forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12453 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -65,9 +65,13 @@
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<I>neigh</I> value = <I>full</I> or <I>half/thread</I> or <I>half</I> or <I>n2</I> or <I>full/cluster</I>
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<I>comm/exchange</I> value = <I>no</I> or <I>host</I> or <I>device</I>
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<I>comm/forward</I> value = <I>no</I> or <I>host</I> or <I>device</I>
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<I>omp</I> args = Nthreads mode
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<I>omp</I> args = Nthreads keyword value ...
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Nthreads = # of OpenMP threads to associate with each MPI process
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mode = force or force/neigh (optional)
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zero or more keyword/value pairs may be appended
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keywords = <I>neigh</I>
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<I>neigh</I> value = <I>yes</I> or <I>no</I>
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<I>yes</I> = threaded neighbor list build (default)
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<I>no</I> = non-threaded neighbor list build
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</PRE>
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</UL>
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@ -80,8 +84,8 @@ package gpu force/neigh 0 1 -1.0
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package cuda gpu/node/special 2 0 2
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package cuda test 3948
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package kokkos neigh half/thread comm/forward device
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package omp * force/neigh
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package omp 4 force
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package omp 0 neigh yes
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package omp 4
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package intel * mixed balance -1
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</PRE>
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<P><B>Description:</B>
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@ -349,30 +353,25 @@ multiple threads to pack/unpack communicated data.
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<P>The <I>omp</I> style invokes options associated with the use of the
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USER-OMP package.
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</P>
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<P>The first argument allows to explicitly set the number of OpenMP
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threads to be allocated for each MPI process. For example, if your
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system has nodes with dual quad-core processors, it has a total of 8
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cores per node. You could run MPI on 2 cores on each node (e.g. using
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options for the mpirun command), and set the <I>Nthreads</I> setting to 4.
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This would effectively use all 8 cores on each node. Since each MPI
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process would spawn 4 threads (one of which runs as part of the MPI
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process itself).
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<P>The first argument sets the number of OpenMP threads allocated for
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each MPI process or task. For example, if your system has nodes with
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dual quad-core processors, it has a total of 8 cores per node. You
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could two MPI tasks per node (e.g. using the -ppn option of the mpirun
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command), and set <I>Nthreads</I> = 4. This would effectively use all 8
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cores on each node. Note that the product of MPI tasks * threads/task
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should not exceed the physical number of cores (on a node), otherwise
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performance will suffer.
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</P>
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<P>For performance reasons, you should not set <I>Nthreads</I> to more threads
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than there are physical cores (per MPI task), but LAMMPS cannot check
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for this.
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</P>
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<P>An <I>Nthreads</I> value of '*' instructs LAMMPS to use whatever is the
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<P>An <I>Nthreads</I> value of 0 instructs LAMMPS to use whatever value is the
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default for the given OpenMP environment. This is usually determined
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via the <I>OMP_NUM_THREADS</I> environment variable or the compiler
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runtime. Please note that in most cases the default for OpenMP
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capable compilers is to use one thread for each available CPU core
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when <I>OMP_NUM_THREADS</I> is not set, which can lead to extremely bad
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runtime. Note that in most cases the default for OpenMP capable
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compilers is to use one thread for each available CPU core when
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<I>OMP_NUM_THREADS</I> is not explicitly set, which can lead to poor
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performance.
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</P>
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<P>By default LAMMPS uses 1 thread per MPI task. If the environment
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variable OMP_NUM_THREADS is set to a valid value, this value is used.
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You can set this environment variable when you launch LAMMPS, e.g.
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<P>Here are examples of how to set the environment variable when
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launching LAMMPS:
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</P>
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<PRE>env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
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env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
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@ -383,26 +382,24 @@ All three of these examples use a total of 4 CPU cores.
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</P>
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<P>Note that different MPI implementations have different ways of passing
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the OMP_NUM_THREADS environment variable to all MPI processes. The
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2nd line above is for MPICH; the 3rd line with -x is for OpenMPI.
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Check your MPI documentation for additional details.
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2nd example line above is for MPICH; the 3rd example line with -x is
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for OpenMPI. Check your MPI documentation for additional details.
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</P>
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<P>You can also set the number of threads per MPI task via the <A HREF = "package.html">package
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omp</A> command, which will override any OMP_NUM_THREADS
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setting.
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<P>What combination of threads and MPI tasks gives the best performance
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is difficult to predict and can depend on many components of your
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input. Not all features of LAMMPS support OpenMP threading via the
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USER-OMP packaage and the parallel efficiency can be very different,
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too.
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</P>
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<P>Which combination of threads and MPI tasks gives the best performance
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is difficult to predict and can depend on many components of your input.
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Not all features of LAMMPS support OpenMP and the parallel efficiency
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can be very different, too.
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</P>
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<P>The <I>mode</I> setting specifies where neighbor list calculations will be
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multi-threaded as well. If <I>mode</I> is force, neighbor list calculation
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is performed in serial. If <I>mode</I> is force/neigh, a multi-threaded
|
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neighbor list build is used. Using the force/neigh setting is almost
|
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always faster and should produce idential neighbor lists at the
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expense of using some more memory (neighbor list pages are always
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allocated for all threads at the same time and each thread works on
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its own pages).
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<P>The <I>neigh</I> keyword specifies whether neighbor list building will be
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multi-threaded in addition to force calculations. If <I>neigh</I> is set
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to <I>no</I> then neighbor list calculation is performed only by MPI tasks
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with no OpenMP threading. If <I>mode</I> is <I>yes</I> (the default), a
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multi-threaded neighbor list build is used. Using <I>neigh</I> = <I>yes</I> is
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almost always faster and should produce idential neighbor lists at the
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expense of using more memory. Specifically, neighbor list pages are
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allocated for all threads at the same time and each thread works
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within its own pages.
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</P>
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<HR>
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@ -455,9 +452,10 @@ the "-sf kk" <A HREF = "Section_start.html#start_7">command-line switch</A> is u
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or not.
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</P>
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<P>If the "-sf omp" <A HREF = "Section_start.html#start_7">command-line switch</A> is
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used then it is as if the command "package omp *" were invoked, to
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specify default settings for the USER-OMP package. If the
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command-line switch is not used, then no defaults are set, and you
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must specify the appropriate package command in your input script.
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used then it is as if the command "package omp 0" were invoked, to
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specify settings for the USER-OMP package. The option defaults are
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neigh = yes. If the command-line switch is not used, then no defaults
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are set, and you must specify the appropriate "package omp" command in
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your input script.
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</P>
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</HTML>
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|
|
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@ -60,9 +60,13 @@ args = arguments specific to the style :l
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{neigh} value = {full} or {half/thread} or {half} or {n2} or {full/cluster}
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{comm/exchange} value = {no} or {host} or {device}
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{comm/forward} value = {no} or {host} or {device}
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{omp} args = Nthreads mode
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{omp} args = Nthreads keyword value ...
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Nthreads = # of OpenMP threads to associate with each MPI process
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mode = force or force/neigh (optional) :pre
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zero or more keyword/value pairs may be appended
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keywords = {neigh}
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{neigh} value = {yes} or {no}
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{yes} = threaded neighbor list build (default)
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{no} = non-threaded neighbor list build :pre
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:ule
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[Examples:]
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@ -74,8 +78,8 @@ package gpu force/neigh 0 1 -1.0
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package cuda gpu/node/special 2 0 2
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package cuda test 3948
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package kokkos neigh half/thread comm/forward device
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package omp * force/neigh
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package omp 4 force
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package omp 0 neigh yes
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package omp 4
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package intel * mixed balance -1 :pre
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|
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[Description:]
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|
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@ -343,33 +347,25 @@ multiple threads to pack/unpack communicated data.
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The {omp} style invokes options associated with the use of the
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USER-OMP package.
|
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|
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The first argument allows to explicitly set the number of OpenMP
|
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threads to be allocated for each MPI process. For example, if your
|
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system has nodes with dual quad-core processors, it has a total of 8
|
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cores per node. You could run MPI on 2 cores on each node (e.g. using
|
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options for the mpirun command), and set the {Nthreads} setting to 4.
|
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This would effectively use all 8 cores on each node. Since each MPI
|
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process would spawn 4 threads (one of which runs as part of the MPI
|
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process itself).
|
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The first argument sets the number of OpenMP threads allocated for
|
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each MPI process or task. For example, if your system has nodes with
|
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dual quad-core processors, it has a total of 8 cores per node. You
|
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could two MPI tasks per node (e.g. using the -ppn option of the mpirun
|
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command), and set {Nthreads} = 4. This would effectively use all 8
|
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cores on each node. Note that the product of MPI tasks * threads/task
|
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should not exceed the physical number of cores (on a node), otherwise
|
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performance will suffer.
|
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|
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For performance reasons, you should not set {Nthreads} to more threads
|
||||
than there are physical cores (per MPI task), but LAMMPS cannot check
|
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for this.
|
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|
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An {Nthreads} value of '*' instructs LAMMPS to use whatever is the
|
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An {Nthreads} value of 0 instructs LAMMPS to use whatever value is the
|
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default for the given OpenMP environment. This is usually determined
|
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via the {OMP_NUM_THREADS} environment variable or the compiler
|
||||
runtime. Please note that in most cases the default for OpenMP
|
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capable compilers is to use one thread for each available CPU core
|
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when {OMP_NUM_THREADS} is not set, which can lead to extremely bad
|
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runtime. Note that in most cases the default for OpenMP capable
|
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compilers is to use one thread for each available CPU core when
|
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{OMP_NUM_THREADS} is not explicitly set, which can lead to poor
|
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performance.
|
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|
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|
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|
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|
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By default LAMMPS uses 1 thread per MPI task. If the environment
|
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variable OMP_NUM_THREADS is set to a valid value, this value is used.
|
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You can set this environment variable when you launch LAMMPS, e.g.
|
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Here are examples of how to set the environment variable when
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launching LAMMPS:
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|
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env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
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env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
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@ -378,33 +374,26 @@ mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script :pre
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or you can set it permanently in your shell's start-up script.
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All three of these examples use a total of 4 CPU cores.
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|
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Note that different MPI implementations have different ways of passing
|
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the OMP_NUM_THREADS environment variable to all MPI processes. The
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2nd line above is for MPICH; the 3rd line with -x is for OpenMPI.
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Check your MPI documentation for additional details.
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2nd example line above is for MPICH; the 3rd example line with -x is
|
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for OpenMPI. Check your MPI documentation for additional details.
|
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|
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You can also set the number of threads per MPI task via the "package
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omp"_package.html command, which will override any OMP_NUM_THREADS
|
||||
setting.
|
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What combination of threads and MPI tasks gives the best performance
|
||||
is difficult to predict and can depend on many components of your
|
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input. Not all features of LAMMPS support OpenMP threading via the
|
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USER-OMP packaage and the parallel efficiency can be very different,
|
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too.
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|
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|
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|
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|
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Which combination of threads and MPI tasks gives the best performance
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is difficult to predict and can depend on many components of your input.
|
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Not all features of LAMMPS support OpenMP and the parallel efficiency
|
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can be very different, too.
|
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|
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The {mode} setting specifies where neighbor list calculations will be
|
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multi-threaded as well. If {mode} is force, neighbor list calculation
|
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is performed in serial. If {mode} is force/neigh, a multi-threaded
|
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neighbor list build is used. Using the force/neigh setting is almost
|
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always faster and should produce idential neighbor lists at the
|
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expense of using some more memory (neighbor list pages are always
|
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allocated for all threads at the same time and each thread works on
|
||||
its own pages).
|
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The {neigh} keyword specifies whether neighbor list building will be
|
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multi-threaded in addition to force calculations. If {neigh} is set
|
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to {no} then neighbor list calculation is performed only by MPI tasks
|
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with no OpenMP threading. If {mode} is {yes} (the default), a
|
||||
multi-threaded neighbor list build is used. Using {neigh} = {yes} is
|
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almost always faster and should produce idential neighbor lists at the
|
||||
expense of using more memory. Specifically, neighbor list pages are
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allocated for all threads at the same time and each thread works
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within its own pages.
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|
||||
:line
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||||
|
||||
|
|
@ -457,7 +446,8 @@ the "-sf kk" "command-line switch"_Section_start.html#start_7 is used
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|||
or not.
|
||||
|
||||
If the "-sf omp" "command-line switch"_Section_start.html#start_7 is
|
||||
used then it is as if the command "package omp *" were invoked, to
|
||||
specify default settings for the USER-OMP package. If the
|
||||
command-line switch is not used, then no defaults are set, and you
|
||||
must specify the appropriate package command in your input script.
|
||||
used then it is as if the command "package omp 0" were invoked, to
|
||||
specify settings for the USER-OMP package. The option defaults are
|
||||
neigh = yes. If the command-line switch is not used, then no defaults
|
||||
are set, and you must specify the appropriate "package omp" command in
|
||||
your input script.
|
||||
|
|
|
|||
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