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Merge remote-tracking branch 'origin/master' into cmake_clean_up

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This commit is contained in:
Christoph Junghans
2020-03-25 09:36:36 -06:00
parent ee3249676e 2ac79d4483
commit b9131fcd18
23 changed files with 433 additions and 514 deletions
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12
cmake/CMakeLists.txt
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@ -236,7 +236,15 @@ pkg_depends(USER-LB MPI)
pkg_depends(USER-PHONON KSPACE)
pkg_depends(USER-SCAFACOS MPI)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
endif()
# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30
# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas
@ -246,14 +254,14 @@ find_package(OpenMP QUIET)
if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9))
option(BUILD_OMP "Build with OpenMP support" OFF)
else()
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
endif()
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find required 'omp.h' header file")
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()

2
cmake/Modules/Packages/USER-INTEL.cmake
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@ -31,7 +31,7 @@ if(PKG_USER-INTEL)
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

6
doc/src/Howto_bash.rst
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@ -12,6 +12,10 @@ via apt-get and all files are accessible in both the Windows Explorer and your
Linux shell (bash). This avoids switching to a different operating system or
installing a virtual machine. Everything runs on Windows.
.. seealso::
You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.
Installing Bash on Windows
--------------------------
@ -103,7 +107,7 @@ needed for various LAMMPS features:
.. code-block:: bash
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
Files in Ubuntu on Windows
^^^^^^^^^^^^^^^^^^^^^^^^^^

2
doc/src/bond_oxdna.rst
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@ -32,7 +32,7 @@ Examples
bond_coeff * 2.0 0.25 0.7564
bond_style oxrna2/fene
bond_coeff \* 2.0 0.25 0.76107
bond_coeff * 2.0 0.25 0.76107
Description
"""""""""""

4
doc/src/pair_bop.rst
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@ -132,9 +132,9 @@ and Te. If your LAMMPS simulation has 4 atoms types and you want the
1st 3 to be Cd, and the 4th to be Te, you would use the following
pair_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* CdTe Cd Cd Cd Te
pair_coeff * * CdTe Cd Cd Cd Te
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd

8
doc/src/pair_class2.rst
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@ -60,18 +60,18 @@ Examples
.. code-block:: LAMMPS
pair_style lj/class2 10.0
pair_coeff \* \* 100.0 2.5
pair_coeff 1 2\* 100.0 2.5 9.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0
pair_style lj/class2/coul/cut 10.0
pair_style lj/class2/coul/cut 10.0 8.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description

12
doc/src/pair_coeff.rst
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@ -19,11 +19,11 @@ Examples
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 2.5
pair_coeff 2 \* 1.0 1.0
pair_coeff 3\* 1\*2 1.0 1.0 2.5
pair_coeff \* \* 1.0 1.0
pair_coeff \* \* nialhjea 1 1 2
pair_coeff \* 3 morse.table ENTRY1
pair_coeff 2 * 1.0 1.0
pair_coeff 3* 1*2 1.0 1.0 2.5
pair_coeff * * 1.0 1.0
pair_coeff * * nialhjea 1 1 2
pair_coeff * 3 morse.table ENTRY1
pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
Description
@ -55,7 +55,7 @@ pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
.. code-block:: LAMMPS
pair_coeff \* \* 1.0 1.0 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff 2 3 2.0 1.0 1.12
A line in a data file that specifies pair coefficients uses the exact

2
doc/src/pair_cosine_squared.rst
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@ -31,7 +31,7 @@ Examples
.. code-block:: LAMMPS
pair_style cosine/squared 3.0
pair_coeff \* \* 1.0 1.3
pair_coeff * * 1.0 1.3
pair_coeff 1 3 1.0 1.3 2.0
pair_coeff 1 3 1.0 1.3 wca
pair_coeff 1 3 1.0 1.3 2.0 wca

4
doc/src/pair_meam_sw_spline.rst
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@ -75,7 +75,9 @@ If your LAMMPS simulation has 3 atoms types and they are all to be
treated with this potential, you would use the following pair_coeff
command:
pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti
.. code-block:: LAMMPS
pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element

4
doc/src/pair_nb3b_harmonic.rst
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@ -64,7 +64,9 @@ NULL values are placeholders for atom types that will be used with
other potentials. An example of a pair_coeff command for use with the
*hybrid* pair style is:
pair_coeff \* \* nb3b/harmonic MgOH.nb3b.harmonic Mg O H
.. code-block:: LAMMPS
pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H
Three-body non-bonded harmonic files in the *potentials* directory of
the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that

4
doc/src/pair_polymorphic.rst
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@ -180,9 +180,9 @@ functions for Si-C tersoff potential. If your LAMMPS simulation has 4
atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
would use the following pair_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* SiC_tersoff.poly Si Si Si C
pair_coeff * * SiC_tersoff.poly Si Si Si C
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom
types. The first three Si arguments map LAMMPS atom types 1,2,3 to the

12
doc/src/pair_python.rst
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@ -113,8 +113,8 @@ which the parameters epsilon and sigma are both 1.0:
class LJCutMelt(LAMMPSPairPotential):
def __init__(self):
super(LJCutMelt,self).__init__()
# set coeffs: 48\*eps\*sig\*\*12, 24\*eps\*sig\*\*6,
# 4\*eps\*sig\*\*12, 4\*eps\*sig\*\*6
# set coeffs: 48*eps*sig**12, 24*eps*sig**6,
# 4*eps*sig**12, 4*eps*sig**6
self.units = 'lj'
self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}}
@ -137,18 +137,18 @@ the *LJCutMelt* example, here are the two functions:
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq
r6inv = r2inv\*r2inv\*r2inv
r6inv = r2inv*r2inv*r2inv
lj1 = coeff[0]
lj2 = coeff[1]
return (r6inv \* (lj1\*r6inv - lj2))\*r2inv
return (r6inv * (lj1*r6inv - lj2))*r2inv
def compute_energy(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq
r6inv = r2inv\*r2inv\*r2inv
r6inv = r2inv*r2inv*r2inv
lj3 = coeff[2]
lj4 = coeff[3]
return (r6inv \* (lj3\*r6inv - lj4))
return (r6inv * (lj3*r6inv - lj4))
.. note::

2
doc/src/pair_spin_magelec.rst
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@ -18,7 +18,7 @@ Examples
.. code-block:: LAMMPS
pair_style spin/magelec 4.5
pair_coeff \* \* magelec 4.5 0.00109 1.0 1.0 1.0
pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0
Description
"""""""""""

12
src/KOKKOS/pair_snap_kokkos.h
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@ -37,15 +37,13 @@ struct TagPairSNAPBeta{};
struct TagPairSNAPComputeNeigh{};
struct TagPairSNAPPreUi{};
struct TagPairSNAPComputeUi{};
struct TagPairSNAPComputeUiTot{}; // accumulate ulist into ulisttot separately
struct TagPairSNAPComputeUiCPU{};
struct TagPairSNAPComputeZi{};
struct TagPairSNAPComputeBi{};
struct TagPairSNAPZeroYi{};
struct TagPairSNAPComputeYi{};
struct TagPairSNAPComputeDuidrj{};
struct TagPairSNAPComputeFusedDeidrj{};
struct TagPairSNAPComputeDuidrjCPU{};
struct TagPairSNAPComputeDeidrj{};
struct TagPairSNAPComputeDeidrjCPU{};
template<class DeviceType>
@ -83,9 +81,6 @@ public:
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeUiTot,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiTot>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiCPU>::member_type& team) const;
@ -102,14 +97,11 @@ public:
void operator() (TagPairSNAPComputeYi,const int& ii) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj>::member_type& team) const;
void operator() (TagPairSNAPComputeFusedDeidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrj>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeDuidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrjCPU>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeDeidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrj>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU>::member_type& team) const;

103
src/KOKKOS/pair_snap_kokkos_impl.h
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@ -30,7 +30,6 @@
#include "kokkos.h"
#include "sna.h"
#define MAXLINE 1024
#define MAXWORD 3
@ -255,26 +254,19 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// scratch size: 2 * team_size * (twojmax+1)^2, to cover all `m1`,`m2` values
// 2 is for double buffer
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi> policy_ui(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
const int tile_size = (twojmax+1)*(twojmax+1);
typedef Kokkos::View< SNAcomplex*,
Kokkos::DefaultExecutionSpace::scratch_memory_space,
Kokkos::MemoryTraits<Kokkos::Unmanaged> >
ScratchViewType;
int scratch_size = ScratchViewType::shmem_size( 2 * team_size * (twojmax+1)*(twojmax+1));
int scratch_size = ScratchViewType::shmem_size( 2 * team_size * tile_size );
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi> policy_ui(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
policy_ui = policy_ui.set_scratch_size(0, Kokkos::PerTeam( scratch_size ));
Kokkos::parallel_for("ComputeUi",policy_ui,*this);
// ComputeUitot
vector_length = 1;
team_size = 128;
team_size_max = Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiTot>::team_size_max(*this);
if (team_size*vector_length > team_size_max)
team_size = team_size_max/vector_length;
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiTot> policy_ui_tot(((idxu_max+team_size-1)/team_size)*chunk_size,team_size,vector_length);
Kokkos::parallel_for("ComputeUiTot",policy_ui_tot,*this);
}
@ -316,7 +308,7 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
typename Kokkos::RangePolicy<DeviceType, TagPairSNAPComputeYi> policy_yi(0,chunk_size*idxz_max);
Kokkos::parallel_for("ComputeYi",policy_yi,*this);
//ComputeDuidrj
//ComputeDuidrj and Deidrj
if (lmp->kokkos->ngpus == 0) { // CPU
int vector_length = 1;
int team_size = 1;
@ -324,53 +316,37 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrjCPU> policy_duidrj_cpu(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
snaKK.set_dir(-1); // technically doesn't do anything
Kokkos::parallel_for("ComputeDuidrjCPU",policy_duidrj_cpu,*this);
} else { // GPU, utilize scratch memory and splitting over dimensions
int team_size_max = Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj>::team_size_max(*this);
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU> policy_deidrj_cpu(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
Kokkos::parallel_for("ComputeDeidrjCPU",policy_deidrj_cpu,*this);
} else { // GPU, utilize scratch memory and splitting over dimensions, fused dui and dei
int team_size_max = Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrj>::team_size_max(*this);
int vector_length = 32;
int team_size = 2; // need to cap b/c of shared memory reqs
if (team_size*vector_length > team_size_max)
team_size = team_size_max/vector_length;
// scratch size: 2 * 2 * team_size * (twojmax+1)^2, to cover all `m1`,`m2` values
// scratch size: 2 * 2 * team_size * (twojmax+1)*(twojmax/2+1), to cover half `m1`,`m2` values due to symmetry
// 2 is for double buffer
const int tile_size = (twojmax+1)*(twojmax/2+1);
typedef Kokkos::View< SNAcomplex*,
Kokkos::DefaultExecutionSpace::scratch_memory_space,
Kokkos::MemoryTraits<Kokkos::Unmanaged> >
ScratchViewType;
int scratch_size = ScratchViewType::shmem_size( 4 * team_size * tile_size);
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrj> policy_fused_deidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
policy_fused_deidrj = policy_fused_deidrj.set_scratch_size(0, Kokkos::PerTeam( scratch_size ));
int scratch_size = ScratchViewType::shmem_size( 4 * team_size * (twojmax+1)*(twojmax+1));
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj> policy_duidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
policy_duidrj = policy_duidrj.set_scratch_size(0, Kokkos::PerTeam( scratch_size ));
// Need to call three times, once for each direction
for (int k = 0; k < 3; k++) {
snaKK.set_dir(k);
Kokkos::parallel_for("ComputeDuidrj",policy_duidrj,*this);
Kokkos::parallel_for("ComputeFusedDeidrj",policy_fused_deidrj,*this);
}
}
//ComputeDeidrj
if (lmp->kokkos->ngpus == 0) { // CPU
int vector_length = 1;
int team_size = 1;
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU> policy_deidrj_cpu(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
Kokkos::parallel_for("ComputeDeidrjCPU",policy_deidrj_cpu,*this);
} else { // GPU, different loop strategy internally
int team_size_max = Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrj>::team_size_max(*this);
int vector_length = 32; // coalescing disaster right now, will fix later
int team_size = 8;
if (team_size*vector_length > team_size_max)
team_size = team_size_max/vector_length;
typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrj> policy_deidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);
Kokkos::parallel_for("ComputeDeidrj",policy_deidrj,*this);
}
//ComputeForce
if (eflag) {
if (neighflag == HALF) {
@ -642,25 +618,6 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUi,const typename
my_sna.compute_ui(team,ii,jj);
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUiTot,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiTot>::member_type& team) const {
SNAKokkos<DeviceType> my_sna = snaKK;
// Extract the quantum number
const int idx = team.team_rank() + team.team_size() * (team.league_rank() % ((my_sna.idxu_max+team.team_size()-1)/team.team_size()));
if (idx >= my_sna.idxu_max) return;
// Extract the atomic index
const int ii = team.league_rank() / ((my_sna.idxu_max+team.team_size()-1)/team.team_size());
if (ii >= chunk_size) return;
// Extract the number of neighbors neighbor number
const int ninside = d_ninside(ii);
my_sna.compute_uitot(team,idx,ii,ninside);
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiCPU>::member_type& team) const {
@ -718,7 +675,7 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeBi,const typename
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj>::member_type& team) const {
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeFusedDeidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrj>::member_type& team) const {
SNAKokkos<DeviceType> my_sna = snaKK;
// Extract the atom number
@ -730,7 +687,7 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDuidrj,const type
const int ninside = d_ninside(ii);
if (jj >= ninside) return;
my_sna.compute_duidrj(team,ii,jj);
my_sna.compute_fused_deidrj(team,ii,jj);
}
template<class DeviceType>
@ -750,24 +707,6 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDuidrjCPU,const t
my_sna.compute_duidrj_cpu(team,ii,jj);
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDeidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrj>::member_type& team) const {
SNAKokkos<DeviceType> my_sna = snaKK;
// Extract the atom number
int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((chunk_size+team.team_size()-1)/team.team_size()));
if (ii >= chunk_size) return;
// Extract the neighbor number
const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size());
const int ninside = d_ninside(ii);
if (jj >= ninside) return;
my_sna.compute_deidrj(team,ii,jj);
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU>::member_type& team) const {

20
src/KOKKOS/sna_kokkos.h
View File

@ -135,14 +135,10 @@ inline
KOKKOS_INLINE_FUNCTION
void pre_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team,const int&); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
void compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_ui_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_ui_orig(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_uitot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int, int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_zi(const int&); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void zero_yi(const int&,const int&); // ForceSNAP
@ -155,12 +151,10 @@ inline
// functions for derivatives
KOKKOS_INLINE_FUNCTION
void compute_duidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); //ForceSNAP
void compute_fused_deidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int); //ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_duidrj_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); //ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_deidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_deidrj_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
double compute_sfac(double, double); // add_uarraytot, compute_duarray
@ -251,10 +245,6 @@ inline
KOKKOS_INLINE_FUNCTION
void add_uarraytot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int, double, double, double); // compute_ui
KOKKOS_INLINE_FUNCTION
void compute_uarray(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int,
double, double, double,
double, double); // compute_ui
KOKKOS_INLINE_FUNCTION
void compute_uarray_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int,
double, double, double,
@ -267,12 +257,8 @@ inline
inline
int compute_ncoeff(); // SNAKokkos()
KOKKOS_INLINE_FUNCTION
void compute_duarray(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int,
double, double, double, // compute_duidrj
double, double, double, double, double);
KOKKOS_INLINE_FUNCTION
void compute_duarray_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int,
double, double, double, // compute_duidrj
double, double, double, // compute_duidrj_cpu
double, double, double, double, double);
// Sets the style for the switching function

674
src/KOKKOS/sna_kokkos_impl.h
View File

@ -19,6 +19,7 @@
#include <cmath>
#include <cstring>
#include <cstdlib>
#include <type_traits>
namespace LAMMPS_NS {
@ -231,11 +232,22 @@ void SNAKokkos<DeviceType>::grow_rij(int newnatom, int newnmax)
zlist = t_sna_2c_ll("sna:zlist",idxz_max,natom);
//ulist = t_sna_3c("sna:ulist",natom,nmax,idxu_max);
#ifdef KOKKOS_ENABLE_CUDA
if (std::is_same<DeviceType,Kokkos::Cuda>::value) {
// dummy allocation
ulist = t_sna_3c_ll("sna:ulist",1,1,1);
dulist = t_sna_4c_ll("sna:dulist",1,1,1);
} else {
#endif
ulist = t_sna_3c_ll("sna:ulist",idxu_max,natom,nmax);
dulist = t_sna_4c_ll("sna:dulist",idxu_max,natom,nmax);
#ifdef KOKKOS_ENABLE_CUDA
}
#endif
//ylist = t_sna_2c_lr("sna:ylist",natom,idxu_max);
ylist = t_sna_2c_ll("sna:ylist",idxu_max,natom);
//dulist = t_sna_4c("sna:dulist",natom,nmax,idxu_max);
dulist = t_sna_4c_ll("sna:dulist",idxu_max,natom,nmax);
}
@ -269,14 +281,14 @@ void SNAKokkos<DeviceType>::pre_ui(const typename Kokkos::TeamPolicy<DeviceType>
}
/* ----------------------------------------------------------------------
compute Ui by summing over bispectrum components
compute Ui by computing Wigner U-functions for one neighbor and
accumulating to the total. GPU only.
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor)
void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int iatom, const int jnbor)
{
double rsq, r, x, y, z, z0, theta0;
// utot(j,ma,mb) = 0 for all j,ma,ma
// utot(j,ma,ma) = 1 for all j,ma
@ -284,22 +296,143 @@ void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceT
// compute r0 = (x,y,z,z0)
// utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb
x = rij(iatom,jnbor,0);
y = rij(iatom,jnbor,1);
z = rij(iatom,jnbor,2);
rsq = x * x + y * y + z * z;
r = sqrt(rsq);
// get shared memory offset
const int max_m_tile = (twojmax+1)*(twojmax+1);
const int team_rank = team.team_rank();
const int scratch_shift = team_rank * max_m_tile;
theta0 = (r - rmin0) * rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0);
// double buffer
SNAcomplex* buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0) + scratch_shift;
SNAcomplex* buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0) + scratch_shift;
const double x = rij(iatom,jnbor,0);
const double y = rij(iatom,jnbor,1);
const double z = rij(iatom,jnbor,2);
const double wj_local = wj(iatom, jnbor);
const double rcut = rcutij(iatom, jnbor);
const double rsq = x * x + y * y + z * z;
const double r = sqrt(rsq);
const double theta0 = (r - rmin0) * rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0);
// theta0 = (r - rmin0) * rscale0;
z0 = r / tan(theta0);
const double cs = cos(theta0);
const double sn = sin(theta0);
const double z0 = r * cs / sn; // r / tan(theta0)
compute_uarray(team, iatom, jnbor, x, y, z, z0, r);
// Compute cutoff function
const double sfac = compute_sfac(r, rcut) * wj_local;
// if we're on the GPU, accumulating into uarraytot is done in a separate kernel.
// if we're not, it's more efficient to include it in compute_uarray.
// compute Cayley-Klein parameters for unit quaternion,
// pack into complex number
const double r0inv = 1.0 / sqrt(r * r + z0 * z0);
const SNAcomplex a = { r0inv * z0, -r0inv * z };
const SNAcomplex b = { r0inv * y, -r0inv * x };
// VMK Section 4.8.2
// All writes go to global memory and shared memory
// so we can avoid all global memory reads
Kokkos::single(Kokkos::PerThread(team), [=]() {
//ulist(0,iatom,jnbor) = { 1.0, 0.0 };
buf1[0] = {1.,0.};
Kokkos::atomic_add(&(ulisttot(0,iatom).re), sfac);
});
for (int j = 1; j <= twojmax; j++) {
const int jju = idxu_block[j];
const int jjup = idxu_block[j-1];
// fill in left side of matrix layer from previous layer
// Flatten loop over ma, mb, need to figure out total
// number of iterations
// for (int ma = 0; ma <= j; ma++)
const int n_ma = j+1;
// for (int mb = 0; 2*mb <= j; mb++)
const int n_mb = j/2+1;
// the last (j / 2) can be avoided due to symmetry
const int total_iters = n_ma * n_mb - (j % 2 == 0 ? (j / 2) : 0);
//for (int m = 0; m < total_iters; m++) {
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, total_iters),
[&] (const int m) {
// ma fast, mb slow
int ma = m % n_ma;
int mb = m / n_ma;
// index into global memory array
const int jju_index = jju+m;
//const int jjup_index = jjup+mb*j+ma;
// index into shared memory buffer for this level
const int jju_shared_idx = m;
// index into shared memory buffer for next level
const int jjup_shared_idx = jju_shared_idx - mb;
SNAcomplex u_accum = {0., 0.};
// VMK recursion relation: grab contribution which is multiplied by b*
const double rootpq2 = -rootpqarray(ma, j - mb);
const SNAcomplex u_up2 = (ma > 0)?rootpq2*buf1[jjup_shared_idx-1]:SNAcomplex(0.,0.);
//const SNAcomplex u_up2 = (ma > 0)?rootpq2*ulist(jjup_index-1,iatom,jnbor):SNAcomplex(0.,0.);
caconjxpy(b, u_up2, u_accum);
// VMK recursion relation: grab contribution which is multiplied by a*
const double rootpq1 = rootpqarray(j - ma, j - mb);
const SNAcomplex u_up1 = (ma < j)?rootpq1*buf1[jjup_shared_idx]:SNAcomplex(0.,0.);
//const SNAcomplex u_up1 = (ma < j)?rootpq1*ulist(jjup_index,iatom,jnbor):SNAcomplex(0.,0.);
caconjxpy(a, u_up1, u_accum);
//ulist(jju_index,iatom,jnbor) = u_accum;
// back up into shared memory for next iter
buf2[jju_shared_idx] = u_accum;
Kokkos::atomic_add(&(ulisttot(jju_index,iatom).re), sfac * u_accum.re);
Kokkos::atomic_add(&(ulisttot(jju_index,iatom).im), sfac * u_accum.im);
// copy left side to right side with inversion symmetry VMK 4.4(2)
// u[ma-j,mb-j] = (-1)^(ma-mb)*Conj([u[ma,mb))
// if j is even (-> physical j integer), last element maps to self, skip
//if (!(m == total_iters - 1 && j % 2 == 0)) {
if (m < total_iters - 1 || j % 2 == 1) {
const int sign_factor = (((ma+mb)%2==0)?1:-1);
const int jju_shared_flip = (j+1-mb)*(j+1)-(ma+1);
const int jjup_flip = jju + jju_shared_flip; // jju+(j+1-mb)*(j+1)-(ma+1);
if (sign_factor == 1) {
u_accum.im = -u_accum.im;
} else {
u_accum.re = -u_accum.re;
}
//ulist(jjup_flip,iatom,jnbor) = u_accum;
buf2[jju_shared_flip] = u_accum;
Kokkos::atomic_add(&(ulisttot(jjup_flip,iatom).re), sfac * u_accum.re);
Kokkos::atomic_add(&(ulisttot(jjup_flip,iatom).im), sfac * u_accum.im);
}
});
// In CUDA backend,
// ThreadVectorRange has a __syncwarp (appropriately masked for
// vector lengths < 32) implict at the end
// swap double buffers
auto tmp = buf1; buf1 = buf2; buf2 = tmp;
}
}
/* ----------------------------------------------------------------------
compute Ui by summing over bispectrum components. CPU only.
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_ui_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor)
@ -327,40 +460,8 @@ void SNAKokkos<DeviceType>::compute_ui_cpu(const typename Kokkos::TeamPolicy<Dev
}
/* ----------------------------------------------------------------------
compute UiTot by summing over neighbors
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_uitot(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int idx, int iatom, int ninside)
{
// fuse initialize in, avoid this load?
SNAcomplex utot = ulisttot(idx, iatom);
for (int jnbor = 0; jnbor < ninside; jnbor++) {
const auto x = rij(iatom,jnbor,0);
const auto y = rij(iatom,jnbor,1);
const auto z = rij(iatom,jnbor,2);
const auto rsq = x * x + y * y + z * z;
const auto r = sqrt(rsq);
const double wj_local = wj(iatom, jnbor);
const double rcut = rcutij(iatom, jnbor);
const double sfac = compute_sfac(r, rcut) * wj_local;
auto ulist_local = ulist(idx, iatom, jnbor);
utot.re += sfac * ulist_local.re;
utot.im += sfac * ulist_local.im;
}
ulisttot(idx, iatom) = utot;
}
/* ----------------------------------------------------------------------
compute Zi by summing over products of Ui
not updated yet
------------------------------------------------------------------------- */
template<class DeviceType>
@ -509,72 +610,203 @@ void SNAKokkos<DeviceType>::compute_yi(int iter,
}
/* ----------------------------------------------------------------------
compute dEidRj
Fused calculation of the derivative of Ui w.r.t. atom j
and of dEidRj. GPU only.
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_deidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor)
void SNAKokkos<DeviceType>::compute_fused_deidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int iatom, const int jnbor)
{
t_scalar3<double> final_sum;
// get shared memory offset
const int max_m_tile = (twojmax+1)*(twojmax/2+1);
const int team_rank = team.team_rank();
const int scratch_shift = team_rank * max_m_tile;
// Like in ComputeUi/ComputeDuidrj, regular loop over j.
for (int j = 0; j <= twojmax; j++) {
int jju = idxu_block(j);
// double buffer for ulist
SNAcomplex* ulist_buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0) + scratch_shift;
SNAcomplex* ulist_buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0) + scratch_shift;
// Flatten loop over ma, mb, reduce w/in
// double buffer for dulist
SNAcomplex* dulist_buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0) + scratch_shift;
SNAcomplex* dulist_buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0) + scratch_shift;
const double x = rij(iatom,jnbor,0);
const double y = rij(iatom,jnbor,1);
const double z = rij(iatom,jnbor,2);
const double rsq = x * x + y * y + z * z;
const double r = sqrt(rsq);
const double rcut = rcutij(iatom, jnbor);
const double rscale0 = rfac0 * MY_PI / (rcut - rmin0);
const double theta0 = (r - rmin0) * rscale0;
const double cs = cos(theta0);
const double sn = sin(theta0);
const double z0 = r * cs / sn;
const double dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq;
const double wj_local = wj(iatom, jnbor);
const double sfac = wj_local * compute_sfac(r, rcut);
const double dsfac = wj_local * compute_dsfac(r, rcut);
const double rinv = 1.0 / r;
// extract a single unit vector
const double u = (dir == 0 ? x * rinv : dir == 1 ? y * rinv : z * rinv);
// Compute Cayley-Klein parameters for unit quaternion
const double r0inv = 1.0 / sqrt(r * r + z0 * z0);
const SNAcomplex a = { r0inv * z0, -r0inv * z };
const SNAcomplex b = { r0inv * y, -r0inv * x };
const double dr0invdr = -r0inv * r0inv * r0inv * (r + z0 * dz0dr);
const double dr0inv = dr0invdr * u;
const double dz0 = dz0dr * u;
const SNAcomplex da = { dz0 * r0inv + z0 * dr0inv,
- z * dr0inv + (dir == 2 ? - r0inv : 0.) };
const SNAcomplex db = { y * dr0inv + (dir==1?r0inv:0.),
-x * dr0inv + (dir==0?-r0inv:0.) };
// Accumulate the full contribution to dedr on the fly
const double du_prod = dsfac * u; // chain rule
const SNAcomplex y_local = ylist(0, iatom);
// Symmetry factor of 0.5 b/c 0 element is on diagonal for even j==0
double dedr_full_sum = 0.5 * du_prod * y_local.re;
// single has a warp barrier at the end
Kokkos::single(Kokkos::PerThread(team), [=]() {
//dulist(0,iatom,jnbor,dir) = { dsfac * u, 0. }; // fold in chain rule here
ulist_buf1[0] = {1., 0.};
dulist_buf1[0] = {0., 0.};
});
for (int j = 1; j <= twojmax; j++) {
int jju = idxu_block[j];
int jjup = idxu_block[j-1];
// flatten the loop over ma,mb
// for (int ma = 0; ma <= j; ma++)
const int n_ma = j+1;
// for (int mb = 0; 2*mb <= j; mb++)
const int n_mb = j/2+1;
const int total_iters = n_ma * n_mb;
t_scalar3<double> sum;
double dedr_sum = 0.; // j-local sum
//for (int m = 0; m < total_iters; m++) {
Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team, total_iters),
[&] (const int m, t_scalar3<double>& sum_tmp) {
[&] (const int m, double& sum_tmp) {
// ma fast, mb slow
int ma = m % n_ma;
int mb = m / n_ma;
// get index
const int jju_index = jju+mb+mb*j+ma;
// get ylist, rescale last element by 0.5
SNAcomplex y_local = ylist(jju_index,iatom);
const SNAcomplex du_x = dulist(jju_index,iatom,jnbor,0);
const SNAcomplex du_y = dulist(jju_index,iatom,jnbor,1);
const SNAcomplex du_z = dulist(jju_index,iatom,jnbor,2);
const int jju_index = jju+m;
// Load y_local, apply the symmetry scaling factor
// The "secret" of the shared memory optimization is it eliminates
// all global memory reads to duidrj in lieu of caching values in
// shared memory and otherwise always writing, making the kernel
// ultimately compute bound. We take advantage of that by adding
// some reads back in.
auto y_local = ylist(jju_index,iatom);
if (j % 2 == 0 && 2*mb == j) {
if (ma == mb) { y_local = 0.5*y_local; }
else if (ma > mb) { y_local = { 0., 0. }; }
else if (ma > mb) { y_local = { 0., 0. }; } // can probably avoid this outright
// else the ma < mb gets "double counted", cancelling the 0.5.
}
sum_tmp.x += du_x.re * y_local.re + du_x.im * y_local.im;
sum_tmp.y += du_y.re * y_local.re + du_y.im * y_local.im;
sum_tmp.z += du_z.re * y_local.re + du_z.im * y_local.im;
// index into shared memory
const int jju_shared_idx = m;
const int jjup_shared_idx = jju_shared_idx - mb;
}, sum); // end loop over flattened ma,mb
// Need to compute and accumulate both u and du (mayhaps, we could probably
// balance some read and compute by reading u each time).
SNAcomplex u_accum = { 0., 0. };
SNAcomplex du_accum = { 0., 0. };
final_sum.x += sum.x;
final_sum.y += sum.y;
final_sum.z += sum.z;
const double rootpq2 = -rootpqarray(ma, j - mb);
const SNAcomplex u_up2 = (ma > 0)?rootpq2*ulist_buf1[jjup_shared_idx-1]:SNAcomplex(0.,0.);
caconjxpy(b, u_up2, u_accum);
const double rootpq1 = rootpqarray(j - ma, j - mb);
const SNAcomplex u_up1 = (ma < j)?rootpq1*ulist_buf1[jjup_shared_idx]:SNAcomplex(0.,0.);
caconjxpy(a, u_up1, u_accum);
// Next, spin up du_accum
const SNAcomplex du_up1 = (ma < j) ? rootpq1*dulist_buf1[jjup_shared_idx] : SNAcomplex(0.,0.);
caconjxpy(da, u_up1, du_accum);
caconjxpy(a, du_up1, du_accum);
const SNAcomplex du_up2 = (ma > 0) ? rootpq2*dulist_buf1[jjup_shared_idx-1] : SNAcomplex(0.,0.);
caconjxpy(db, u_up2, du_accum);
caconjxpy(b, du_up2, du_accum);
// No need to save u_accum to global memory
// Cache u_accum, du_accum to scratch memory.
ulist_buf2[jju_shared_idx] = u_accum;
dulist_buf2[jju_shared_idx] = du_accum;
// Directly accumulate deidrj into sum_tmp
//dulist(jju_index,iatom,jnbor,dir) = ((dsfac * u)*u_accum) + (sfac*du_accum);
const SNAcomplex du_prod = ((dsfac * u)*u_accum) + (sfac*du_accum);
sum_tmp += du_prod.re * y_local.re + du_prod.im * y_local.im;
// copy left side to right side with inversion symmetry VMK 4.4(2)
// u[ma-j][mb-j] = (-1)^(ma-mb)*Conj([u[ma][mb])
if (j%2==1 && mb+1==n_mb) {
int sign_factor = (((ma+mb)%2==0)?1:-1);
//const int jjup_flip = jju+(j+1-mb)*(j+1)-(ma+1); // no longer needed b/c we don't update dulist
const int jju_shared_flip = (j+1-mb)*(j+1)-(ma+1);
if (sign_factor == 1) {
u_accum.im = -u_accum.im;
du_accum.im = -du_accum.im;
} else {
u_accum.re = -u_accum.re;
du_accum.re = -du_accum.re;
}
Kokkos::single(Kokkos::PerThread(team), [&] () {
dedr(iatom,jnbor,0) = final_sum.x*2.0;
dedr(iatom,jnbor,1) = final_sum.y*2.0;
dedr(iatom,jnbor,2) = final_sum.z*2.0;
});
// We don't need the second half of the tile for the deidrj accumulation.
// That's taken care of by the symmetry factor above.
//dulist(jjup_flip,iatom,jnbor,dir) = ((dsfac * u)*u_accum) + (sfac*du_accum);
// We do need it for ortho polynomial generation, though
ulist_buf2[jju_shared_flip] = u_accum;
dulist_buf2[jju_shared_flip] = du_accum;
}
}, dedr_sum);
// swap buffers
auto tmp = ulist_buf1; ulist_buf1 = ulist_buf2; ulist_buf2 = tmp;
tmp = dulist_buf1; dulist_buf1 = dulist_buf2; dulist_buf2 = tmp;
// Accumulate dedr. This "should" be in a single, but
// a Kokkos::single call implies a warp sync, and we may
// as well avoid that. This does no harm as long as the
// final assignment is in a single block.
//Kokkos::single(Kokkos::PerThread(team), [=]() {
dedr_full_sum += dedr_sum;
//});
}
// Store the accumulated dedr.
Kokkos::single(Kokkos::PerThread(team), [&] () {
dedr(iatom,jnbor,dir) = dedr_full_sum*2.0;
});
}
/* ----------------------------------------------------------------------
compute dEidRj, CPU path only.
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_deidrj_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor)
@ -708,28 +940,6 @@ void SNAKokkos<DeviceType>::compute_bi(const typename Kokkos::TeamPolicy<DeviceT
calculate derivative of Ui w.r.t. atom j
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_duidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor)
{
double rsq, r, x, y, z, z0, theta0, cs, sn;
double dz0dr;
x = rij(iatom,jnbor,0);
y = rij(iatom,jnbor,1);
z = rij(iatom,jnbor,2);
rsq = x * x + y * y + z * z;
r = sqrt(rsq);
double rscale0 = rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0);
theta0 = (r - rmin0) * rscale0;
cs = cos(theta0);
sn = sin(theta0);
z0 = r * cs / sn;
dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq;
compute_duarray(team, iatom, jnbor, x, y, z, z0, r, dz0dr, wj(iatom,jnbor), rcutij(iatom,jnbor));
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_duidrj_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor)
@ -774,119 +984,6 @@ void SNAKokkos<DeviceType>::add_uarraytot(const typename Kokkos::TeamPolicy<Devi
compute Wigner U-functions for one neighbor
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_uarray(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor,
double x, double y, double z,
double z0, double r)
{
// define size of scratch memory buffer
const int max_m_tile = (twojmax+1)*(twojmax+1);
const int team_rank = team.team_rank();
// get scratch memory double buffer
SNAcomplex* buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0);
SNAcomplex* buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0);
// compute Cayley-Klein parameters for unit quaternion,
// pack into complex number
double r0inv = 1.0 / sqrt(r * r + z0 * z0);
SNAcomplex a = { r0inv * z0, -r0inv * z };
SNAcomplex b = { r0inv * y, -r0inv * x };
// VMK Section 4.8.2
// All writes go to global memory and shared memory
// so we can avoid all global memory reads
Kokkos::single(Kokkos::PerThread(team), [=]() {
ulist(0,iatom,jnbor) = { 1.0, 0.0 };
buf1[max_m_tile*team_rank] = {1.,0.};
});
for (int j = 1; j <= twojmax; j++) {
const int jju = idxu_block[j];
int jjup = idxu_block[j-1];
// fill in left side of matrix layer from previous layer
// Flatten loop over ma, mb, need to figure out total
// number of iterations
// for (int ma = 0; ma <= j; ma++)
const int n_ma = j+1;
// for (int mb = 0; 2*mb <= j; mb++)
const int n_mb = j/2+1;
const int total_iters = n_ma * n_mb;
//for (int m = 0; m < total_iters; m++) {
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, total_iters),
[&] (const int m) {
// ma fast, mb slow
int ma = m % n_ma;
int mb = m / n_ma;
// index into global memory array
const int jju_index = jju+mb+mb*j+ma;
// index into shared memory buffer for previous level
const int jju_shared_idx = max_m_tile*team_rank+mb+mb*j+ma;
// index into shared memory buffer for next level
const int jjup_shared_idx = max_m_tile*team_rank+mb*j+ma;
SNAcomplex u_accum = {0., 0.};
// VMK recursion relation: grab contribution which is multiplied by a*
const double rootpq1 = rootpqarray(j - ma, j - mb);
const SNAcomplex u_up1 = (ma < j)?rootpq1*buf1[jjup_shared_idx]:SNAcomplex(0.,0.);
caconjxpy(a, u_up1, u_accum);
// VMK recursion relation: grab contribution which is multiplied by b*
const double rootpq2 = -rootpqarray(ma, j - mb);
const SNAcomplex u_up2 = (ma > 0)?rootpq2*buf1[jjup_shared_idx-1]:SNAcomplex(0.,0.);
caconjxpy(b, u_up2, u_accum);
ulist(jju_index,iatom,jnbor) = u_accum;
// We no longer accumulate into ulisttot in this kernel.
// Instead, we have a separate kernel which avoids atomics.
// Running two separate kernels is net faster.
// back up into shared memory for next iter
if (j != twojmax) buf2[jju_shared_idx] = u_accum;
// copy left side to right side with inversion symmetry VMK 4.4(2)
// u[ma-j,mb-j] = (-1)^(ma-mb)*Conj([u[ma,mb))
// We can avoid this if we're on the last row for an integer j
if (!(n_ma % 2 == 1 && (mb+1) == n_mb)) {
int sign_factor = ((ma%2==0)?1:-1)*(mb%2==0?1:-1);
const int jjup_flip = jju+(j+1-mb)*(j+1)-(ma+1);
const int jju_shared_flip = max_m_tile*team_rank+(j+1-mb)*(j+1)-(ma+1);
if (sign_factor == 1) {
u_accum.im = -u_accum.im;
} else {
u_accum.re = -u_accum.re;
}
ulist(jjup_flip,iatom,jnbor) = u_accum;
if (j != twojmax) buf2[jju_shared_flip] = u_accum;
}
});
// In CUDA backend,
// ThreadVectorRange has a __syncwarp (appropriately masked for
// vector lengths < 32) implicit at the end
// swap double buffers
auto tmp = buf1; buf1 = buf2; buf2 = tmp;
//std::swap(buf1, buf2); // throws warnings
}
}
// CPU version
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_uarray_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor,
@ -976,152 +1073,9 @@ void SNAKokkos<DeviceType>::compute_uarray_cpu(const typename Kokkos::TeamPolicy
/* ----------------------------------------------------------------------
compute derivatives of Wigner U-functions for one neighbor
see comments in compute_uarray()
see comments in compute_uarray_cpu()
------------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_duarray(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor,
double x, double y, double z,
double z0, double r, double dz0dr,
double wj, double rcut)
{
// get shared memory offset
const int max_m_tile = (twojmax+1)*(twojmax+1);
const int team_rank = team.team_rank();
// double buffer for ulist
SNAcomplex* ulist_buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0);
SNAcomplex* ulist_buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0);
// double buffer for dulist
SNAcomplex* dulist_buf1 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0);
SNAcomplex* dulist_buf2 = (SNAcomplex*)team.team_shmem( ).get_shmem(team.team_size()*max_m_tile*sizeof(SNAcomplex), 0);
const double sfac = wj * compute_sfac(r, rcut);
const double dsfac = wj * compute_dsfac(r, rcut);
const double rinv = 1.0 / r;
// extract a single unit vector
const double u = (dir == 0 ? x * rinv : dir == 1 ? y * rinv : z * rinv);
// Compute Cayley-Klein parameters for unit quaternion
const double r0inv = 1.0 / sqrt(r * r + z0 * z0);
const SNAcomplex a = { r0inv * z0, -r0inv * z };
const SNAcomplex b = { r0inv * y, -r0inv * x };
const double dr0invdr = -r0inv * r0inv * r0inv * (r + z0 * dz0dr);
const double dr0inv = dr0invdr * u;
const double dz0 = dz0dr * u;
const SNAcomplex da = { dz0 * r0inv + z0 * dr0inv,
- z * dr0inv + (dir == 2 ? - r0inv : 0.) };
const SNAcomplex db = { y * dr0inv + (dir==1?r0inv:0.),
-x * dr0inv + (dir==0?-r0inv:0.) };
// single has a warp barrier at the end
Kokkos::single(Kokkos::PerThread(team), [=]() {
dulist(0,iatom,jnbor,dir) = { dsfac * u, 0. }; // fold in chain rule here
ulist_buf1[max_m_tile*team_rank] = {1., 0.};
dulist_buf1[max_m_tile*team_rank] = {0., 0.};
});
for (int j = 1; j <= twojmax; j++) {
int jju = idxu_block[j];
int jjup = idxu_block[j-1];
// flatten the loop over ma,mb
// for (int ma = 0; ma <= j; ma++)
const int n_ma = j+1;
// for (int mb = 0; 2*mb <= j; mb++)
const int n_mb = j/2+1;
const int total_iters = n_ma * n_mb;
//for (int m = 0; m < total_iters; m++) {
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, total_iters),
[&] (const int m) {
// ma fast, mb slow
int ma = m % n_ma;
int mb = m / n_ma;
const int jju_index = jju+mb+mb*j+ma;
// index into shared memory
const int jju_shared_idx = max_m_tile*team_rank+mb+mb*j+ma;
const int jjup_shared_idx = max_m_tile*team_rank+mb*j+ma;
// Need to compute and accumulate both u and du (mayhaps, we could probably
// balance some read and compute by reading u each time).
SNAcomplex u_accum = { 0., 0. };
SNAcomplex du_accum = { 0., 0. };
const double rootpq1 = rootpqarray(j - ma, j - mb);
const SNAcomplex u_up1 = (ma < j)?rootpq1*ulist_buf1[jjup_shared_idx]:SNAcomplex(0.,0.);
caconjxpy(a, u_up1, u_accum);
const double rootpq2 = -rootpqarray(ma, j - mb);
const SNAcomplex u_up2 = (ma > 0)?rootpq2*ulist_buf1[jjup_shared_idx-1]:SNAcomplex(0.,0.);
caconjxpy(b, u_up2, u_accum);
// No need to save u_accum to global memory
if (j != twojmax) ulist_buf2[jju_shared_idx] = u_accum;
// Next, spin up du_accum
const SNAcomplex du_up1 = (ma < j) ? rootpq1*dulist_buf1[jjup_shared_idx] : SNAcomplex(0.,0.);
caconjxpy(da, u_up1, du_accum);
caconjxpy(a, du_up1, du_accum);
const SNAcomplex du_up2 = (ma > 0) ? rootpq2*dulist_buf1[jjup_shared_idx-1] : SNAcomplex(0.,0.);
caconjxpy(db, u_up2, du_accum);
caconjxpy(b, du_up2, du_accum);
dulist(jju_index,iatom,jnbor,dir) = ((dsfac * u)*u_accum) + (sfac*du_accum);
if (j != twojmax) dulist_buf2[jju_shared_idx] = du_accum;
// copy left side to right side with inversion symmetry VMK 4.4(2)
// u[ma-j][mb-j] = (-1)^(ma-mb)*Conj([u[ma][mb])
int sign_factor = ((ma%2==0)?1:-1)*(mb%2==0?1:-1);
const int jjup_flip = jju+(j+1-mb)*(j+1)-(ma+1);
const int jju_shared_flip = max_m_tile*team_rank+(j+1-mb)*(j+1)-(ma+1);
if (sign_factor == 1) {
//ulist_alt(iatom,jnbor,jjup_flip).re = u_accum.re;
//ulist_alt(iatom,jnbor,jjup_flip).im = -u_accum.im;
u_accum.im = -u_accum.im;
du_accum.im = -du_accum.im;
} else {
//ulist_alt(iatom,jnbor,jjup_flip).re = -u_accum.re;
//ulist_alt(iatom,jnbor,jjup_flip).im = u_accum.im;
u_accum.re = -u_accum.re;
du_accum.re = -du_accum.re;
}
dulist(jjup_flip,iatom,jnbor,dir) = ((dsfac * u)*u_accum) + (sfac*du_accum);
if (j != twojmax) {
ulist_buf2[jju_shared_flip] = u_accum;
dulist_buf2[jju_shared_flip] = du_accum;
}
});
// swap buffers
auto tmp = ulist_buf1; ulist_buf1 = ulist_buf2; ulist_buf2 = tmp;
tmp = dulist_buf1; dulist_buf1 = dulist_buf2; dulist_buf2 = tmp;
}
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_duarray_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int iatom, int jnbor,
@ -1680,11 +1634,17 @@ double SNAKokkos<DeviceType>::memory_usage()
bytes += jdimpq*jdimpq * sizeof(double); // pqarray
bytes += idxcg_max * sizeof(double); // cglist
#ifdef KOKKOS_ENABLE_CUDA
if (!std::is_same<DeviceType,Kokkos::Cuda>::value) {
#endif
bytes += natom * idxu_max * sizeof(double) * 2; // ulist
bytes += natom * idxu_max * 3 * sizeof(double) * 2; // dulist
#ifdef KOKKOS_ENABLE_CUDA
}
#endif
bytes += natom * idxu_max * sizeof(double) * 2; // ulisttot
if (!Kokkos::Impl::is_same<typename DeviceType::array_layout,Kokkos::LayoutRight>::value)
bytes += natom * idxu_max * sizeof(double) * 2; // ulisttot_lr
bytes += natom * idxu_max * 3 * sizeof(double) * 2; // dulist
bytes += natom * idxz_max * sizeof(double) * 2; // zlist
bytes += natom * idxb_max * sizeof(double); // blist

4
src/KSPACE/msm.cpp
View File

@ -2920,7 +2920,7 @@ void MSM::compute_phis_and_dphis(const double &dx, const double &dy,
/* ----------------------------------------------------------------------
compute phi using interpolating polynomial
see Eq 7 from Parallel Computing 35 (2009) 164<EFBFBD>177
see Eq 7 from Parallel Computing 35 (2009) 164-177
and Hardy's thesis
------------------------------------------------------------------------- */
@ -2999,7 +2999,7 @@ inline double MSM::compute_phi(const double &xi)
/* ----------------------------------------------------------------------
compute the derivative of phi
phi is an interpolating polynomial
see Eq 7 from Parallel Computing 35 (2009) 164<EFBFBD>177
see Eq 7 from Parallel Computing 35 (2009) 164-177
and Hardy's thesis
------------------------------------------------------------------------- */

2
src/USER-INTEL/pair_tersoff_intel.cpp
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Markus H<EFBFBD>hnerbach (RWTH)
Contributing author: Markus Höhnerbach (RWTH)
------------------------------------------------------------------------- */
#include <cmath>

8
src/USER-INTEL/verlet_lrt_intel.cpp
View File

@ -185,7 +185,7 @@ void VerletLRTIntel::setup(int flag)
_kspace_done = 0;
pthread_mutex_unlock(&_kmutex);
#elif defined(_LMP_INTEL_LRT_11)
kspace_thread.join();
_kspace_thread.join();
#endif
if (kspace_compute_flag) _intel_kspace->compute_second(eflag,vflag);
@ -298,9 +298,9 @@ void VerletLRTIntel::run(int n)
pthread_cond_signal(&_kcond);
pthread_mutex_unlock(&_kmutex);
#elif defined(_LMP_INTEL_LRT_11)
std::thread kspace_thread;
std::thread _kspace_thread;
if (kspace_compute_flag)
kspace_thread=std::thread([=] {
_kspace_thread=std::thread([=] {
_intel_kspace->compute_first(eflag, vflag);
timer->stamp(Timer::KSPACE);
} );
@ -332,7 +332,7 @@ void VerletLRTIntel::run(int n)
pthread_mutex_unlock(&_kmutex);
#elif defined(_LMP_INTEL_LRT_11)
if (kspace_compute_flag)
kspace_thread.join();
_kspace_thread.join();
#endif
if (kspace_compute_flag) {

6
src/USER-SMTBQ/pair_smtbq.cpp
View File

@ -13,7 +13,7 @@
/* ----------------------------------------------------------------------
The SMTBQ code has been developed with the financial support of CNRS and
of the Regional Council of Burgundy (Convention n<EFBFBD> 2010-9201AAO037S03129)
of the Regional Council of Burgundy (Convention n¡ 2010-9201AAO037S03129)
Copyright (2015)
Universite de Bourgogne : Nicolas SALLES, Olivier POLITANO
@ -943,7 +943,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
3 -> Short int. Ox-Ox
4 -> Short int. SMTB (repulsion)
5 -> Covalent energy SMTB
6 -> Somme des Q(i)<EFBFBD>
6 -> Somme des Q(i)²
------------------------------------------------------------------------- */
/* -------------- N-body forces Calcul --------------- */
@ -3022,7 +3022,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
ngp = igp = 0; nelt[ngp] = 0;
// On prend un oxyg<EFBFBD>ne
// On prend un oxygène
// printf ("[me %d] On prend un oxygene\n",me);
for (ii = 0; ii < inum; ii++) {

1
src/atom_vec.cpp
View File

@ -36,6 +36,7 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
forceclearflag = 0;
size_data_bonus = 0;
maxexchange = 0;
molecular = 0;
kokkosable = 0;

33
src/variable.cpp
View File

@ -661,6 +661,8 @@ int Variable::next(int narg, char **arg)
} else if (istyle == UNIVERSE || istyle == ULOOP) {
uloop_again:
// wait until lock file can be created and owned by proc 0 of this world
// rename() is not atomic in practice, but no known simple fix
// means multiple procs can read/write file at the same time (bad!)
@ -669,7 +671,7 @@ int Variable::next(int narg, char **arg)
// delay for random fraction of 1 second before subsequent tries
// when successful, read next available index and Bcast it within my world
int nextindex;
int nextindex = -1;
if (me == 0) {
int seed = 12345 + universe->me + which[find(arg[0])];
RanMars *random = new RanMars(lmp,seed);
@ -682,10 +684,33 @@ int Variable::next(int narg, char **arg)
}
delete random;
FILE *fp = fopen("tmp.lammps.variable.lock","r");
fscanf(fp,"%d",&nextindex);
//printf("READ %d %d\n",universe->me,nextindex);
// if the file cannot be found, we may have a race with some
// other MPI rank that has called rename at the same time
// and we have to start over.
// if the read is short (we need at least one byte) we try reading again.
FILE *fp;
char buf[64];
for (int loopmax = 0; loopmax < 100; ++loopmax) {
fp = fopen("tmp.lammps.variable.lock","r");
if (fp == NULL) goto uloop_again;
buf[0] = buf[1] = '\0';
fread(buf,1,64,fp);
fclose(fp);
if (strlen(buf) > 0) {
nextindex = atoi(buf);
break;
}
delay = (int) (1000000*random->uniform());
usleep(delay);
}
if (nextindex < 0)
error->one(FLERR,"Unexpected error while incrementing uloop "
"style variable. Please contact LAMMPS developers.");
//printf("READ %d %d\n",universe->me,nextindex);
fp = fopen("tmp.lammps.variable.lock","w");
fprintf(fp,"%d\n",nextindex+1);
//printf("WRITE %d %d\n",universe->me,nextindex+1);