Datatype class: H5T_FLOAT F0413 08:54:40.661201 17769 hdf5_data_layer.cpp:53] Check failed: hdf_blobs_[i] ->shape(0) == num (1 vs. 1024)

Question

My data set is a HDF5 file consists of data with shape [129028,1,12,1024] and label of shape [129028,1,1,1].
But when I run solver.prototxt, I get the error message:

I0413 08:54:34.689985 17769 hdf5.cpp:32] Datatype class: H5T_FLOAT
F0413 08:54:40.661201 17769 hdf5_data_layer.cpp:53] Check failed:   
hdf_blobs_[i] -&gt;shape(0) == num (1 vs. 1024) 
*** Check failure stack trace: ***

please run in shell `h5ls` to see the actual shape of your stored arrays — Shai, Apr 13 '16 at 15:31
Possible duplicate of [\[caffe\]: check fails: Check failed: hdf\_blobs\_\[i\]->shape(0) == num (200 vs. 6000)](http://stackoverflow.com/questions/34418027/caffe-check-fails-check-failed-hdf-blobs-i-shape0-num-200-vs-6000) — Shai, Apr 13 '16 at 15:39

score 2 · Accepted Answer · edited May 23 '17 at 10:33

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It looks like you saved your hdf5 from matlab, rather than python (judging by your previous question).
When saving data from Matlab one has to remember that Matlab stores multi-dimensions arrays in memory in colums-first fashion (fortran style), while python, caffe and many other applications expects multi-dimension arrays in row-first fashion (C style).
Thus, you need to permute the data in matlab before saving it to hdf5 for caffe. See this answer for more details.

I suspect that if you run h5ls in shell on the hdf5 file you stored you'll notice that the shape of the stored arrays are actually

data   [1024, 12, 1, 129028]
label  [1, 1, 1, 129028]

edited May 23 '17 at 10:33

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answered Apr 13 '16 at 15:37

Shai

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You are right! I saved data set in matlab using permute. I think I misunderstood what you told me before so that I got the error.Thank you very much! – Zhao Wulanaren Apr 14 '16 at 07:33
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Now I can train my data without any error! Thanks again! – Zhao Wulanaren Apr 14 '16 at 07:45
@ Shai Hello, can you give me some advice about my new question? – Zhao Wulanaren Apr 18 '16 at 05:43

Datatype class: H5T_FLOAT F0413 08:54:40.661201 17769 hdf5_data_layer.cpp:53] Check failed: hdf_blobs_[i] ->shape(0) == num (1 vs. 1024)

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