h5read() error, I'm not sure how to fix this?

Hi all,

I am having problems opening a dataset from .h5 files. The code is below.

filename = 'r0184KB.h5';

rawSpectra = h5read(filename, '/K_alpha/spectra');

This is strange because sometimes this code runs with no problem whereas other times I get this error message:

Error using h5readc

The HDF5 library encountered an error and produced the following stack trace information:

H5FD_sec2_read file read failed: time = Thu Jun 23 12:54:52 2022

, filename = 'Z:\Projects\XES\Reduced Data\r0184KB.h5', file descriptor = 3, errno =

22, error message = 'Invalid argument', buf = 000001D1E4447060, total read size = 102875136, bytes

this sub-read = 102875136, bytes actually read = 18446744073709551615, offset = 104616

H5FD_read driver read request failed

H5F_accum_read driver read request failed

H5F_block_read read through metadata accumulator failed

H5D__contig_readvv_sieve_cb block read failed

H5V_opvv can't perform operation

H5D__contig_readvv can't perform vectorized sieve buffer read

H5D__select_io read error

H5D__select_read read error

H5D__contig_read contiguous read failed

H5D__read can't read data

H5Dread can't read data

Error in h5read (line 66)

[data,var_class] = h5readc(Filename,Dataset,start,count,stride);

Error in ExtractingXESDataFromH5Files (line 13)

rawSpectra = h5read(filename, '/K_alpha/spectra');

Does anyone know how to fix this problem? I think it could be a memory problem as it works everytime when I read in smaller dataset but only sometimes when I read the larger ones.

Thanks!

[per isakson]

Is 'Z:\Projects\XES\Reduced Data\r0184KB.h5', correct?

It's safer without blanks in filespecs.

Try with a full file specification.

[Kyle Barlow]

Thanks for the reply.

Yes, it's correct, it works for the other datasets in the h5 files absolutely fine just not this one. I've also tried with full fule specification and it still has the same error.

As I say, this code sometimes works and sometimes throws up that error, I don't know therefore if it's a problem with the code or something else.

[per isakson]

"just not this one" and "sometimes works and sometimes". What differs between the cases when it works and when it doesn't? Hard to answer, I guess.

I don't understand the details of the error message.

Do you use HDFView? I use it all the time when I create code, which reads and writes to h5-files. Does HDFView open the file without problems? Inspect the content of the file with HDFView. Does it look OK? Is it what you expected?

[Kyle Barlow]

There is no difference between the two cases. It seems to work one moment then fail the next seemingly random. I have lots of h5 files and the ones that are smaller in size seem to work all the time but as the files get larger they fail more often. But again, this is random, with no changes in the code inbetween.

I also do not understand the error message.

Yes, I use HDFView, everything looks exactly like I expect it to.

[per isakson]

And HDFView has no problems to open the file?

I once made a Matlab program that invoked a simulation program in a loop. It ran for hours. I used a gaming PC, which someone else had configured. The simulation program fairly often returned erroneous results. I found that the frequency of errors depended on the air temperature in the room. Lowering the CPU clock frequency and removing some dust solved the problem.

Is Z: mapped to something on the net, a server somewhere?

Answer 1

[Shuba Nandini]

Hi Kyle,

It is my understanding that you are facing sporadic issues due to size of the dataset that you are using with “h5read” function. Here are few possible reasons that could give the error:

• Error might occur when you are trying to read more data than what’s available in the dataset. To fix this, you need to adjust your start and count parameters appropriately using this command

data = h5read(filename,ds,start,count);

• Memory Issues: If your dataset is very large, it might exceed the available memory on your computer. This could potentially lead to errors. You might need to consider reading the data in smaller chunks.
• Make sure the dataset path you are providing exists in your file. If the path doesn’t exist, h5read will throw an error.

Please refer to the following documentation to know more about “h5read” function:

Read data from HDF5 dataset - MATLAB h5read - MathWorks India

Read a single file in HDF5 container with Matlab

I hope this helps you to resolve the issue!

Regards,

Shuba Nandini