Closed CooperStansbury closed 3 months ago
Verified LD_LIBRARY_PATH: I've set LD_LIBRARY_PATH to include a compatible libstdc++.so.6 prior to installing graph-tool via conda.
There should be no need to set LD_LIBRARY_PATH
, and it is probably a bad idea. Your own conda environment will include a compatible libstdc++.so
in its own lib/
directory. Judging from your error message above, it should be here:
/home/cstansbu/miniconda3/lib/libstdc++.so
BTW, it appears that you have installed graph-tool
into your miniconda base
environment. You should probably try installing it to a dedicated environment, at least for testing purposes.
First, make sure your version of conda
is up-to-date. Since you appear to have multiple conda installations on your machine, be careful to work with your own base
environment:
source /home/cstansbu/miniconda3/bin/activate base
conda install -n base 'conda>=24.5.0'
And then try installing graph-tool-base
with the following command:
conda create -n gt --override-channels -c conda-forge 'graph-tool-base>=2.68'
And check to see if it was installed properly:
conda activate gt
python -c 'import graph_tool.all as gt'
If that works, you can try installing the full graph-tool
package (which includes drawing dependencies).
conda install -n gt --override-channels -c conda-forge `graph-tool>=2.68`
If you're still having trouble, please reply with the output of conda info
, along with a transcript of the commands you tried.
A fresh conda install worked. I will close.
Best,
Comment:
Summary:
I'm attempting to use
graph-tool
(version 2.58) installed via conda-forge on my University's HPC system, but I'm encountering an import error due to an incompatiblelibstdc++.so.6
version.Error Message:
Troubleshooting Steps:
LD_LIBRARY_PATH
: I've setLD_LIBRARY_PATH
to include a compatiblelibstdc++.so.6
prior to installinggraph-tool
viaconda
.ldd libgraph_tool_core.so
indicates the shared object is correctly linked to the compatiblelibstdc++.so.6
.libstdc++.so.6
in a standard path that is taking precedence.Request:
I'd appreciate guidance on diagnosing the root cause: Why is the incompatible system
libstdc++.so.6
being used despite the correct linkage?System Specifications:
Additional Notes: