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

28 次查看（过去 30 天）
Kyle Barlow
Kyle Barlow 2022-6-23
回答： Shuba Nandini 2023-10-3
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!
  5 个评论
显示 3更早的评论
Kyle Barlow
Kyle Barlow 2022-6-23
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
per isakson 2022-6-23
编辑：per isakson 2022-6-23
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?

请先登录，再进行评论。

请先登录，再回答此问题。

回答（1 个）

Shuba Nandini
Shuba Nandini 2023-10-3
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

类别

在 Help Center 和 File Exchange 中查找有关 HDF5 Files 的更多信息

标签

产品


版本

R2020a

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by