-ID universe-ID original-ID: I J K: name
|
2011-12-13 23:58:47 +08:00
|
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|
</P>
|
2011-12-14 02:30:06 +08:00
|
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|
<P>The IDs are the processor's rank in this simulation (the world), the
|
2011-12-13 23:58:47 +08:00
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|
universe (of multiple simulations), and the original MPI communicator
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|
used to instantiate LAMMPS, respectively. The world and universe IDs
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|
will only be different if you are running on more than one partition;
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|
see the <A HREF = "Section_start.html#start_6">-partition command-line switch</A>.
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The universe and original IDs will only be different if you used the
|
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|
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|
<A HREF = "Section_start.html#start_6">-reorder command-line switch</A> to reorder
|
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|
|
|
the processors differently than their rank in the original
|
2011-12-14 02:30:06 +08:00
|
|
|
communicator LAMMPS was instantiated with.
|
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|
|
|
</P>
|
|
|
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|
<P>I,J,K are the indices of the processor in the 3d logical grid, each
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|
|
from 1 to Nd, where Nd is the number of processors in that dimension
|
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|
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|
of the grid.
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|
</P>
|
|
|
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|
<P>The <I>name</I> is what is returned by a call to MPI_Get_processor_name()
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|
|
and should represent an identifier relevant to the physical processors
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|
in your machine. Note that depending on the MPI implementation,
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|
|
multiple cores can have the same <I>name</I>.
|
2011-12-13 23:58:47 +08:00
|
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|
</P>
|
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|
<HR>
|
|
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|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Restrictions:</B>
|
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|
|
|
</P>
|
|
|
|
|
<P>This command cannot be used after the simulation box is defined by a
|
|
|
|
|
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
|
|
|
|
|
It can be used before a restart file is read to change the 3d
|
|
|
|
|
processor grid from what is specified in the restart file.
|
|
|
|
|
</P>
|
2011-12-14 01:51:57 +08:00
|
|
|
<P>The <I>grid numa</I> keyword only currently works with the <I>map cart</I>
|
|
|
|
|
option.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>part</I> keyword (for the receiving partition) only works with the
|
2011-12-15 00:32:06 +08:00
|
|
|
<I>grid onelevel</I> or <I>grid twolevel</I> options.
|
2011-12-13 23:58:47 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
2011-12-10 00:47:47 +08:00
|
|
|
</P>
|
2011-12-13 23:58:47 +08:00
|
|
|
<P><A HREF = "partition.html">partition</A>, <A HREF = "Section_start.html#start_6">-reorder command-line
|
|
|
|
|
switch</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
2011-12-14 01:51:57 +08:00
|
|
|
<P>The option defaults are Px Py Pz = * * *, grid = onelevel, and map =
|
|
|
|
|
cart.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
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|
</HTML>
|
