From 5b521b045bcc8cb9e4ddd984e8126b9719cb1ce2 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Wed, 7 Feb 2018 20:57:11 -0500
Subject: [PATCH] sPuReMD: fixes to remove compilatoin warnings. Replace
standard library functions with safer versions to avoid buffer overruns.
Safer use of placeholders in format strings for printing.
---
sPuReMD/src/analyze.c | 8 +++++++-
sPuReMD/src/ffield.c | 2 +-
sPuReMD/src/geo_tools.c | 6 +++---
sPuReMD/src/init_md.c | 4 ++--
sPuReMD/src/lin_alg.c | 6 ++++++
sPuReMD/src/print_utils.c | 22 +++++++++++-----------
sPuReMD/src/tool_box.c | 18 +++++++++++++-----
sPuReMD/src/tool_box.h | 2 +-
sPuReMD/src/traj.c | 8 ++++----
9 files changed, 48 insertions(+), 28 deletions(-)
diff --git a/sPuReMD/src/analyze.c b/sPuReMD/src/analyze.c
index 9fcd54f7..675e9007 100644
--- a/sPuReMD/src/analyze.c
+++ b/sPuReMD/src/analyze.c
@@ -21,6 +21,8 @@
#include "analyze.h"
+#include <ctype.h>
+
#include "box.h"
#include "list.h"
#include "tool_box.h"
@@ -580,8 +582,12 @@ void Analyze_Fragments( reax_system *system, control_params *control,
/* output the results of fragment analysis */
for ( i = 0; i < num_fragment_types; ++i )
- if ( strlen(fragments[i]) )
+ {
+ if ( strnlen(fragments[i], MAX_ATOM_TYPES) )
+ {
fprintf( fout, "%d of %s\n", fragment_count[i], fragments[i] );
+ }
+ }
fprintf( fout, "\n" );
fflush( fout );
diff --git a/sPuReMD/src/ffield.c b/sPuReMD/src/ffield.c
index 7aab5c52..1fb05c45 100644
--- a/sPuReMD/src/ffield.c
+++ b/sPuReMD/src/ffield.c
@@ -167,7 +167,7 @@ char Read_Force_Field( FILE* fp, reax_interaction* reax )
fgets( s, MAX_LINE, fp );
Tokenize( s, &tmp );
- for ( j = 0; j < strlen( tmp[0] ); ++j )
+ for ( j = 0; j < strnlen( tmp[0], MAX_TOKEN_LEN ); ++j )
reax->sbp[i].name[j] = toupper( tmp[0][j] );
val = atof(tmp[1]);
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 740a9648..549d29ff 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -365,7 +365,7 @@ char Read_PDB( const char * const pdb_file, reax_system* system, control_params
pdb_serial = (int) strtod( &serial[0], &endptr );
workspace->orig_id[top] = pdb_serial;
- Trim_Spaces( element );
+ Trim_Spaces( element, 9 );
atom->type = Get_Atom_Type( &(system->reaxprm), element );
strcpy( atom->name, atom_name );
@@ -492,7 +492,7 @@ char Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
{
p_atom = &(system->atoms[i]);
strncpy(name, p_atom->name, 8);
- Trim_Spaces(name);
+ Trim_Spaces( name, 8 );
snprintf( line, MAX_STR, PDB_ATOM_FORMAT_O,
"ATOM ", workspace->orig_id[i], p_atom->name, ' ', "REX", ' ', 1, ' ',
p_atom->x[0], p_atom->x[1], p_atom->x[2],
@@ -711,7 +711,7 @@ char Read_BGF( const char * const bgf_file, reax_system* system, control_params
/* atom name and type */
strcpy( system->atoms[atom_cnt].name, atom_name );
- Trim_Spaces( element );
+ Trim_Spaces( element, 10 );
system->atoms[atom_cnt].type =
Get_Atom_Type( &(system->reaxprm), element );
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 93fed761..c071a46f 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -773,11 +773,11 @@ void Init_Out_Controls( reax_system *system, control_params *control,
/* Init molecular analysis file */
if ( control->molec_anal )
{
- snprintf( temp, TEMP_SIZE + 4, "%s.mol", control->sim_name );
+ snprintf( temp, TEMP_SIZE, "%.*s.mol", TEMP_SIZE - 5, control->sim_name );
out_control->mol = fopen( temp, "w" );
if ( control->num_ignored )
{
- snprintf( temp, TEMP_SIZE + 4, "%s.ign", control->sim_name );
+ snprintf( temp, TEMP_SIZE, "%.*s.ign", TEMP_SIZE - 5, control->sim_name );
out_control->ign = fopen( temp, "w" );
}
}
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 110c43a3..5c5b7f47 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -3294,6 +3294,12 @@ int GMRES_HouseHolder( const static_storage * const workspace,
reduction(+: t_ortho, t_pa, t_spmv, t_ts, t_vops)
#endif
{
+ t_ortho = 0.0;
+ t_pa = 0.0;
+ t_spmv = 0.0;
+ t_ts = 0.0;
+ t_vops = 0.0;
+
t_start = Get_Time( );
bnorm = Norm( b, N );
t_vops += Get_Timing_Info( t_start );
diff --git a/sPuReMD/src/print_utils.c b/sPuReMD/src/print_utils.c
index 383fdb89..d37fe5ea 100644
--- a/sPuReMD/src/print_utils.c
+++ b/sPuReMD/src/print_utils.c
@@ -406,7 +406,7 @@ void Print_Near_Neighbors( reax_system *system, control_params *control,
FILE *fout;
reax_list *near_nbrs = &((*lists)[NEAR_NBRS]);
- snprintf( fname, MAX_STR, "%s.near_nbrs", control->sim_name );
+ snprintf( fname, MAX_STR, "%.*s.near_nbrs", MAX_STR - 11, control->sim_name );
fout = fopen( fname, "w" );
for ( i = 0; i < system->N; ++i )
@@ -440,7 +440,7 @@ void Print_Near_Neighbors2( reax_system *system, control_params *control,
FILE *fout;
reax_list *near_nbrs = &((*lists)[NEAR_NBRS]);
- snprintf( fname, MAX_STR, "%s.near_nbrs_lgj", control->sim_name );
+ snprintf( fname, MAX_STR, "%.*s.near_nbrs_lgj", MAX_STR - 15, control->sim_name );
fout = fopen( fname, "w" );
for ( i = 0; i < system->N; ++i )
@@ -475,7 +475,7 @@ void Print_Far_Neighbors( reax_system *system, control_params *control,
FILE *fout;
reax_list *far_nbrs = &((*lists)[FAR_NBRS]);
- snprintf( fname, MAX_STR, "%s.far_nbrs", control->sim_name );
+ snprintf( fname, MAX_STR, "%.*s.far_nbrs", MAX_STR - 10, control->sim_name );
fout = fopen( fname, "w" );
for ( i = 0; i < system->N; ++i )
@@ -520,7 +520,7 @@ void Print_Far_Neighbors2( reax_system *system, control_params *control,
FILE *fout;
reax_list *far_nbrs = &((*lists)[FAR_NBRS]);
- snprintf( fname, MAX_STR, "%s.far_nbrs_lgj", control->sim_name );
+ snprintf( fname, MAX_STR, "%.*s.far_nbrs_lgj", MAX_STR - 14, control->sim_name );
fout = fopen( fname, "w" );
int num = 0;
int temp[500];
@@ -553,7 +553,7 @@ void Print_Total_Force( reax_system *system, control_params *control,
int i;
#if !defined(TEST_FORCES)
char temp[1000];
- snprintf( temp, 1000, "%s.ftot", control->sim_name );
+ snprintf( temp, 1000, "%.*s.ftot", 994, control->sim_name );
out_control->ftot = fopen( temp, "w" );
#endif
@@ -735,7 +735,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
sparse_matrix *H;
FILE *out;
- snprintf( fname, 100, "%s.state%d.out", control->sim_name, step );
+ snprintf( fname, 100, "%.*s.state%10d.out", 79, control->sim_name, step );
out = fopen( fname, "w" );
for ( i = 0; i < system->N_cm; i++ )
@@ -753,7 +753,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
// fprintf( out, "%g\n", workspace->s_t[i+system->N] );
// fclose( out );
- snprintf( fname, 100, "%s.H%d.out", control->sim_name, step );
+ snprintf( fname, 100, "%.*s.H%10d.out", 83, control->sim_name, step );
out = fopen( fname, "w" );
H = workspace->H;
@@ -776,7 +776,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
fclose( out );
- snprintf( fname, 100, "%s.H_sp%d.out", control->sim_name, step );
+ snprintf( fname, 100, "%.*s.H_sp%10d.out", 80, control->sim_name, step );
out = fopen( fname, "w" );
H = workspace->H_sp;
@@ -799,13 +799,13 @@ void Print_Linear_System( reax_system *system, control_params *control,
fclose( out );
- /*snprintf( fname, 100, "%s.b_s%d", control->sim_name, step );
+ /*snprintf( fname, 100, "%.*s.b_s%10d", 84, control->sim_name, step );
out = fopen( fname, "w" );
for( i = 0; i < system->N; i++ )
fprintf( out, "%12.7f\n", workspace->b_s[i] );
fclose( out );
- snprintf( fname, 100, "%s.b_t%d", control->sim_name, step );
+ snprintf( fname, 100, "%.*s.b_t%10d", 84, control->sim_name, step );
out = fopen( fname, "w" );
for( i = 0; i < system->N; i++ )
fprintf( out, "%12.7f\n", workspace->b_t[i] );
@@ -820,7 +820,7 @@ void Print_Charges( reax_system *system, control_params *control,
char fname[100];
FILE *fout;
- snprintf( fname, 100, "%s.q%d", control->sim_name, step );
+ snprintf( fname, 100, "%.*s.q%10d", 87, control->sim_name, step );
fout = fopen( fname, "w" );
for ( i = 0; i < system->N; ++i )
diff --git a/sPuReMD/src/tool_box.c b/sPuReMD/src/tool_box.c
index 3853c270..c0a61f51 100644
--- a/sPuReMD/src/tool_box.c
+++ b/sPuReMD/src/tool_box.c
@@ -19,7 +19,6 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "mytypes.h"
#include "tool_box.h"
#include <ctype.h>
@@ -273,13 +272,22 @@ int Check_Input_Range( int val, int lo, int hi, char *message )
}
-void Trim_Spaces( char *element )
+void Trim_Spaces( char * const element, const size_t size )
{
- int i, j;
+ int i, j, n;
+
+ n = strnlen( element, size );
+
+ /* buffer not NULL-terminated, abort */
+ if ( n == size )
+ {
+ return;
+ }
- for ( i = 0; element[i] == ' '; ++i ); // skip initial space chars
+ for ( i = 0; element[i] == ' '; ++i )
+ ; // skip initial space chars
- for ( j = i; j < (int)(strlen(element)) && element[j] != ' '; ++j )
+ for ( j = i; j < n && element[j] != ' '; ++j )
{
element[j - i] = toupper( element[j] ); // make uppercase, offset to 0
}
diff --git a/sPuReMD/src/tool_box.h b/sPuReMD/src/tool_box.h
index d1b15f64..29781e00 100644
--- a/sPuReMD/src/tool_box.h
+++ b/sPuReMD/src/tool_box.h
@@ -56,7 +56,7 @@ int is_Valid_Serial( static_storage*, int );
int Check_Input_Range( int, int, int, char* );
-void Trim_Spaces( char* );
+void Trim_Spaces( char * const, const size_t );
/* from system_props.h */
real Get_Time( );
diff --git a/sPuReMD/src/traj.c b/sPuReMD/src/traj.c
index 14e2a36b..7972d086 100644
--- a/sPuReMD/src/traj.c
+++ b/sPuReMD/src/traj.c
@@ -79,7 +79,7 @@ int Write_Custom_Header( reax_system *system, control_params *control,
control->molec_anal,
control->freq_molec_anal );
- control_block_len = strlen( control_block );
+ control_block_len = strnlen( control_block, SIZE1 );
snprintf( frame_format, SIZE1, "Frame Format: %d\n%s\n%s\n",
@@ -123,7 +123,7 @@ int Write_Custom_Header( reax_system *system, control_params *control,
}
strcat( frame_format, angle_format );
- frame_format_len = strlen( frame_format );
+ frame_format_len = strnlen( frame_format, SIZE1 );
header_len = HEADER_INIT_LEN + (control_block_len + SIZE_INFO_LEN2) +
@@ -309,7 +309,7 @@ int Append_Custom_Frame( reax_system *system, control_params *control,
data->E_Ang, data->E_Pen, data->E_Coa, data->E_HB,
data->E_Tor, data->E_Con,
data->E_vdW, data->E_Ele, data->E_Pol );
- frame_globals_len = strlen( buffer );
+ frame_globals_len = strnlen( buffer, SIZE );
frame_len = frame_globals_len +
write_atoms * SIZE_INFO_LEN3 + system->N * atom_line_len +
@@ -507,7 +507,7 @@ void Read_Traj( output_controls *out_control, char *traj_name )
fprintf( stderr, "read line\n" );
- if ( strlen( size_buffer ) >= SIZE_INFO_LEN3 )
+ if ( strnlen( size_buffer, 50 ) >= SIZE_INFO_LEN3 )
{
sscanf( size_buffer, "%d %d %d", &skip_all, &skip_part, &n );
}
--
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