help > Deep Neuron binary instantiation fail on Ubuntu 16.04
Showing 1-4 of 4 posts
Aug 13, 2018 05:08 PM | ZHANGCAN DING - Bournemouth University
Deep Neuron binary instantiation fail on Ubuntu 16.04
Hi all,
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
Aug 13, 2018 05:08 PM | Zhi Zhou
RE: Deep Neuron binary instantiation fail on Ubuntu 16.04
You don't have to install
Caffe.
Please run the "start_vaa3d.sh" in the folder "Vaa3D_CentOS_64bit_DeepNeuron" as mentioned in the instruction.
Originally posted by ZHANGCAN DING:
Please run the "start_vaa3d.sh" in the folder "Vaa3D_CentOS_64bit_DeepNeuron" as mentioned in the instruction.
Originally posted by ZHANGCAN DING:
Hi all,
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
Aug 14, 2018 04:08 PM | ZHANGCAN DING - Bournemouth University
RE: Deep Neuron binary instantiation fail on Ubuntu 16.04
Hi Zhi,
Thank you for your reply. Sorry I did not mention that I have tried with ./start_vaa3d.sh but it still failed to load the plug in. The error is:
./start_vaa3d.sh
ERROR: ld.so: object '/data/mat/zhi/VAA3D/Vaa3D_CentOS_64bit_deeplearning/libstdc++.so.6' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libgstbase-0.10.so.0: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
renaming the libstdc++.so.6. changes nothing. It seems something goes wrong with the LD_PRELOAD, after I typed unset LD_PROLOAD;ls the result is
unset LD_PROLOAD;ls
libatlas.so.3 liblbfgs.so libQtGui.so.4
libboost_filesystem.so.1.63.0 libleveldb.so.1 libQtNetwork.so.4
libboost_system.so.1.63.0 liblmdb.so libQtOpenGL.so.4
libboost_thread.so.1.63.0 libneurolabi_debug.so libQtSvg.so.4
libcaffe.so.1.0.0-rc3 libopencv_core.so libQtXml.so.4
libcblas.so.3 libopencv_core.so.2.4 libsnappy.so.1
libconfig++.so.9 libopencv_core.so.3.0 libstdc++.so.6
libcublas.so.8.0 libopencv_core.so.3.0.0 libstdc++.so.6.0.13
libcudart.so.8.0 libopencv_highgui.so.2.4 libstdc++.so.6.0.17
libcudnn.so.5 libopencv_imgproc.so libtiff.so.3
libcurand.so.8.0 libopencv_imgproc.so.2.4 libtiff.so.5
libfftw3f.so.3 libopencv_imgproc.so.3.0 libtiff.so.5.1.0
libfftw3f_threads.so.3 libopencv_imgproc.so.3.0.0 plugins
libfftw3.so.3 libopencv_ml.so start_vaa3d.sh
libglog.so.0 libopencv_ml.so.3.0 start_vaa3d.sh~
libhdf5_hl.so.10 libopencv_ml.so.3.0.0 v3d_version.xml
libhdf5.so.10 libprotobuf.so.11 vaa3d
liblbfgs-1.10.so libQtCore.so.4
So what can I do next to properly load the plug-in please? Thank you so much.
Best,
Zhangcan
Originally posted by Zhi Zhou:
Thank you for your reply. Sorry I did not mention that I have tried with ./start_vaa3d.sh but it still failed to load the plug in. The error is:
./start_vaa3d.sh
ERROR: ld.so: object '/data/mat/zhi/VAA3D/Vaa3D_CentOS_64bit_deeplearning/libstdc++.so.6' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libgstbase-0.10.so.0: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
renaming the libstdc++.so.6. changes nothing. It seems something goes wrong with the LD_PRELOAD, after I typed unset LD_PROLOAD;ls the result is
unset LD_PROLOAD;ls
libatlas.so.3 liblbfgs.so libQtGui.so.4
libboost_filesystem.so.1.63.0 libleveldb.so.1 libQtNetwork.so.4
libboost_system.so.1.63.0 liblmdb.so libQtOpenGL.so.4
libboost_thread.so.1.63.0 libneurolabi_debug.so libQtSvg.so.4
libcaffe.so.1.0.0-rc3 libopencv_core.so libQtXml.so.4
libcblas.so.3 libopencv_core.so.2.4 libsnappy.so.1
libconfig++.so.9 libopencv_core.so.3.0 libstdc++.so.6
libcublas.so.8.0 libopencv_core.so.3.0.0 libstdc++.so.6.0.13
libcudart.so.8.0 libopencv_highgui.so.2.4 libstdc++.so.6.0.17
libcudnn.so.5 libopencv_imgproc.so libtiff.so.3
libcurand.so.8.0 libopencv_imgproc.so.2.4 libtiff.so.5
libfftw3f.so.3 libopencv_imgproc.so.3.0 libtiff.so.5.1.0
libfftw3f_threads.so.3 libopencv_imgproc.so.3.0.0 plugins
libfftw3.so.3 libopencv_ml.so start_vaa3d.sh
libglog.so.0 libopencv_ml.so.3.0 start_vaa3d.sh~
libhdf5_hl.so.10 libopencv_ml.so.3.0.0 v3d_version.xml
libhdf5.so.10 libprotobuf.so.11 vaa3d
liblbfgs-1.10.so libQtCore.so.4
So what can I do next to properly load the plug-in please? Thank you so much.
Best,
Zhangcan
Originally posted by Zhi Zhou:
You don't have
to install Caffe.
Please run the "start_vaa3d.sh" in the folder "Vaa3D_CentOS_64bit_DeepNeuron" as mentioned in the instruction.
Originally posted by ZHANGCAN DING:
Please run the "start_vaa3d.sh" in the folder "Vaa3D_CentOS_64bit_DeepNeuron" as mentioned in the instruction.
Originally posted by ZHANGCAN DING:
Hi all,
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
Aug 15, 2018 12:08 AM | Zhi Zhou
RE: Deep Neuron binary instantiation fail on Ubuntu 16.04
The error is from here
"libgstbase-0.10.so.0: cannot open shared object file: No such file
or directory) ".
You may have to install GStreamer on your Ubuntu.
Originally posted by ZHANGCAN DING:
You may have to install GStreamer on your Ubuntu.
Originally posted by ZHANGCAN DING:
Hi Zhi,
Thank you for your reply. Sorry I did not mention that I have tried with ./start_vaa3d.sh but it still failed to load the plug in. The error is:
./start_vaa3d.sh
ERROR: ld.so: object '/data/mat/zhi/VAA3D/Vaa3D_CentOS_64bit_deeplearning/libstdc++.so.6' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libgstbase-0.10.so.0: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
renaming the libstdc++.so.6. changes nothing. It seems something goes wrong with the LD_PRELOAD, after I typed unset LD_PROLOAD;ls the result is
unset LD_PROLOAD;ls
libatlas.so.3 liblbfgs.so libQtGui.so.4
libboost_filesystem.so.1.63.0 libleveldb.so.1 libQtNetwork.so.4
libboost_system.so.1.63.0 liblmdb.so libQtOpenGL.so.4
libboost_thread.so.1.63.0 libneurolabi_debug.so libQtSvg.so.4
libcaffe.so.1.0.0-rc3 libopencv_core.so libQtXml.so.4
libcblas.so.3 libopencv_core.so.2.4 libsnappy.so.1
libconfig++.so.9 libopencv_core.so.3.0 libstdc++.so.6
libcublas.so.8.0 libopencv_core.so.3.0.0 libstdc++.so.6.0.13
libcudart.so.8.0 libopencv_highgui.so.2.4 libstdc++.so.6.0.17
libcudnn.so.5 libopencv_imgproc.so libtiff.so.3
libcurand.so.8.0 libopencv_imgproc.so.2.4 libtiff.so.5
libfftw3f.so.3 libopencv_imgproc.so.3.0 libtiff.so.5.1.0
libfftw3f_threads.so.3 libopencv_imgproc.so.3.0.0 plugins
libfftw3.so.3 libopencv_ml.so start_vaa3d.sh
libglog.so.0 libopencv_ml.so.3.0 start_vaa3d.sh~
libhdf5_hl.so.10 libopencv_ml.so.3.0.0 v3d_version.xml
libhdf5.so.10 libprotobuf.so.11 vaa3d
liblbfgs-1.10.so libQtCore.so.4
So what can I do next to properly load the plug-in please? Thank you so much.
Best,
Zhangcan
Originally posted by Zhi Zhou:
Thank you for your reply. Sorry I did not mention that I have tried with ./start_vaa3d.sh but it still failed to load the plug in. The error is:
./start_vaa3d.sh
ERROR: ld.so: object '/data/mat/zhi/VAA3D/Vaa3D_CentOS_64bit_deeplearning/libstdc++.so.6' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libgstbase-0.10.so.0: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
renaming the libstdc++.so.6. changes nothing. It seems something goes wrong with the LD_PRELOAD, after I typed unset LD_PROLOAD;ls the result is
unset LD_PROLOAD;ls
libatlas.so.3 liblbfgs.so libQtGui.so.4
libboost_filesystem.so.1.63.0 libleveldb.so.1 libQtNetwork.so.4
libboost_system.so.1.63.0 liblmdb.so libQtOpenGL.so.4
libboost_thread.so.1.63.0 libneurolabi_debug.so libQtSvg.so.4
libcaffe.so.1.0.0-rc3 libopencv_core.so libQtXml.so.4
libcblas.so.3 libopencv_core.so.2.4 libsnappy.so.1
libconfig++.so.9 libopencv_core.so.3.0 libstdc++.so.6
libcublas.so.8.0 libopencv_core.so.3.0.0 libstdc++.so.6.0.13
libcudart.so.8.0 libopencv_highgui.so.2.4 libstdc++.so.6.0.17
libcudnn.so.5 libopencv_imgproc.so libtiff.so.3
libcurand.so.8.0 libopencv_imgproc.so.2.4 libtiff.so.5
libfftw3f.so.3 libopencv_imgproc.so.3.0 libtiff.so.5.1.0
libfftw3f_threads.so.3 libopencv_imgproc.so.3.0.0 plugins
libfftw3.so.3 libopencv_ml.so start_vaa3d.sh
libglog.so.0 libopencv_ml.so.3.0 start_vaa3d.sh~
libhdf5_hl.so.10 libopencv_ml.so.3.0.0 v3d_version.xml
libhdf5.so.10 libprotobuf.so.11 vaa3d
liblbfgs-1.10.so libQtCore.so.4
So what can I do next to properly load the plug-in please? Thank you so much.
Best,
Zhangcan
Originally posted by Zhi Zhou:
You don't have
to install Caffe.
Please run the "start_vaa3d.sh" in the folder "Vaa3D_CentOS_64bit_DeepNeuron" as mentioned in the instruction.
Originally posted by ZHANGCAN DING:
Please run the "start_vaa3d.sh" in the folder "Vaa3D_CentOS_64bit_DeepNeuron" as mentioned in the instruction.
Originally posted by ZHANGCAN DING:
Hi all,
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan
I was trying to start the bianry version of Deep Neuron from https://github.com/Vaa3D/Vaa3D_Data/rele... on my linux (Ubuntu 16.04), but the plugin failed to be loaded.
The error is:
Fail instantiation( Cannot load library /home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so: (libcaffe.so.1.0.0-rc3: cannot open shared object file: No such file or directory) ): "/home/ynie02/Downloads/vaa3d_Test/deepneuron/Vaa3D_CentOS_64bit_DeepNeuron/plugins/DeepNeuron_toolbox/libDeep_Neuron.so"
Searching ./plugins done.
Do anyone have any ideas for this problem please? I referred to a similar issue in https://www.nitrc.org/forum/forum.php?thread_id=9118&forum_id=1553 , which renames the particular .so file to force using the one in system lib, but I think it's not applicable for this issue as I do not have caffe lib in my system. Or should I install caffe first?
Thank you so much.
Best,
Zhangcan