Which version of hdf5 library is recommended?

[gachiemchiep]

Hello caffe. Thank you for your great software.

I am using hdf5 file as input for our network.

I use the python script from https://github.com/BVLC/caffe/blob/master/src/caffe/test/test_data/generate_sample_data.py to generate sample data. Sample data is fine and readable by matlab.

But when i used generated sample data as input data layer. The following error appeared.

WARNING: Logging before InitGoogleLogging() is written to STDERR
E1203 14:27:21.852881 21368 extract_features.cpp:54] Using CPU
I1203 14:27:21.988205 21368 net.cpp:75] Creating Layer data
I1203 14:27:21.988236 21368 net.cpp:111] data -> data
I1203 14:27:21.988248 21368 net.cpp:111] data -> label
I1203 14:27:21.988260 21368 hdf5_data_layer.cpp:63] Loading filename from /host_home/yanai-lab/Sotsuken13/vugia/git/caffe/caffe/test/sample_data.h5
I1203 14:27:21.988638 21368 hdf5_data_layer.cpp:75] Number of files: 269
I1203 14:27:21.988652 21368 hdf5_data_layer.cpp:32] Loading HDF5 file�HDF
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 140426434959680:
#000: ../../../src/H5F.c line 1514 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#1: ../../../src/H5F.c line 1218 in H5F_open(): unable to open file
major: File accessability
minor: Unable to open file
#2: ../../../src/H5FD.c line 1079 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#3: ../../../src/H5FDsec2.c line 365 in H5FD_sec2_open(): unable to open file
major: File accessability
minor: Unable to open file
#4: ../../../src/H5FDsec2.c line 365 in H5FD_sec2_open(): No such file or directory
major: Internal error (too specific to document in detail)
minor: System error message
E1203 14:27:21.989533 21368 hdf5_data_layer.cpp:35] Failed opening HDF5 file�HDF
which file is load: �HDF
I1203 14:27:21.989578 21368 hdf5_data_layer.cpp:89] output data size: 1,0,0,0
I1203 14:27:21.989591 21368 net.cpp:126] Top shape: 1 0 0 0 (0)
I1203 14:27:21.989606 21368 net.cpp:126] Top shape: 1 0 0 0 (0)
I1203 14:27:21.989614 21368 net.cpp:157] data does not need backward computation.
I1203 14:27:21.989627 21368 net.cpp:75] Creating Layer conv1
I1203 14:27:21.989635 21368 net.cpp:85] conv1 <- data
I1203 14:27:21.989647 21368 net.cpp:111] conv1 -> conv1
F1203 14:27:21.989676 21368 blob.cpp:18] Check failed: height >= 0 (-1 vs. 0)
*** Check failure stack trace: ***
Abort (core dumped)

The path of hdf5 file is totally correct and it is readable.

gp02:~/git/caffe/caffe/test> ls -al /host_home/yanai-lab/Sotsuken13/vugia/git/caffe/caffe/test/sample_data.h5
-rwxrwxrwx 1 vugia YANAI_LAB 11784 12月 3 14:23 /host_home/yanai-lab/Sotsuken13/vugia/git/caffe/caffe/test/sample_data.h5

I think this is some bug of hdf5 library.
The version of hdf5 library is 1.8.4. Is this version is outdated? Should i update hdf5 library to newer version?
If anyone has working hdf5 library, please let me know your computer's environtment detail.
That will be very helpful.

[kklots]

hi, i just make the same mistake like this, you should load .txt file in prototxt file, not .h5 file directly.
the context in txt file looks like that:
$caffedir/examples/hdf5/train.h5

[gachiemchiep]

Hi kklots.
Thank you for your answer.
You are right. "Loading from txt file in prototxt file" did solve my problem.