MATLAB: Ncwrite/nccreate unable to open file for writing/netcdf.create error: Permission denied (13)

Question

Hi everybody,

I wrote a script that averages data from many netcdf files. Opening them with ncwrite out of the folder NCEP_Reanalysis works fine and all the calculations are excuted perfectly. However, trying to save the averaged data seems to be a problem. The names of the different properties I'm averaging are saved in the cell array properties and are accessed in the loop via the variable property.

Using the following code:

        nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),sprintf('%s',properties{property}),propNEW)
        nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'lon',LON)
        nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'lat',LAT)
        nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'level',LEVEL)
        nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'time',TIME)

returns the following error:

Error using internal.matlab.imagesci.nc/openToWrite (line 1176) Unable to open NCEP_Reanalysisverage.air.nc for writing.

Error in internal.matlab.imagesci.nc/openToAppend (line 1243) this.openToWrite();

Error in internal.matlab.imagesci.nc (line 123) this.openToAppend();

Error in nccreate (line 120) ncObj = internal.matlab.imagesci.nc(ncFile,'a', formatStr);

Error in averageNCEP (line 74) nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),sprintf('%s',properties{property}),propNEW)

So I tried something similar using this code:

        ncidout = netcdf.create(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'NETCDF4');
        dimidlon = netcdf.defDim(ncidout,'lon',144);
        dimidlat = netcdf.defDim(ncidout,'lat',73);
        dimidlevel = netcdf.defDim(ncidout,'level',17);
        dimidtime = netcdf.defDim(ncidout,'time',1464);
        lon_ID=netcdf.defVar(ncidout,'lon','double',[dimidlon]);
        lat_ID=netcdf.defVar(ncidout,'lat','double',[dimidlat]);
        level_ID=netcdf.defVar(ncidout,'level','double',[dimidlevel]);
        time_ID=netcdf.defVar(ncidout,'time','double',[dimidtime]);
        prop_ID = netcdf.defVar(ncid,sprintf('%s',properties{property}),'double',[dimidlon dimidlat dimidlevel dimidtime]);
        netcdf.endDef(ncidout);
        netcdf.putVar(ncidout,lon_ID,LON);
        netcdf.putVar(ncidout,lat_ID,LAT);
        netcdf.putVar(ncidout,level_ID,LEVEL);
        netcdf.putVar(ncidout,time_ID,TIME);
        netcdf.putVar(ncidout,prop_ID,propNEW);
        netcdf.close(ncidout)

which gives me this error:

Error using netcdflib The NetCDF library encountered an error during execution of 'create' function – 'Permission denied (13)'.

Error in netcdf.create (line 53) ncid = netcdflib('create', filename, mode);

Error in averageNCEP (line 80) ncidout = netcdf.create(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'NETCDF4');

I tried removing read-only attributes of the folder NCEP_Reanalysis and all folders further up the hierarchy with the console and the command (Operating system: Windows 7):

      attrib -r +s E:\VM_Ubuntu_16.04.1_shared_folder\NCEP_Reanalysis

without success. The error occurs in the first iterartion and everything before it works fine. I'm attaching the whole code anyway even so it's over a hundred lines just to give you the big picture:

      %%Average the NCEP-Reanalysis Data from 1948 to 2015, does not work for different interval of years
      LON = ncread('NCEP_Reanalysis\1948\air.1948.nc','lon');
      LAT = ncread('NCEP_Reanalysis\1948\air.1948.nc','lat');
      LEVEL = ncread('NCEP_Reanalysis\1948\air.1948.nc','level');
      TIME = ncread('NCEP_Reanalysis\1948\air.1948.nc','time');
      properties = {'air','hgt','omega','rhum','shum','uwind','vwind'};
      propNEW = zeros(144,73,17,1464);
      nextpropertyFLAG = 1; % 1=next property, else = current property
      LeapYearCompensator = zeros(144,73,17,4);
      for property = 1:length(properties)
          disp('++++++++++++++++++++++++++++++++++++')
          for year = 1948:2014
              disp('******************************************************')
              fprintf('loading %s.%d.nc\n',properties{property},year)
              if nextpropertyFLAG == 1
                  prop1 = ncread(['NCEP_Reanalysis\' sprintf('%d',year) '\' sprintf('%s.%d.nc',properties{property},year)],sprintf('%s',properties{property}));
              else
                  prop1  = propNEW;
              end
              fprintf('loading %s.%d.nc\n',properties{property},year+1)
              prop2 = ncread(['NCEP_Reanalysis\' sprintf('%d',year+1) '\' sprintf('%s.%d.nc',properties{property},year+1)],sprintf('%s',properties{property}));
              [d11,d12,d13,d14] = size(prop1);
              [d21,d22,d23,d24] = size(prop2);
              if d11 ~= d21
                  error(['longitutdes of do not match\n' 'lon of ' sprintf('%s.%d.nc',properties{property},year) ' = ' sprintf('%d',d11) '\n' 'lon of ' sprintf('%s.%d.nc',properties{property},year+1) ' = ' sprintf('%d',d21)])
              end
              if d12 ~= d22
                  error(['latitudes of do not match\n' 'lat of ' sprintf('%s.%d.nc',properties{property},year) ' = ' sprintf('%d',d12) '\n' 'lat of ' sprintf('%s.%d.nc',properties{property},year+1) ' = ' sprintf('%d',d22)])
              end
              if d13 ~= d23
                  error(['levels of do not match\n' 'levels of ' sprintf('%s.%d.nc',properties{property},year) ' = ' sprintf('%d',d13) '\n' 'levels of ' sprintf('%s.%d.nc',properties{property},year+1) ' = ' sprintf('%d',d23)])
              end
              if d11 ~= 144
                  error('more than 144 longitude values -> preallocated array not big enough')
              end
              if d12 ~= 73
                  error('more than 73 latitude values -> preallocated array not big enough')
              end
              if d13 ~= 17
                  error('more than 17 levels -> preallocated array not big enough')
              end
              if d14 ~= 1460 && d14 ~= 1464
                  error(sprintf('invalid time steps in %s.%d.nc',properties{property},year))
              end
              if d24 ~= 1460 && d24 ~= 1464
                 error(sprintf('invalid time steps in %s.%d.nc',properties{property},year+1))
              end
              if d14 == 1460 % prop1 is data contained in a leap year
                  prop1 = cat(4,prop1(:,:,:,1:(31+28)*4),LeapYearCompensator,prop1(:,:,:,((31+28)*4+1):1460)); % complement the extra day with values of 0

              elseif d24 == 1460
                   prop2 = cat(4,prop2(:,:,:,1:(31+28)*4),LeapYearCompensator,prop2(:,:,:,((31+28)*4+1):1460)); % complement the extra day with values of 0
              end
        for time = 1:1464
            if mod(time,4) == 0
                fprintf('finished\t property:\t %s,\t years:\t %d\t and\t %d,\t day:\t %d\n',properties{property},year,year+1,time/4)
            end
            for lon = 1:144
                for lat = 1:73
                    for level = 1:17
                      propNEW(lon,lat,level,time) = (prop1(lon,lat,level,time)+prop2(lon,lat,level,time))/2;
                    end
                end
            end
        end
        % Save average property
        fprintf('saving average.%s.nc\n',properties{property})
%         nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),sprintf('%s',properties{property}),propNEW)
%         nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'lon',LON)
%         nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'lat',LAT)
%         nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'level',LEVEL)
%         nccreate(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'time',TIME)
        ncidout = netcdf.create(sprintf('NCEP_Reanalysis\average.%s.nc',properties{property}),'NETCDF4');
        dimidlon = netcdf.defDim(ncidout,'lon',144);
        dimidlat = netcdf.defDim(ncidout,'lat',73);
        dimidlevel = netcdf.defDim(ncidout,'level',17);
        dimidtime = netcdf.defDim(ncidout,'time',1464);
        lon_ID=netcdf.defVar(ncidout,'lon','double',[dimidlon]);
        lat_ID=netcdf.defVar(ncidout,'lat','double',[dimidlat]);
        level_ID=netcdf.defVar(ncidout,'level','double',[dimidlevel]);
        time_ID=netcdf.defVar(ncidout,'time','double',[dimidtime]);
        prop_ID = netcdf.defVar(ncid,sprintf('%s',properties{property}),'double',[dimidlon dimidlat dimidlevel dimidtime]);
        netcdf.endDef(ncidout);
        netcdf.putVar(ncidout,lon_ID,LON);
        netcdf.putVar(ncidout,lat_ID,LAT);
        netcdf.putVar(ncidout,level_ID,LEVEL);
        netcdf.putVar(ncidout,time_ID,TIME);
        netcdf.putVar(ncidout,prop_ID,propNEW);
        netcdf.close(ncidout)
        nextpropertyFLAG = nextpropertyFLAG + 1;
        disp('******************************************************')
  end
    nextpropertyFLAG = 1;
    disp('++++++++++++++++++++++++++++++++++++')
end

Any ideas on how to fix this?

Answer 1

Instead of putting function inside functions, like sprintf() inside the argument list to nccreate(), create the filenames outside, in advance, and see what they are. See if they look "right" and are not in a folder where you can't save things, like under the Program Files folder.

baseFileName = sprintf('NCEP_Reanalysis/average.%s.nc',properties{property})
fullFileName = fullfile(pwd, baseFileName)
string = sprintf('%s',properties{property})
nccreate(fullFileName, string, propNEW)

See what gets spit out to the command window (since I left off the semicolons) and see if the filenames look right. Tell me what one is.