Matlab/Octave interface: function "h5readatt_octave" not found, trying to run "setup"

[warsea94]

I am trying to run the file Rect_Waveguide.m from the Tutorials. I have added the installation path for interface to work.
When the command PlotHDF5FieldData(dump_file, PlotArgs) is executed, I get the following error, which is same as the one specified in this issue .

PlotHDF5FieldData(dump_file, PlotArgs)

warning: function "h5readatt_octave" not found, trying to run "setup"
warning: called from
    ReadHDF5Attribute at line 15 column 9
    ReadHDF5FieldData>ReadHDF5FieldData_octave at line 97 column 34
    ReadHDF5FieldData at line 29 column 19
    PlotHDF5FieldData at line 25 column 8
setting up openEMS matlab/octave interface
compiling oct files
HDF5 library path found at: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/openmpi
HDF5 include path found at: /usr/include/hdf5/serial
/usr/bin/ld: cannot open output file h5readatt_octave.oct: Permission denied
collect2: error: ld returned 1 exit status
sh: 2: /usr/lib/x86_64-linux-gnu/hdf5/openmpi: Permission denied
warning: mkoctfile: building exited with failure status
error: 'h5readatt_octave' undefined near line 22 column 19
error: called from
    ReadHDF5Attribute at line 22 column 10
    ReadHDF5FieldData>ReadHDF5FieldData_octave at line 97 column 34
    ReadHDF5FieldData at line 29 column 19
    PlotHDF5FieldData at line 25 column 8

I guess the setup.m file is updated based on this issue, but I somehow still get the same error. Is there something I am missing out ? Do help me with the issue.
Thanks in advance.

[thliebig]

Well you have a permission denied error. Maybe you need to run "setup.m" again but with admin rights? Not ideal for sure.
Otherwise if you build from source, make sure to build e.g. in your home dir or somewhere with full rights...

[DatKnight]

I'm also having the same issue, when I run the octave script as sudo I don't get the permission denied errors but I do get the following:

Create FDTD operator (compressed SSE + multi-threading)
FDTD simulation size: 27x12x122 --> 39528 FDTD cells 
FDTD timestep is: 7.79642e-13 s; Nyquist rate: 24 timesteps @2.67217e+10 Hz
Excitation signal length is: 1225 timesteps (9.55062e-10s)
Max. number of timesteps: 10000 ( --> 8.16327 * Excitation signal length)
Create FDTD engine (compressed SSE + multi-threading)
Running FDTD engine... this may take a while... grab a cup of coffee?!?
[@        4s] Timestep:         4920 || Speed:   48.6 MC/s (8.132e-04 s/TS) || Energy: ~1.85e-30 (-78.94dB)
Time for 4920 iterations with 39528.00 cells : 4.00 sec
Speed: 48.60 MCells/s 
warning: legend: 'best' not yet implemented for location specifier, using 'northeast' instead
warning: legend: 'best' not yet implemented for location specifier, using 'northeast' instead
warning: function "h5readatt_octave" not found, trying to run "setup"
warning: called from
    ReadHDF5Attribute at line 15 column 9
    ReadHDF5FieldData>ReadHDF5FieldData_octave at line 97 column 34
    ReadHDF5FieldData at line 29 column 19
    PlotHDF5FieldData at line 25 column 8
    waveguide at line 96 column 1

setting up openEMS matlab/octave interface
compiling oct files
error: running "setup" failed...
error: called from
    ReadHDF5Attribute at line 19 column 13
    ReadHDF5FieldData>ReadHDF5FieldData_octave at line 97 column 34
    ReadHDF5FieldData at line 29 column 19
    PlotHDF5FieldData at line 25 column 8
    waveguide at line 96 column 1

I'm not sure where I can find setup.m if I need to run that, I've followed the install instructions as best I could.

[DatKnight]

I've done a bit more research and I figured out the issue:
The octave development package wasn't installed, I'm not sure if this is something I missed in the tutorial but I just fixed it by running (in fedora):
sudo dnf install octave-devel
Then running octave as root, making sure to add the openEMS paths, and running setup

[morganepm]

Hi,
I have similar error message but unfortunately the steps described above do not seem to resolve the problem. Here is the error message I am getting:

calculating far field at phi=[0 90] deg...
CalcNF2FF: Reading nf2ff data only...
warning: load: '/home/xxxx/opt/openEMS/share/openEMS/matlab/Tutorials/tmp_Horn_Antenna/nf2ff.h5' found by searching load path
warning: called from
    ReadHDF5Mesh>ReadHDF5Mesh_octave at line 57 column 5
    ReadHDF5Mesh at line 19 column 14
    ReadNF2FF at line 15 column 10
    CalcNF2FF at line 111 column 11
    Horn_Antenna at line 164 column 7

warning: function "h5readatt_octave" not found, trying to run "setup"
warning: called from
    ReadHDF5Attribute at line 15 column 9
    ReadNF2FF at line 22 column 12
    CalcNF2FF at line 111 column 11
    Horn_Antenna at line 164 column 7

setting up openEMS matlab/octave interface
compiling oct files
HDF5 library path found at: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5 include path found at: /usr/include/hdf5/serial
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/Scrt1.o: in function `_start':
(.text+0x1b): undefined reference to `main'
collect2: error: ld returned 1 exit status
sh: 2: /usr/lib/x86_64-linux-gnu/hdf5/serial: Permission denied
error: running "setup" failed...
error: called from
    ReadHDF5Attribute at line 19 column 13
    ReadNF2FF at line 22 column 12
    CalcNF2FF at line 111 column 11
    Horn_Antenna at line 164 column 7

Do you have any insights for me?

[ivantaran]

Hi all!
I've the same issue.

compiling oct files
HDF5 library path found at: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5 include path found at: /usr/include/hdf5/serial
sh: 2: /usr/lib/x86_64-linux-gnu/hdf5/serial: Permission denied
error: mkoctfile: building exited with failure status

It seems that the problem in ~/.local/share/openEMS/matlab/setup.m
I added -shared to mkoctfile parameters and explicitly specified the hdf5inc_dir and hdf5lib_dir paths

            hdf5inc_dir = "/usr/include/hdf5/serial"
            hdf5lib_dir = "/usr/lib/x86_64-linux-gnu/hdf5/serial"
            mkoctfile("h5readatt_octave.cc", ["-L" hdf5lib_dir], ["-I" hdf5inc_dir], "-lhdf5", "-shared")

And it compiled successfully

>> setup

setting up openEMS matlab/octave interface
compiling oct files
HDF5 library path found at: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5 include path found at: /usr/include/hdf5/serial
hdf5inc_dir = /usr/include/hdf5/serial
hdf5lib_dir = /usr/lib/x86_64-linux-gnu/hdf5/serial