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blob size exceeds INT_MAX: did you have had this error? #5

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sara-eb opened this issue Jun 28, 2018 · 3 comments
Open

blob size exceeds INT_MAX: did you have had this error? #5

sara-eb opened this issue Jun 28, 2018 · 3 comments

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@sara-eb
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sara-eb commented Jun 28, 2018

Hi, I tried to run the code in 3D-Unet with your pretrained model.
I am asking this question

I0625 14:51:07.611187 11147 net.cpp:400] conv_d0b-c -> d0c
F0625 14:51:07.612490 11147 blob.cpp:33] Check failed: shape[i] <= 0x7fffffff / count_ (385 vs. 89) blob size exceeds INT_MAX
*** Check failure stack trace: ***
    @     0x7f483a8105cd  google::LogMessage::Fail()
    @     0x7f483a812433  google::LogMessage::SendToLog()
    @     0x7f483a81015b  google::LogMessage::Flush()
    @     0x7f483a812e1e  google::LogMessageFatal::~LogMessageFatal()
    @     0x7f483aed0e60  caffe::Blob<>::Reshape()
    @     0x7f483afbe205  caffe::BaseConvolutionLayer<>::Reshape()
    @     0x7f483aebe48f  caffe::Net<>::Init()
    @     0x7f483aebfd11  caffe::Net<>::Net()
    @     0x7f483ae2014a  caffe::Solver<>::InitTrainNet()
    @     0x7f483ae214b7  caffe::Solver<>::Init()
    @     0x7f483ae2185a  caffe::Solver<>::Solver()
    @     0x7f483ae35823  caffe::Creator_SGDSolver<>()
    @           0x40a6d8  train()
    @           0x4075a8  main
    @     0x7f48392c4830  __libc_start_main
    @           0x407d19  _start
    @              (nil)  (unknown)
Aborted (core dumped)

Did you face with this error? I tried to apply your pre-trained model on my data. If yes, could you please guide me? I have installed 3d-Unet patch on caffe. Then I tried to install opencl-caffe that I was not successful. Thanks
@holgerroth
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This is common problem with Caffe and/or hdf5, see BVLC/caffe#3084.
How large are your images and how many are you saving in a hdf5 file?

@sara-eb
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sara-eb commented Jul 11, 2018 •
edited

@holgerroth I installed opencl-caffe, and could solve the issue with that error. I have one volume in each .h5 file, but I have the list of paths to 90 volumes in train.txt file. I am still not able to rain the model on my data. The input volumes have different width, height, and depth from each other and varies patient to patient. The input shape of the first volumes to the network, for example, is NxCxDxHxW (N:batch size, C: channels, D: depth, H: height, W: width), and the size of D, H, and W are not same. the issue that I am facing now is related to architecture, and i am getting the following error:

I0708 22:19:59.143136 30282 layer_factory.cpp:74] Creating layer loaddata
I0708 22:19:59.143214 30282 net.cpp:185] Creating Layer loaddata
I0708 22:19:59.143275 30282 net.cpp:515] loaddata -> data
I0708 22:19:59.143400 30282 net.cpp:515] loaddata -> label
I0708 22:19:59.143479 30282 hdf5_data_layer.cpp:85] Loading list of HDF5 filenames from: /home/user/workspace/create_lmdb/SK/3D_HDF5/train_list.txt
I0708 22:19:59.151377 30282 hdf5_data_layer.cpp:99] Number of HDF5 files: 90
I0708 22:19:59.204767 30282 hdf5.cpp:33] Datatype class: H5T_FLOAT
I0708 22:19:59.460875 30282 hdf5.cpp:36] Datatype class: H5T_INTEGER
I0708 22:19:59.531133 30282 net.cpp:223] Setting up loaddata
I0708 22:19:59.531157 30282 net.cpp:233] Top shape: 1 1 104 281 389 (11368136)
I0708 22:19:59.531162 30282 net.cpp:233] Top shape: 1 1 104 281 389 (11368136)
I0708 22:19:59.531177 30282 layer_factory.cpp:74] Creating layer conv_d0a-b
I0708 22:19:59.531195 30282 net.cpp:185] Creating Layer conv_d0a-b
I0708 22:19:59.531200 30282 net.cpp:549] conv_d0a-b <- data
I0708 22:19:59.531214 30282 net.cpp:515] conv_d0a-b -> d0b
I0708 22:19:59.545521 30282 net.cpp:223] Setting up conv_d0a-b
I0708 22:19:59.545558 30282 net.cpp:233] Top shape: 1 32 102 279 387 (352423872)
I0708 22:19:59.545604 30282 layer_factory.cpp:74] Creating layer bn_d0b
I0708 22:19:59.545646 30282 net.cpp:185] Creating Layer bn_d0b
I0708 22:19:59.545650 30282 net.cpp:549] bn_d0b <- d0b
I0708 22:19:59.545655 30282 net.cpp:515] bn_d0b -> normd0b
I0708 22:19:59.559860 30282 net.cpp:223] Setting up bn_d0b
I0708 22:19:59.559887 30282 net.cpp:233] Top shape: 1 32 102 279 387 (352423872)
I0708 22:19:59.559916 30282 layer_factory.cpp:74] Creating layer sc_d0b
I0708 22:19:59.559931 30282 net.cpp:185] Creating Layer sc_d0b
I0708 22:19:59.559936 30282 net.cpp:549] sc_d0b <- normd0b
I0708 22:19:59.559942 30282 net.cpp:515] sc_d0b -> scaled0b
I0708 22:19:59.559963 30282 layer_factory.cpp:74] Creating layer sc_d0b
I0708 22:19:59.607246 30282 net.cpp:223] Setting up sc_d0b
I0708 22:19:59.607280 30282 net.cpp:233] Top shape: 1 32 102 279 387 (352423872)
I0708 22:19:59.607300 30282 layer_factory.cpp:74] Creating layer relu_d0b
I0708 22:19:59.607311 30282 net.cpp:185] Creating Layer relu_d0b
I0708 22:19:59.607319 30282 net.cpp:549] relu_d0b <- scaled0b
I0708 22:19:59.607327 30282 net.cpp:502] relu_d0b -> scaled0b (in-place)
I0708 22:19:59.610675 30282 net.cpp:223] Setting up relu_d0b
I0708 22:19:59.610707 30282 net.cpp:233] Top shape: 1 32 102 279 387 (352423872)
I0708 22:19:59.610723 30282 layer_factory.cpp:74] Creating layer conv_d0b-c
I0708 22:19:59.610735 30282 net.cpp:185] Creating Layer conv_d0b-c
I0708 22:19:59.610740 30282 net.cpp:549] conv_d0b-c <- scaled0b
I0708 22:19:59.610749 30282 net.cpp:515] conv_d0b-c -> d0c
I0708 22:19:59.611543 30282 net.cpp:223] Setting up conv_d0b-c
I0708 22:19:59.611553 30282 net.cpp:233] Top shape: 1 64 100 277 385 (682528000)
I0708 22:19:59.611564 30282 layer_factory.cpp:74] Creating layer bn_d0c
I0708 22:19:59.611573 30282 net.cpp:185] Creating Layer bn_d0c
I0708 22:19:59.611578 30282 net.cpp:549] bn_d0c <- d0c
I0708 22:19:59.611584 30282 net.cpp:515] bn_d0c -> normd0c
I0708 22:19:59.625416 30282 net.cpp:223] Setting up bn_d0c
I0708 22:19:59.625437 30282 net.cpp:233] Top shape: 1 64 100 277 385 (682528000)
I0708 22:19:59.625464 30282 layer_factory.cpp:74] Creating layer sc_d0c
I0708 22:19:59.625476 30282 net.cpp:185] Creating Layer sc_d0c
I0708 22:19:59.625480 30282 net.cpp:549] sc_d0c <- normd0c
I0708 22:19:59.625488 30282 net.cpp:515] sc_d0c -> scaled0c
I0708 22:19:59.625509 30282 layer_factory.cpp:74] Creating layer sc_d0c
I0708 22:19:59.652434 30282 net.cpp:223] Setting up sc_d0c
I0708 22:19:59.652472 30282 net.cpp:233] Top shape: 1 64 100 277 385 (682528000)
I0708 22:19:59.652489 30282 layer_factory.cpp:74] Creating layer relu_d0c
I0708 22:19:59.652498 30282 net.cpp:185] Creating Layer relu_d0c
I0708 22:19:59.652500 30282 net.cpp:549] relu_d0c <- scaled0c
I0708 22:19:59.652505 30282 net.cpp:502] relu_d0c -> scaled0c (in-place)
I0708 22:19:59.652720 30282 net.cpp:223] Setting up relu_d0c
I0708 22:19:59.652729 30282 net.cpp:233] Top shape: 1 64 100 277 385 (682528000)
I0708 22:19:59.652755 30282 layer_factory.cpp:74] Creating layer scaled0c_relu_d0c_0_split
I0708 22:19:59.652776 30282 net.cpp:185] Creating Layer scaled0c_relu_d0c_0_split
I0708 22:19:59.652781 30282 net.cpp:549] scaled0c_relu_d0c_0_split <- scaled0c
I0708 22:19:59.652786 30282 net.cpp:515] scaled0c_relu_d0c_0_split -> scaled0c_relu_d0c_0_split_0
I0708 22:19:59.652796 30282 net.cpp:515] scaled0c_relu_d0c_0_split -> scaled0c_relu_d0c_0_split_1
I0708 22:19:59.652813 30282 net.cpp:223] Setting up scaled0c_relu_d0c_0_split
I0708 22:19:59.652818 30282 net.cpp:233] Top shape: 1 64 100 277 385 (682528000)
I0708 22:19:59.652822 30282 net.cpp:233] Top shape: 1 64 100 277 385 (682528000)
I0708 22:19:59.652832 30282 layer_factory.cpp:74] Creating layer pool_d0c-1a
I0708 22:19:59.652844 30282 net.cpp:185] Creating Layer pool_d0c-1a
I0708 22:19:59.652848 30282 net.cpp:549] pool_d0c-1a <- scaled0c_relu_d0c_0_split_0
I0708 22:19:59.652853 30282 net.cpp:515] pool_d0c-1a -> d1a
I0708 22:19:59.679503 30282 net.cpp:223] Setting up pool_d0c-1a
I0708 22:19:59.679546 30282 net.cpp:233] Top shape: 1 64 50 139 193 (85846400)
I0708 22:19:59.679584 30282 layer_factory.cpp:74] Creating layer conv_d1a-b
I0708 22:19:59.679613 30282 net.cpp:185] Creating Layer conv_d1a-b
I0708 22:19:59.679633 30282 net.cpp:549] conv_d1a-b <- d1a
I0708 22:19:59.679657 30282 net.cpp:515] conv_d1a-b -> d1b
I0708 22:19:59.685448 30282 net.cpp:223] Setting up conv_d1a-b
I0708 22:19:59.685487 30282 net.cpp:233] Top shape: 1 64 48 137 191 (80385024)
I0708 22:19:59.685528 30282 layer_factory.cpp:74] Creating layer bn_d1b
I0708 22:19:59.685556 30282 net.cpp:185] Creating Layer bn_d1b
I0708 22:19:59.685575 30282 net.cpp:549] bn_d1b <- d1b
I0708 22:19:59.685595 30282 net.cpp:515] bn_d1b -> normd1b
I0708 22:19:59.690904 30282 net.cpp:223] Setting up bn_d1b
I0708 22:19:59.690953 30282 net.cpp:233] Top shape: 1 64 48 137 191 (80385024)
I0708 22:19:59.691015 30282 layer_factory.cpp:74] Creating layer sc_d1b
I0708 22:19:59.691056 30282 net.cpp:185] Creating Layer sc_d1b
I0708 22:19:59.691076 30282 net.cpp:549] sc_d1b <- normd1b
I0708 22:19:59.691099 30282 net.cpp:515] sc_d1b -> scaled1b
I0708 22:19:59.691148 30282 layer_factory.cpp:74] Creating layer sc_d1b
I0708 22:19:59.699025 30282 net.cpp:223] Setting up sc_d1b
I0708 22:19:59.699053 30282 net.cpp:233] Top shape: 1 64 48 137 191 (80385024)
I0708 22:19:59.699076 30282 layer_factory.cpp:74] Creating layer relu_d1b
I0708 22:19:59.699090 30282 net.cpp:185] Creating Layer relu_d1b
I0708 22:19:59.699096 30282 net.cpp:549] relu_d1b <- scaled1b
I0708 22:19:59.699105 30282 net.cpp:502] relu_d1b -> scaled1b (in-place)
I0708 22:19:59.699471 30282 net.cpp:223] Setting up relu_d1b
I0708 22:19:59.699486 30282 net.cpp:233] Top shape: 1 64 48 137 191 (80385024)
I0708 22:19:59.699502 30282 layer_factory.cpp:74] Creating layer conv_d1b-c
I0708 22:19:59.699517 30282 net.cpp:185] Creating Layer conv_d1b-c
I0708 22:19:59.699523 30282 net.cpp:549] conv_d1b-c <- scaled1b
I0708 22:19:59.699532 30282 net.cpp:515] conv_d1b-c -> d1c
I0708 22:19:59.705317 30282 net.cpp:223] Setting up conv_d1b-c
I0708 22:19:59.705332 30282 net.cpp:233] Top shape: 1 128 46 135 189 (150232320)
I0708 22:19:59.705344 30282 layer_factory.cpp:74] Creating layer bn_d1c
I0708 22:19:59.705355 30282 net.cpp:185] Creating Layer bn_d1c
I0708 22:19:59.705359 30282 net.cpp:549] bn_d1c <- d1c
I0708 22:19:59.705368 30282 net.cpp:515] bn_d1c -> normd1c
I0708 22:19:59.707568 30282 net.cpp:223] Setting up bn_d1c
I0708 22:19:59.707582 30282 net.cpp:233] Top shape: 1 128 46 135 189 (150232320)
I0708 22:19:59.707598 30282 layer_factory.cpp:74] Creating layer sc_d1c
I0708 22:19:59.707608 30282 net.cpp:185] Creating Layer sc_d1c
I0708 22:19:59.707612 30282 net.cpp:549] sc_d1c <- normd1c
I0708 22:19:59.707617 30282 net.cpp:515] sc_d1c -> scaled1c
I0708 22:19:59.707638 30282 layer_factory.cpp:74] Creating layer sc_d1c
I0708 22:19:59.712186 30282 net.cpp:223] Setting up sc_d1c
I0708 22:19:59.712204 30282 net.cpp:233] Top shape: 1 128 46 135 189 (150232320)
I0708 22:19:59.712221 30282 layer_factory.cpp:74] Creating layer relu_d1c
I0708 22:19:59.712247 30282 net.cpp:185] Creating Layer relu_d1c
I0708 22:19:59.712252 30282 net.cpp:549] relu_d1c <- scaled1c
I0708 22:19:59.712257 30282 net.cpp:502] relu_d1c -> scaled1c (in-place)
I0708 22:19:59.712501 30282 net.cpp:223] Setting up relu_d1c
I0708 22:19:59.712510 30282 net.cpp:233] Top shape: 1 128 46 135 189 (150232320)
I0708 22:19:59.712519 30282 layer_factory.cpp:74] Creating layer scaled1c_relu_d1c_0_split
I0708 22:19:59.712527 30282 net.cpp:185] Creating Layer scaled1c_relu_d1c_0_split
I0708 22:19:59.712530 30282 net.cpp:549] scaled1c_relu_d1c_0_split <- scaled1c
I0708 22:19:59.712534 30282 net.cpp:515] scaled1c_relu_d1c_0_split -> scaled1c_relu_d1c_0_split_0
I0708 22:19:59.712543 30282 net.cpp:515] scaled1c_relu_d1c_0_split -> scaled1c_relu_d1c_0_split_1
I0708 22:19:59.712560 30282 net.cpp:223] Setting up scaled1c_relu_d1c_0_split
I0708 22:19:59.712565 30282 net.cpp:233] Top shape: 1 128 46 135 189 (150232320)
I0708 22:19:59.712569 30282 net.cpp:233] Top shape: 1 128 46 135 189 (150232320)
I0708 22:19:59.712577 30282 layer_factory.cpp:74] Creating layer pool_d1c-2a
I0708 22:19:59.712589 30282 net.cpp:185] Creating Layer pool_d1c-2a
I0708 22:19:59.712594 30282 net.cpp:549] pool_d1c-2a <- scaled1c_relu_d1c_0_split_0
I0708 22:19:59.712602 30282 net.cpp:515] pool_d1c-2a -> d2a
I0708 22:19:59.714496 30282 net.cpp:223] Setting up pool_d1c-2a
I0708 22:19:59.714509 30282 net.cpp:233] Top shape: 1 128 23 68 95 (19018240)
I0708 22:19:59.714519 30282 layer_factory.cpp:74] Creating layer conv_d2a-b
I0708 22:19:59.714529 30282 net.cpp:185] Creating Layer conv_d2a-b
I0708 22:19:59.714532 30282 net.cpp:549] conv_d2a-b <- d2a
I0708 22:19:59.714537 30282 net.cpp:515] conv_d2a-b -> d2b
I0708 22:19:59.722410 30282 net.cpp:223] Setting up conv_d2a-b
I0708 22:19:59.722425 30282 net.cpp:233] Top shape: 1 128 21 66 93 (16498944)
I0708 22:19:59.722440 30282 layer_factory.cpp:74] Creating layer bn_d2b
I0708 22:19:59.722446 30282 net.cpp:185] Creating Layer bn_d2b
I0708 22:19:59.722450 30282 net.cpp:549] bn_d2b <- d2b
I0708 22:19:59.722453 30282 net.cpp:515] bn_d2b -> normd2b
I0708 22:19:59.722640 30282 net.cpp:223] Setting up bn_d2b
I0708 22:19:59.722647 30282 net.cpp:233] Top shape: 1 128 21 66 93 (16498944)
I0708 22:19:59.722658 30282 layer_factory.cpp:74] Creating layer sc_d2b
I0708 22:19:59.722666 30282 net.cpp:185] Creating Layer sc_d2b
I0708 22:19:59.722668 30282 net.cpp:549] sc_d2b <- normd2b
I0708 22:19:59.722672 30282 net.cpp:515] sc_d2b -> scaled2b
I0708 22:19:59.722682 30282 layer_factory.cpp:74] Creating layer sc_d2b
I0708 22:19:59.723462 30282 net.cpp:223] Setting up sc_d2b
I0708 22:19:59.723472 30282 net.cpp:233] Top shape: 1 128 21 66 93 (16498944)
I0708 22:19:59.723481 30282 layer_factory.cpp:74] Creating layer relu_d2b
I0708 22:19:59.723487 30282 net.cpp:185] Creating Layer relu_d2b
I0708 22:19:59.723489 30282 net.cpp:549] relu_d2b <- scaled2b
I0708 22:19:59.723493 30282 net.cpp:502] relu_d2b -> scaled2b (in-place)
I0708 22:19:59.723675 30282 net.cpp:223] Setting up relu_d2b
I0708 22:19:59.723682 30282 net.cpp:233] Top shape: 1 128 21 66 93 (16498944)
I0708 22:19:59.723690 30282 layer_factory.cpp:74] Creating layer conv_d2b-c
I0708 22:19:59.723697 30282 net.cpp:185] Creating Layer conv_d2b-c
I0708 22:19:59.723701 30282 net.cpp:549] conv_d2b-c <- scaled2b
I0708 22:19:59.723704 30282 net.cpp:515] conv_d2b-c -> d2c
I0708 22:19:59.735688 30282 net.cpp:223] Setting up conv_d2b-c
I0708 22:19:59.735697 30282 net.cpp:233] Top shape: 1 256 19 64 91 (28327936)
I0708 22:19:59.735720 30282 layer_factory.cpp:74] Creating layer bn_d2c
I0708 22:19:59.735725 30282 net.cpp:185] Creating Layer bn_d2c
I0708 22:19:59.735728 30282 net.cpp:549] bn_d2c <- d2c
I0708 22:19:59.735735 30282 net.cpp:515] bn_d2c -> normd2c
I0708 22:19:59.735910 30282 net.cpp:223] Setting up bn_d2c
I0708 22:19:59.735916 30282 net.cpp:233] Top shape: 1 256 19 64 91 (28327936)
I0708 22:19:59.735942 30282 layer_factory.cpp:74] Creating layer sc_d2c
I0708 22:19:59.735949 30282 net.cpp:185] Creating Layer sc_d2c
I0708 22:19:59.735951 30282 net.cpp:549] sc_d2c <- normd2c
I0708 22:19:59.735965 30282 net.cpp:515] sc_d2c -> scaled2c
I0708 22:19:59.735980 30282 layer_factory.cpp:74] Creating layer sc_d2c
I0708 22:19:59.736647 30282 net.cpp:223] Setting up sc_d2c
I0708 22:19:59.736655 30282 net.cpp:233] Top shape: 1 256 19 64 91 (28327936)
I0708 22:19:59.736677 30282 layer_factory.cpp:74] Creating layer relu_d2c
I0708 22:19:59.736682 30282 net.cpp:185] Creating Layer relu_d2c
I0708 22:19:59.736685 30282 net.cpp:549] relu_d2c <- scaled2c
I0708 22:19:59.736688 30282 net.cpp:502] relu_d2c -> scaled2c (in-place)
I0708 22:19:59.736865 30282 net.cpp:223] Setting up relu_d2c
I0708 22:19:59.736871 30282 net.cpp:233] Top shape: 1 256 19 64 91 (28327936)
I0708 22:19:59.736893 30282 layer_factory.cpp:74] Creating layer scaled2c_relu_d2c_0_split
I0708 22:19:59.736898 30282 net.cpp:185] Creating Layer scaled2c_relu_d2c_0_split
I0708 22:19:59.736901 30282 net.cpp:549] scaled2c_relu_d2c_0_split <- scaled2c
I0708 22:19:59.736904 30282 net.cpp:515] scaled2c_relu_d2c_0_split -> scaled2c_relu_d2c_0_split_0
I0708 22:19:59.736912 30282 net.cpp:515] scaled2c_relu_d2c_0_split -> scaled2c_relu_d2c_0_split_1
I0708 22:19:59.736924 30282 net.cpp:223] Setting up scaled2c_relu_d2c_0_split
I0708 22:19:59.736929 30282 net.cpp:233] Top shape: 1 256 19 64 91 (28327936)
I0708 22:19:59.736933 30282 net.cpp:233] Top shape: 1 256 19 64 91 (28327936)
I0708 22:19:59.736941 30282 layer_factory.cpp:74] Creating layer pool_d2c-3a
I0708 22:19:59.736948 30282 net.cpp:185] Creating Layer pool_d2c-3a
I0708 22:19:59.736950 30282 net.cpp:549] pool_d2c-3a <- scaled2c_relu_d2c_0_split_0
I0708 22:19:59.736954 30282 net.cpp:515] pool_d2c-3a -> d3a
I0708 22:19:59.738168 30282 net.cpp:223] Setting up pool_d2c-3a
I0708 22:19:59.738175 30282 net.cpp:233] Top shape: 1 256 10 32 46 (3768320)
I0708 22:19:59.738183 30282 layer_factory.cpp:74] Creating layer conv_d3a-b
I0708 22:19:59.738190 30282 net.cpp:185] Creating Layer conv_d3a-b
I0708 22:19:59.738193 30282 net.cpp:549] conv_d3a-b <- d3a
I0708 22:19:59.738198 30282 net.cpp:515] conv_d3a-b -> d3b
I0708 22:19:59.761819 30282 net.cpp:223] Setting up conv_d3a-b
I0708 22:19:59.761839 30282 net.cpp:233] Top shape: 1 256 8 30 44 (2703360)
I0708 22:19:59.761855 30282 layer_factory.cpp:74] Creating layer bn_d3b
I0708 22:19:59.761864 30282 net.cpp:185] Creating Layer bn_d3b
I0708 22:19:59.761868 30282 net.cpp:549] bn_d3b <- d3b
I0708 22:19:59.761874 30282 net.cpp:515] bn_d3b -> normd3b
I0708 22:19:59.761909 30282 net.cpp:223] Setting up bn_d3b
I0708 22:19:59.761914 30282 net.cpp:233] Top shape: 1 256 8 30 44 (2703360)
I0708 22:19:59.761924 30282 layer_factory.cpp:74] Creating layer sc_d3b
I0708 22:19:59.761930 30282 net.cpp:185] Creating Layer sc_d3b
I0708 22:19:59.761934 30282 net.cpp:549] sc_d3b <- normd3b
I0708 22:19:59.761937 30282 net.cpp:515] sc_d3b -> scaled3b
I0708 22:19:59.761948 30282 layer_factory.cpp:74] Creating layer sc_d3b
I0708 22:19:59.762456 30282 net.cpp:223] Setting up sc_d3b
I0708 22:19:59.762465 30282 net.cpp:233] Top shape: 1 256 8 30 44 (2703360)
I0708 22:19:59.762486 30282 layer_factory.cpp:74] Creating layer relu_d3b
I0708 22:19:59.762491 30282 net.cpp:185] Creating Layer relu_d3b
I0708 22:19:59.762495 30282 net.cpp:549] relu_d3b <- scaled3b
I0708 22:19:59.762501 30282 net.cpp:502] relu_d3b -> scaled3b (in-place)
I0708 22:19:59.762678 30282 net.cpp:223] Setting up relu_d3b
I0708 22:19:59.762686 30282 net.cpp:233] Top shape: 1 256 8 30 44 (2703360)
I0708 22:19:59.762707 30282 layer_factory.cpp:74] Creating layer conv_d3b-c
I0708 22:19:59.762713 30282 net.cpp:185] Creating Layer conv_d3b-c
I0708 22:19:59.762717 30282 net.cpp:549] conv_d3b-c <- scaled3b
I0708 22:19:59.762722 30282 net.cpp:515] conv_d3b-c -> d3c
I0708 22:19:59.809218 30282 net.cpp:223] Setting up conv_d3b-c
I0708 22:19:59.809253 30282 net.cpp:233] Top shape: 1 512 6 28 42 (3612672)
I0708 22:19:59.809269 30282 layer_factory.cpp:74] Creating layer bn_d3c
I0708 22:19:59.809278 30282 net.cpp:185] Creating Layer bn_d3c
I0708 22:19:59.809281 30282 net.cpp:549] bn_d3c <- d3c
I0708 22:19:59.809288 30282 net.cpp:515] bn_d3c -> normd3c
I0708 22:19:59.809360 30282 net.cpp:223] Setting up bn_d3c
I0708 22:19:59.809366 30282 net.cpp:233] Top shape: 1 512 6 28 42 (3612672)
I0708 22:19:59.809379 30282 layer_factory.cpp:74] Creating layer sc_d3c
I0708 22:19:59.809388 30282 net.cpp:185] Creating Layer sc_d3c
I0708 22:19:59.809393 30282 net.cpp:549] sc_d3c <- normd3c
I0708 22:19:59.809397 30282 net.cpp:515] sc_d3c -> scaled3c
I0708 22:19:59.809414 30282 layer_factory.cpp:74] Creating layer sc_d3c
I0708 22:19:59.809927 30282 net.cpp:223] Setting up sc_d3c
I0708 22:19:59.809936 30282 net.cpp:233] Top shape: 1 512 6 28 42 (3612672)
I0708 22:19:59.809943 30282 layer_factory.cpp:74] Creating layer relu_d3c
I0708 22:19:59.809949 30282 net.cpp:185] Creating Layer relu_d3c
I0708 22:19:59.809952 30282 net.cpp:549] relu_d3c <- scaled3c
I0708 22:19:59.809957 30282 net.cpp:502] relu_d3c -> scaled3c (in-place)
I0708 22:19:59.810125 30282 net.cpp:223] Setting up relu_d3c
I0708 22:19:59.810132 30282 net.cpp:233] Top shape: 1 512 6 28 42 (3612672)
I0708 22:19:59.810140 30282 layer_factory.cpp:74] Creating layer upconv_d3c_u2a
I0708 22:19:59.810148 30282 net.cpp:185] Creating Layer upconv_d3c_u2a
I0708 22:19:59.810150 30282 net.cpp:549] upconv_d3c_u2a <- scaled3c
I0708 22:19:59.810154 30282 net.cpp:515] upconv_d3c_u2a -> u2a
I0708 22:19:59.810273 30282 net.cpp:223] Setting up upconv_d3c_u2a
I0708 22:19:59.810279 30282 net.cpp:233] Top shape: 1 512 12 56 84 (28901376)
I0708 22:19:59.810300 30282 layer_factory.cpp:74] Creating layer bn_u2a
I0708 22:19:59.810307 30282 net.cpp:185] Creating Layer bn_u2a
I0708 22:19:59.810308 30282 net.cpp:549] bn_u2a <- u2a
I0708 22:19:59.810312 30282 net.cpp:515] bn_u2a -> normu2a
I0708 22:19:59.810431 30282 net.cpp:223] Setting up bn_u2a
I0708 22:19:59.810437 30282 net.cpp:233] Top shape: 1 512 12 56 84 (28901376)
I0708 22:19:59.810461 30282 layer_factory.cpp:74] Creating layer sc_u2a
I0708 22:19:59.810465 30282 net.cpp:185] Creating Layer sc_u2a
I0708 22:19:59.810469 30282 net.cpp:549] sc_u2a <- normu2a
I0708 22:19:59.810473 30282 net.cpp:515] sc_u2a -> scaleu2a
I0708 22:19:59.810487 30282 layer_factory.cpp:74] Creating layer sc_u2a
I0708 22:19:59.810976 30282 net.cpp:223] Setting up sc_u2a
I0708 22:19:59.810983 30282 net.cpp:233] Top shape: 1 512 12 56 84 (28901376)
I0708 22:19:59.810992 30282 layer_factory.cpp:74] Creating layer relu_u2a
I0708 22:19:59.810997 30282 net.cpp:185] Creating Layer relu_u2a
I0708 22:19:59.810999 30282 net.cpp:549] relu_u2a <- scaleu2a
I0708 22:19:59.811002 30282 net.cpp:502] relu_u2a -> scaleu2a (in-place)
I0708 22:19:59.811174 30282 net.cpp:223] Setting up relu_u2a
I0708 22:19:59.811182 30282 net.cpp:233] Top shape: 1 512 12 56 84 (28901376)
I0708 22:19:59.811188 30282 layer_factory.cpp:74] Creating layer concat_d2c_u2a-b
I0708 22:19:59.811198 30282 net.cpp:185] Creating Layer concat_d2c_u2a-b
I0708 22:19:59.811200 30282 net.cpp:549] concat_d2c_u2a-b <- scaleu2a
I0708 22:19:59.811203 30282 net.cpp:549] concat_d2c_u2a-b <- scaled2c_relu_d2c_0_split_1
I0708 22:19:59.811208 30282 net.cpp:515] concat_d2c_u2a-b -> u2b
F0708 22:19:59.811223 30282 concat_layer.cpp:45] Check failed: top_shape[j] == bottom[i]->shape(j) (12 vs. 19) All inputs must have the same shape, except at concat_axis.
*** Check failure stack trace: ***
    @     0x7f54a41e35cd  google::LogMessage::Fail()
    @     0x7f54a41e5433  google::LogMessage::SendToLog()
    @     0x7f54a41e315b  google::LogMessage::Flush()
    @     0x7f54a41e5e1e  google::LogMessageFatal::~LogMessageFatal()
    @     0x7f54a4cb9a11  caffe::ConcatLayer<>::Reshape()
    @     0x7f54a4bd5ac6  caffe::Layer<>::SetUp()
    @     0x7f54a4c01d2f  caffe::Net<>::Init()
    @     0x7f54a4c0384e  caffe::Net<>::Net()
    @     0x7f54a4c0d87c  caffe::Solver<>::InitTrainNet()
    @     0x7f54a4c0ec25  caffe::Solver<>::Init()
    @     0x7f54a4c0ef6a  caffe::Solver<>::Solver()
    @     0x7f54a495ed65  caffe::Creator_SGDSolver<>()
    @     0x7f54a4dece6d  caffe::SolverRegistry<>::CreateSolver()
    @           0x41296f  train()
    @           0x410a0f  main
    @     0x7f54a315e830  __libc_start_main
    @           0x411339  _start
    @              (nil)  (unknown)

The input shape of the first volume in HDF5 dataset is 1 1 104 281 389 (NxCxDxHxW), when it reaches to the Concat layer (concat_d2c_u2a-b), it is raising an error, which it is inputs are with the following two shapes:

1 256 19 64 91 scaled2c_relu_d2c_0_split_1
1 512 12 56 84 scaleu2a
How can I solve this issue?

@holgerroth
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Can you share your prototxt file as well please?

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@holgerroth @sara-eb