Problem on test set

[bioinfo-dirty-jobs]

Dear All,
I try to install on Ubuntu 18 using conda with python3.6:
here the error for sh test.sh

`lugins: xdist-2.1.0, cov-2.10.1, forked-1.3.0
collected 7 items                                                                                                                                                             

tests/test_resnet3d.py FFFFF.F                                                                                                                                          [100%]

================================================================================== FAILURES ===================================================================================
______________________________________________________________________________ test_resnet3d_18 _______________________________________________________________________________

resnet3d_test = <function resnet3d_test.<locals>.f at 0x7f3c1abbd048>

    def test_resnet3d_18(resnet3d_test):
        """Test 18."""
        K.set_image_data_format('channels_last')
>       model = Resnet3DBuilder.build_resnet_18((224, 224, 224, 1), 2)

tests/test_resnet3d.py:20: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
resnet3d/resnet3d.py:273: in build_resnet_18
    [2, 2, 2, 2], reg_factor=reg_factor)
resnet3d/resnet3d.py:243: in build
    )(block)
resnet3d/resnet3d.py:113: in f
    )(input)
resnet3d/resnet3d.py:140: in f
    return _shortcut3d(input, residual)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

input = <tf.Tensor 'max_pooling3d/MaxPool3D:0' shape=(None, 56, 56, 56, 64) dtype=float32>
residual = <tf.Tensor 'conv3d_2/BiasAdd:0' shape=(None, 56, 56, 56, 64) dtype=float32>

    def _shortcut3d(input, residual):
        """3D shortcut to match input and residual and merges them with "sum"."""
>       stride_dim1 = ceil(input._keras_shape[DIM1_AXIS] \
            / residual._keras_shape[DIM1_AXIS])
E       AttributeError: 'Tensor' object has no attribute '_keras_shape'

resnet3d/resnet3d.py:80: AttributeError
---------------------------------------------------------------------------- Captured stderr call -----------------------------------------------------------------------------
2020-10-15 17:33:12.626916: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcuda.so.1
2020-10-15 17:33:12.672638: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:982] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2020-10-15 17:33:12.672836: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1716] Found device 0 with properties: 
pciBusID: 0000:01:00.0 name: Quadro RTX 4000 computeCapability: 7.5
coreClock: 1.545GHz coreCount: 36 deviceMemorySize: 7.79GiB deviceMemoryBandwidth: 387.49GiB/s
2020-10-15 17:33:12.672879: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.672911: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcublas.so.10'; dlerror: libcublas.so.10: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.672942: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcufft.so.10'; dlerror: libcufft.so.10: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.672972: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcurand.so.10'; dlerror: libcurand.so.10: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.673001: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcusolver.so.10'; dlerror: libcusolver.so.10: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.673029: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcusparse.so.10'; dlerror: libcusparse.so.10: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.673059: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudnn.so.7'; dlerror: libcudnn.so.7: cannot open shared object file: No such file or directory
2020-10-15 17:33:12.673065: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1753] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...
2020-10-15 17:33:12.673215: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN)to use the following CPU instructions in performance-critical operations:  AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2020-10-15 17:33:12.697604: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 3600000000 Hz
2020-10-15 17:33:12.698881: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55f1090d5040 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-10-15 17:33:12.698894: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version
2020-10-15 17:33:12.699862: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1257] Device interconnect StreamExecutor with strength 1 edge matrix:
2020-10-15 17:33:12.699871: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1263]      
______________________________________________________________________________ test_resnet3d_34 _______________________________________________________________________________

resnet3d_test = <function resnet3d_test.<locals>.f at 0x7f3c184f0ae8>

    def test_resnet3d_34(resnet3d_test):
        """Test 34."""
        K.set_image_data_format('channels_last')
>       model = Resnet3DBuilder.build_resnet_34((224, 224, 224, 1), 2)

tests/test_resnet3d.py:30: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
resnet3d/resnet3d.py:279: in build_resnet_34
    [3, 4, 6, 3], reg_factor=reg_factor)
resnet3d/resnet3d.py:243: in build
    )(block)
resnet3d/resnet3d.py:113: in f
    )(input)
resnet3d/resnet3d.py:140: in f
    return _shortcut3d(input, residual)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

input = <tf.Tensor 'max_pooling3d_1/MaxPool3D:0' shape=(None, 56, 56, 56, 64) dtype=float32>
residual = <tf.Tensor 'conv3d_5/BiasAdd:0' shape=(None, 56, 56, 56, 64) dtype=float32>

    def _shortcut3d(input, residual):
        """3D shortcut to match input and residual and merges them with "sum"."""
>       stride_dim1 = ceil(input._keras_shape[DIM1_AXIS] \
            / residual._keras_shape[DIM1_AXIS])
E       AttributeError: 'Tensor' object has no attribute '_keras_shape'

resnet3d/resnet3d.py:80: AttributeError
______________________________________________________________________________ test_resnet3d_50 _______________________________________________________________________________

resnet3d_test = <function resnet3d_test.<locals>.f at 0x7f3c1aa8cb70>

    def test_resnet3d_50(resnet3d_test):
        """Test 50."""
        K.set_image_data_format('channels_last')
>       model = Resnet3DBuilder.build_resnet_50((224, 224, 224, 1), 1, 1e-2)

tests/test_resnet3d.py:40: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
resnet3d/resnet3d.py:285: in build_resnet_50
    [3, 4, 6, 3], reg_factor=reg_factor)
resnet3d/resnet3d.py:243: in build
    )(block)
resnet3d/resnet3d.py:113: in f
    )(input)
resnet3d/resnet3d.py:169: in f
    return _shortcut3d(input, residual)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

input = <tf.Tensor 'max_pooling3d_2/MaxPool3D:0' shape=(None, 56, 56, 56, 64) dtype=float32>
residual = <tf.Tensor 'conv3d_9/BiasAdd:0' shape=(None, 56, 56, 56, 256) dtype=float32>

    def _shortcut3d(input, residual):
        """3D shortcut to match input and residual and merges them with "sum"."""
>       stride_dim1 = ceil(input._keras_shape[DIM1_AXIS] \
            / residual._keras_shape[DIM1_AXIS])
E       AttributeError: 'Tensor' object has no attribute '_keras_shape'

resnet3d/resnet3d.py:80: AttributeError
______________________________________________________________________________ test_resnet3d_101 ______________________________________________________________________________

resnet3d_test = <function resnet3d_test.<locals>.f at 0x7f3c1abbd0d0>

    def test_resnet3d_101(resnet3d_test):
        """Test 101."""
        K.set_image_data_format('channels_last')
>       model = Resnet3DBuilder.build_resnet_101((224, 224, 224, 1), 2)

tests/test_resnet3d.py:50: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
resnet3d/resnet3d.py:291: in build_resnet_101
    [3, 4, 23, 3], reg_factor=reg_factor)
resnet3d/resnet3d.py:243: in build
    )(block)
resnet3d/resnet3d.py:113: in f
    )(input)
resnet3d/resnet3d.py:169: in f
    return _shortcut3d(input, residual)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

input = <tf.Tensor 'max_pooling3d_3/MaxPool3D:0' shape=(None, 56, 56, 56, 64) dtype=float32>
residual = <tf.Tensor 'conv3d_13/BiasAdd:0' shape=(None, 56, 56, 56, 256) dtype=float32>

    def _shortcut3d(input, residual):
        """3D shortcut to match input and residual and merges them with "sum"."""
>       stride_dim1 = ceil(input._keras_shape[DIM1_AXIS] \
            / residual._keras_shape[DIM1_AXIS])
E       AttributeError: 'Tensor' object has no attribute '_keras_shape'

resnet3d/resnet3d.py:80: AttributeError
______________________________________________________________________________ test_resnet3d_152 ______________________________________________________________________________

resnet3d_test = <function resnet3d_test.<locals>.f at 0x7f3c184b2f28>

    def test_resnet3d_152(resnet3d_test):
        """Test 152."""
        K.set_image_data_format('channels_last')
>       model = Resnet3DBuilder.build_resnet_152((224, 224, 224, 1), 2)

tests/test_resnet3d.py:60: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
resnet3d/resnet3d.py:297: in build_resnet_152
    [3, 8, 36, 3], reg_factor=reg_factor)
resnet3d/resnet3d.py:243: in build
    )(block)
resnet3d/resnet3d.py:113: in f
    )(input)
resnet3d/resnet3d.py:169: in f
    return _shortcut3d(input, residual)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

input = <tf.Tensor 'max_pooling3d_4/MaxPool3D:0' shape=(None, 56, 56, 56, 64) dtype=float32>
residual = <tf.Tensor 'conv3d_17/BiasAdd:0' shape=(None, 56, 56, 56, 256) dtype=float32>

    def _shortcut3d(input, residual):
        """3D shortcut to match input and residual and merges them with "sum"."""
>       stride_dim1 = ceil(input._keras_shape[DIM1_AXIS] \
            / residual._keras_shape[DIM1_AXIS])
E       AttributeError: 'Tensor' object has no attribute '_keras_shape'

resnet3d/resnet3d.py:80: AttributeError
_______________________________________________________________________________ test_get_block ________________________________________________________________________________

    def test_get_block():
        """Test get residual block."""
        K.set_image_data_format('channels_last')
        Resnet3DBuilder.build((224, 224, 224, 1), 2, 'bottleneck',
>                             [2, 2, 2, 2], reg_factor=1e-4)

tests/test_resnet3d.py:78: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
resnet3d/resnet3d.py:243: in build
    )(block)
resnet3d/resnet3d.py:113: in f
    )(input)
resnet3d/resnet3d.py:169: in f
    return _shortcut3d(input, residual)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

input = <tf.Tensor 'max_pooling3d_5/MaxPool3D:0' shape=(None, 56, 56, 56, 64) dtype=float32>
residual = <tf.Tensor 'conv3d_21/BiasAdd:0' shape=(None, 56, 56, 56, 256) dtype=float32>

    def _shortcut3d(input, residual):
        """3D shortcut to match input and residual and merges them with "sum"."""
>       stride_dim1 = ceil(input._keras_shape[DIM1_AXIS] \
            / residual._keras_shape[DIM1_AXIS])
E       AttributeError: 'Tensor' object has no attribute '_keras_shape'

resnet3d/resnet3d.py:80: AttributeError
============================================================================== warnings summary ===============================================================================
../../../../home/thor/miniconda3/envs/keras3d/lib/python3.6/site-packages/tensorflow/python/autograph/utils/testing.py:21
  /home/thor/miniconda3/envs/keras3d/lib/python3.6/site-packages/tensorflow/python/autograph/utils/testing.py:21: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
    import imp

-- Docs: https://docs.pytest.org/en/stable/warnings.html

---------- coverage: platform linux, python 3.6.11-final-0 -----------
Name                   Stmts   Miss  Cover   Missing
----------------------------------------------------
resnet3d/__init__.py       1      0   100%
resnet3d/resnet3d.py     124     25    80%   82-99, 108, 114, 131, 157, 185-188, 195, 244-267
----------------------------------------------------
TOTAL                    125     25    80%

=========================================================================== short test summary info ===========================================================================
FAILED tests/test_resnet3d.py::test_resnet3d_18 - AttributeError: 'Tensor' object has no attribute '_keras_shape'
FAILED tests/test_resnet3d.py::test_resnet3d_34 - AttributeError: 'Tensor' object has no attribute '_keras_shape'
FAILED tests/test_resnet3d.py::test_resnet3d_50 - AttributeError: 'Tensor' object has no attribute '_keras_shape'
FAILED tests/test_resnet3d.py::test_resnet3d_101 - AttributeError: 'Tensor' object has no attribute '_keras_shape'
FAILED tests/test_resnet3d.py::test_resnet3d_152 - AttributeError: 'Tensor' object has no attribute '_keras_shape'
FAILED tests/test_resnet3d.py::test_get_block - AttributeError: 'Tensor' object has no attribute '_keras_shape'`