[netCDF #AFZ-136343]: NetCDF error

the primary problem is that you are not allocating memory
big enough to hold the total contents of the "coordinates" variable.
You have allocated:
  float Vec[3*na*40] where na = 3000.
But in fact you need to allocate 
  float Vec[2*na*nf]

This means that memory past the Vec variable will be overwritten
which is probably causing the fault.



> I'm trying to read trajectory data made by Molecular Dynamics program 
> 'AMBER', whose file format is NetCDF.I tried to read variable called 
> "coordinates".
> The dimensions of coordinates are as follow:
> dimensions
> frame = UNLIMITED ; // (20000 currently)        spatial = 3 ;        atom = 
> 3000 ;
> variablesfloat coordinates(frame, atom, spatial) ; 
> I tried to read and write the data by following C language code, but 
> segmentation fault occured. If I reduced data size that I try to read by 
> changing count vector, It worked. Are data size which can be read at once 
> limited? then Are there any way to read whole data?
> 
> #include <stdio.h>#include <netcdf.h>
> #define ERR(e) {printf("Error: %s\n", nc_strerror(e)); return 2;}#define 
> FILE_NAME "w1000.tp3.nvtmd2.nc"
> intmain(){int ncid, retval, VecCoord;int na=3000, nf=20000;static size_t 
> iv_strt[] = {0, 0, 0};static size_t iv_cnt[] = {20000, 3000, 3}; // 1, 2, 
> 3float Vec[3*na*40];int i, j, rec, k, l;
> /*Open the file. NC_NOWRITE tells netCDF we want read-only access  * to the 
> file*/
>   if ((retval = nc_open(FILE_NAME, NC_NOWRITE, &ncid)))      ERR(retval);
>   if ((retval = nc_inq_varid(ncid, "coordinates", &VecCoord)))    ERR(retval);
>   if ((retval = nc_get_vara_float(ncid, VecCoord,iv_strt, iv_cnt, &Vec[0])))
> 
> 
> 
> if ((retval=nc_close(ncid)))   ERR(retval);
> FILE *fout;//fout= fopen("home/janghm17/NetCDF/DataFile.txt", "wt");
> 
> fout= fopen("DataFile.txt", "wt");  if(fout==NULL) {      printf("Error: 
> Can't open output file.\n");          exit(1);            }           
> printf("start\n");
>             for(j=0; j<na*40; j++){              fprintf(fout, "%f %f %f\n", 
> Vec[3*j], Vec[3*j+1], Vec[3*j+2]);              }              
> printf("end\n");
>                 fclose(fout); return 0;}
> 
> Thanks,
> 
> 

=Dennis Heimbigner
  Unidata


Ticket Details
===================
Ticket ID: AFZ-136343
Department: Support netCDF
Priority: Normal
Status: Open
===================
NOTE: All email exchanges with Unidata User Support are recorded in the Unidata 
inquiry tracking system and then made publicly available through the web.  If 
you do not want to have your interactions made available in this way, you must 
let us know in each email you send to us.