moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of github.com:RRZE-HPC/MD-Bench

Browse Source
This commit is contained in:
JanLJL 2023-02-09 17:33:42 +01:00
commit 98583cdade
7 changed files with 3098 additions and 15 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1541
asm/unused/force_lj_lammps_avx512_dp_no_newton_raphson.s Normal file
View File

File diff suppressed because it is too large Load Diff

1466
asm/unused/force_lj_lammps_avx512_sp_no_newton_raphson.s Normal file
View File

File diff suppressed because it is too large Load Diff

35
gromacs/force_lj.c
View File

@ -35,9 +35,12 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp parallel for
#pragma omp for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
int ci_cj1 = CJ1_FROM_CI(ci);
@ -119,6 +122,8 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ end\n");
return E-S;
@ -149,9 +154,12 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp parallel for
#pragma omp for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
#if CLUSTER_M > CLUSTER_N
@ -266,6 +274,8 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ_2xnn end\n");
return E-S;
@ -296,9 +306,12 @@ double computeForceLJ_2xnn_full(Parameter *param, Atom *atom, Neighbor *neighbor
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp parallel for
#pragma omp for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
#if CLUSTER_M > CLUSTER_N
@ -398,6 +411,8 @@ double computeForceLJ_2xnn_full(Parameter *param, Atom *atom, Neighbor *neighbor
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ_2xnn end\n");
return E-S;
@ -435,9 +450,12 @@ double computeForceLJ_4xn_half(Parameter *param, Atom *atom, Neighbor *neighbor,
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp parallel for
#pragma omp for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
#if CLUSTER_M > CLUSTER_N
@ -591,6 +609,8 @@ double computeForceLJ_4xn_half(Parameter *param, Atom *atom, Neighbor *neighbor,
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ_4xn end\n");
return E-S;
@ -620,9 +640,12 @@ double computeForceLJ_4xn_full(Parameter *param, Atom *atom, Neighbor *neighbor,
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp parallel for
#pragma omp for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
#if CLUSTER_M > CLUSTER_N
@ -751,6 +774,8 @@ double computeForceLJ_4xn_full(Parameter *param, Atom *atom, Neighbor *neighbor,
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ_4xn end\n");
return E-S;

2
include_ICX.mk
View File

@ -11,7 +11,7 @@ endif
ifeq ($(ISA),AVX2)
OPTS = -Ofast -xCORE-AVX2 $(PROFILE)
#OPTS = -Ofast -xAVX2 $(PROFILE)
#OPTS = -Ofast -xHost $(PROFILE)
#OPTS = -Ofast -march=core-avx2 $(PROFILE)
endif

14
lammps/force_eam.c
View File

@ -31,8 +31,12 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot;
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force_eam_fp");
#pragma omp parallel for
#pragma omp for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
@ -95,13 +99,19 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
}
LIKWID_MARKER_STOP("force_eam_fp");
}
// We still need to update fp for PBC atoms
for(int i = 0; i < atom->Nghost; i++) {
fp[Nlocal + i] = fp[atom->border_map[i]];
}
#pragma omp parallel
{
LIKWID_MARKER_START("force_eam");
#pragma omp for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
@ -192,6 +202,8 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
}
LIKWID_MARKER_STOP("force_eam");
}
double E = getTimeStamp();
return E-S;
}

25
lammps/force_lj.c
View File

@ -36,9 +36,12 @@ double computeForceLJFullNeigh_plain_c(Parameter *param, Atom *atom, Neighbor *n
atom_fz(i) = 0.0;
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp parallel for
#pragma omp for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
@ -92,6 +95,8 @@ double computeForceLJFullNeigh_plain_c(Parameter *param, Atom *atom, Neighbor *n
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
return E-S;
}
@ -112,8 +117,12 @@ double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("forceLJ-halfneigh");
#pragma omp for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
@ -173,6 +182,8 @@ double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
}
LIKWID_MARKER_STOP("forceLJ-halfneigh");
}
double E = getTimeStamp();
return E-S;
}
@ -191,7 +202,6 @@ double computeForceLJFullNeigh_simd(Parameter *param, Atom *atom, Neighbor *neig
}
double S = getTimeStamp();
LIKWID_MARKER_START("force");
#ifndef __SIMD_KERNEL__
fprintf(stderr, "Error: SIMD kernel not implemented for specified instruction set!");
@ -203,7 +213,12 @@ double computeForceLJFullNeigh_simd(Parameter *param, Atom *atom, Neighbor *neig
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
#pragma omp parallel for
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
@ -244,9 +259,11 @@ double computeForceLJFullNeigh_simd(Parameter *param, Atom *atom, Neighbor *neig
atom_fy(i) += simd_h_reduce_sum(fiy);
atom_fz(i) += simd_h_reduce_sum(fiz);
}
#endif
LIKWID_MARKER_STOP("force");
}
#endif
double E = getTimeStamp();
return E-S;
}

30
util/evaluate_latency_and_cfd.sh
View File

@ -1,16 +1,36 @@
#!/bin/bash
# Adjustable variables
TAG="${TAG:-ICC}"
OPT_SCHEME="${OPT_SCHEME:-lammps}"
[[ -z "$1" ]] && echo "Use: $0 <binary> [-c <core>] [-f <freq>] [-n <nruns>] [-l <log>] [-s]" && exit
[[ ! -f "$1" ]] && echo "Binary file not found, make sure to use 'make'" && exit
[[ ! -f "$1-stub" ]] && echo "Binary file for stubbed case not found, make sure to use 'make VARIANT=stub'" && exit
MDBENCH_BIN=$1
BIN_INFO="${MDBENCH_BIN#*-}" # $OPT_SCHEME-$TAG-$ISA-$PREC
OPT_SCHEME="${BIN_INFO%%-*}"
PREC="${BIN_INFO##*-}"
BIN_INFO="${BIN_INFO#*-}" # $TAG-$ISA-$PREC
BIN_INFO="${BIN_INFO%-*}" # $TAG-$ISA
TAG="${BIN_INFO%%-*}"
ISA="${BIN_INFO##*-}"
CORE="${CORE:-0}"
FREQ="${FREQ:-2.4}"
NRUNS="${NRUNS:-3}"
LOG="${LOG:-latencies_and_cfds.log}"
STUB_ONLY="${STUB_ONLY:-false}"
OPTIND=2
while getopts "c:f:n:l:s" flag; do
case "${flag}" in
c) CORE=${OPTARG};;
f) FREQ=${OPTARG};;
n) NRUNS=${OPTARG};;
l) LOG=${OPTARG};;
s) STUB_ONLY=true;;
esac
done
# Other useful variables
MDBENCH_BIN=./MDBench-$TAG-$OPT_SCHEME
MDBENCH_BIN=./MDBench-$OPT_SCHEME-$TAG-$ISA-$PREC
FIXED_PARAMS="--freq $FREQ"
CPU_VENDOR=$(lscpu | grep "Vendor ID" | tr -s ' ' | cut -d ' ' -f3)
@ -46,6 +66,8 @@ function run_benchmark() {
echo "Tag: $TAG" | tee -a $LOG
echo "Optimization scheme: $OPT_SCHEME" | tee -a $LOG
echo "Instruction set: $ISA" | tee -a $LOG
echo "Precision: $PREC" | tee -a $LOG
echo "Binary: $MDBENCH_BIN(-stub)" | tee -a $LOG
echo "Frequency: $FREQ" | tee -a $LOG
echo "Number of runs: $NRUNS" | tee -a $LOG