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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9002 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-10-25 15:35:14 +00:00
parent 13dd457ae7
commit 6dcb5fb23d
8 changed files with 88 additions and 125 deletions
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2
examples/COUPLE/README
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@ -32,7 +32,7 @@ lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
library collection of useful inter-code communication routines
simple simple example of driver code calling LAMMPS as library
fortran a wrapper on the LAMMPS library API that
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
fortran2 a more sophisticated wrapper on the LAMMPS library API that
can be called from Fortran

4
src/Makefile.shlib
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File diff suppressed because one or more lines are too long

18
src/REPLICA/verlet_split.cpp
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@ -1,4 +1,4 @@
/* -------------------------------------------------------------------------
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -32,6 +32,7 @@
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "fix.h"
#include "modify.h"
#include "timer.h"
#include "memory.h"
@ -260,7 +261,8 @@ void VerletSplit::setup_minimal(int flag)
void VerletSplit::run(int n)
{
int nflag,ntimestep,sortflag;
bigint ntimestep;
int nflag,sortflag;
// sync both partitions before start timer
@ -272,6 +274,13 @@ void VerletSplit::run(int n)
rk_setup();
// check if OpenMP support fix defined
Fix *fix_omp;
int ifix = modify->find_fix("package_omp");
if (ifix < 0) fix_omp = NULL;
else fix_omp = modify->fix[ifix];
// flags for timestepping iterations
int n_post_integrate = modify->n_post_integrate;
@ -360,6 +369,11 @@ void VerletSplit::run(int n)
}
} else {
// run FixOMP as sole pre_force fix, if defined
if (fix_omp) fix_omp->pre_force(vflag);
if (force->kspace) {
timer->stamp();
force->kspace->compute(eflag,vflag);

5
src/USER-OMP/Install.sh
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@ -1,10 +1,9 @@
# Install/unInstall package files in LAMMPS
# do not install child files if parent does not exist
for file in *_omp.cpp *_omp.h pppm*proxy.h pppm*proxy.cpp; do
for file in *_omp.cpp *_omp.h ; do
# let us see if the "rain man" can count the toothpicks...
ofile=`echo $file | sed -e s,_pppm_tip4p_omp,_long_tip4p_omp, \
-e s,pppm.\\*_proxy,pppm_omp, -e s,_pppm_omp,_long_omp, \
ofile=`echo $file | sed \
-e s,\\\\\\(.\\*\\\\\\)_omp\\\\.h,\\\\1.h, \
-e s,\\\\\\(.\\*\\\\\\)_omp\\\\.cpp,\\\\1.cpp,`
if (test $1 = 1) then

5
src/USER-OMP/Package.sh
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@ -4,10 +4,9 @@
# not exist. Do remove OpenMP style files that have no matching
# non-OpenMP version installed, e.g. after a package has been
# removed
for file in *_omp.cpp *_omp.h pppm*proxy.h pppm*proxy.cpp thr_data.h thr_data.cpp; do
for file in *_omp.cpp *_omp.h thr_data.h thr_data.cpp; do
# let us see if the "rain man" can count the toothpicks...
ofile=`echo $file | sed -e s,_pppm_tip4p_omp,_long_tip4p_omp, \
-e s,pppm.\\*_proxy,pppm_omp, -e s,_pppm_omp,_long_omp, \
ofile=`echo $file | sed \
-e s,\\\\\\(.\\*\\\\\\)_omp\\\\.\\\\\\(h\\\\\\|cpp\\\\\\),\\\\1.\\\\2,`
if (test $file = "thr_omp.h") || (test $file = "thr_omp.cpp") \
|| (test $file = "thr_data.h") || (test $file = "thr_data.cpp") then

96
src/USER-OMP/fix_omp.cpp
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@ -22,6 +22,7 @@
#include "force.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "integrate.h"
#include "min.h"
@ -194,61 +195,76 @@ void FixOMP::init()
if (strstr(update->integrate_style,"respa") != NULL)
error->all(FLERR,"Cannot use r-RESPA with /omp styles");
int check_hybrid;
int check_hybrid, kspace_split;
last_pair_hybrid = NULL;
last_omp_style = NULL;
const char *last_omp_name = NULL;
const char *last_hybrid_name = NULL;
const char *last_force_name = NULL;
// support for verlet/split operation.
// kspace_split == 0 : regular processing
// kspace_split < 0 : master partition, does not do kspace
// kspace_split > 0 : slave partition, only does kspace
if (strstr(update->integrate_style,"verlet/split") != NULL) {
if (universe->iworld == 0) kspace_split = -1;
else kspace_split = 1;
} else {
kspace_split = 0;
}
// determine which is the last force style with OpenMP
// support as this is the one that has to reduce the forces
#define CheckStyleForOMP(name) \
check_hybrid = 0; \
if (force->name) { \
if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
check_hybrid=1; \
if (force->name->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \
last_omp_name = force->name ## _style; \
last_omp_style = (void *) force->name; \
} \
#define CheckStyleForOMP(name) \
check_hybrid = 0; \
if (force->name) { \
if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
(strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
check_hybrid=1; \
if (force->name->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \
last_omp_name = force->name ## _style; \
last_omp_style = (void *) force->name; \
} \
}
#define CheckHybridForOMP(name,Class) \
if (check_hybrid) { \
Class ## Hybrid *style = (Class ## Hybrid *) force->name; \
for (int i=0; i < style->nstyles; i++) { \
if (style->styles[i]->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \
last_omp_name = style->keywords[i]; \
last_omp_style = style->styles[i]; \
} \
} \
#define CheckHybridForOMP(name,Class) \
if (check_hybrid) { \
Class ## Hybrid *style = (Class ## Hybrid *) force->name; \
for (int i=0; i < style->nstyles; i++) { \
if (style->styles[i]->suffix_flag & Suffix::OMP) { \
last_force_name = (const char *) #name; \
last_omp_name = style->keywords[i]; \
last_omp_style = style->styles[i]; \
} \
} \
}
CheckStyleForOMP(pair);
CheckHybridForOMP(pair,Pair);
if (check_hybrid) {
last_pair_hybrid = last_omp_style;
last_hybrid_name = last_omp_name;
if (kspace_split <= 0) {
CheckStyleForOMP(pair);
CheckHybridForOMP(pair,Pair);
if (check_hybrid) {
last_pair_hybrid = last_omp_style;
last_hybrid_name = last_omp_name;
}
CheckStyleForOMP(bond);
CheckHybridForOMP(bond,Bond);
CheckStyleForOMP(angle);
CheckHybridForOMP(angle,Angle);
CheckStyleForOMP(dihedral);
CheckHybridForOMP(dihedral,Dihedral);
CheckStyleForOMP(improper);
CheckHybridForOMP(improper,Improper);
}
CheckStyleForOMP(bond);
CheckHybridForOMP(bond,Bond);
CheckStyleForOMP(angle);
CheckHybridForOMP(angle,Angle);
CheckStyleForOMP(dihedral);
CheckHybridForOMP(dihedral,Dihedral);
CheckStyleForOMP(improper);
CheckHybridForOMP(improper,Improper);
CheckStyleForOMP(kspace);
if (kspace_split >= 0) {
CheckStyleForOMP(kspace);
}
#undef CheckStyleForOMP
#undef CheckHybridForOMP

72
src/USER-OMP/thr_omp.cpp
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@ -147,7 +147,7 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
---------------------------------------------------------------------- */
void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
ThrData *const thr, const int nproxy)
ThrData *const thr)
{
const int nlocal = lmp->atom->nlocal;
const int nghost = lmp->atom->nghost;
@ -172,12 +172,7 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
if (pair->vflag_fdotr) {
if (style == fix->last_pair_hybrid) {
// pair_style hybrid will compute fdotr for us
// but we first need to reduce the forces
data_reduce_thr(&(f[0][0]), nall, nthreads, 3, tid);
need_force_reduce = 0;
}
if (fix->last_pair_hybrid) return;
// this is a non-hybrid pair style. compute per thread fdotr
if (fix->last_pair_hybrid == NULL) {
@ -205,67 +200,7 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
thr->virial_pair[i] = 0.0;
}
}
if (eflag & 2) {
data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
}
if (vflag & 4) {
data_reduce_thr(&(pair->vatom[0][0]), nall, nthreads, 6, tid);
}
}
}
break;
case THR_PAIR|THR_PROXY: {
Pair * const pair = lmp->force->pair;
if (tid >= nproxy && pair->vflag_fdotr) {
if (fix->last_pair_hybrid) {
if (tid == nproxy)
lmp->error->all(FLERR,
"Cannot use hybrid pair style with kspace proxy");
else return;
}
// this is a non-hybrid pair style. compute per thread fdotr
if (fix->last_pair_hybrid == NULL) {
if (lmp->neighbor->includegroup == 0)
thr->virial_fdotr_compute(x, nlocal, nghost, -1);
else
thr->virial_fdotr_compute(x, nlocal, nghost, nfirst);
}
}
if (evflag) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (tid < nproxy) {
// nothing to collect for kspace proxy threads
// just reset pair accumulators to 0.0.
if (eflag & 1) {
thr->eng_vdwl = 0.0;
thr->eng_coul = 0.0;
}
if (vflag & 3)
for (int i=0; i < 6; ++i) {
thr->virial_pair[i] = 0.0;
}
} else {
if (eflag & 1) {
pair->eng_vdwl += thr->eng_vdwl;
pair->eng_coul += thr->eng_coul;
thr->eng_vdwl = 0.0;
thr->eng_coul = 0.0;
}
if (vflag & 3)
for (int i=0; i < 6; ++i) {
pair->virial[i] += thr->virial_pair[i];
thr->virial_pair[i] = 0.0;
}
}
}
if (eflag & 2) {
data_reduce_thr(&(pair->eatom[0]), nall, nthreads, 1, tid);
}
@ -439,9 +374,8 @@ void ThrOMP::reduce_thr(void *style, const int eflag, const int vflag,
}
break;
case THR_KSPACE|THR_PROXY: // fallthrough
case THR_KSPACE:
// nothing to do
// nothing to do. XXX need to add support for per-atom info
break;
default:

11
src/USER-OMP/thr_omp.h
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@ -58,7 +58,8 @@ class ThrOMP {
enum {THR_NONE=0,THR_PAIR=1,THR_BOND=1<<1,THR_ANGLE=1<<2,
THR_DIHEDRAL=1<<3,THR_IMPROPER=1<<4,THR_KSPACE=1<<5,
THR_CHARMM=1<<6,THR_PROXY=1<<7,THR_HYBRID=1<<8,THR_FIX=1<<9};
THR_CHARMM=1<<6, /*THR_PROXY=1<<7,*/ THR_HYBRID=1<<8,
THR_FIX=1<<9};
protected:
// extra ev_tally setup work for threaded styles
@ -71,7 +72,7 @@ class ThrOMP {
// reduce per thread data as needed
void reduce_thr(void * const style, const int eflag, const int vflag,
ThrData * const thr, const int nproxy=0);
ThrData * const thr);
// thread safe variant error abort support.
// signals an error condition in any thread by making
@ -167,14 +168,14 @@ class ThrOMP {
// set loop range thread id, and force array offset for threaded runs.
static inline void loop_setup_thr(int &ifrom, int &ito, int &tid,
int inum, int nthreads, int nproxy=0)
int inum, int nthreads)
{
#if defined(_OPENMP)
tid = omp_get_thread_num();
// each thread works on a fixed chunk of atoms.
const int idelta = 1 + inum/(nthreads-nproxy);
ifrom = (tid-nproxy)*idelta;
const int idelta = 1 + inum/nthreads;
ifrom = tid*idelta;
ito = ((ifrom + idelta) > inum) ? inum : ifrom + idelta;
#else
tid = 0;