Installing vrn in Fedora. /lib64/libmatio.so.2: undefined symbol: H5T_NATIVE_SCHAR_g

[fpradom]

Hello, Aaron

I desisted from use Fedora 29, while F29 and F28 have python3 preinstalled as default and internal use so installing python 2.7 was inutil.

I have made a clean installation from Fedora 27 that have python 2.7.15 preinstalled.

The full installation elements are as follow: Prerequisites:

sudo -i dnf install kernel-devel kernel-headers gcc gcc-c++ make dkms acpid libglvnd-glx libglvnd-opengl libglvnd-devel pkgconfig dnf install cmake wget git ImageMagick-devel dnf install openssl-devel bzip2-devel glog-devel boost-devel

NVidia driver for GeForce GTX 750 Ti

dnf install mesa-libGLU-devel libX11-devel libXi-devel libXmu-devel cuda 8.0 and cudnn 5.1 for coda 8

For python: dnf install python-devel

pip install visvis pip install imageio pip install numpy pip install dlib pip install matplotlib

Added gcc53-c++-5.3.0 for Torch installation

Installed Torch 7 from https://github.com/torch/distro.git

Installed THPP from https://github.com/1adrianb/thpp.git

Installed fb.python from https://github.com/facebook/fblualib.git

Installed VRN from https://github.com/AaronJackson/vrn.git

On running run.sh I had the Fatal Python error: ceval: tstate mix-up github

I surfed your Issues and finded in #59 your recomendation to remove from main.lua:

from mpl_toolkits.mplot3d import Axes3D import matplotlib.pyplot as plt import matplotlib.patches as patches

and replace on vrn/face-alignment/facedetection_dlib.lua:

local detections = py.reval('[np.asarray([d.left(), d.top(), d.right(), d.bottom()]) for i, d in enumerate(dets)]',{dets=dets})
with local detections = py.reval('[np.asarray([d.left(), d.top(), d.right(), d.bottom()],dtype=float) for i, d in enumerate(dets)]',{dets=dets})

main.lua needs npy4th and matio so,

---- installing npy4th ---- git clone https://github.com/htwaijry/npy4th.git cd npy4th luarocks make

---- installing matio ---- downloaded matio-1.5.2-7.fc23.x86_64.rpm from https://rpm.pbone.net/ sudo rpm -ihv --nodeps --force matio-1.5.2-7.fc23.x86_64.rpm luarocks install matio

---

With this done I tryed the run.sh again with following result:

[f_prado@localhost vrn]$ ./run.sh ...rado/usr/local/torch/install/share/lua/5.1/matio/ffi.lua:20: /lib64/libmatio.so.2: undefined symbol: H5T_NATIVE_SCHAR_g stack traceback: [C]: in function 'load' ...rado/usr/local/torch/install/share/lua/5.1/matio/ffi.lua:20: in function <...rado/usr/local/torch/install/share/lua/5.1/matio/ffi.lua:20> [C]: in function 'xpcall' ...rado/usr/local/torch/install/share/lua/5.1/matio/ffi.lua:20: in main chunk [C]: at 0x0044e490 [C]: in function 'pcall' ...ado/usr/local/torch/install/share/lua/5.1/trepl/init.lua:385: in function 'require' ...ado/usr/local/torch/install/share/lua/5.1/matio/init.lua:3: in main chunk [C]: at 0x0044e490 [C]: in function 'pcall' ...ado/usr/local/torch/install/share/lua/5.1/trepl/init.lua:385: in function 'require' ...rado/usr/local/torch/install/share/lua/5.1/xlua/init.lua:360: in function <...rado/usr/local/torch/install/share/lua/5.1/xlua/init.lua:360> [C]: in function 'pcall' ...rado/usr/local/torch/install/share/lua/5.1/xlua/init.lua:361: in function 'xrequire' main.lua:16: in main chunk [C]: in function 'dofile' ...ocal/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk [C]: at 0x004059e0 ...ado/usr/local/torch/install/share/lua/5.1/trepl/init.lua:389: ...ado/usr/local/torch/install/share/lua/5.1/trepl/init.lua:389: ...rado/usr/local/torch/install/share/lua/5.1/matio/ffi.lua:24: Could not find libmatio. Please make sure that you installd MatIO and you have the shared libraries (libmatio.so or libmatio.dylib) in your library path warning: could not be loaded (is it installed?) Scanning directory for data... Found 5 images 5 images require a face detector Initialising python libs...
Initialising detector...
/home/f_prado/usr/local/torch/install/bin/luajit: getrf : Lapack library not found in compile time
at /home/f_prado/usr/local/torch/pkg/torch/lib/TH/generic/THLapack.c:140
stack traceback:
[C]: at 0x7f8a18f8e350
[C]: in function 'inverse'
./utils.lua:51: in function 'transform'
./utils.lua:59: in function 'crop'
main.lua:58: in main chunk
[C]: in function 'dofile'
...ocal/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk
[C]: at 0x004059e0 ls: no se puede acceder a '.txt': No such file or directory ls: no se puede acceder a '.raw': No such file or directory

I have libmatio.so.2 in /lib64/

Can you please help me?

[AaronJackson]

Hmm, interesting. Thanks for your detailed report. Instead of fixing the issue, it might be easier to remove any dependency on matio from the face-alignment code. VRN doesn't depend need to access any MAT files.

[fpradom]

Hi Aaron eliminated line 16 in main.lua: -- xrequire('matio') -- matlab

now the run.sh execution gives: [f_prado@localhost vrn]$ ./run.sh Scanning directory for data... Found 5 images 5 images require a face detector Initialising python libs... Initialising detector... /home/f_prado/usr/local/torch/install/bin/luajit: getrf : Lapack library not found in compile time at /home/f_prado/usr/local/torch/pkg/torch/lib/TH/generic/THLapack.c:140 stack traceback: [C]: at 0x7f47635b9350 [C]: in function 'inverse' ./utils.lua:51: in function 'transform' ./utils.lua:59: in function 'crop' main.lua:58: in main chunk [C]: in function 'dofile' ...ocal/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk [C]: at 0x004059e0 ls: no se puede acceder a '.txt': No such file or directory ls: no se puede acceder a '.raw': No such file or directory

Any idea how to progress? Thanks in advance.

[AaronJackson]

Not sure about that one. I have not seen it under CentOS. Maybe try making sure *blas-devel is installed and trying to reinstall Torch7?

fpradom writes:

Hi Aaron eliminated line 16 in main.lua: -- xrequire('matio') -- matlab

now the run.sh execution gives: [f_prado@localhost vrn]$ ./run.sh Scanning directory for data... Found 5 images 5 images require a face detector Initialising python libs... Initialising detector... /home/f_prado/usr/local/torch/install/bin/luajit: getrf : Lapack library not found in compile time at /home/f_prado/usr/local/torch/pkg/torch/lib/TH/generic/THLapack.c:140 stack traceback: [C]: at 0x7f47635b9350 [C]: in function 'inverse' ./utils.lua:51: in function 'transform' ./utils.lua:59: in function 'crop' main.lua:58: in main chunk [C]: in function 'dofile' ...ocal/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk [C]: at 0x004059e0 ls: no se puede acceder a '.txt': No such file or directory ls: no se puede acceder a '.raw': No such file or directory

Any idea how to progress? Thanks in advance.

-- Aaron Jackson - M6PIU http://aaronsplace.co.uk/

[fpradom]

Will try, Thanks

[fpradom]

Hi Aaron:

Solved the previous error by executing: CMAKE_LIBRARY_PATH=/opt/OpenBLAS/include:/opt/OpenBLAS/lib:$CMAKE_LIBRARY_PATH luarocks install torch

now a new error appears:

f_prado@localhost vrn]$ ./run.sh Scanning directory for data... /home/f_prado/usr/local/torch/install/bin/luajit: ...o/usr/local/torch/install/share/lua/5.1/torch/Tensor.lua:466: Wrong size for view. Input size: 1x68x2. Output size: 2 stack traceback: [C]: in function 'error' ...o/usr/local/torch/install/share/lua/5.1/torch/Tensor.lua:466: in function 'view' ./utils.lua:178: in function 'bounding_box' ./utils.lua:300: in function 'getFileList' main.lua:25: in main chunk [C]: in function 'dofile' ...ocal/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk [C]: at 0x004059e0 ls: no se puede acceder a '.txt': No such file or directory ls: no se puede acceder a '.raw': No such file or directory Any suggestion? Thanks in advance

[AaronJackson]

Can you make sure nothing else changed in utils.lua? other than the matio stuff

[fpradom]

I have restored the original utils.lua and removed the above indicated lines. The error is the same

[AaronJackson]

Hmm, I can't think why that would happen. Check that run.sh still contains

th main.lua -model 2D-FAN-300W.t7 \
   -input ../$INPUT/ \
   -detectFaces true \
   -mode generate \
   -output ../$INPUT/ \
   -device gpu \
-outputFormat txt

and that you didn't remove or change any of the lines there.

Are you using the included example images? Or are you using a different folder, perhaps one that contains some txt files?

[fpradom]

Hi Aaron: All lines are present in run.sh I am using your images in the examples directory and there are not .txt files but .t7, one for each .jpg image.

[fpradom]

in the file ../usr/local/torch/install/share/lua/5.1/torch/Tensor.lua the line that gives the error is in a function that has as comment "-- TODO : This should be implemented in TH and and wrapped." Can this have an influence in the process?

[AaronJackson]

It shouldn't be calling it anyway. The t7 files shouldn't be there so I am wondering if you had run it outside of the script in the past for testing or something. Anyway, delete the t7 files and try again. The face-alignment code thinks they are facial landmarks and is trying to use them as a bounding box.

[fpradom]

Hi Aaron: You are right. I have made many tries. After deleting the t7 files the program has continue until an out of memory error appeared. I have changed the gpu device with cpu, and now the output is: [f_prado@localhost vrn]$ ./run.sh Scanning directory for data... Found 5 images 5 images require a face detector Initialising python libs... Initialising detector... Cropped and scaled AFLW_image00046.jpg Cropped and scaled AFLW_image00095.jpg Cropped and scaled AFLW_image00190.jpg Cropped and scaled AFLW_image00656.jpg Cropped and scaled asj.jpg Processed AFLW_image00190. Processed asj. Processed AFLW_image00046. Processed AFLW_image00656. Processed AFLW_image00095. Traceback (most recent call last): File "../vis.py", line 20, in t = vv.imshow(im) File "/usr/lib/python2.7/site-packages/visvis/functions/imshow.py", line 57, in imshow axes = vv.gca() File "/usr/lib/python2.7/site-packages/visvis/functions/gca.py", line 19, in gca f = vv.gcf() File "/usr/lib/python2.7/site-packages/visvis/functions/gcf.py", line 23, in gcf return vv.figure() File "/usr/lib/python2.7/site-packages/visvis/functions/figure.py", line 23, in figure backends.use() File "/usr/lib/python2.7/site-packages/visvis/backends/init.py", line 229, in use raise RuntimeError("None of the backends could be loaded. "+tmp) RuntimeError: None of the backends could be loaded. Install PySide, PyQt4, wxPython, GTK, or fltk. Traceback (most recent call last): File "../vis.py", line 20, in t = vv.imshow(im) File "/usr/lib/python2.7/site-packages/visvis/functions/imshow.py", line 57, in imshow axes = vv.gca() File "/usr/lib/python2.7/site-packages/visvis/functions/gca.py", line 19, in gca f = vv.gcf() File "/usr/lib/python2.7/site-packages/visvis/functions/gcf.py", line 23, in gcf return vv.figure() File "/usr/lib/python2.7/site-packages/visvis/functions/figure.py", line 23, in figure backends.use() File "/usr/lib/python2.7/site-packages/visvis/backends/init.py", line 229, in use raise RuntimeError("None of the backends could be loaded. "+tmp) RuntimeError: None of the backends could be loaded. Install PySide, PyQt4, wxPython, GTK, or fltk. Traceback (most recent call last): File "../vis.py", line 20, in t = vv.imshow(im) File "/usr/lib/python2.7/site-packages/visvis/functions/imshow.py", line 57, in imshow axes = vv.gca() File "/usr/lib/python2.7/site-packages/visvis/functions/gca.py", line 19, in gca f = vv.gcf() File "/usr/lib/python2.7/site-packages/visvis/functions/gcf.py", line 23, in gcf return vv.figure() File "/usr/lib/python2.7/site-packages/visvis/functions/figure.py", line 23, in figure backends.use() File "/usr/lib/python2.7/site-packages/visvis/backends/init.py", line 229, in use raise RuntimeError("None of the backends could be loaded. "+tmp) RuntimeError: None of the backends could be loaded. Install PySide, PyQt4, wxPython, GTK, or fltk. Traceback (most recent call last): File "../vis.py", line 20, in t = vv.imshow(im) File "/usr/lib/python2.7/site-packages/visvis/functions/imshow.py", line 57, in imshow axes = vv.gca() File "/usr/lib/python2.7/site-packages/visvis/functions/gca.py", line 19, in gca f = vv.gcf() File "/usr/lib/python2.7/site-packages/visvis/functions/gcf.py", line 23, in gcf return vv.figure() File "/usr/lib/python2.7/site-packages/visvis/functions/figure.py", line 23, in figure backends.use() File "/usr/lib/python2.7/site-packages/visvis/backends/init.py", line 229, in use raise RuntimeError("None of the backends could be loaded. "+tmp) RuntimeError: None of the backends could be loaded. Install PySide, PyQt4, wxPython, GTK, or fltk. Traceback (most recent call last): File "../vis.py", line 20, in t = vv.imshow(im) File "/usr/lib/python2.7/site-packages/visvis/functions/imshow.py", line 57, in imshow axes = vv.gca() File "/usr/lib/python2.7/site-packages/visvis/functions/gca.py", line 19, in gca f = vv.gcf() File "/usr/lib/python2.7/site-packages/visvis/functions/gcf.py", line 23, in gcf return vv.figure() File "/usr/lib/python2.7/site-packages/visvis/functions/figure.py", line 23, in figure backends.use() File "/usr/lib/python2.7/site-packages/visvis/backends/init.py", line 229, in use raise RuntimeError("None of the backends could be loaded. "+tmp) RuntimeError: None of the backends could be loaded. Install PySide, PyQt4, wxPython, GTK, or fltk.

Are PySide, PyQt4, wxPython, GTK, or fltk. necessary?

[fpradom]

After this, I have .txt files in examples, jpg files in scaled and .raw files in output.

[AaronJackson]

Doesn't look like an out of memory error to me. Are you connecting to a linux box without X forwarding? Instead you could use the raw2obj script and then open with something like Meshlab.

[fpradom]

Hi Aaron: When I installed the nvidia driver I mused uninstall the xorg-x11 library. I proved to use the raw2obj script with following script:

ls -1 output/*.raw | sed 's/.raw//' | while read fname ; do python raw2obj.py \ --volume output/"$i".raw \ --image examples/scaled/"$i".jpg \ --obj output/"$i".obj done

but this give me following error: [f_prado@localhost vrn]$ ./r2o.sh Traceback (most recent call last): File "raw2obj.py", line 2, in import scipy.misc ImportError: No module named scipy.misc

I can not find scipy.misc in my HD

[fpradom]

Sorry, I instaled scipy and now the error is:

[f_prado@localhost vrn]$ ./r2o.sh Traceback (most recent call last): File "raw2obj.py", line 2, in import scipy.misc ImportError: No module named scipy.misc Haw can I install mcubes module?

[fpradom]

I make a mistake in the comment . The output is: [f_prado@localhost vrn]$ ./r2o.sh Traceback (most recent call last): File "raw2obj.py", line 3, in import mcubes ImportError: No module named mcubes

[fpradom]

Hi Aaron Found the PyMcubes and installed. Now all seems to run well.