forked from lijiext/lammps
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200 lines
8.5 KiB
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<HTML>
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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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<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 a 3d grid
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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>numa</I> or <I>part</I>
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<PRE> <I>grid</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 layout 3d grid of procs with reorder = 0
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cart/reorder = use MPI_Cart() methods to layout 3d grid of procs with reorder = 1
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xyz,xzy,yxz,yzx,zxy,zyx = layout 3d grid of procs in IJK order, where I varies fastest, then J, and K slowest
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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 layout will be multiple of Precv layout in each dimension
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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 2 4 4
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processors * * 5
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processors * * * grid xyz
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processors * * * numa
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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 (with MPI ranks 0 to
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P-1) are mapped to the logical grid so that each grid cell is a
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processor. The arguments to this command control each of these 2
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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. It will do
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this based on the size and shape of the global simulation box so as to
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minimize the surface-to-volume ratio of each processor's 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, this choosing explicit values for Px or Py or
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Pz can be used to override the LAMMPS default if it is known to be
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sub-optimal for a particular problem. For example, a problem where
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the extent of atoms will change dramatically in a particular dimension
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over the 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. If multiple partitions are being used then P is the number
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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.
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</P>
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<P>Note that if you run on a large, prime number of processors P, then a
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grid 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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<HR>
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<P>The <I>grid</I> keyword affects how processor IDs are mapped to the 3d grid
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of processors.
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</P>
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<P>The <I>cart</I> style uses the family of MPI Cartesian functions to do
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this, namely MPI_Cart_create(), MPI_Cart_get(), MPI_Cart_shift(), and
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MPI_Cart_rank(). It invokes the MPI_Cart_create() function with its
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reorder flag = 0, so that MPI is 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 is free to 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 explicitly maps the P
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processors to the grid so that the processor ID in the I direction
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varies fastest, the processor ID in the J direction varies next
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fastest, and the processor ID in the K direction varies slowest. For
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example, if you select style <I>xyz</I> and you have a 2x2x2 grid of 8
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processors, the assignments of the 8 octants of the simulation domain
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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. However
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in practice, few if any MPI implementations actually do this. So it
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is likely that the <I>cart</I> and <I>cart/reorder</I> styles simply give the
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same result as one of the IJK styles.
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</P>
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<HR>
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<P>The <I>numa</I> keyword affects both the factorization of P into Px,Py,Pz
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and the mapping of processors to the 3d grid.
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</P>
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<P>It will perform a two-level factorization of the simulation box to
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minimize inter-node communication. This can improve parallel
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efficiency by reducing network traffic. When this keyword is set, the
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simulation box is first divided across nodes. Then within each node,
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the subdomain is further divided between the cores of each node.
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</P>
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<P>The numa setting will be ignored if (a) there are less than 4 cores
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per node, or (b) the number of MPI processes is not divisible by the
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number of cores used per node, or (c) only 1 node is allocated, or (d)
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any of the Px or Py of Pz values is greater than 1.
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</P>
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<HR>
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<P>The <I>part</I> keyword can be useful when running in multi-partition mode,
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e.g. with the <A HREF = "run_style.html<A HREF = "Section_start.html#start_6">-partition">>run_style verlet/split</A> command. It
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specifies a dependency bewteen a sending partition <I>Psend</I> and a
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receiving partition <I>Precv</I> which is enforced when each is setting up
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their own mapping of the partitions processors to the simulation box.
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Each of <I>Psend</I> and <I>Precv</I> must be integers from 1 to Np, where Np is
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the number of partitions you have defined via the <A HREF = </A>
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command-line 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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<HR>
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<P>Note that you can use the <A HREF = "partition.html">partition</A> command to
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specify 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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<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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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This command cannot be used after the simulation box is defined by a
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<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
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It can be used before a restart file is read to change the 3d
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processor grid from what is specified in the restart file.
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are Px Py Pz = * * *, grid = cart, numa = 0.
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</P>
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</HTML>
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