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pt_test.c
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pt_test.c
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#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <unistd.h>
#include "mpi.h"
#include "adios.h"
#include "adios_read.h"
#include "adios_error.h"
#include "pt_structs.h"
ADIOS_FILE *adios_open_state(char *adios_file, enum ADIOS_READ_METHOD read_method, char *opts, MPI_Comm comm)
{
adios_read_init_method(read_method, comm, opts);
ADIOS_FILE* afile = adios_read_open_file(adios_file, read_method, comm);
return afile;
}
int adios_read_state(ADIOS_FILE *afile, pt_atoms *atoms_array, int proc_no, int time_step)
{
int num_atoms, num_types;
adios_schedule_read (afile, NULL, "num_atoms", 0, 1, &num_atoms);
adios_schedule_read (afile, NULL, "num_types", 0, 1, &num_types);
adios_perform_reads (afile, 1);
printf("I am here %d %d....\n",num_atoms,num_types);
if (alloc_atoms_array(atoms_array,num_atoms,num_types)!=0) return 1;
// printf("Next set of reads.: %d %d\n",proc_no,time_step);
uint64_t start[2];
uint64_t count[2];
start[0] = proc_no; start[1] = 0;
count[0] = 1; count[1] = 6;
ADIOS_SELECTION *sel_dims = adios_selection_boundingbox (2,start,count);
adios_schedule_read (afile, sel_dims, "cell_dims", time_step,1,atoms_array->cell_dims);
adios_perform_reads (afile, 1);
printf("I am after cell_dims...\n"); fflush(stdout);
uint64_t start1[2], count1[2];
start1[0] = proc_no; start1[0] = 0;
count1[0] = 1; count1[1] = atoms_array->num_types;
ADIOS_SELECTION *sel_types = adios_selection_boundingbox (2,start1,count1);
adios_schedule_read (afile, sel_types, "type_id", time_step,1,atoms_array->type_id);
adios_schedule_read (afile, sel_types, "masses", time_step,1,atoms_array->masses);
adios_perform_reads (afile, 1);
printf("I am here...\n");
uint64_t start2[2], count2[2];
start2[0] = proc_no; start2[1] = 0;
count2[0] = 1; count2[1] = atoms_array->num_atoms;
ADIOS_SELECTION *sel_atoms = adios_selection_boundingbox (2,start2,count2);
adios_schedule_read (afile, sel_atoms, "atom_id", time_step,1,atoms_array->atom_id);
adios_schedule_read (afile, sel_atoms, "atom_type", time_step,1,atoms_array->atom_type);
adios_schedule_read (afile, sel_atoms, "px", time_step,1,atoms_array->px);
adios_schedule_read (afile, sel_atoms, "py", time_step,1,atoms_array->py);
adios_schedule_read (afile, sel_atoms, "pz", time_step,1,atoms_array->pz);
adios_schedule_read (afile, sel_atoms, "imx", time_step,1,atoms_array->imx);
adios_schedule_read (afile, sel_atoms, "imy", time_step,1,atoms_array->imy);
adios_schedule_read (afile, sel_atoms, "imz", time_step,1,atoms_array->imz);
adios_schedule_read (afile, sel_atoms, "atom_vid", time_step,1,atoms_array->atom_vid);
adios_schedule_read (afile, sel_atoms, "vx", time_step,1,atoms_array->vx);
adios_schedule_read (afile, sel_atoms, "vy", time_step,1,atoms_array->vy);
adios_schedule_read (afile, sel_atoms, "vz", time_step,1,atoms_array->vz);
adios_perform_reads (afile, 1);
return 0;
}
int text_write_state(FILE *fp, pt_atoms *atoms_array)
{
int i;
fprintf(fp,"%s",atoms_array->header_str);
fprintf(fp,"\n");
fprintf(fp,"%d atoms\n",atoms_array->num_atoms);
fprintf(fp,"%d atom types\n",atoms_array->num_types);
fprintf(fp,"\n");
fprintf(fp,"%.16e %.16e xlo xhi\n",atoms_array->cell_dims[0][0],atoms_array->cell_dims[0][1]);
fprintf(fp,"%.16e %.16e ylo yhi\n",atoms_array->cell_dims[1][0],atoms_array->cell_dims[1][1]);
fprintf(fp,"%.16e %.16e zlo zhi\n",atoms_array->cell_dims[2][0],atoms_array->cell_dims[2][1]);
fprintf(fp,"\n");
fprintf(fp,"Masses\n");
fprintf(fp,"\n");
for (i=0;i<atoms_array->num_types;i++)
fprintf(fp,"%d %lg\n",atoms_array->type_id[i],atoms_array->masses[i]);
fprintf(fp,"\n");
fprintf(fp,"Atoms # atomic\n");
fprintf(fp,"\n");
for (i=0;i<atoms_array->num_atoms;i++) {
fprintf(fp,"%d %d %.16le %.16le %.16le %d %d %d\n",
atoms_array->atom_id[i],
atoms_array->atom_type[i],
atoms_array->px[i],
atoms_array->py[i],
atoms_array->pz[i],
atoms_array->imx[i],
atoms_array->imy[i],
atoms_array->imz[i]);
}
fprintf(fp,"\n");
fprintf(fp,"Velocities\n");
fprintf(fp,"\n");
for (i=0;i<atoms_array->num_atoms;i++) {
fprintf(fp,"%d %.16le %.16le %.16le\n",
atoms_array->atom_vid[i],
atoms_array->vx[i],
atoms_array->vy[i],
atoms_array->vz[i]);
}
return 0;
}
int main(int argc, char *argv[])
{
pt_atoms atoms_out;
MPI_Comm comm = MPI_COMM_WORLD;
int comm_rank, comm_size;
enum ADIOS_READ_METHOD read_method = ADIOS_READ_METHOD_BP;
int i;
char filename[256];
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &comm_rank);
MPI_Comm_size (comm, &comm_size);
if (argc!=5) {
printf("Usage: %s <bp file> <output file> <select_id> <time step>\n",argv[0]);
return 1;
}
char *bp_file = argv[1];
char *out_file = argv[2];
int select_id = atoi(argv[3]);
int time_step = atoi(argv[4]);
printf("Reading the file....\n"); fflush(stdout);
adios_init_noxml(comm);
FILE *fpo = fopen(out_file,"w");
if (fpo==NULL) return 1;
int len = strlen(HEADER_STRING)+1;
strcpy(atoms_out.header_str,HEADER_STRING);
ADIOS_FILE *afile = adios_open_state(bp_file, read_method, (char*)"", comm);
if (afile==NULL) return 1;
adios_read_state(afile,&atoms_out,select_id,time_step);
adios_read_close(afile);
MPI_Barrier(comm);
adios_read_finalize_method(read_method);
if (text_write_state(fpo,&atoms_out)!=0) {
printf("Write error....\n");
return 1;
}
fclose(fpo);
MPI_Finalize ();
return 0;
}