Error during running example_kinetics.py

[Zhang Zihao]

collect2: error: ld returned 1 exit status
CMakeFiles/F.dir/build.make:101: recipe for target 'F' failed
make[2]: *** [F] Error 1
CMakeFiles/Makefile2:82: recipe for target 'CMakeFiles/F.dir/all' failed
make[1]: *** [CMakeFiles/F.dir/all] Error 2
Makefile:90: recipe for target 'all' failed
make: *** [all] Error 2
Traceback (most recent call last):
File "/workspace/OpenCap/opencap-processing-main/example_kinetics.py", line 166, in <module>
settings = processInputsOpenSimAD(baseDir, dataFolder, session_id, trial_name,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/workspace/OpenCap/opencap-processing-main/UtilsDynamicSimulations/OpenSimAD/utilsOpenSimAD.py", line 2321, in processInputsOpenSimAD
generateExternalFunction(baseDir, dataFolder, session_id,
File "/workspace/OpenCap/opencap-processing-main/UtilsDynamicSimulations/OpenSimAD/utilsOpenSimAD.py", line 1544, in generateExternalFunction
buildExternalFunction(
File "/workspace/OpenCap/opencap-processing-main/UtilsDynamicSimulations/OpenSimAD/utilsOpenSimAD.py", line 1795, in buildExternalFunction
shutil.copy2(path_external_filename_foo, CPP_DIR)
File "/opt/conda/envs/opencap-processing/lib/python3.11/shutil.py", line 448, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/opt/conda/envs/opencap-processing/lib/python3.11/shutil.py", line 256, in copyfile
with open(src, 'rb') as fsrc:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/workspace/OpenCap/opencap-processing-main/UtilsDynamicSimulations/OpenSimAD/build-ExpressionGraphF/foo.py'

I use the docker, all steps are carried out according to the instructions but it just can't work.

[Matt Petrucci]

Hi Zhang,

Is your repo up to date?

This was an issue in the past: https://github.com/stanfordnmbl/opencap ... issues/113

Hope this helps,
Matt

[Matt Petrucci]

Hi Zhang,

Quick question, are you running this on Mac or Windows? If Mac, which OS?

Thanks!
Matt

[Zhang Zihao]

I am running this project on Linux and have installed libopenblas-base inside the docker container

[Matt Petrucci]

Hi Zhang,

Are you creating your own docker container? If yes, we haven't tested the compiler within a docker container.

The code should work without a docker container if a python environment is set up as outlined in the README of the Github repository. But if you run into issues with that let us know.

Thanks,
Matt

[Zhang Zihao]

Well, I managed to get it working on Windows, thanks for your help

[Matt Petrucci]

Great! Yes Windows should work well. We're looking into the problem on Linux.