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Revert "reorganize memory (de-)allocation and fix substantial memory leak in MSM"

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This reverts commit f78671c1a4.
This commit is contained in:
Axel Kohlmeyer
2020-06-22 19:15:28 -04:00
parent 3fffe20463
commit afe6484c44
1 changed files with 100 additions and 95 deletions
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195
src/KSPACE/msm.cpp
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@ -28,8 +28,6 @@
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "math_const.h"
@ -65,6 +63,9 @@ MSM::MSM(LAMMPS *lmp) : KSpace(lmp),
factors[0] = 2;
MPI_Comm_rank(world,&me);
procneigh_levels = NULL;
world_levels = NULL;
active_flag = NULL;
phi1d = dphi1d = NULL;
@ -80,7 +81,15 @@ MSM::MSM(LAMMPS *lmp) : KSpace(lmp),
v0_direct_top = v1_direct_top = v2_direct_top = NULL;
v3_direct_top = v4_direct_top = v5_direct_top = NULL;
cg_all = cg_peratom_all = NULL;
cg = cg_peratom = NULL;
ngrid = NULL;
cg = NULL;
cg_peratom = NULL;
procneigh_levels = NULL;
world_levels = NULL;
active_flag = NULL;
alpha = betax = betay = betaz = NULL;
nx_msm = ny_msm = nz_msm = NULL;
@ -141,7 +150,10 @@ MSM::~MSM()
void MSM::init()
{
if (me == 0) utils::logmesg(lmp,"MSM initialization ...\n");
if (me == 0) {
if (screen) fprintf(screen,"MSM initialization ...\n");
if (logfile) fprintf(logfile,"MSM initialization ...\n");
}
// error check
@ -157,8 +169,13 @@ void MSM::init()
if ((slabflag == 1) && (me == 0))
error->warning(FLERR,"Slab correction not needed for MSM");
if ((order < 4) || (order > 10) || (order%2 != 0))
error->all(FLERR,"MSM order must be 4, 6, 8, or 10");
if (order < 4 || order > 10) {
char str[128];
sprintf(str,"MSM order must be 4, 6, 8, or 10");
error->all(FLERR,str);
}
if (order%2 != 0) error->all(FLERR,"MSM order must be 4, 6, 8, or 10");
if (sizeof(FFT_SCALAR) != 8)
error->all(FLERR,"Cannot (yet) use single precision with MSM "
@ -204,14 +221,33 @@ void MSM::init()
MPI_Allreduce(&ngrid[0],&ngrid_max,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
std::string mesg = fmt::format(" 3d grid size/proc = {}\n", ngrid_max);
mesg += fmt::format(" estimated absolute RMS force accuracy = {}\n",
estimated_error);
mesg += fmt::format(" estimated relative force accuracy = {}\n",
estimated_error/two_charge_force);
mesg += fmt::format(" grid = {} {} {}\n",nx_msm[0],ny_msm[0],nz_msm[0]);
mesg += fmt::format(" order = {}\n",order);
utils::logmesg(lmp,mesg);
if (screen) {
fprintf(screen," 3d grid size/proc = %d\n",
ngrid_max);
fprintf(screen," estimated absolute RMS force accuracy = %g\n",
estimated_error);
fprintf(screen," estimated relative force accuracy = %g\n",
estimated_error/two_charge_force);
}
if (logfile) {
fprintf(logfile," 3d grid size/proc = %d\n",
ngrid_max);
fprintf(logfile," estimated absolute RMS force accuracy = %g\n",
estimated_error);
fprintf(logfile," estimated relative force accuracy = %g\n",
estimated_error/two_charge_force);
}
}
if (me == 0) {
if (screen) {
fprintf(screen," grid = %d %d %d\n",nx_msm[0],ny_msm[0],nz_msm[0]);
fprintf(screen," order = %d\n",order);
}
if (logfile) {
fprintf(logfile," grid = %d %d %d\n",nx_msm[0],ny_msm[0],nz_msm[0]);
fprintf(logfile," order = %d\n",order);
}
}
}
@ -362,6 +398,7 @@ void MSM::setup()
nmax_direct = 8*(nxhi_direct+1)*(nyhi_direct+1)*(nzhi_direct+1);
deallocate();
if (peratom_allocate_flag) deallocate_peratom();
// compute direct sum interaction weights
@ -612,8 +649,6 @@ void MSM::compute(int eflag, int vflag)
void MSM::allocate()
{
deallocate();
// interpolation coeffs
order_allocated = order;
@ -635,9 +670,9 @@ void MSM::allocate()
// allocate memory for each grid level
for (int n=0; n<levels; n++) {
memory->create3d_offset(qgrid[n],nzlo_out[n],nzhi_out[n],
nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:qgrid");
memory->create3d_offset(egrid[n],nzlo_out[n],nzhi_out[n],
nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:egrid");
@ -660,23 +695,24 @@ void MSM::allocate()
void MSM::deallocate()
{
delete cg_all;
cg_all = nullptr;
memory->destroy2d_offset(phi1d,-order_allocated);
memory->destroy2d_offset(dphi1d,-order_allocated);
if (cg_all) delete cg_all;
for (int n=0; n<levels; n++) {
memory->destroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
memory->destroy3d_offset(egrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
if (qgrid[n])
memory->destroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
if (world_levels[n] != MPI_COMM_NULL)
MPI_Comm_free(&world_levels[n]);
world_levels[n] = MPI_COMM_NULL;
active_flag[n] = 0;
if (egrid[n])
memory->destroy3d_offset(egrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
delete cg[n];
cg[n] = nullptr;
if (world_levels)
if (world_levels[n] != MPI_COMM_NULL)
MPI_Comm_free(&world_levels[n]);
if (cg)
if (cg[n]) delete cg[n];
}
}
@ -765,7 +801,6 @@ void MSM::deallocate_peratom()
void MSM::allocate_levels()
{
deallocate_levels();
ngrid = new int[levels];
cg = new GridComm*[levels];
@ -815,21 +850,21 @@ void MSM::allocate_levels()
v5grid = new double***[levels];
for (int n=0; n<levels; n++) {
cg[n] = nullptr;
cg[n] = NULL;
world_levels[n] = MPI_COMM_NULL;
active_flag[n] = 0;
cg_peratom[n] = nullptr;
cg_peratom[n] = NULL;
qgrid[n] = nullptr;
egrid[n] = nullptr;
qgrid[n] = NULL;
egrid[n] = NULL;
v0grid[n] = nullptr;
v1grid[n] = nullptr;
v2grid[n] = nullptr;
v3grid[n] = nullptr;
v4grid[n] = nullptr;
v5grid[n] = nullptr;
v0grid[n] = NULL;
v1grid[n] = NULL;
v2grid[n] = NULL;
v3grid[n] = NULL;
v4grid[n] = NULL;
v5grid[n] = NULL;
}
}
/* ----------------------------------------------------------------------
@ -838,9 +873,7 @@ void MSM::allocate_levels()
void MSM::deallocate_levels()
{
if (cg) deallocate();
delete [] ngrid;
ngrid = nullptr;
memory->destroy(procneigh_levels);
delete [] world_levels;
@ -886,50 +919,6 @@ void MSM::deallocate_levels()
delete [] v3grid;
delete [] v4grid;
delete [] v5grid;
world_levels = nullptr;
active_flag = nullptr;
cg = nullptr;
cg_peratom = nullptr;
alpha = nullptr;
betax = nullptr;
betay = nullptr;
betaz = nullptr;
nx_msm = nullptr;
ny_msm = nullptr;
nz_msm = nullptr;
nxlo_in = nullptr;
nylo_in = nullptr;
nzlo_in = nullptr;
nxhi_in = nullptr;
nyhi_in = nullptr;
nzhi_in = nullptr;
nxlo_out = nullptr;
nylo_out = nullptr;
nzlo_out = nullptr;
nxhi_out = nullptr;
nyhi_out = nullptr;
nzhi_out = nullptr;
delxinv = nullptr;
delyinv = nullptr;
delzinv = nullptr;
qgrid = nullptr;
egrid = nullptr;
v0grid = nullptr;
v1grid = nullptr;
v2grid = nullptr;
v3grid = nullptr;
v4grid = nullptr;
v5grid = nullptr;
}
/* ----------------------------------------------------------------------
@ -1064,9 +1053,9 @@ void MSM::set_grid_global()
double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp);
*p_cutoff = cutoff;
if (me == 0)
error->warning(FLERR,fmt::format("Adjusting Coulombic cutoff for "
"MSM, new cutoff = {}", cutoff));
char str[128];
sprintf(str,"Adjusting Coulombic cutoff for MSM, new cutoff = %g",cutoff);
if (me == 0) error->warning(FLERR,str);
}
if (triclinic == 0) {
@ -1105,6 +1094,7 @@ void MSM::set_grid_global()
if (!domain->nonperiodic) levels -= 1;
deallocate_levels();
allocate_levels();
// find number of grid levels in each direction
@ -1328,8 +1318,8 @@ void MSM::set_grid_local()
void MSM::set_proc_grid(int n)
{
for (int i=0; i<3; i++)
myloc[i] = comm->myloc[i];
for (int i=0; i<3; i++)
myloc[i] = comm->myloc[i];
// size of inner MSM grid owned by this proc
@ -1372,7 +1362,6 @@ void MSM::set_proc_grid(int n)
// define a new MPI communicator for this grid level that only includes active procs
if(world_levels[n] != MPI_COMM_NULL) MPI_Comm_free(&world_levels[n]);
MPI_Comm_split(world,color,me,&world_levels[n]);
if (!active_flag[n]) return;
@ -1490,13 +1479,16 @@ void MSM::particle_map()
void MSM::make_rho()
{
//fprintf(screen,"MSM aninterpolation\n\n");
int i,l,m,n,nx,ny,nz,mx,my,mz;
double dx,dy,dz,x0,y0,z0;
// clear 3d density array
double ***qgrid0 = qgrid[0];
memset(&(qgrid0[nzlo_out[0]][nylo_out[0]][nxlo_out[0]]),0,ngrid[0]*sizeof(double));
double ***qgridn = qgrid[0];
memset(&(qgridn[nzlo_out[0]][nylo_out[0]][nxlo_out[0]]),0,ngrid[0]*sizeof(double));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@ -1527,7 +1519,7 @@ void MSM::make_rho()
x0 = y0*phi1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
qgrid0[mz][my][mx] += x0*phi1d[0][l];
qgridn[mz][my][mx] += x0*phi1d[0][l];
}
}
}
@ -1542,6 +1534,8 @@ void MSM::make_rho()
void MSM::direct(int n)
{
//fprintf(screen,"Direct contribution on level %i\n\n",n);
double ***qgridn = qgrid[n];
double ***egridn = egrid[n];
double ***v0gridn = v0grid[n];
@ -1774,6 +1768,8 @@ void MSM::direct(int n)
void MSM::direct_peratom(int n)
{
//fprintf(screen,"Direct contribution on level %i\n\n",n);
double ***qgridn = qgrid[n];
double ***v0gridn = v0grid[n];
double ***v1gridn = v1grid[n];
@ -1896,6 +1892,8 @@ void MSM::direct_peratom(int n)
void MSM::direct_top(int n)
{
//fprintf(screen,"Direct contribution on level %i\n\n",n);
double ***qgridn = qgrid[n];
double ***egridn = egrid[n];
double ***v0gridn = v0grid[n];
@ -2259,6 +2257,8 @@ void MSM::direct_peratom_top(int n)
void MSM::restriction(int n)
{
//fprintf(screen,"Restricting from level %i to %i\n\n",n,n+1);
const int p = order-1;
double ***qgrid1 = qgrid[n];
@ -2281,7 +2281,8 @@ void MSM::restriction(int n)
// zero out charge on coarser grid
memset(&(qgrid2[nzlo_out[n+1]][nylo_out[n+1]][nxlo_out[n+1]]),0,ngrid[n+1]*sizeof(double));
memset(&(qgrid2[nzlo_out[n+1]][nylo_out[n+1]][nxlo_out[n+1]]),0,
ngrid[n+1]*sizeof(double));
for (kp = nzlo_in[n+1]; kp <= nzhi_in[n+1]; kp++)
for (jp = nylo_in[n+1]; jp <= nyhi_in[n+1]; jp++)
@ -2330,6 +2331,8 @@ void MSM::restriction(int n)
void MSM::prolongation(int n)
{
//fprintf(screen,"Prolongating from level %i to %i\n\n",n+1,n);
const int p = order-1;
double ***egrid1 = egrid[n];
@ -2718,6 +2721,8 @@ void MSM::unpack_reverse(int flag, double *buf, int nlist, int *list)
void MSM::fieldforce()
{
//fprintf(screen,"MSM interpolation\n\n");
double ***egridn = egrid[0];
int i,l,m,n,nx,ny,nz,mx,my,mz;