diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index 4b4838ba70..b64c88ca40 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -190,55 +190,16 @@ from the GPU package, you can either append "gpu" to the style name switch, or use the suffix command.

-

The fix gpu command controls the GPU selection and -initialization steps. +

The package gpu command must be used near the beginning +of your script to control the GPU selection and initialization steps. +It also enables asynchronous splitting of force computations between +the CPUs and GPUs.

-

The format for the fix is: -

-
fix fix-ID all gpu mode first last split 
-
-

where fix-ID is the name for the fix. The gpu fix must be the first -fix specified for a given run, otherwise LAMMPS will exit with an -error. The gpu fix does not have any effect on runs that do not use -GPU acceleration, so there should be no problem specifying the fix -first in any input script. -

-

The mode setting can be either "force" or "force/neigh". In the -former, neighbor list calculation is performed on the CPU using the -standard LAMMPS routines. In the latter, the neighbor list calculation -is performed on the GPU. The GPU neighbor list can be used for better -performance, however, it cannot not be used with a triclinic box or -with hybrid pair styles. -

-

There are cases when it may be more efficient to select the CPU for -neighbor list builds. If a non-GPU enabled style (e.g. a fix or -compute) requires a neighbor list, it will also be built using CPU -routines. Redundant CPU and GPU neighbor list calculations will -typically be less efficient. -

-

The first setting is the ID (as reported by -lammps/lib/gpu/nvc_get_devices) of the first GPU that will be used on -each node. The last setting is the ID of the last GPU that will be -used on each node. If you have only one GPU per node, first and -last will typically both be 0. Selecting a non-sequential set of GPU -IDs (e.g. 0,1,3) is not currently supported. -

-

The split setting is the fraction of particles whose forces, -torques, energies, and/or virials will be calculated on the GPU. This -can be used to perform CPU and GPU force calculations simultaneously, -e.g. on a hybrid node with a multicore CPU and a GPU(s). If split -is negative, the software will attempt to calculate the optimal -fraction automatically every 25 timesteps based on CPU and GPU -timings. Because the GPU speedups are dependent on the number of -particles, automatic calculation of the split can be less efficient, -but typically results in loop times within 20% of an optimal fixed -split. -

-

As an example, if you have two GPUs per node, 8 CPU cores per node, +

As an example, if you have two GPUs per node and 8 CPU cores per node, and would like to run on 4 nodes (32 cores) with dynamic balancing of -force calculation across CPU and GPU cores, the fix might be +force calculation across CPU and GPU cores, you could specify

-
fix 0 all gpu force/neigh 0 1 -1 
+
package gpu force/neigh 0 1 -1 
 

 
In this case, all CPU cores and GPU devices on the nodes would be
 utilized.  Each GPU device would be shared by 4 CPU cores. The CPU
@@ -246,39 +207,14 @@ cores would perform force calculations for some fraction of the
 particles at the same time the GPUs performed force calculation for
 the other particles.
 

-
Asynchronous pair computation on GPU and CPU
-

-
The GPU accelerated pair styles can perform pair style force
-calculation on the GPU at the same time other force calculations
-within LAMMPS are being performed on the CPU.  These include pair,
-bond, angle, etc forces as well as long-range Coulombic forces.  This
-is enabled by the split setting in the gpu fix as described above.
-

-
With a split setting less than 1.0, a portion of the pair-wise force
-calculations will also be performed on the CPU.  When the CPU finishes
-its pair style computations (if any), the next LAMMPS force
-computation will begin (bond, angle, etc), possibly before the GPU has
-finished its pair style computations.
-

-
This means that if split is set to 1.0, the GPU will begin the
-LAMMPS force computation immediately. This can be used to run a
-hybrid GPU pair style at the same time as a hybrid
-CPU pair style. In this case, the GPU pair style should be first in
-the hybrid command in order to perform simultaneous calculations. This
-also allows bond, angle,
-dihedral, improper, and
-long-range force computations to run
-simultaneously with the GPU pair style.  If all CPU force computations
-complete before the GPU, LAMMPS will block until the GPU has finished
-before continuing the timestep.
-

 
Timing output:
 

-
As noted above, GPU accelerated pair styles can perform computations
-asynchronously with CPU computations. The "Pair" time reported by
-LAMMPS will be the maximum of the time required to complete the CPU
-pair style computations and the time required to complete the GPU pair
-style computations. Any time spent for GPU-enabled pair styles for
+
As described by the package gpu command, GPU
+accelerated pair styles can perform computations asynchronously with
+CPU computations. The "Pair" time reported by LAMMPS will be the
+maximum of the time required to complete the CPU pair style
+computations and the time required to complete the GPU pair style
+computations. Any time spent for GPU-enabled pair styles for
 computations that run simultaneously with bond,
 angle, dihedral,
 improper, and long-range
diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt
index c67655f13e..b348fe207d 100644
--- a/doc/Section_accelerate.txt
+++ b/doc/Section_accelerate.txt
@@ -185,55 +185,16 @@ from the GPU package, you can either append "gpu" to the style name
 switch"_Section_start.html#2_6, or use the "suffix"_suffix.html
 command.
 
-The "fix gpu"_fix_gpu.html command controls the GPU selection and
-initialization steps.
+The "package gpu"_package.html command must be used near the beginning
+of your script to control the GPU selection and initialization steps.
+It also enables asynchronous splitting of force computations between
+the CPUs and GPUs.
 
-The format for the fix is:
-
-fix fix-ID all gpu {mode} {first} {last} {split} :pre
-
-where fix-ID is the name for the fix. The gpu fix must be the first
-fix specified for a given run, otherwise LAMMPS will exit with an
-error. The gpu fix does not have any effect on runs that do not use
-GPU acceleration, so there should be no problem specifying the fix
-first in any input script.
-
-The {mode} setting can be either "force" or "force/neigh". In the
-former, neighbor list calculation is performed on the CPU using the
-standard LAMMPS routines. In the latter, the neighbor list calculation
-is performed on the GPU. The GPU neighbor list can be used for better
-performance, however, it cannot not be used with a triclinic box or
-with "hybrid"_pair_hybrid.html pair styles.
-
-There are cases when it may be more efficient to select the CPU for
-neighbor list builds. If a non-GPU enabled style (e.g. a fix or
-compute) requires a neighbor list, it will also be built using CPU
-routines.  Redundant CPU and GPU neighbor list calculations will
-typically be less efficient.
-
-The {first} setting is the ID (as reported by
-lammps/lib/gpu/nvc_get_devices) of the first GPU that will be used on
-each node. The {last} setting is the ID of the last GPU that will be
-used on each node. If you have only one GPU per node, {first} and
-{last} will typically both be 0. Selecting a non-sequential set of GPU
-IDs (e.g. 0,1,3) is not currently supported.
-
-The {split} setting is the fraction of particles whose forces,
-torques, energies, and/or virials will be calculated on the GPU. This
-can be used to perform CPU and GPU force calculations simultaneously,
-e.g. on a hybrid node with a multicore CPU and a GPU(s).  If {split}
-is negative, the software will attempt to calculate the optimal
-fraction automatically every 25 timesteps based on CPU and GPU
-timings. Because the GPU speedups are dependent on the number of
-particles, automatic calculation of the split can be less efficient,
-but typically results in loop times within 20% of an optimal fixed
-split.
-
-As an example, if you have two GPUs per node, 8 CPU cores per node,
+As an example, if you have two GPUs per node and 8 CPU cores per node,
 and would like to run on 4 nodes (32 cores) with dynamic balancing of
-force calculation across CPU and GPU cores, the fix might be
+force calculation across CPU and GPU cores, you could specify
 
-fix 0 all gpu force/neigh 0 1 -1 :pre
+package gpu force/neigh 0 1 -1 :pre
 
 In this case, all CPU cores and GPU devices on the nodes would be
 utilized.  Each GPU device would be shared by 4 CPU cores. The CPU
@@ -241,39 +202,14 @@ cores would perform force calculations for some fraction of the
 particles at the same time the GPUs performed force calculation for
 the other particles.
 
-[Asynchronous pair computation on GPU and CPU]
-
-The GPU accelerated pair styles can perform pair style force
-calculation on the GPU at the same time other force calculations
-within LAMMPS are being performed on the CPU.  These include pair,
-bond, angle, etc forces as well as long-range Coulombic forces.  This
-is enabled by the {split} setting in the gpu fix as described above.
-
-With a {split} setting less than 1.0, a portion of the pair-wise force
-calculations will also be performed on the CPU.  When the CPU finishes
-its pair style computations (if any), the next LAMMPS force
-computation will begin (bond, angle, etc), possibly before the GPU has
-finished its pair style computations.
-
-This means that if {split} is set to 1.0, the GPU will begin the
-LAMMPS force computation immediately. This can be used to run a
-"hybrid"_pair_hybrid.html GPU pair style at the same time as a hybrid
-CPU pair style. In this case, the GPU pair style should be first in
-the hybrid command in order to perform simultaneous calculations. This
-also allows "bond"_bond_style.html, "angle"_angle_style.html,
-"dihedral"_dihedral_style.html, "improper"_improper_style.html, and
-"long-range"_kspace_style.html force computations to run
-simultaneously with the GPU pair style.  If all CPU force computations
-complete before the GPU, LAMMPS will block until the GPU has finished
-before continuing the timestep.
-
 [Timing output:]
 
-As noted above, GPU accelerated pair styles can perform computations
-asynchronously with CPU computations. The "Pair" time reported by
-LAMMPS will be the maximum of the time required to complete the CPU
-pair style computations and the time required to complete the GPU pair
-style computations. Any time spent for GPU-enabled pair styles for
+As described by the "package gpu"_package.html command, GPU
+accelerated pair styles can perform computations asynchronously with
+CPU computations. The "Pair" time reported by LAMMPS will be the
+maximum of the time required to complete the CPU pair style
+computations and the time required to complete the GPU pair style
+computations. Any time spent for GPU-enabled pair styles for
 computations that run simultaneously with "bond"_bond_style.html,
 "angle"_angle_style.html, "dihedral"_dihedral_style.html,
 "improper"_improper_style.html, and "long-range"_kspace_style.html
diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 941b2a1de2..0618a5d250 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -338,15 +338,14 @@ of each style or click on the style itself for a full description:
 

-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+

 
adaptaddforceaveforceave/atomave/correlateave/histoave/spatialave/time

 
bond/breakbond/createbond/swapbox/relaxdeformdepositdragdt/reset
efieldenforce2devaporateexternalfreezegpugravityheat
indentlangevinlineforcemomentummovemsstnebnph
nph/aspherenph/spherenptnpt/aspherenpt/spherenvenve/aspherenve/limit
nve/noforcenve/spherenvtnvt/aspherenvt/sllodnvt/sphereorient/fccplaneforce
poemspourpress/berendsenprintqeq/combreax/bondsrecenterrigid
rigid/nverigid/nvtsetforceshakespringspring/rgspring/selfsrd
store/forcestore/statetemp/berendsentemp/rescalethermal/conductivitytmdttmviscosity
viscouswall/colloidwall/granwall/harmonicwall/lj126wall/lj93wall/reflectwall/region
wall/srd 
+
efieldenforce2devaporateexternalfreezegravityheatindent
langevinlineforcemomentummovemsstnebnphnph/asphere
nph/spherenptnpt/aspherenpt/spherenvenve/aspherenve/limitnve/noforce
nve/spherenvtnvt/aspherenvt/sllodnvt/sphereorient/fccplaneforcepoems
pourpress/berendsenprintqeq/combreax/bondsrecenterrigidrigid/nve
rigid/nvtsetforceshakespringspring/rgspring/selfsrdstore/force
store/statetemp/berendsentemp/rescalethermal/conductivitytmdttmviscosityviscous
wall/colloidwall/granwall/harmonicwall/lj126wall/lj93wall/reflectwall/regionwall/srd 
 

 
 
These are fix styles contributed by users, which can be used if
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 3635a753f5..f9b9b1a189 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -418,7 +418,6 @@ of each style or click on the style itself for a full description:
 "evaporate"_fix_evaporate.html,
 "external"_fix_external.html,
 "freeze"_fix_freeze.html,
-"gpu"_fix_gpu.html,
 "gravity"_fix_gravity.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
diff --git a/doc/fix_gpu.html b/doc/fix_gpu.html
deleted file mode 100644
index d48e510798..0000000000
--- a/doc/fix_gpu.html
+++ /dev/null
@@ -1,112 +0,0 @@
-
-
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
-

-
-
-
-
-
-
-

-
-
fix gpu command 
-

-
Syntax:
-

-
fix ID group-ID gpu mode first last split 
-

-
-
Examples:
-

-
fix 0 all gpu force 0 0 1.0
-fix 0 all gpu force 0 0 0.75
-fix 0 all gpu force/neigh 0 0 1.0
-fix 0 all gpu force/neigh 0 1 -1.0 
-

-
Description:
-

-
Select and initialize GPUs to be used for acceleration and configure
-GPU acceleration in LAMMPS. This fix is required in order to use
-any style with GPU acceleration. The fix must be the first fix
-specified for a run or an error will be generated. The fix will not have an 
-effect on any LAMMPS computations that do not use GPU acceleration, so there 
-should not be any problems with specifying this fix first in input scripts.
-

-
The mode setting specifies where neighbor list calculations will be
-performed.  If mode is force, neighbor list calculation is performed
-on the CPU. If mode is force/neigh, neighbor list calculation is
-performed on the GPU. GPU neighbor list calculation currently cannot
-be used with a triclinic box. GPU neighbor list calculation currently
-cannot be used with hybrid pair styles.  GPU
-neighbor lists are not compatible with styles that are not
-GPU-enabled.  When a non-GPU enabled style requires a neighbor list,
-it will also be built using CPU routines. In these cases, it will
-typically be more efficient to only use CPU neighbor list builds.
-

-
The first and last settings specify the GPUs that will be used for
-simulation.  On each node, the GPU IDs in the inclusive range from
-first to last will be used.
-

-
The split setting can be used for load balancing force calculation
-work between CPU and GPU cores in GPU-enabled pair styles. If
-0<split<1.0, a fixed fraction of particles is offloaded to the GPU
-while force calculation for the other particles occurs simulataneously
-on the CPU. If split<0, the optimal fraction (based on CPU and GPU
-timings) is calculated every 25 timesteps. If split=1.0, all force
-calculations for GPU accelerated pair styles are performed on the
-GPU. In this case, hybrid, bond,
-angle, dihedral,
-improper, and long-range
-calculations can be performed on the CPU while the GPU is performing
-force calculations for the GPU-enabled pair style.
-

-
In order to use GPU acceleration, a GPU enabled style must be selected
-in the input script in addition to this fix.  Currently, this is
-limited to a few pair styles and the PPPM kspace
-style.
-

-
See this section of the manual for more
-details about using the GPU package.
-

-
Restart, fix_modify, output, run start/stop, minimize info:
-

-
This fix is part of the "gpu" package.  It is only enabled if LAMMPS
-was built with that package.  See the Making
-LAMMPS section for more info.
-

-
No information about this fix is written to binary restart
-files.  None of the fix_modify options
-are relevant to this fix.
-

-
No parameter of this fix can be used with the start/stop keywords of
-the run command.
-

-
Restrictions: 
-

-
The fix must be the first fix specified for a given run. The
-force/neigh mode should not be used with a triclinic box or
-hybrid pair styles.
-

-
The split setting must be positive when using
-hybrid pair styles.
-

-
Currently, group-ID must be all.
-

-
Related commands: none
-

-
Default: none
-

-
diff --git a/doc/fix_gpu.txt b/doc/fix_gpu.txt
deleted file mode 100644
index 6abf729e74..0000000000
--- a/doc/fix_gpu.txt
+++ /dev/null
@@ -1,102 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-fix gpu command :h3
-
-[Syntax:]
-
-fix ID group-ID gpu mode first last split :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-gpu = style name of this fix command :l
-mode = force or force/neigh :l
-first = ID of first GPU to be used on each node :l
-last = ID of last GPU to be used on each node :l
-split = fraction of particles assigned to the GPU :l
-:ule
-
-[Examples:]
-
-fix 0 all gpu force 0 0 1.0
-fix 0 all gpu force 0 0 0.75
-fix 0 all gpu force/neigh 0 0 1.0
-fix 0 all gpu force/neigh 0 1 -1.0 :pre
-
-[Description:]
-
-Select and initialize GPUs to be used for acceleration and configure
-GPU acceleration in LAMMPS. This fix is required in order to use
-any style with GPU acceleration. The fix must be the first fix
-specified for a run or an error will be generated. The fix will not have an 
-effect on any LAMMPS computations that do not use GPU acceleration, so there 
-should not be any problems with specifying this fix first in input scripts.
-
-The {mode} setting specifies where neighbor list calculations will be
-performed.  If {mode} is force, neighbor list calculation is performed
-on the CPU. If {mode} is force/neigh, neighbor list calculation is
-performed on the GPU. GPU neighbor list calculation currently cannot
-be used with a triclinic box. GPU neighbor list calculation currently
-cannot be used with "hybrid"_pair_hybrid.html pair styles.  GPU
-neighbor lists are not compatible with styles that are not
-GPU-enabled.  When a non-GPU enabled style requires a neighbor list,
-it will also be built using CPU routines. In these cases, it will
-typically be more efficient to only use CPU neighbor list builds.
-
-The {first} and {last} settings specify the GPUs that will be used for
-simulation.  On each node, the GPU IDs in the inclusive range from
-{first} to {last} will be used.
-
-The {split} setting can be used for load balancing force calculation
-work between CPU and GPU cores in GPU-enabled pair styles. If
-0<{split}<1.0, a fixed fraction of particles is offloaded to the GPU
-while force calculation for the other particles occurs simulataneously
-on the CPU. If {split}<0, the optimal fraction (based on CPU and GPU
-timings) is calculated every 25 timesteps. If {split}=1.0, all force
-calculations for GPU accelerated pair styles are performed on the
-GPU. In this case, "hybrid"_pair_hybrid.html, "bond"_bond_style.html,
-"angle"_angle_style.html, "dihedral"_dihedral_style.html,
-"improper"_improper_style.html, and "long-range"_kspace_style.html
-calculations can be performed on the CPU while the GPU is performing
-force calculations for the GPU-enabled pair style.
-
-In order to use GPU acceleration, a GPU enabled style must be selected
-in the input script in addition to this fix.  Currently, this is
-limited to a few "pair styles"_pair_style.html and the PPPM "kspace
-style"_kspace_style.html.
-
-See "this section"_doc/Section_accerate.html of the manual for more
-details about using the GPU package.
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-This fix is part of the "gpu" package.  It is only enabled if LAMMPS
-was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
-
-No information about this fix is written to "binary restart
-files"_restart.html.  None of the "fix_modify"_fix_modify.html options
-are relevant to this fix.
-
-No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.
-
-[Restrictions:] 
-
-The fix must be the first fix specified for a given run. The
-force/neigh {mode} should not be used with a triclinic box or
-"hybrid"_pair_hybrid.html pair styles.
-
-The {split} setting must be positive when using
-"hybrid"_pair_hybrid.html pair styles.
-
-Currently, group-ID must be all.
-
-[Related commands:] none
-
-[Default:] none
-
diff --git a/doc/package.html b/doc/package.html
index 814340bc81..c1b5b0bebf 100644
--- a/doc/package.html
+++ b/doc/package.html
@@ -15,39 +15,136 @@
 

 
package style args 
 

-