Undefined Symbol Error while running argos.py

[Komal0103]

I have been trying to run argos.py as given in the tutorial: python $MAP_BASE/helios/pipeViewer/pipe_view/argos.py -d small_core_pipeout -l ../layouts/small_core.alf.

However, running this command gives me the following errors: /usr/local/lib/libsimdb.so: undefined symbol: _ZN5simdb5Table8NS_DELIME, or

ImportError: /home/komals/sparta/map/helios/pipeViewer/pipe_view/logsearch.cpython-38-x86_64-linux-gnu.so: undefined symbol: _ZTI8wxThread.

I have built the Helios and Sparta frameworks as given in the map repository. There were issues while building the simdb submodule, so I separately built it using CMake. I get these errors even after reinstalling the dependencies multiple times, and checking for incorrect paths.

I apologize for the novice question, but it would be great if anyone could help me with this!

[klingaard]

Those are new issues

Looks like you're running directly from the build (as per the tutorial). This should be ok, but TBH I haven't tested that in a long while. We moved to an installed version of argos in the main repo. I'll look into it.

Can you try installing the pipe viewer? In other words, try this:

cmake --install . --prefix=$CONDA_PREFIX

then try this:

argos -d small_core_pipeout -l ../layouts/small_core.alf

[Komal0103]

Thank you for your reply! I tried using this. I get the same error:

Traceback (most recent call last):
  File "/home/komals/miniconda3/envs/sparta/bin/argos", line 5, in <module>
    from pipe_view.argos import main
  File "/home/komals/miniconda3/envs/sparta/lib/python3.12/site-packages/pipe_view/argos.py", line 41, in <module>
    from pipe_view.gui.dialogs.select_layout_dlg import SelectLayoutDlg  # noqa: E402, E501
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/komals/miniconda3/envs/sparta/lib/python3.12/site-packages/pipe_view/gui/dialogs/select_layout_dlg.py", line 9, in <module>
    from ...model.layout import Layout
  File "/home/komals/miniconda3/envs/sparta/lib/python3.12/site-packages/pipe_view/model/layout.py", line 11, in <module>
    from .import element_types as etypes
  File "/home/komals/miniconda3/envs/sparta/lib/python3.12/site-packages/pipe_view/model/element_types.py", line 2, in <module>
    from .element import FakeElement, BoxElement, ImageElement
  File "/home/komals/miniconda3/envs/sparta/lib/python3.12/site-packages/pipe_view/model/element.py", line 30, in <module>
    from ..logsearch import LogSearch  # Argos module for searching logfiles
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: /home/komals/miniconda3/envs/sparta/lib/python3.12/site-packages/pipe_view/logsearch.cpython-312-x86_64-linux-gnu.so: undefined symbol: _ZTI8wxThread

This is the same I get while using directly from the build.

[klingaard]

What linux are you using?

[Komal0103]

I am using Ubuntu 20.04.

[klingaard]

Ok, it used to work fine on 20, but I’m using 22.  Anyway, I assume you’re using a conda environment?  Also what compiler / version are you using?