mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7273 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
5a968ac62e
commit
143aa917f2
|
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@ -181,6 +181,12 @@ the bond topologies you have defined.
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<DD>GPU acceleration requires fix gpu in the input script.
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<DT><I>Accelerator sharing is not currently supported on system.</I>
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<DD>You cannot use more MPI processes than accelerators on the
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system as currently configured. For NVIDIA GPUs, the compute
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mode must be changed using nvidia-smi to support sharing.
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<DT><I>All angle coeffs are not set</I>
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<DD>All angle coefficients must be set in the data file or by the
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@ -1205,6 +1211,11 @@ in LAMMPS.
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<DD>No atoms in system have a non-zero charge.
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<DT><I>Cannot use neigh_modify exclude with GPU neighbor builds</I>
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<DD>This is a current limitation of the GPU implementation
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in LAMMPS.
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<DT><I>Cannot use neighbor bins - box size << cutoff</I>
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<DD>Too many neighbor bins will be created. This typically happens when
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@ -5799,6 +5810,12 @@ length in that dimension. E.g. the xy tilt must be between -half and
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<DD>Self-explanatory.
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<DT><I>Unable to initialize accelerator for use</I>
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<DD>One or more specified accelerator(s) cannot currently be used by LAMMPS.
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This can happen if the accelerator is already in use by another
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process.
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<DT><I>Unbalanced quotes in input line</I>
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<DD>No matching end double quote was found following a leading double
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|
|
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@ -178,6 +178,12 @@ the bond topologies you have defined. :dd
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GPU acceleration requires fix gpu in the input script. :dd
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{Accelerator sharing is not currently supported on system.} :dt
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You cannot use more MPI processes than accelerators on the
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system as currently configured. For NVIDIA GPUs, the compute
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mode must be changed using nvidia-smi to support sharing. :dd
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{All angle coeffs are not set} :dt
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All angle coefficients must be set in the data file or by the
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@ -1202,6 +1208,11 @@ in LAMMPS. :dd
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No atoms in system have a non-zero charge. :dd
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{Cannot use neigh_modify exclude with GPU neighbor builds} :dt
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This is a current limitation of the GPU implementation
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in LAMMPS. :dd
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{Cannot use neighbor bins - box size << cutoff} :dt
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Too many neighbor bins will be created. This typically happens when
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@ -5796,6 +5807,12 @@ Self-explanatory. :dd
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Self-explanatory. :dd
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{Unable to initialize accelerator for use} :dt
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One or more specified accelerator(s) cannot currently be used by LAMMPS.
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This can happen if the accelerator is already in use by another
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process. :dd
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{Unbalanced quotes in input line} :dt
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No matching end double quote was found following a leading double
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|
|
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@ -998,12 +998,22 @@ lj/cut</A> variant, with style names lj/cut/opt, lj/cut/omp,
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lj/cut/gpu, or lj/cut/cuda. A variant styles can be specified
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explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
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-suffix switch is used, you do not need to modify your input script.
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The specified suffix (opt,omp,gpu,cuda) is automatically appended whenever
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your input script command creates a new <A HREF = "atom_style.html">atom</A>,
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<A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>, <A HREF = "compute.html">compute</A>, or
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<A HREF = "run_style.html">run</A> style. atom, pair, fix, compute, or integrate
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style. If the variant version does not exist, the standard version is
|
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created.
|
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The specified suffix (opt,omp,gpu,cuda) is automatically appended
|
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whenever your input script command creates a new
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<A HREF = "atom_style.html">atom</A>, <A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>,
|
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<A HREF = "compute.html">compute</A>, or <A HREF = "run_style.html">run</A> style. If the variant
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version does not exist, the standard version is created.
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</P>
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<P>For the GPU package, using this command-line switch also invokes the
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default GPU settings, as if the command "package gpu force/neigh 0 0
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1" were used at the top of your input script. These settings can be
|
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changed by using the <A HREF = "pacakge.html">package gpu</A> command in your script
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if desired.
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</P>
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<P>For the OMP package, using this command-line switch also invokes the
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default OMP settings, as if the command "package omp *" were used at
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the top of your input script. These settings can be changed by using
|
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the <A HREF = "pacakge.html">package omp</A> command in your script if desired.
|
||||
</P>
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||||
<P>The <A HREF = "suffix.html">suffix</A> command can also set a suffix and it can also
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turn off/on any suffix setting made via the command line.
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||||
|
|
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|
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@ -990,12 +990,22 @@ lj/cut"_pair_lj.html variant, with style names lj/cut/opt, lj/cut/omp,
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lj/cut/gpu, or lj/cut/cuda. A variant styles can be specified
|
||||
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
|
||||
-suffix switch is used, you do not need to modify your input script.
|
||||
The specified suffix (opt,omp,gpu,cuda) is automatically appended whenever
|
||||
your input script command creates a new "atom"_atom_style.html,
|
||||
"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or
|
||||
"run"_run_style.html style. atom, pair, fix, compute, or integrate
|
||||
style. If the variant version does not exist, the standard version is
|
||||
created.
|
||||
The specified suffix (opt,omp,gpu,cuda) is automatically appended
|
||||
whenever your input script command creates a new
|
||||
"atom"_atom_style.html, "pair"_pair_style.html, "fix"_fix.html,
|
||||
"compute"_compute.html, or "run"_run_style.html style. If the variant
|
||||
version does not exist, the standard version is created.
|
||||
|
||||
For the GPU package, using this command-line switch also invokes the
|
||||
default GPU settings, as if the command "package gpu force/neigh 0 0
|
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1" were used at the top of your input script. These settings can be
|
||||
changed by using the "package gpu"_pacakge.html command in your script
|
||||
if desired.
|
||||
|
||||
For the OMP package, using this command-line switch also invokes the
|
||||
default OMP settings, as if the command "package omp *" were used at
|
||||
the top of your input script. These settings can be changed by using
|
||||
the "package omp"_pacakge.html command in your script if desired.
|
||||
|
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The "suffix"_suffix.html command can also set a suffix and it can also
|
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turn off/on any suffix setting made via the command line.
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||||
|
|
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113
doc/package.html
113
doc/package.html
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@ -24,7 +24,18 @@
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first = ID of first GPU to be used on each node
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last = ID of last GPU to be used on each node
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split = fraction of particles assigned to the GPU
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<I>cuda</I> args = to be determined
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<I>cuda</I> args = one or more keyword/value pairs may be appended
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keywords = <I>gpu/node</I> or <I>gpu/node/special</I> or <I>timing</I> or <I>test</I> or <I>override/bpa</I>
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gpu/node values = N
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N = number of GPUs to be used per node
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gpu/node/special values = N gpu1 .. gpuN
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N = number of GPUs to be used per node
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gpu1 .. gpuN = N IDs of the GPUs to use
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timing values = none
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test values = id
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id = atom-ID of a test particle
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override/bpa values = flag
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flag = 0 for TpA algorithm, 1 for BpA algorithm
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<I>omp</I> args = Nthreads mode
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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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@ -45,17 +56,25 @@ package omp 4 force
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<P>This command invokes package-specific settings. Currently the
|
||||
following packages use it: GPU, USER-CUDA, and USER-OMP.
|
||||
</P>
|
||||
<P>To use the accelerated GPU and USER-OMP styles, the use of the package
|
||||
command is required. However, as described in the "Defaults" section
|
||||
below, if you use the "-sf gpu" or "-sf omp" <A HREF = "Section_start.html#start_6">command-line
|
||||
options</A> to enable use of these styles,
|
||||
then default package settings are enabled. In that case you only need
|
||||
to use the package command if you want to change the defaults.
|
||||
</P>
|
||||
<P>To use the accelerate USER-CUDA styles, the package command is not
|
||||
required as defaults are assigned internally. You only need to use
|
||||
the package command if you want to change the defaults.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
|
||||
details about using these various packages for accelerating
|
||||
a LAMMPS calculation.
|
||||
details about using these various packages for accelerating LAMMPS
|
||||
calculations.
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||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>gpu</I> style invokes options associated with the use of the GPU
|
||||
package. It allows you to select and initialize GPUs to be used for
|
||||
acceleration via this package and configure how the GPU acceleration
|
||||
is performed. These settings are required in order to use any style
|
||||
with GPU acceleration.
|
||||
package.
|
||||
</P>
|
||||
<P>The <I>mode</I> setting specifies where neighbor list calculations will be
|
||||
performed. If <I>mode</I> is force, neighbor list calculation is performed
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||||
|
|
@ -102,7 +121,54 @@ the other particles.
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|||
<HR>
|
||||
|
||||
<P>The <I>cuda</I> style invokes options associated with the use of the
|
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USER-CUDA package. These still need to be documented.
|
||||
USER-CUDA package.
|
||||
</P>
|
||||
<P>The <I>gpu/node</I> setting specifies the number <I>N</I> of GPUs to be used on
|
||||
each node. An MPI process with rank <I>K</I> will use the GPU (K mod N).
|
||||
This implies that processes should be assigned with successive ranks
|
||||
on each node, which is the default with most (or even all) MPI
|
||||
implementations. The default value for <I>N</I> is 2.
|
||||
</P>
|
||||
<P>The <I>gpu/node/special</I> setting also specifies the number (N) of GPUs
|
||||
to be used on each node, but allows more control over their
|
||||
specification. An MPI process with rank <I>K</I> will use the GPU <I>gpuI</I>
|
||||
with l = (K mod N) + 1. This implies that processes should be assigned
|
||||
with successive ranks on each node, which is the default with most (or
|
||||
even all) MPI implementations. For example if you have three GPUs on
|
||||
a machine, one of which is used for the X-Server (the GPU with the ID
|
||||
1) while the others (with IDs 0 and 2) are used for computations you
|
||||
would specify:
|
||||
</P>
|
||||
<PRE>package cuda gpu/node/special 2 0 2
|
||||
</PRE>
|
||||
<P>A main purpose of the <I>gpu/node/special</I> option is to allow two (or
|
||||
more) simulations to be run on one workstation. In that case one
|
||||
would set the first simulation to use GPU 0 and the second to use GPU
|
||||
1. This is not necessary though, if the GPUs are in what is called
|
||||
<I>compute exclusive</I> mode. Using that setting, every process will get
|
||||
its own GPU automatically. This <I>compute exclusive</I> mode can be set
|
||||
as root using the <I>nvidia-smi</I> tool which is part of the CUDA
|
||||
installation.
|
||||
</P>
|
||||
<P>Note that if the <I>gpu/node/special</I> keyword is not used, the USER-CUDA
|
||||
package sorts existing GPUs on each node according to their number of
|
||||
multiprocessors. This way, compute GPUs will be priorized over
|
||||
X-Server GPUs.
|
||||
</P>
|
||||
<P>Use of the <I>timing</I> keyword will output detailed timing information
|
||||
for various subroutines.
|
||||
</P>
|
||||
<P>The <I>test</I> keyword will output info for the the specified atom at
|
||||
several points during each time step. This is mainly usefull for
|
||||
debugging purposes. Note that the simulation will be severly slowed
|
||||
down if this option is used.
|
||||
</P>
|
||||
<P>The <I>override/bpa</I> keyword can be used to specify which mode is used
|
||||
for pair-force evaluation. TpA = one thread per atom; BpA = one block
|
||||
per atom. If this keyword is not used, a short test at the begin of
|
||||
each run will determine which method is more effective (the result of
|
||||
this test is part of the LAMMPS output). Therefore it is usually not
|
||||
necessary to use this setting.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -153,22 +219,15 @@ its own pages).
|
|||
</P>
|
||||
<P>The cuda style of this command can only be invoked if LAMMPS was built
|
||||
with the USER-CUDA package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info. When using
|
||||
styles in the USER-CUDA package, use of the "package cuda" command in
|
||||
your input script is not required.
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>The gpu style of this command can only be invoked if LAMMPS was built
|
||||
with the GPU package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info. When using
|
||||
styles in the GPU package, use of the "package gpu" command in your
|
||||
input script is currently required.
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>The omp style of this command can only be invoked if LAMMPS was built
|
||||
with the USER-OMP package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info. When using
|
||||
styles in the USER-OMP package, use of the "package omp" command in
|
||||
your input script is not required. See the information on default
|
||||
settings below.
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
@ -176,10 +235,20 @@ settings below.
|
|||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>If the "-sf omp" <A HREF = "Section_start.html#start_6">command-line switch</A> is
|
||||
used then "package omp *" is also auto-invoked to specify default OMP
|
||||
settings.
|
||||
<P>If the "-sf gpu" <A HREF = "Section_start.html#start_6">command-line switch</A> is
|
||||
used then it is as if the command "package gpu force/neigh 0 0 1" were
|
||||
invoked, to specify default settings for the GPU 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.
|
||||
</P>
|
||||
<P>The other styles have no defaults.
|
||||
<P>The default settings for the USER CUDA package are "package cuda gpu
|
||||
2". This is the case whether the "-sf cuda" <A HREF = "Section_start.html#start_6">command-line
|
||||
switch</A> is used or not.
|
||||
</P>
|
||||
<P>If the "-sf omp" <A HREF = "Section_start.html#start_6">command-line switch</A> 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.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
113
doc/package.txt
113
doc/package.txt
|
|
@ -19,7 +19,18 @@ args = arguments specific to the style :l
|
|||
first = ID of first GPU to be used on each node
|
||||
last = ID of last GPU to be used on each node
|
||||
split = fraction of particles assigned to the GPU
|
||||
{cuda} args = to be determined
|
||||
{cuda} args = one or more keyword/value pairs may be appended
|
||||
keywords = {gpu/node} or {gpu/node/special} or {timing} or {test} or {override/bpa}
|
||||
gpu/node values = N
|
||||
N = number of GPUs to be used per node
|
||||
gpu/node/special values = N gpu1 .. gpuN
|
||||
N = number of GPUs to be used per node
|
||||
gpu1 .. gpuN = N IDs of the GPUs to use
|
||||
timing values = none
|
||||
test values = id
|
||||
id = atom-ID of a test particle
|
||||
override/bpa values = flag
|
||||
flag = 0 for TpA algorithm, 1 for BpA algorithm
|
||||
{omp} args = Nthreads mode
|
||||
Nthreads = # of OpenMP threads to associate with each MPI process
|
||||
mode = force or force/neigh (optional) :pre
|
||||
|
|
@ -39,17 +50,25 @@ package omp 4 force :pre
|
|||
This command invokes package-specific settings. Currently the
|
||||
following packages use it: GPU, USER-CUDA, and USER-OMP.
|
||||
|
||||
To use the accelerated GPU and USER-OMP styles, the use of the package
|
||||
command is required. However, as described in the "Defaults" section
|
||||
below, if you use the "-sf gpu" or "-sf omp" "command-line
|
||||
options"_Section_start.html#start_6 to enable use of these styles,
|
||||
then default package settings are enabled. In that case you only need
|
||||
to use the package command if you want to change the defaults.
|
||||
|
||||
To use the accelerate USER-CUDA styles, the package command is not
|
||||
required as defaults are assigned internally. You only need to use
|
||||
the package command if you want to change the defaults.
|
||||
|
||||
See "this section"_Section_accelerate.html of the manual for more
|
||||
details about using these various packages for accelerating
|
||||
a LAMMPS calculation.
|
||||
details about using these various packages for accelerating LAMMPS
|
||||
calculations.
|
||||
|
||||
:line
|
||||
|
||||
The {gpu} style invokes options associated with the use of the GPU
|
||||
package. It allows you to select and initialize GPUs to be used for
|
||||
acceleration via this package and configure how the GPU acceleration
|
||||
is performed. These settings are required in order to use any style
|
||||
with GPU acceleration.
|
||||
package.
|
||||
|
||||
The {mode} setting specifies where neighbor list calculations will be
|
||||
performed. If {mode} is force, neighbor list calculation is performed
|
||||
|
|
@ -96,7 +115,54 @@ the other particles.
|
|||
:line
|
||||
|
||||
The {cuda} style invokes options associated with the use of the
|
||||
USER-CUDA package. These still need to be documented.
|
||||
USER-CUDA package.
|
||||
|
||||
The {gpu/node} setting specifies the number {N} of GPUs to be used on
|
||||
each node. An MPI process with rank {K} will use the GPU (K mod N).
|
||||
This implies that processes should be assigned with successive ranks
|
||||
on each node, which is the default with most (or even all) MPI
|
||||
implementations. The default value for {N} is 2.
|
||||
|
||||
The {gpu/node/special} setting also specifies the number (N) of GPUs
|
||||
to be used on each node, but allows more control over their
|
||||
specification. An MPI process with rank {K} will use the GPU {gpuI}
|
||||
with l = (K mod N) + 1. This implies that processes should be assigned
|
||||
with successive ranks on each node, which is the default with most (or
|
||||
even all) MPI implementations. For example if you have three GPUs on
|
||||
a machine, one of which is used for the X-Server (the GPU with the ID
|
||||
1) while the others (with IDs 0 and 2) are used for computations you
|
||||
would specify:
|
||||
|
||||
package cuda gpu/node/special 2 0 2 :pre
|
||||
|
||||
A main purpose of the {gpu/node/special} option is to allow two (or
|
||||
more) simulations to be run on one workstation. In that case one
|
||||
would set the first simulation to use GPU 0 and the second to use GPU
|
||||
1. This is not necessary though, if the GPUs are in what is called
|
||||
{compute exclusive} mode. Using that setting, every process will get
|
||||
its own GPU automatically. This {compute exclusive} mode can be set
|
||||
as root using the {nvidia-smi} tool which is part of the CUDA
|
||||
installation.
|
||||
|
||||
Note that if the {gpu/node/special} keyword is not used, the USER-CUDA
|
||||
package sorts existing GPUs on each node according to their number of
|
||||
multiprocessors. This way, compute GPUs will be priorized over
|
||||
X-Server GPUs.
|
||||
|
||||
Use of the {timing} keyword will output detailed timing information
|
||||
for various subroutines.
|
||||
|
||||
The {test} keyword will output info for the the specified atom at
|
||||
several points during each time step. This is mainly usefull for
|
||||
debugging purposes. Note that the simulation will be severly slowed
|
||||
down if this option is used.
|
||||
|
||||
The {override/bpa} keyword can be used to specify which mode is used
|
||||
for pair-force evaluation. TpA = one thread per atom; BpA = one block
|
||||
per atom. If this keyword is not used, a short test at the begin of
|
||||
each run will determine which method is more effective (the result of
|
||||
this test is part of the LAMMPS output). Therefore it is usually not
|
||||
necessary to use this setting.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -147,22 +213,15 @@ This command cannot be used after the simulation box is defined by a
|
|||
|
||||
The cuda style of this command can only be invoked if LAMMPS was built
|
||||
with the USER-CUDA package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info. When using
|
||||
styles in the USER-CUDA package, use of the "package cuda" command in
|
||||
your input script is not required.
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
The gpu style of this command can only be invoked if LAMMPS was built
|
||||
with the GPU package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info. When using
|
||||
styles in the GPU package, use of the "package gpu" command in your
|
||||
input script is currently required.
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
The omp style of this command can only be invoked if LAMMPS was built
|
||||
with the USER-OMP package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info. When using
|
||||
styles in the USER-OMP package, use of the "package omp" command in
|
||||
your input script is not required. See the information on default
|
||||
settings below.
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
@ -170,9 +229,19 @@ settings below.
|
|||
|
||||
[Default:]
|
||||
|
||||
If the "-sf gpu" "command-line switch"_Section_start.html#start_6 is
|
||||
used then it is as if the command "package gpu force/neigh 0 0 1" were
|
||||
invoked, to specify default settings for the GPU 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.
|
||||
|
||||
The default settings for the USER CUDA package are "package cuda gpu
|
||||
2". This is the case whether the "-sf cuda" "command-line
|
||||
switch"_Section_start.html#start_6 is used or not.
|
||||
|
||||
If the "-sf omp" "command-line switch"_Section_start.html#start_6 is
|
||||
used then "package omp *" is also auto-invoked to specify default OMP
|
||||
settings.
|
||||
|
||||
The other styles have no defaults.
|
||||
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.
|
||||
|
||||
|
|
|
|||
|
|
@ -19,16 +19,17 @@
|
|||
</H3>
|
||||
<H3>pair_style coul/long command
|
||||
</H3>
|
||||
<H3>pair_style coul/long/gpu command
|
||||
</H3>
|
||||
<H3>pair_style coul/long/omp command
|
||||
</H3>
|
||||
<H3>pair_style coul/long/gpu command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<P>pair_style coul/cut cutoff
|
||||
<PRE>pair_style coul/cut cutoff
|
||||
pair_style coul/debye kappa cutoff
|
||||
pair_style coul/long cutoff
|
||||
</P>
|
||||
pair_style coul/long/gpu cutoff
|
||||
</PRE>
|
||||
<UL><LI>cutoff = global cutoff for Coulombic interactions
|
||||
<LI>kappa = Debye length (inverse distance units)
|
||||
</UL>
|
||||
|
|
|
|||
|
|
@ -11,14 +11,15 @@ pair_style coul/cut/omp command :h3
|
|||
pair_style coul/debye command :h3
|
||||
pair_style coul/debye/omp command :h3
|
||||
pair_style coul/long command :h3
|
||||
pair_style coul/long/gpu command :h3
|
||||
pair_style coul/long/omp command :h3
|
||||
pair_style coul/long/gpu command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style coul/cut cutoff
|
||||
pair_style coul/debye kappa cutoff
|
||||
pair_style coul/long cutoff
|
||||
pair_style coul/long/gpu cutoff :pre
|
||||
|
||||
cutoff = global cutoff for Coulombic interactions
|
||||
kappa = Debye length (inverse distance units) :ul
|
||||
|
|
|
|||
Loading…
Reference in New Issue