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[netCDF #AFZ-136343]: NetCDF error
- Subject: [netCDF #AFZ-136343]: NetCDF error
- Date: Thu, 26 Apr 2018 13:52:57 -0600
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
===================
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