Pre-processing stage key error

[nvlabs]

Pre-processing stage key error

[jdppthk]

Thanks @Melissa3248. I would recommend pre-populating the empty hdf5 files. Before running the parallel_copy_small_set.py file. I will push a script to do that. It should just do the following:

time_steps = 52
with h5py.File('filename.h5', 'w') as f:
f.create_dataset('fields', shape = (time_steps, 20, 720, 1440), dtype='f')

look through the h5py docs for more details https://docs.h5py.org/en/stable/high/dataset.html

[TeunZoer]

Hi everyone, I ran into the exact same error with the example code but have no idea how to solve it. Does someone know what is causing the error?

[Afshinshafei]

I am searching for more than one week that what can cause this error and the most recommendation was data corruption which is not our case I think.
if someone knows how to solve it, it can save so much time for us thank you very much.

[Melissa3248]

I ran into the same problem running the parallel_copy_small_set.py file, and I was able to fix the issue by adding two lines in the writetofile() function:

def writetofile(src, dest, channel_idx, varslist, src_idx=0, frmt='nc'):
    if os.path.isfile(src):
        batch = 2**4
        rank = MPI.COMM_WORLD.rank
        Nproc = MPI.COMM_WORLD.size
        Nimgtot = 52#src_shape[0]

        Nimg = Nimgtot//Nproc
        base = rank*Nimg
        end = (rank+1)*Nimg if rank<Nproc - 1 else Nimgtot
        idx = base

        fdest = h5py.File(dest, 'a', driver='mpio', comm=MPI.COMM_WORLD)
        fdest['fields'] = np.empty((1,20,720,1440))

        for variable_name in varslist:

            if frmt == 'nc':
                fsrc = DS(src, 'r', format="NETCDF4").variables[variable_name]
            elif frmt == 'h5':
                fsrc = h5py.File(src, 'r')[varslist[0]]
            #print("fsrc shape", fsrc.shape)
            fdest = h5py.File(dest, 'a', driver='mpio', comm=MPI.COMM_WORLD)

            start = time.time()
            while idx<end:
                if end - idx < batch:
                    if len(fsrc.shape) == 4:
                        ims = fsrc[idx:end,src_idx]
                    else:
                        ims = fsrc[idx:end]
                    print(ims.shape)
                    fdest['fields'][idx:end, channel_idx, :, :] = ims
                    break
                else:
                    if len(fsrc.shape) == 4:
                        ims = fsrc[idx:idx+batch,src_idx]
                    else:
                        ims = fsrc[idx:idx+batch]
                    #ims = fsrc[idx:idx+batch]
                    print("ims shape", ims.shape)
                    fdest['fields'][idx:idx+batch, channel_idx, :, :] = ims
                    idx+=batch
                    ttot = time.time() - start
                    eta = (end - base)/((idx - base)/ttot)
                    hrs = eta//3600
                    mins = (eta - 3600*hrs)//60
                    secs = (eta - 3600*hrs - 60*mins)

            ttot = time.time() - start
            hrs = ttot//3600
            mins = (ttot - 3600*hrs)//60
            secs = (ttot - 3600*hrs - 60*mins)
            channel_idx += 1

The two lines I added are:
fdest = h5py.File(dest, 'a', driver='mpio', comm=MPI.COMM_WORLD)
fdest['fields'] = np.empty((1,20,720,1440))

This initializes the destination file with a shape of (timepoint, # features, latitude, longitude). The code then appends data for each time point, so in the 13 day example, you obtain a dataset with size (52,20,720,1440). Hope this fix also works for you!

[TeunZoer]

Thanks @Melissa3248 and @jdppthk for your solutions. Melissa her solution (with a small adjustment in the empty numpy array) only worked for the first variable, from the second variable ('v10') I then get the following error:

File "/home/teun/Documents/TUD/FourCastNet/FourCastNet-0.0.0/data_process/parallel_copy_small_set_Melissa.py", line 119, in
writetofile(src, dest, 1, ['v10'])
File "/home/teun/Documents/TUD/FourCastNet/FourCastNet-0.0.0/data_process/parallel_copy_small_set_Melissa.py", line 71, in writetofile
fdest['fields'] = np.empty((16,20,721,1440))
File "/home/teun/miniconda3/lib/python3.9/site-packages/h5py/_hl/group.py", line 433, in setitem
h5o.link(ds.id, self.id, name, lcpl=lcpl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 202, in h5py.h5o.link
OSError: Unable to create link (name already exists)

For me the pre-populating proposed by jdppthk worked!

[jdppthk]

Glad it works for you. Closing this issue.