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@ -28,8 +28,8 @@
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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 = inname
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inname = file containing grid layout
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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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@ -40,8 +40,8 @@
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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 = outname
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outname = name of file to write 3d grid of processors to
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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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@ -112,12 +112,12 @@ 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 multi-core nodes
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to minimize off-node communication. It insures that contiguous
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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
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of the 3d grid will correspond to the cores of each node. This
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affects both the factorization and mapping steps.
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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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@ -156,7 +156,7 @@ any of the Px or Py of Pz values is greater than 1.
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the MPI ranks of processors LAMMPS is running on are ordered by core
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and then by node. See the same note for the <I>twolevel</I> keyword.
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</P>
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<P>The <I>custom</I> style uses the file <I>inname</I> to define both the 3d
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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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@ -268,11 +268,11 @@ setup phase if this error has been made.
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</P>
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<HR>
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<P>The <I>out</I> keyword writes the mapping of the factorization of P
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<P>The <I>file</I> keyword writes the mapping of the factorization of P
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processors and their mapping to the 3d grid to the specified file
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<I>fname</I>. This is useful to check that you assigned physical
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<I>outfile</I>. This is useful to check that you assigned physical
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processors in the manner you desired, which can be tricky to figure
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out, especially when running on multiple partitions or on a multicore
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out, especially when running on multiple partitions or on, a multicore
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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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@ -282,10 +282,9 @@ to a different file, e.g. using a <A HREF = "variable.html">world-style variable
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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:
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</P>
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<P>I J K: world-ID universe-ID original-ID: name
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<P>world-ID universe-ID original-ID: I J K: name
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</P>
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<P>I,J,K are the indices of the processor in the 3d logical grid. The
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IDs are the processor's rank in this simulation (the world), the
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<P>The IDs are the processor's rank in this simulation (the world), the
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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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@ -293,11 +292,16 @@ 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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<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
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communicator LAMMPS was instantiated with. The <I>name</I> is what is
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returned by a call to MPI_Get_processor_name() and should represent an
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identifier relevant to the physical processors in your machine. Note
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that depending on the MPI implementation, multiple cores can have the
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same <I>name</I>.
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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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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>.
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</P>
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<HR>
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@ -22,8 +22,8 @@ keyword = {grid} or {map} or {part} or {file} :l
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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 = inname
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inname = file containing grid layout
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custom params = infile
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infile = file containing grid layout
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{map} arg = {cart} or {cart/reorder} or {xyz} or {xzy} or {yxz} or {yzx} or {zxy} or {zyx}
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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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@ -34,8 +34,8 @@ keyword = {grid} or {map} or {part} or {file} :l
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Precv = partition # (1 to Np) which will recv the processor layout
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cstyle = {multiple}
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{multiple} = Psend grid will be multiple of Precv grid in each dimension
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{file} arg = outname
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outname = name of file to write 3d grid of processors to :pre
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{file} arg = outfile
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outfile = name of file to write 3d grid of processors to :pre
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:ule
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[Examples:]
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@ -105,12 +105,12 @@ 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 {map} keyword setting.
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The {twolevel} style can be used on machines with multi-core nodes
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to minimize off-node communication. It insures that contiguous
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The {twolevel} 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 {Nc} is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections
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of the 3d grid will correspond to the cores of each node. This
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affects both the factorization and mapping steps.
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For example if {Nc} 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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The {Cx}, {Cy}, {Cz} settings are similar to the {Px}, {Py}, {Pz}
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settings, only their product should equal {Nc}. Any of the 3
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@ -149,7 +149,7 @@ IMPORTANT NOTE: For the {numa} style to work correctly, it assumes
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the MPI ranks of processors LAMMPS is running on are ordered by core
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and then by node. See the same note for the {twolevel} keyword.
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The {custom} style uses the file {inname} to define both the 3d
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The {custom} style uses the file {infile} to define both the 3d
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factorization and the mapping of processors to the grid.
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The file should have the following format. Any number of initial
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@ -261,11 +261,11 @@ setup phase if this error has been made.
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:line
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The {out} keyword writes the mapping of the factorization of P
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The {file} keyword writes the mapping of the factorization of P
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processors and their mapping to the 3d grid to the specified file
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{fname}. This is useful to check that you assigned physical
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{outfile}. This is useful to check that you assigned physical
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processors in the manner you desired, which can be tricky to figure
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out, especially when running on multiple partitions or on a multicore
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out, especially when running on multiple partitions or on, a multicore
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machine or when the processor ranks were reordered by use of the
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"-reorder command-line switch"_Section_start.html#start_6 or due to
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use of MPI-specific launch options such as a config file.
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@ -275,10 +275,9 @@ to a different file, e.g. using a "world-style variable"_variable.html
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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:
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I J K: world-ID universe-ID original-ID: name
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world-ID universe-ID original-ID: I J K: name
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I,J,K are the indices of the processor in the 3d logical grid. The
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IDs are the processor's rank in this simulation (the world), the
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The IDs are the processor's rank in this simulation (the world), the
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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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@ -286,11 +285,16 @@ see the "-partition command-line switch"_Section_start.html#start_6.
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The universe and original IDs will only be different if you used the
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"-reorder command-line switch"_Section_start.html#start_6 to reorder
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the processors differently than their rank in the original
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communicator LAMMPS was instantiated with. The {name} is what is
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returned by a call to MPI_Get_processor_name() and should represent an
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identifier relevant to the physical processors in your machine. Note
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that depending on the MPI implementation, multiple cores can have the
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same {name}.
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communicator LAMMPS was instantiated with.
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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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of the grid.
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The {name} 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 {name}.
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:line
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