From 5e63860cc2f61d86e1b2ccd443a67bf75614d755 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Fri, 2 Feb 2018 14:27:58 -0500
Subject: [PATCH] sPuReMD: more memory management changes.
---
sPuReMD/src/init_md.c | 114 ++++++++++++++++++++++++++++--------------
sPuReMD/src/lin_alg.c | 7 +--
sPuReMD/src/lookup.c | 18 ++++---
sPuReMD/src/restart.c | 44 +++++++++++-----
4 files changed, 122 insertions(+), 61 deletions(-)
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 96243efe..3e814309 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -345,22 +345,33 @@ void Init_Workspace( reax_system *system, control_params *control,
if ( control->cm_solver_pre_comp_type == ICHOLT_PC ||
control->cm_solver_pre_comp_type == ILUT_PAR_PC )
{
- workspace->droptol = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->droptol = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->droptol" );
}
//TODO: check if unused
- //workspace->w = (real *) calloc( cm_lin_sys_size, sizeof( real ) );
+ //workspace->w = (real *) scalloc( cm_lin_sys_size, sizeof( real ),
+ //"Init_Workspace::workspace->droptol" );
//TODO: check if unused
- workspace->b = (real *) calloc( system->N_cm * 2, sizeof( real ) );
- workspace->b_s = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->b_t = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->b_prc = (real *) calloc( system->N_cm * 2, sizeof( real ) );
- workspace->b_prm = (real *) calloc( system->N_cm * 2, sizeof( real ) );
- workspace->s = (real**) calloc( 5, sizeof( real* ) );
- workspace->t = (real**) calloc( 5, sizeof( real* ) );
+ workspace->b = (real *) scalloc( system->N_cm * 2, sizeof( real ),
+ "Init_Workspace::workspace->b" );
+ workspace->b_s = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->b_s" );
+ workspace->b_t = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->b_t" );
+ workspace->b_prc = (real *) scalloc( system->N_cm * 2, sizeof( real ),
+ "Init_Workspace::workspace->b_prc" );
+ workspace->b_prm = (real *) scalloc( system->N_cm * 2, sizeof( real ),
+ "Init_Workspace::workspace->b_prm" );
+ workspace->s = (real**) scalloc( 5, sizeof( real* ),
+ "Init_Workspace::workspace->s" );
+ workspace->t = (real**) scalloc( 5, sizeof( real* ),
+ "Init_Workspace::workspace->t" );
for ( i = 0; i < 5; ++i )
{
- workspace->s[i] = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->t[i] = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->s[i] = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->s[i]" );
+ workspace->t[i] = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->t[i]" );
}
switch ( control->charge_method )
@@ -422,40 +433,62 @@ void Init_Workspace( reax_system *system, control_params *control,
/* GMRES storage */
case GMRES_S:
case GMRES_H_S:
- workspace->y = (real *) calloc( control->cm_solver_restart + 1, sizeof( real ) );
- workspace->z = (real *) calloc( control->cm_solver_restart + 1, sizeof( real ) );
- workspace->g = (real *) calloc( control->cm_solver_restart + 1, sizeof( real ) );
- workspace->h = (real **) calloc( control->cm_solver_restart + 1, sizeof( real*) );
- workspace->hs = (real *) calloc( control->cm_solver_restart + 1, sizeof( real ) );
- workspace->hc = (real *) calloc( control->cm_solver_restart + 1, sizeof( real ) );
- workspace->rn = (real **) calloc( control->cm_solver_restart + 1, sizeof( real*) );
- workspace->v = (real **) calloc( control->cm_solver_restart + 1, sizeof( real*) );
+ workspace->y = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
+ "Init_Workspace::workspace->y" );
+ workspace->z = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
+ "Init_Workspace::workspace->z" );
+ workspace->g = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
+ "Init_Workspace::workspace->g" );
+ workspace->h = (real **) scalloc( control->cm_solver_restart + 1, sizeof( real*),
+ "Init_Workspace::workspace->h" );
+ workspace->hs = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
+ "Init_Workspace::workspace->hs" );
+ workspace->hc = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
+ "Init_Workspace::workspace->hc" );
+ workspace->rn = (real **) scalloc( control->cm_solver_restart + 1, sizeof( real*),
+ "Init_Workspace::workspace->rn" );
+ workspace->v = (real **) scalloc( control->cm_solver_restart + 1, sizeof( real*),
+ "Init_Workspace::workspace->v" );
for ( i = 0; i < control->cm_solver_restart + 1; ++i )
{
- workspace->h[i] = (real *) calloc( control->cm_solver_restart + 1, sizeof( real ) );
- workspace->rn[i] = (real *) calloc( system->N_cm * 2, sizeof( real ) );
- workspace->v[i] = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->h[i] = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
+ "Init_Workspace::workspace->h[i]" );
+ workspace->rn[i] = (real *) scalloc( system->N_cm * 2, sizeof( real ),
+ "Init_Workspace::workspace->rn[i]" );
+ workspace->v[i] = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->v[i]" );
}
- workspace->r = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->d = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->q = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->p = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->r = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->r" );
+ workspace->d = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->d" );
+ workspace->q = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->q" );
+ workspace->p = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->p" );
break;
/* CG storage */
case CG_S:
- workspace->r = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->d = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->q = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->p = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->r = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->r" );
+ workspace->d = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->d" );
+ workspace->q = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->q" );
+ workspace->p = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->p" );
break;
case SDM_S:
- workspace->r = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->d = (real *) calloc( system->N_cm, sizeof( real ) );
- workspace->q = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->r = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->r" );
+ workspace->d = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->d" );
+ workspace->q = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->q" );
break;
default:
@@ -480,8 +513,10 @@ void Init_Workspace( reax_system *system, control_params *control,
/* storage for analysis */
if ( control->molec_anal || control->diffusion_coef )
{
- workspace->mark = (int *) calloc( system->N, sizeof(int) );
- workspace->old_mark = (int *) calloc( system->N, sizeof(int) );
+ workspace->mark = (int *) scalloc( system->N, sizeof(int),
+ "Init_Workspace::workspace->mark" );
+ workspace->old_mark = (int *) scalloc( system->N, sizeof(int),
+ "Init_Workspace::workspace->old_mark" );
}
else
{
@@ -490,7 +525,8 @@ void Init_Workspace( reax_system *system, control_params *control,
if ( control->diffusion_coef )
{
- workspace->x_old = (rvec *) calloc( system->N, sizeof( rvec ) );
+ workspace->x_old = (rvec *) scalloc( system->N, sizeof( rvec ),
+ "Init_Workspace::workspace->x_old" );
}
else
{
@@ -563,8 +599,10 @@ void Init_Lists( reax_system *system, control_params *control,
Generate_Neighbor_Lists(system, control, data, workspace, lists, out_control);
Htop = 0;
- hb_top = (int*) calloc( system->N, sizeof(int) );
- bond_top = (int*) calloc( system->N, sizeof(int) );
+ hb_top = (int*) scalloc( system->N, sizeof(int),
+ "Init_Lists::hb_top" );
+ bond_top = (int*) scalloc( system->N, sizeof(int),
+ "Init_Lists::bond_top" );
num_3body = 0;
Estimate_Storage_Sizes( system, control, lists, &Htop,
hb_top, bond_top, &num_3body );
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 01cb1798..32ec6741 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -1894,11 +1894,8 @@ void Transpose( const sparse_matrix * const A, sparse_matrix * const A_t )
{
unsigned int i, j, pj, *A_t_top;
- if ( (A_t_top = (unsigned int*) calloc( A->n + 1, sizeof(unsigned int))) == NULL )
- {
- fprintf( stderr, "Not enough space for matrix tranpose. Terminating...\n" );
- exit( INSUFFICIENT_MEMORY );
- }
+ A_t_top = (unsigned int*) scalloc( A->n + 1, sizeof(unsigned int),
+ "Transpose::A_t_top" );
memset( A_t->start, 0, (A->n + 1) * sizeof(unsigned int) );
diff --git a/sPuReMD/src/lookup.c b/sPuReMD/src/lookup.c
index 7990169c..7ec372f4 100644
--- a/sPuReMD/src/lookup.c
+++ b/sPuReMD/src/lookup.c
@@ -271,12 +271,18 @@ void Make_LR_Lookup_Table( reax_system *system, control_params *control )
num_atom_types = system->reaxprm.num_atom_types;
dr = control->r_cut / control->tabulate;
- h = (real*) calloc( (control->tabulate + 1), sizeof(real) );
- fh = (real*) calloc( (control->tabulate + 1), sizeof(real) );
- fvdw = (real*) calloc( (control->tabulate + 1), sizeof(real) );
- fCEvd = (real*) calloc( (control->tabulate + 1), sizeof(real) );
- fele = (real*) calloc( (control->tabulate + 1), sizeof(real) );
- fCEclmb = (real*) calloc( (control->tabulate + 1), sizeof(real) );
+ h = (real*) scalloc( (control->tabulate + 1), sizeof(real),
+ "Make_LR_Lookup_Table::h" );
+ fh = (real*) scalloc( (control->tabulate + 1), sizeof(real),
+ "Make_LR_Lookup_Table::fh" );
+ fvdw = (real*) scalloc( (control->tabulate + 1), sizeof(real),
+ "Make_LR_Lookup_Table::fvdw" );
+ fCEvd = (real*) scalloc( (control->tabulate + 1), sizeof(real),
+ "Make_LR_Lookup_Table::fCEvd" );
+ fele = (real*) scalloc( (control->tabulate + 1), sizeof(real),
+ "Make_LR_Lookup_Table::fele" );
+ fCEclmb = (real*) scalloc( (control->tabulate + 1), sizeof(real),
+ "Make_LR_Lookup_Table::fCEclmb" );
/* allocate Long-Range LookUp Table space based on
number of atom types in the ffield file */
diff --git a/sPuReMD/src/restart.c b/sPuReMD/src/restart.c
index 0f7b1c5b..82474a8b 100644
--- a/sPuReMD/src/restart.c
+++ b/sPuReMD/src/restart.c
@@ -20,7 +20,9 @@
----------------------------------------------------------------------*/
#include "restart.h"
+
#include "box.h"
+#include "tool_box.h"
#include "vector.h"
@@ -101,17 +103,25 @@ void Read_Binary_Restart( char *fname, reax_system *system,
#endif
/* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+ system->atoms = (reax_atom*) scalloc( system->N, sizeof(reax_atom),
+ "Read_Binary_Restart::system->atoms" );
- workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
+ workspace->map_serials = (int*) scalloc( MAX_ATOM_ID, sizeof(int),
+ "Read_Binary_Restart::workspace->map_serials" );
for ( i = 0; i < MAX_ATOM_ID; ++i )
workspace->map_serials[i] = -1;
- workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
+ workspace->orig_id = (int*) scalloc( system->N, sizeof(int),
+ "Read_Binary_Restart::workspace->orig_id" );
+ workspace->restricted = (int*) scalloc( system->N, sizeof(int),
+ "Read_Binary_Restart::workspace->restricted" );
+ workspace->restricted_list = (int**) scalloc( system->N, sizeof(int*),
+ "Read_Binary_Restart::workspace->restricted_list" );
for ( i = 0; i < system->N; ++i )
- workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
+ {
+ workspace->restricted_list[i] = (int*) scalloc( MAX_RESTRICT, sizeof(int),
+ "Read_Binary_Restart::workspace->restricted_list[i]" );
+ }
for ( i = 0; i < system->N; ++i )
{
@@ -207,17 +217,27 @@ void Read_ASCII_Restart( char *fname, reax_system *system,
#endif
/* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+ system->atoms = (reax_atom*) scalloc( system->N, sizeof(reax_atom),
+ "Read_ASCII_Restart::system->atoms" );
- workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
+ workspace->map_serials = (int*) scalloc( MAX_ATOM_ID, sizeof(int),
+ "Read_ASCII_Restart::workspace->map_serials" );
for ( i = 0; i < MAX_ATOM_ID; ++i )
+ {
workspace->map_serials[i] = -1;
+ }
- workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
+ workspace->orig_id = (int*) scalloc( system->N, sizeof(int),
+ "Read_ASCII_Restart::workspace->orig_id" );
+ workspace->restricted = (int*) scalloc( system->N, sizeof(int),
+ "Read_ASCII_Restart::workspace->restricted" );
+ workspace->restricted_list = (int**) scalloc( system->N, sizeof(int*),
+ "Read_ASCII_Restart::workspace->restricted_list" );
for ( i = 0; i < system->N; ++i )
- workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
+ {
+ workspace->restricted_list[i] = (int*) scalloc( MAX_RESTRICT, sizeof(int),
+ "Read_ASCII_Restart::workspace->restricted_list[i]" );
+ }
for ( i = 0; i < system->N; ++i )
{
--
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