How to install Parallel HDF5 with Jetson Nano?

Robotics & Edge Computing Jetson & Embedded Systems Jetson Nano
1

I have some problem when running tensorflow:

Traceback (most recent call last):
File “/usr/lib/python3.6/contextlib.py”, line 99, in exit
self.gen.throw(type, value, traceback)
File “/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py”, line 5652, in get_controller
yield g
File “/home/jetsonnano2/Desktop/TTRobot_Proj_20200207/yolo.py”, line 70, in generate
self.yolo_model = load_model(model_path, compile=False)
File “/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py”, line 458, in load_wrapper
return load_function(*args, **kwargs)
File “/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py”, line 550, in load_model
model = _deserialize_model(h5dict, custom_objects, compile)
File “/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py”, line 239, in _deserialize_model
model_config = h5dict[‘model_config’]
File “/usr/local/lib/python3.6/dist-packages/keras/utils/io_utils.py”, line 298, in getitem
elif attr in self.data:
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “/usr/local/lib/python3.6/dist-packages/h5py/_hl/group.py”, line 415, in contains
return self._e(name) in self.id
File “h5py/h5g.pyx”, line 461, in h5py.h5g.GroupID.contains
File “h5py/h5g.pyx”, line 462, in h5py.h5g.GroupID.contains
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “h5py/h5g.pyx”, line 531, in h5py.h5g._path_valid
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “h5py/h5l.pyx”, line 212, in h5py.h5l.LinkProxy.exists
KeyError: ‘Unable to get link info (bad symbol table node signature)’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “TTRobot2.0__with_APP.py”, line 557, in
table_locate = PP.yolo_predict(video,reffrence_frames)
File “/home/jetsonnano2/Desktop/TTRobot_Proj_20200207/PingPong_lib_yolo_v1.py”, line 86, in yolo_predict
yolo = YOLO()
File “/home/jetsonnano2/Desktop/TTRobot_Proj_20200207/yolo.py”, line 45, in init
self.boxes, self.scores, self.classes = self.generate()
File “/home/jetsonnano2/Desktop/TTRobot_Proj_20200207/yolo.py”, line 74, in generate
self.yolo_model.load_weights(self.model_path) # make sure model, anchors and classes match
File “/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py”, line 458, in load_wrapper
return load_function(*args, **kwargs)
File “/usr/local/lib/python3.6/dist-packages/keras/engine/network.py”, line 1217, in load_weights
f, self.layers, reshape=reshape)
File “/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py”, line 1162, in load_weights_from_hdf5_group
g = f[name]
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “/usr/local/lib/python3.6/dist-packages/h5py/_hl/group.py”, line 264, in getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “h5py/h5o.pyx”, line 190, in h5py.h5o.open
KeyError: ‘Unable to open object (bad symbol table node signature)’

2

Hi,

Please try the following command to see if works:

sudo apt-get install libhdf5-serial-dev hdf5-tools

Thanks.

3

I have installed the package before, so it didn’t work.

4

Hi,

Sorry for the late.

Maybe you can try to install parallel hdf5 from source.
This will require you to install MPI on Jetson first.

https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel

Thanks.