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npair_half_bin_newton_tri_intel.cpp
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Sat, Jun 29, 05:59
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15 KB
Mime Type
text/x-c++
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Mon, Jul 1, 05:59 (2 d)
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rLAMMPS lammps
npair_half_bin_newton_tri_intel.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include "npair_half_bin_newton_tri_intel.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonTriIntel
::
NPairHalfBinNewtonTriIntel
(
LAMMPS
*
lmp
)
:
NPairIntel
(
lmp
)
{}
/* ----------------------------------------------------------------------
binned neighbor list construction with Newton's 3rd law for triclinic
each owned atom i checks its own bin and other bins in triclinic stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void
NPairHalfBinNewtonTriIntel
::
build
(
NeighList
*
list
)
{
if
(
nstencil
>
INTEL_MAX_STENCIL
)
error
->
all
(
FLERR
,
"Too many neighbor bins for USER-INTEL package."
);
#ifdef _LMP_INTEL_OFFLOAD
if
(
exclude
)
error
->
all
(
FLERR
,
"Exclusion lists not yet supported for Intel offload"
);
#endif
if
(
_fix
->
precision
()
==
FixIntel
::
PREC_MODE_MIXED
)
hbnti
(
list
,
_fix
->
get_mixed_buffers
());
else
if
(
_fix
->
precision
()
==
FixIntel
::
PREC_MODE_DOUBLE
)
hbnti
(
list
,
_fix
->
get_double_buffers
());
else
hbnti
(
list
,
_fix
->
get_single_buffers
());
_fix
->
stop_watch
(
TIME_HOST_NEIGHBOR
);
}
template
<
class
flt_t
,
class
acc_t
>
void
NPairHalfBinNewtonTriIntel
::
hbnti
(
NeighList
*
list
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
)
{
const
int
nlocal
=
(
includegroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
list
->
inum
=
nlocal
;
int
host_start
=
_fix
->
host_start_neighbor
();
const
int
off_end
=
_fix
->
offload_end_neighbor
();
#ifdef _LMP_INTEL_OFFLOAD
if
(
off_end
)
grow_stencil
();
if
(
_fix
->
full_host_list
())
host_start
=
0
;
int
offload_noghost
=
_fix
->
offload_noghost
();
#endif
buffers
->
grow_list
(
list
,
atom
->
nlocal
,
comm
->
nthreads
,
off_end
);
int
need_ic
=
0
;
if
(
atom
->
molecular
)
dminimum_image_check
(
need_ic
,
neighbor
->
cutneighmax
,
neighbor
->
cutneighmax
,
neighbor
->
cutneighmax
);
#ifdef _LMP_INTEL_OFFLOAD
if
(
need_ic
)
{
if
(
offload_noghost
)
{
hbnti
<
flt_t
,
acc_t
,
1
,
1
>
(
1
,
list
,
buffers
,
0
,
off_end
);
hbnti
<
flt_t
,
acc_t
,
1
,
1
>
(
0
,
list
,
buffers
,
host_start
,
nlocal
,
off_end
);
}
else
{
hbnti
<
flt_t
,
acc_t
,
0
,
1
>
(
1
,
list
,
buffers
,
0
,
off_end
);
hbnti
<
flt_t
,
acc_t
,
0
,
1
>
(
0
,
list
,
buffers
,
host_start
,
nlocal
);
}
}
else
{
if
(
offload_noghost
)
{
hbnti
<
flt_t
,
acc_t
,
1
,
0
>
(
1
,
list
,
buffers
,
0
,
off_end
);
hbnti
<
flt_t
,
acc_t
,
1
,
0
>
(
0
,
list
,
buffers
,
host_start
,
nlocal
,
off_end
);
}
else
{
hbnti
<
flt_t
,
acc_t
,
0
,
0
>
(
1
,
list
,
buffers
,
0
,
off_end
);
hbnti
<
flt_t
,
acc_t
,
0
,
0
>
(
0
,
list
,
buffers
,
host_start
,
nlocal
);
}
}
#else
if
(
need_ic
)
hbnti
<
flt_t
,
acc_t
,
0
,
1
>
(
0
,
list
,
buffers
,
host_start
,
nlocal
);
else
hbnti
<
flt_t
,
acc_t
,
0
,
0
>
(
0
,
list
,
buffers
,
host_start
,
nlocal
);
#endif
}
template
<
class
flt_t
,
class
acc_t
,
int
offload_noghost
,
int
need_ic
>
void
NPairHalfBinNewtonTriIntel
::
hbnti
(
const
int
offload
,
NeighList
*
list
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
,
const
int
astart
,
const
int
aend
,
const
int
offload_end
)
{
if
(
aend
-
astart
==
0
)
return
;
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
int
pad
=
1
;
int
nall_t
=
nall
;
#ifdef _LMP_INTEL_OFFLOAD
if
(
offload_noghost
&&
offload
)
nall_t
=
atom
->
nlocal
;
if
(
offload
)
{
if
(
INTEL_MIC_NBOR_PAD
>
1
)
pad
=
INTEL_MIC_NBOR_PAD
*
sizeof
(
float
)
/
sizeof
(
flt_t
);
}
else
#endif
if
(
INTEL_NBOR_PAD
>
1
)
pad
=
INTEL_NBOR_PAD
*
sizeof
(
float
)
/
sizeof
(
flt_t
);
const
int
pad_width
=
pad
;
const
ATOM_T
*
_noalias
const
x
=
buffers
->
get_x
();
int
*
_noalias
const
firstneigh
=
buffers
->
firstneigh
(
list
);
const
int
e_nall
=
nall_t
;
const
int
molecular
=
atom
->
molecular
;
int
*
ns
=
NULL
;
tagint
*
s
=
NULL
;
int
tag_size
=
0
,
special_size
;
if
(
buffers
->
need_tag
())
tag_size
=
e_nall
;
if
(
molecular
)
{
s
=
atom
->
special
[
0
];
ns
=
atom
->
nspecial
[
0
];
special_size
=
aend
;
}
else
{
s
=
&
buffers
->
_special_holder
;
ns
=
&
buffers
->
_nspecial_holder
;
special_size
=
0
;
}
const
tagint
*
_noalias
const
special
=
s
;
const
int
*
_noalias
const
nspecial
=
ns
;
const
int
maxspecial
=
atom
->
maxspecial
;
const
tagint
*
_noalias
const
tag
=
atom
->
tag
;
int
*
_noalias
const
ilist
=
list
->
ilist
;
int
*
_noalias
numneigh
=
list
->
numneigh
;
int
*
_noalias
const
cnumneigh
=
buffers
->
cnumneigh
(
list
);
const
int
nstencil
=
this
->
nstencil
;
const
int
*
_noalias
const
stencil
=
this
->
stencil
;
const
flt_t
*
_noalias
const
cutneighsq
=
buffers
->
get_cutneighsq
()[
0
];
const
int
ntypes
=
atom
->
ntypes
+
1
;
const
int
nlocal
=
atom
->
nlocal
;
#ifndef _LMP_INTEL_OFFLOAD
int
*
const
mask
=
atom
->
mask
;
tagint
*
const
molecule
=
atom
->
molecule
;
#endif
int
tnum
;
int
*
overflow
;
double
*
timer_compute
;
#ifdef _LMP_INTEL_OFFLOAD
if
(
offload
)
{
timer_compute
=
_fix
->
off_watch_neighbor
();
tnum
=
buffers
->
get_off_threads
();
overflow
=
_fix
->
get_off_overflow_flag
();
_fix
->
stop_watch
(
TIME_HOST_NEIGHBOR
);
_fix
->
start_watch
(
TIME_OFFLOAD_LATENCY
);
}
else
#
endif
{
tnum
=
comm
->
nthreads
;
overflow
=
_fix
->
get_overflow_flag
();
}
const
int
nthreads
=
tnum
;
const
int
maxnbors
=
buffers
->
get_max_nbors
();
int
*
_noalias
const
atombin
=
buffers
->
get_atombin
();
const
int
*
_noalias
const
binpacked
=
buffers
->
get_binpacked
();
const
int
xperiodic
=
domain
->
xperiodic
;
const
int
yperiodic
=
domain
->
yperiodic
;
const
int
zperiodic
=
domain
->
zperiodic
;
const
flt_t
xprd_half
=
domain
->
xprd_half
;
const
flt_t
yprd_half
=
domain
->
yprd_half
;
const
flt_t
zprd_half
=
domain
->
zprd_half
;
#ifdef _LMP_INTEL_OFFLOAD
const
int
*
_noalias
const
binhead
=
this
->
binhead
;
const
int
*
_noalias
const
bins
=
this
->
bins
;
const
int
cop
=
_fix
->
coprocessor_number
();
const
int
separate_buffers
=
_fix
->
separate_buffers
();
#pragma offload target(mic:cop) if(offload) \
in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
in(tag:length(tag_size) alloc_if(0) free_if(0)) \
in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
in(firstneigh:length(0) alloc_if(0) free_if(0)) \
in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
out(numneigh:length(0) alloc_if(0) free_if(0)) \
in(ilist:length(0) alloc_if(0) free_if(0)) \
in(atombin:length(aend) alloc_if(0) free_if(0)) \
in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
in(maxnbors,nthreads,maxspecial,nstencil,offload_end,pad_width,e_nall) \
in(offload,separate_buffers, astart, aend, nlocal, molecular, ntypes) \
in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
out(overflow:length(5) alloc_if(0) free_if(0)) \
out(timer_compute:length(1) alloc_if(0) free_if(0)) \
signal(tag)
#endif
{
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
*
timer_compute
=
MIC_Wtime
();
#endif
#ifdef _LMP_INTEL_OFFLOAD
overflow
[
LMP_LOCAL_MIN
]
=
astart
;
overflow
[
LMP_LOCAL_MAX
]
=
aend
-
1
;
overflow
[
LMP_GHOST_MIN
]
=
e_nall
;
overflow
[
LMP_GHOST_MAX
]
=
-
1
;
#endif
int
nstencilp
=
0
;
int
binstart
[
INTEL_MAX_STENCIL
],
binend
[
INTEL_MAX_STENCIL
];
for
(
int
k
=
0
;
k
<
nstencil
;
k
++
)
{
binstart
[
nstencilp
]
=
stencil
[
k
];
int
end
=
stencil
[
k
]
+
1
;
for
(
int
kk
=
k
+
1
;
kk
<
nstencil
;
kk
++
)
{
if
(
stencil
[
kk
-
1
]
+
1
==
stencil
[
kk
])
{
end
++
;
k
++
;
}
else
break
;
}
binend
[
nstencilp
]
=
end
;
nstencilp
++
;
}
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(numneigh, overflow, nstencilp, binstart, binend)
#endif
{
#ifdef _LMP_INTEL_OFFLOAD
int
lmin
=
e_nall
,
lmax
=
-
1
,
gmin
=
e_nall
,
gmax
=
-
1
;
#endif
const
int
num
=
aend
-
astart
;
int
tid
,
ifrom
,
ito
;
IP_PRE_omp_range_id
(
ifrom
,
ito
,
tid
,
num
,
nthreads
);
ifrom
+=
astart
;
ito
+=
astart
;
int
which
;
const
int
list_size
=
(
ito
+
tid
*
2
+
2
)
*
maxnbors
;
int
ct
=
(
ifrom
+
tid
*
2
)
*
maxnbors
;
int
*
neighptr
=
firstneigh
+
ct
;
const
int
obound
=
maxnbors
*
3
;
for
(
int
i
=
ifrom
;
i
<
ito
;
i
++
)
{
const
flt_t
xtmp
=
x
[
i
].
x
;
const
flt_t
ytmp
=
x
[
i
].
y
;
const
flt_t
ztmp
=
x
[
i
].
z
;
const
int
itype
=
x
[
i
].
w
;
const
int
ioffset
=
ntypes
*
itype
;
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
const
int
ibin
=
atombin
[
i
];
int
raw_count
=
maxnbors
;
for
(
int
k
=
0
;
k
<
nstencilp
;
k
++
)
{
const
int
bstart
=
binhead
[
ibin
+
binstart
[
k
]];
const
int
bend
=
binhead
[
ibin
+
binend
[
k
]];
for
(
int
jj
=
bstart
;
jj
<
bend
;
jj
++
)
{
const
int
j
=
binpacked
[
jj
];
#ifdef _LMP_INTEL_OFFLOAD
if
(
offload_noghost
)
{
if
(
j
<
nlocal
)
{
if
(
i
<
offload_end
)
continue
;
}
else
if
(
offload
)
continue
;
}
#endif
if
(
x
[
j
].
z
<
ztmp
)
continue
;
if
(
x
[
j
].
z
==
ztmp
)
{
if
(
x
[
j
].
y
<
ytmp
)
continue
;
if
(
x
[
j
].
y
==
ytmp
)
{
if
(
x
[
j
].
x
<
xtmp
)
continue
;
if
(
x
[
j
].
x
==
xtmp
&&
j
<=
i
)
continue
;
}
}
#ifndef _LMP_INTEL_OFFLOAD
if
(
exclude
)
{
const
int
jtype
=
x
[
j
].
w
;
if
(
exclusion
(
i
,
j
,
itype
,
jtype
,
mask
,
molecule
))
continue
;
}
#endif
neighptr
[
raw_count
++
]
=
j
;
}
}
if
(
raw_count
>
obound
)
*
overflow
=
1
;
#if defined(LMP_SIMD_COMPILER)
#ifdef _LMP_INTEL_OFFLOAD
int
vlmin
=
lmin
,
vlmax
=
lmax
,
vgmin
=
gmin
,
vgmax
=
gmax
;
#if __INTEL_COMPILER+0 > 1499
#pragma vector aligned
#pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
#endif
#else
#pragma vector aligned
#pragma simd
#endif
#endif
for
(
int
u
=
maxnbors
;
u
<
raw_count
;
u
++
)
{
int
j
=
neighptr
[
u
];
const
flt_t
delx
=
xtmp
-
x
[
j
].
x
;
const
flt_t
dely
=
ytmp
-
x
[
j
].
y
;
const
flt_t
delz
=
ztmp
-
x
[
j
].
z
;
const
int
jtype
=
x
[
j
].
w
;
const
flt_t
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
if
(
rsq
>
cutneighsq
[
ioffset
+
jtype
])
neighptr
[
u
]
=
e_nall
;
else
{
if
(
need_ic
)
{
int
no_special
;
ominimum_image_check
(
no_special
,
delx
,
dely
,
delz
);
if
(
no_special
)
neighptr
[
u
]
=
-
j
-
1
;
}
#ifdef _LMP_INTEL_OFFLOAD
if
(
j
<
nlocal
)
{
if
(
j
<
vlmin
)
vlmin
=
j
;
if
(
j
>
vlmax
)
vlmax
=
j
;
}
else
{
if
(
j
<
vgmin
)
vgmin
=
j
;
if
(
j
>
vgmax
)
vgmax
=
j
;
}
#endif
}
}
int
n
=
0
,
n2
=
maxnbors
;
for
(
int
u
=
maxnbors
;
u
<
raw_count
;
u
++
)
{
const
int
j
=
neighptr
[
u
];
int
pj
=
j
;
if
(
pj
<
e_nall
)
{
if
(
need_ic
)
if
(
pj
<
0
)
pj
=
-
pj
-
1
;
if
(
pj
<
nlocal
)
neighptr
[
n
++
]
=
j
;
else
neighptr
[
n2
++
]
=
j
;
}
}
int
ns
=
n
;
for
(
int
u
=
maxnbors
;
u
<
n2
;
u
++
)
neighptr
[
n
++
]
=
neighptr
[
u
];
ilist
[
i
]
=
i
;
cnumneigh
[
i
]
=
ct
;
ns
+=
n2
-
maxnbors
;
int
edge
=
(
ns
%
pad_width
);
if
(
edge
)
{
const
int
pad_end
=
ns
+
(
pad_width
-
edge
);
#if defined(LMP_SIMD_COMPILER)
#pragma loop_count min=1, max=15, avg=8
#endif
for
(
;
ns
<
pad_end
;
ns
++
)
neighptr
[
ns
]
=
e_nall
;
}
numneigh
[
i
]
=
ns
;
ct
+=
ns
;
const
int
alignb
=
(
INTEL_DATA_ALIGN
/
sizeof
(
int
));
edge
=
(
ct
%
alignb
);
if
(
edge
)
ct
+=
alignb
-
edge
;
neighptr
=
firstneigh
+
ct
;
if
(
ct
+
obound
>
list_size
)
{
if
(
i
<
ito
-
1
)
{
*
overflow
=
1
;
ct
=
(
ifrom
+
tid
*
2
)
*
maxnbors
;
}
}
}
if
(
*
overflow
==
1
)
for
(
int
i
=
ifrom
;
i
<
ito
;
i
++
)
numneigh
[
i
]
=
0
;
#ifdef _LMP_INTEL_OFFLOAD
if
(
separate_buffers
)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if
(
lmin
<
overflow
[
LMP_LOCAL_MIN
])
overflow
[
LMP_LOCAL_MIN
]
=
lmin
;
if
(
lmax
>
overflow
[
LMP_LOCAL_MAX
])
overflow
[
LMP_LOCAL_MAX
]
=
lmax
;
if
(
gmin
<
overflow
[
LMP_GHOST_MIN
])
overflow
[
LMP_GHOST_MIN
]
=
gmin
;
if
(
gmax
>
overflow
[
LMP_GHOST_MAX
])
overflow
[
LMP_GHOST_MAX
]
=
gmax
;
}
#pragma omp barrier
}
int
ghost_offset
=
0
,
nall_offset
=
e_nall
;
if
(
separate_buffers
)
{
int
nghost
=
overflow
[
LMP_GHOST_MAX
]
+
1
-
overflow
[
LMP_GHOST_MIN
];
if
(
nghost
<
0
)
nghost
=
0
;
if
(
offload
)
{
ghost_offset
=
overflow
[
LMP_GHOST_MIN
]
-
overflow
[
LMP_LOCAL_MAX
]
-
1
;
nall_offset
=
overflow
[
LMP_LOCAL_MAX
]
+
1
+
nghost
;
}
else
{
ghost_offset
=
overflow
[
LMP_GHOST_MIN
]
-
nlocal
;
nall_offset
=
nlocal
+
nghost
;
}
}
#endif
if
(
molecular
)
{
for
(
int
i
=
ifrom
;
i
<
ito
;
++
i
)
{
int
*
_noalias
jlist
=
firstneigh
+
cnumneigh
[
i
];
const
int
jnum
=
numneigh
[
i
];
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for
(
int
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
const
int
j
=
jlist
[
jj
];
if
(
need_ic
&&
j
<
0
)
{
which
=
0
;
jlist
[
jj
]
=
-
j
-
1
;
}
else
ofind_special
(
which
,
special
,
nspecial
,
i
,
tag
[
j
]);
#ifdef _LMP_INTEL_OFFLOAD
if
(
j
>=
nlocal
)
{
if
(
j
==
e_nall
)
jlist
[
jj
]
=
nall_offset
;
else
if
(
which
)
jlist
[
jj
]
=
(
j
-
ghost_offset
)
^
(
which
<<
SBBITS
);
else
jlist
[
jj
]
-=
ghost_offset
;
}
else
#endif
if
(
which
)
jlist
[
jj
]
=
j
^
(
which
<<
SBBITS
);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else
if
(
separate_buffers
)
{
for
(
int
i
=
ifrom
;
i
<
ito
;
++
i
)
{
int
*
_noalias
jlist
=
firstneigh
+
cnumneigh
[
i
];
const
int
jnum
=
numneigh
[
i
];
int
jj
=
0
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
if
(
jlist
[
jj
]
>=
nlocal
)
break
;
while
(
jj
<
jnum
)
{
if
(
jlist
[
jj
]
==
e_nall
)
jlist
[
jj
]
=
nall_offset
;
else
jlist
[
jj
]
-=
ghost_offset
;
jj
++
;
}
}
}
#endif
}
// end omp
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
*
timer_compute
=
MIC_Wtime
()
-
*
timer_compute
;
#endif
}
// end offload
#ifdef _LMP_INTEL_OFFLOAD
if
(
offload
)
{
_fix
->
stop_watch
(
TIME_OFFLOAD_LATENCY
);
_fix
->
start_watch
(
TIME_HOST_NEIGHBOR
);
for
(
int
n
=
0
;
n
<
aend
;
n
++
)
{
ilist
[
n
]
=
n
;
numneigh
[
n
]
=
0
;
}
}
else
{
for
(
int
i
=
astart
;
i
<
aend
;
i
++
)
list
->
firstneigh
[
i
]
=
firstneigh
+
cnumneigh
[
i
];
if
(
separate_buffers
)
{
_fix
->
start_watch
(
TIME_PACK
);
_fix
->
set_neighbor_host_sizes
();
buffers
->
pack_sep_from_single
(
_fix
->
host_min_local
(),
_fix
->
host_used_local
(),
_fix
->
host_min_ghost
(),
_fix
->
host_used_ghost
());
_fix
->
stop_watch
(
TIME_PACK
);
}
}
#else
for
(
int
i
=
astart
;
i
<
aend
;
i
++
)
list
->
firstneigh
[
i
]
=
firstneigh
+
cnumneigh
[
i
];
#endif
}
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