src/external/tng_io/src/tests/tng_parallel_read.c

   1 #ifdef TNG_BUILD_OPENMP_EXAMPLES
   2
   3 /* This code is part of the tng binary trajectory format.
   4  *
   5  * Written by Magnus Lundborg
   6  * Copyright (c) 2012-2013, The GROMACS development team.
   7  * Check out http://www.gromacs.org for more information.
   8  *
   9  *
  10  * This program is free software; you can redistribute it and/or
  11  * modify it under the terms of the Revised BSD License.
  12  */
  13
  14 #include "tng/tng_io.h"
  15
  16 #include <stdlib.h>
  17 #include <stdio.h>
  18
  19
  20 /* N.B. this code is for testing parallel reading of trajectory frame sets. The
  21  * performance is not improved very much and is to a large extent limited by
  22  * disk i/o. It can however be used as inspiration for writing parallel code
  23  * using the TNG library. The code is NOT fully tested and may behave strangely. */
  24
  25 int main(int argc, char **argv)
  26 {
  27     tng_trajectory_t traj, local_traj = 0;
  28     union data_values ***local_positions = 0; // A 3-dimensional array to be populated
  29     union data_values **particle_pos = 0;
  30     int64_t n_particles, n_values_per_frame, n_frame_sets, n_frames;
  31     int64_t n_frames_per_frame_set, tot_n_frames = 0;
  32     char data_type;
  33     int i, j, fail;
  34     int64_t particle = 0, local_first_frame, local_last_frame;
  35     char atom_name[64], res_name[64];
  36     tng_trajectory_frame_set_t frame_set = 0;
  37
  38     if(argc <= 1)
  39     {
  40         printf("No file specified\n");
  41         printf("Usage:\n");
  42         printf("tng_parallel_read <tng_file> [particle number = %"PRId64"]\n",
  43                particle);
  44         exit(1);
  45     }
  46
  47     // A reference must be passed to allocate memory
  48     if(tng_trajectory_init(&traj) != TNG_SUCCESS)
  49     {
  50         tng_trajectory_destroy(&traj);
  51         exit(1);
  52     }
  53     tng_input_file_set(traj, argv[1]);
  54
  55     tng_current_frame_set_get(traj, &frame_set);
  56
  57     // Read the file headers
  58     tng_file_headers_read(traj, TNG_USE_HASH);
  59
  60     if(argc >= 3)
  61     {
  62         particle = strtoll(argv[2], 0, 10);
  63     }
  64
  65     tng_num_frame_sets_get(traj, &n_frame_sets);
  66     tng_num_frames_per_frame_set_get(traj, &n_frames_per_frame_set);
  67
  68     particle_pos = malloc(sizeof(union data_values *) * n_frame_sets *
  69     n_frames_per_frame_set);
  70     for(i = n_frame_sets * n_frames_per_frame_set; i--;)
  71     {
  72         /* Assume 3 values per frame even if it's not determined yet */
  73         particle_pos[i] = malloc(sizeof(union data_values) * 3);
  74     }
  75
  76     printf("%"PRId64" frame sets\n", n_frame_sets);
  77
  78     if(tng_atom_name_of_particle_nr_get(traj, particle, atom_name,
  79                                         sizeof(atom_name)) ==
  80        TNG_SUCCESS &&
  81        tng_residue_name_of_particle_nr_get(traj, particle, res_name,
  82                                            sizeof(res_name)) ==
  83        TNG_SUCCESS)
  84     {
  85         printf("Particle: %s (%s)\n", atom_name, res_name);
  86     }
  87     else
  88     {
  89         printf("Particle name not found\n");
  90     }
  91
  92     fail = 0;
  93
  94 #pragma omp parallel \
  95 private (n_frames, n_particles, n_values_per_frame, \
  96          local_first_frame, local_last_frame, j, fail) \
  97 firstprivate (local_traj, local_positions, frame_set)\
  98 shared(data_type, traj, n_frame_sets, particle_pos, particle, i, tot_n_frames)\
  99 default(none)
 100 {
 101     /* Each tng_trajectory_t keeps its own file pointers and i/o positions.
 102      * Therefore there must be a copy for each thread. */
 103     tng_trajectory_init_from_src(traj, &local_traj);
 104 #pragma omp for
 105     for(i = 0; i < n_frame_sets; i++)
 106     {
 107         if(tng_frame_set_nr_find(local_traj, i) != TNG_SUCCESS)
 108         {
 109             printf("FAILED finding frame set %d!\n", i);
 110             tot_n_frames = 0;
 111             fail = 1;
 112         }
 113         if(tng_particle_data_get(local_traj, TNG_TRAJ_POSITIONS, &local_positions,
 114                                  &n_frames, &n_particles, &n_values_per_frame,
 115                                  &data_type) != TNG_SUCCESS)
 116         {
 117             printf("FAILED getting particle data\n");
 118             tot_n_frames = 0;
 119             fail = 1;
 120         }
 121         if(!fail)
 122         {
 123             tng_current_frame_set_get(local_traj, &frame_set);
 124             tng_frame_set_frame_range_get(local_traj, frame_set, &local_first_frame, &local_last_frame);
 125     //         printf("Frame %"PRId64"-%"PRId64":\n", local_first_frame, local_last_frame);
 126     //         printf("%"PRId64" %"PRId64" %"PRId64"\n", n_frames, n_particles, n_values_per_frame);
 127             tot_n_frames += n_frames;
 128             for(j = 0; j < n_frames; j++)
 129             {
 130                 particle_pos[local_first_frame + j][0] = local_positions[j][particle][0];
 131                 particle_pos[local_first_frame + j][1] = local_positions[j][particle][1];
 132                 particle_pos[local_first_frame + j][2] = local_positions[j][particle][2];
 133             }
 134         }
 135     }
 136
 137     // Free memory
 138     if(local_positions)
 139     {
 140         tng_particle_data_values_free(local_traj, local_positions, n_frames, n_particles,
 141                                       n_values_per_frame, data_type);
 142     }
 143     tng_trajectory_destroy(&local_traj);
 144 }
 145     switch(data_type)
 146     {
 147     case TNG_INT_DATA:
 148         for(j = 0; j < tot_n_frames; j++)
 149         {
 150             printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", particle_pos[j][0].i,
 151                    particle_pos[j][1].i, particle_pos[j][2].i);
 152         }
 153         break;
 154     case TNG_FLOAT_DATA:
 155         for(j = 0; j < tot_n_frames; j++)
 156         {
 157             printf("\t%f\t%f\t%f\n", particle_pos[j][0].f,
 158                    particle_pos[j][1].f, particle_pos[j][2].f);
 159         }
 160         break;
 161     case TNG_DOUBLE_DATA:
 162         for(j = 0; j < tot_n_frames; j++)
 163         {
 164             printf("\t%f\t%f\t%f\n", particle_pos[j][0].d,
 165                    particle_pos[j][1].d, particle_pos[j][2].d);
 166         }
 167         break;
 168     default:
 169         break;
 170     }
 171
 172     /* Free more memory */
 173     for(i = n_frame_sets * n_frames_per_frame_set; i--;)
 174     {
 175         free(particle_pos[i]);
 176     }
 177     free(particle_pos);
 178
 179     tng_trajectory_destroy(&traj);
 180
 181     return(0);
 182 }
 183
 184 #endif