Error using fclose Invalid file identifier.

Hi Matlab's Community,

I'm a new user of Matlab. I'm practicing my program, but I got the error:

Error using fclose

Invalid file identifier. Use fopen to generate a valid file identifier.

Error in nc_interface (line 98)

fclose(fid);

Error in nc_getatt (line 61)

[method,~,~] = nc_interface(ncfile);

Error in nc_inq (line 69)

A = nc_getatt(ncfile); % NetCDF file global attributes

Error in get_roms_grid (line 98)

Ginfo = nc_inq(Ginp);

Error in coarse2fine (line 59)

C = get_roms_grid(Ginp);

Error in wrf2roms_mw_ref (line 26)

coarse2fine(ParROMSFile,theROMSFile,eval(num2str(pgratio)),eval(num2str(pistart)),eval(num2str(piend)),eval(num2str(pjstart)),eval(n str(pjend)))

Error in generate_roms_grid (line 123)

[rho,projection] =

wrf2roms_mw_ref(theWRFFile,theROMSFile,rlim,npass,order,mini_depth,bathy_source,mod_dom,corr_ocean_mask,num_passes)

Error in run (line 86)

evalin('caller', [script ';']);

Please help me to resolve this problem. I'm really appreciated that.

I'm really sorry because it's quite specific.

Thanks all.

Answer 1

[Walter Roberson]

        if (ne(fid,-1)),
            signature = fread(fid,8,'uint8=>uint8');
            if (strcmp(char(signature(1:3))', 'CDF')),
                if (signature(4) == 1)
                    ftype = 'NetCDF';                           % NetCDF classic
                elseif (signature(4) == 2)
                    ftype = 'NetCDF';                           % NetCDF 64bit offset
                end
            elseif (strcmp(char(signature(2:4))', 'HDF'))
                ftype = 'NetCDF4';                            % NetCDF4/HDF5
            end
        end
        fclose(fid);

That code uses fclose() even if the fopen() failed.

In short, the file it is trying to open does not exist.

[Manh Nguyen]

Dear Mr. Walter,

Thank you for your fast reply. Can you kindly give me the way to avoid this error?

[Walter Roberson]

        if fid < 0
            error('Failed to open file |%s|', ncfile);
        end
        signature = fread(fid,8,'uint8=>uint8');
        if (strcmp(char(signature(1:3))', 'CDF')),
            if (signature(4) == 1)
                ftype = 'NetCDF';                           % NetCDF classic
            elseif (signature(4) == 2)
                ftype = 'NetCDF';                           % NetCDF 64bit offset
            end
        elseif (strcmp(char(signature(2:4))', 'HDF'))
            ftype = 'NetCDF4';                            % NetCDF4/HDF5
        else
            fclose(fid);
            error('Unknown signature for file |%s|', ncfile);
        end

        fclose(fid);

[Manh Nguyen]

Dear Mr. Walter,

Thank you for your help.

After I alter the program according to your suggestion, the error don't appear again.

Thank you very much!

[Manh Nguyen]

Dear Mr. Walter,

Thank to your modified command, the error didn't appear again.

Can you kindly help me to debug my code? I can not know how to fix that.

>> run generate_roms_grid.m
ROMS domain 2 information is to be saved to ROMS_COAWST_grd2.nc

theWRFFile =

    'wrfinput_d02'

Error using nc_interface (line 87)
Failed to open file |ROMS_COAWST_grd1.nc|

My idea is that I create the ROMS_COAWST_grd1.nc file from wrfinput_d01 then to ROMS_COAWST_grd2.nc from wrfinput_d02. But in the program, it create the 2nd grid before generating the 1st grid leading to this error.

Please help me to solve this problem. I'm really appreciated your help.

I attach all of scripts in the attachments and the wrfinput files are in this link (https://drive.google.com/file/d/1lTPkJyrVYwn8MHrSwXYA4SFVRPCXWxCP/view?usp=sharing)

Thank you again.

[Walter Roberson]

The output you posted was for

mod_dom = 2;

but the code you posted was for

mod_dom = 1;

This makes a difference because the ROMS file name

fname=['ROMS_COAWST_grd',num2str(mod_dom),'.nc'];  %Name of output ROMS model NetCDF file

would have been

ROMS_COAWST_grd2.nc

if mod_dom were 2, but the error message is as if fname were ROMS_COAWST_grd1.nc

You seem to have a conflict between your posted code and the messages you posted.

[Manh Nguyen]

Dear Mr. Walter.

I'm really sorry because there are many conflicts between the codes and the messages I posted. With mod_dom = 1 option, my code can work successfully. However, if I change mod_dom = 2, the program will get the error:

>> run generate_roms_grid.m
ROMS domain 2 information is to be saved to ROMS_COAWST_grd2.nc

theWRFFile =

    'wrfinput_d02'

Error using nc_interface (line 87)
Failed to open file |ROMS_COAWST_grd1.nc|

Error in nc_getatt (line 61)
[method,~,~] = nc_interface(ncfile);

Error in nc_inq (line 69)
A = nc_getatt(ncfile);            % NetCDF file global attributes

Error in get_roms_grid (line 98)
  Ginfo = nc_inq(Ginp);

Error in coarse2fine (line 59)
C = get_roms_grid(Ginp);

Error in wrf2roms_mw_ref (line 26)
   coarse2fine(ParROMSFile,theROMSFile,eval(num2str(pgratio)),eval(num2str(pistart)),eval(num2str(piend)),eval(num2str(pjstart)),eval(n   str(pjend)))

Error in generate_roms_grid (line 126)
   [rho,projection] =
   wrf2roms_mw_ref(theWRFFile,theROMSFile,rlim,npass,order,mini_depth,bathy_source,mod_dom,corr_ocean_mask,num_passes)

Error in run (line 86)
evalin('caller', [script ';']);

This error reported that I did not have the ROMS_COAWST_grd1.nc file. My ideal when using these codes is that creates the 2 file ROMS_COAWST_grd1.nc and ROMS_COAWST_grd2.nc, in which the ROMS_COAWST_grd2.nc is generated after the ROMS_COAWST_grd1.nc file.

Can you kindly help me to address this issue?

Thank you very much.

[Walter Roberson]

Error using internal.matlab.imagesci.nc/openToRead (line 1274)

Could not open wrfinput_d02_nicholls for reading.

I do not have any of your datasets to test with.

[Manh Nguyen]

The input datasets are on the Drive, please download them from this link ( https://drive.google.com/file/d/1lTPkJyrVYwn8MHrSwXYA4SFVRPCXWxCP/view?usp=sharing ). I'm so sorry about this inconvenience.

Thank you for your help.

[Walter Roberson]

wrf2roms_mw_ref() reads the PARENT_ID attribute from the NC file you tell it to read, and uses that parent ID to form the name of the ROMS_COAWST_grd file to read. In this case, the parent ID stored in the file is 1, so it needs ROMS_COAWST_grd1.nc

But even if it used 2 instead of 1 there: coarse2fine() needs to be able to read from the file to get values needed to create the new ROMS file, so if it used 2 at that point, it would be trying to read from ROMS_COAWST_grd2.nc before that file had been created.

The work flow cannot be used to create a new initial ROMS file; it can be used to create a new ROMS file from a wrf file using a different ROMS file as a base

[Manh Nguyen]

Thank you for your help.

Although the codes can not run for my cases, I'm really appreciated your help.

I have another idea is that I use these codes to create the ROMS_COAWST_grd1.nc with mod_dom = 1 option then I change mod_dom = 2 to generate the ROMS_COAWST_grd2.nc file. I don't know whether it have any problem but I can run without problem.

Answer 2

[KSSV]

You need not to use fopen and fclose etc for reading ncfiles in MATLAB. Reading ncfiles is very simple in MATLAB. You just need to know two functions: ncinfo/ ncdisp and ncread. Read about these functions.

[Manh Nguyen]

Dear Dr. KSSV,

Thank you for your reply. Can you kindly help me with fopen and fclose command?

I'm really appreciated that.