Fixed TNG memory alignment problem and reset pointers.

This is a temporary fix to the memory alignment problems on some
platforms. In the main TNG repository the whole I/O system is
rewritten to address this problem. This fix is to avoid the
problems without making too large changes.

There are also some pointers that were not reset after memory
was freed. This is also fixed in here.

This commit does not correspond to any commit in the TNG
repository.

Fixes #1542, #1546, #1547 and #1559.

Change-Id: I90a6406cccbc43fd57d4423c2b661019cf7763e8

diff --git a/src/external/tng_io/src/lib/tng_io.c b/src/external/tng_io/src/lib/tng_io.c
index d0028bd69fcd17cd1943608cb8c4a9eb0ed0b465..001521b6c0efe32888d3dae45c12a5555b254489 100644 (file)
--- a/src/external/tng_io/src/lib/tng_io.c
+++ b/src/external/tng_io/src/lib/tng_io.c
@@ -4762,8 +4762,8 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
     int nalgo;
     int new_len;
     int *alt_algo = 0;
-    char *dest, *temp;
-    int64_t algo_find_n_frames;
+    char *dest, *temp, *temp_data_contents;
+    int64_t algo_find_n_frames, compressed_len;
     unsigned long offset;
     float f_precision;
     double d_precision;
@@ -4791,6 +4791,17 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
     f_precision = 1/(float)tng_data->compression_precision;
     d_precision = 1/tng_data->compression_precision;
 
+    compressed_len = block->block_contents_size - (int64_t)((char *)start_pos - (char *)block->block_contents);
+    temp_data_contents = malloc(compressed_len);
+    if(!temp_data_contents)
+    {
+        fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+                compressed_len, __FILE__, __LINE__);
+        return(TNG_CRITICAL);
+    }
+
+    memcpy(temp_data_contents, (char *)start_pos, compressed_len);
+
     if(block->id == TNG_TRAJ_POSITIONS)
     {
         /* If there is only one frame in this frame set and there might be more
@@ -4802,7 +4813,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             alt_algo=malloc(nalgo * sizeof *tng_data->compress_algo_pos);
             if(type == TNG_FLOAT_DATA)
             {
-                dest = tng_compress_pos_float_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_pos_float_find_algo((float *)temp_data_contents, (int)n_particles,
                                                         (int)n_frames,
                                                         f_precision,
                                                         0, alt_algo,
@@ -4811,7 +4822,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             }
             else
             {
-                dest = tng_compress_pos_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_pos_find_algo((double *)temp_data_contents, (int)n_particles,
                                            (int)n_frames,
                                            d_precision,
                                            0, alt_algo,
@@ -4834,7 +4845,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
                                            sizeof *tng_data->compress_algo_pos);
             if(type == TNG_FLOAT_DATA)
             {
-                dest = tng_compress_pos_float_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_pos_float_find_algo((float *)temp_data_contents, (int)n_particles,
                                                         (int)algo_find_n_frames,
                                                         f_precision,
                                                         0, tng_data->
@@ -4843,7 +4854,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
 
                 if(algo_find_n_frames < n_frames)
                 {
-                    dest = tng_compress_pos_float(start_pos, (int)n_particles,
+                    dest = tng_compress_pos_float((float *)temp_data_contents, (int)n_particles,
                                                   (int)n_frames,
                                                   f_precision,
                                                   0, tng_data->compress_algo_pos,
@@ -4852,7 +4863,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             }
             else
             {
-                dest = tng_compress_pos_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_pos_find_algo((double *)temp_data_contents, (int)n_particles,
                                            (int)algo_find_n_frames,
                                            d_precision,
                                            0, tng_data->
@@ -4861,7 +4872,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
 
                 if(algo_find_n_frames < n_frames)
                 {
-                    dest = tng_compress_pos(start_pos, (int)n_particles,
+                    dest = tng_compress_pos((double *)temp_data_contents, (int)n_particles,
                                             (int)n_frames,
                                             d_precision, 0,
                                             tng_data->compress_algo_pos,
@@ -4873,14 +4884,14 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
         {
             if(type == TNG_FLOAT_DATA)
             {
-                dest = tng_compress_pos_float(start_pos, (int)n_particles,
+                dest = tng_compress_pos_float((float *)temp_data_contents, (int)n_particles,
                                               (int)n_frames,
                                               f_precision, 0,
                                               tng_data->compress_algo_pos, &new_len);
             }
             else
             {
-                dest = tng_compress_pos(start_pos, (int)n_particles,
+                dest = tng_compress_pos((double *)temp_data_contents, (int)n_particles,
                                         (int)n_frames,
                                         d_precision, 0,
                                         tng_data->compress_algo_pos,
@@ -4899,7 +4910,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             alt_algo=malloc(nalgo * sizeof *tng_data->compress_algo_pos);
             if(type == TNG_FLOAT_DATA)
             {
-                dest = tng_compress_vel_float_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_vel_float_find_algo((float *)temp_data_contents, (int)n_particles,
                                                         (int)n_frames,
                                                         f_precision,
                                                         0, alt_algo,
@@ -4908,7 +4919,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             }
             else
             {
-                dest = tng_compress_vel_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_vel_find_algo((double *)temp_data_contents, (int)n_particles,
                                                   (int)n_frames,
                                                   d_precision,
                                                   0, alt_algo,
@@ -4932,7 +4943,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
 
             if(type == TNG_FLOAT_DATA)
             {
-                dest = tng_compress_vel_float_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_vel_float_find_algo((float *)temp_data_contents, (int)n_particles,
                                                         (int)algo_find_n_frames,
                                                         f_precision,
                                                         0, tng_data->
@@ -4940,7 +4951,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
                                                         &new_len);
                 if(algo_find_n_frames < n_frames)
                 {
-                    dest = tng_compress_vel_float(start_pos, (int)n_particles,
+                    dest = tng_compress_vel_float((float *)temp_data_contents, (int)n_particles,
                                                   (int)n_frames,
                                                   f_precision,
                                                   0, tng_data->compress_algo_vel,
@@ -4949,7 +4960,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             }
             else
             {
-                dest = tng_compress_vel_find_algo(start_pos, (int)n_particles,
+                dest = tng_compress_vel_find_algo((double *)temp_data_contents, (int)n_particles,
                                                   (int)algo_find_n_frames,
                                                   d_precision,
                                                   0, tng_data->
@@ -4957,7 +4968,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
                                                   &new_len);
                 if(algo_find_n_frames < n_frames)
                 {
-                    dest = tng_compress_vel(start_pos, (int)n_particles,
+                    dest = tng_compress_vel((double *)temp_data_contents, (int)n_particles,
                                             (int)n_frames,
                                             d_precision,
                                             0, tng_data->compress_algo_vel,
@@ -4969,7 +4980,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
         {
             if(type == TNG_FLOAT_DATA)
             {
-                dest = tng_compress_vel_float(start_pos, (int)n_particles,
+                dest = tng_compress_vel_float((float *)temp_data_contents, (int)n_particles,
                                               (int)n_frames,
                                               f_precision,
                                               0, tng_data->
@@ -4978,7 +4989,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
             }
             else
             {
-                dest = tng_compress_vel(start_pos, (int)n_particles,
+                dest = tng_compress_vel((double *)temp_data_contents, (int)n_particles,
                                         (int)n_frames,
                                         d_precision,
                                         0, tng_data->
@@ -4990,6 +5001,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
     else
     {
         fprintf(stderr, "TNG library: Can only compress positions and velocities using TNG-MF1 algorithms.\n");
+        free(temp_data_contents);
         return(TNG_FAILURE);
     }
 
@@ -5002,6 +5014,8 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
 
     block->block_contents_size = new_len + offset;
 
+    free(temp_data_contents);
+
     temp = realloc(block->block_contents, block->block_contents_size);
     if(!temp)
     {
@@ -5032,7 +5046,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
                                           void *start_pos,
                                           const unsigned long uncompressed_len)
 {
-    char *temp;
+    char *temp, *temp_data_contents;
     double *d_dest = 0;
     float *f_dest = 0;
     unsigned long offset;
@@ -5054,6 +5068,16 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
         return(TNG_FAILURE);
     }
 
+    temp_data_contents = malloc(uncompressed_len);
+    if(!temp_data_contents)
+    {
+        fprintf(stderr, "TNG library: Cannot allocate memory (%lu bytes). %s: %d\n",
+                uncompressed_len, __FILE__, __LINE__);
+        return(TNG_CRITICAL);
+    }
+
+    memcpy(temp_data_contents, (char *)start_pos, uncompressed_len);
+
     if(type == TNG_FLOAT_DATA)
     {
         f_dest = malloc(uncompressed_len);
@@ -5061,9 +5085,10 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
         {
             fprintf(stderr, "TNG library: Cannot allocate memory (%lu bytes). %s: %d\n",
                 uncompressed_len, __FILE__, __LINE__);
+            free(temp_data_contents);
             return(TNG_CRITICAL);
         }
-        result = tng_compress_uncompress_float(start_pos, f_dest);
+        result = tng_compress_uncompress_float(temp_data_contents, f_dest);
     }
     else
     {
@@ -5072,14 +5097,16 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
         {
             fprintf(stderr, "TNG library: Cannot allocate memory (%lu bytes). %s: %d\n",
                 uncompressed_len, __FILE__, __LINE__);
+            free(temp_data_contents);
             return(TNG_CRITICAL);
         }
-        result = tng_compress_uncompress(start_pos, d_dest);
+        result = tng_compress_uncompress(temp_data_contents, d_dest);
     }
 
     if(result == 1)
     {
         fprintf(stderr, "TNG library: Cannot uncompress TNG compressed block.\n");
+        free(temp_data_contents);
         return(TNG_FAILURE);
     }
 
@@ -5102,6 +5129,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
         }
         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
                block->block_contents_size, __FILE__, __LINE__);
+        free(temp_data_contents);
         return(TNG_CRITICAL);
     }
 
@@ -5116,6 +5144,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
 
     block->block_contents = temp;
 
+    free(temp_data_contents);
     if(d_dest)
     {
         free(d_dest);
@@ -11668,6 +11697,10 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
     *n = tng_data->n_trajectory_frame_sets = cnt;
 
     *frame_set = orig_frame_set;
+    /* The mapping block in the original frame set has been freed when reading
+     * other frame sets. */
+    frame_set->mappings = 0;
+    frame_set->n_mapping_blocks = 0;
 
     fseek(tng_data->input_file,
           (long)tng_data->first_trajectory_frame_set_input_file_pos,