Missing library during RMG's RMS install on Explorer

[sevyharris]

Bug Description

I finally got around to installing the latest RMG version on Northeastern's explorer cluster (post-Python 3.9 update. I know I know I shouldn't have waited this long)

And I get this error during the source install_rms.sh step-- after Julia's installed and it's trying to install ReactionMechanismSimulator

ERROR: LoadError: InitError: Python: ImportError: /home/harris.se/.julia/juliaup/julia-1.10.10+0.x64.linux.gnu/bin/../lib/julia/libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/harris.se/anaconda3/envs/rmg_20250812/lib/python3.9/site-packages/rdkit/Chem/../../../../libRDKitFileParsers.so.1)
Python stacktrace:
 [1] <module>
   @ ~/anaconda3/envs/rmg_20250812/lib/python3.9/site-packages/rdkit/Chem/__init__.py:23
Stacktrace:
  [1] pythrow()
    @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/err.jl:89
  [2] errcheck
    @ ~/.julia/packages/PythonCall/avYrV/src/Core/err.jl:10 [inlined]
  [3] pyimport(m::String)
    @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/builtins.jl:1560
  [4] __init__()
    @ ReactionMechanismSimulator ~/.julia/packages/ReactionMechanismSimulator/lzNw6/src/ReactionMechanismSimulator.jl:32
  [5] include(mod::Module, _path::String)
    @ Base ./Base.jl:495
  [6] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2084
  [7] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1882
  [8] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
  [9] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [10] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1873
 [11] macro expansion
    @ ./loading.jl:1860 [inlined]
 [12] macro expansion
    @ ./lock.jl:267 [inlined]
 [13] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1823
 [14] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [15] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1816
during initialization of module ReactionMechanismSimulator
in expression starting at /home/harris.se/.julia/packages/ReactionMechanismSimulator/lzNw6/src/ReactionMechanismSimulator.jl:1

How To Reproduce

Try installing RMG on Northeastern's Explorer cluster, including the install_rms.sh step.

Expected Behavior

This should run without errors

Installation Information

Describe your installation method and system information.

• OS: NAME="Rocky Linux", VERSION="9.3 (Blue Onyx)"
• Installation method: source
• RMG version information:
  • RMG-Py: 6cf97c3
  • RMG-database: 987eb83638de8f522bb4bab26579742364499d40

Additional Context

These are technically my own experimental branches, but I don't see any reason they'd affect the RMS install.

This issue is mostly for me to keep track of my own debugging process.

I suspect the problem is that the RC compute folks haven't gotten around to building out all of the c/c++ libraries for Explorer like they had for Discovery. Let's see if I can find a workaround.

[sevyharris]

Interesting, I added to the LD_LIBRARY path in my .bashrc export LD_LIBRARY_PATH="/home/harris.se/anaconda3/envs/rmg_20250812/lib/:$LD_LIBRARY_PATH and got a segmentation fault instead of the above error:

julia> using ReactionMechanismSimulator
Segmentation fault (core dumped)

Removing the LD_LIBRARY_PATH change stops the segmentation fault and reverts to the previous error

[sevyharris]

Looks like the problem is that the $LD_LIBRARY_PATH needs to be pointing to some updated version of libstdc++.so.6, but where is it??

[sevyharris]

This is the version of rdkit I'm using that seems to be causing the problem:

[sevyharris]

But I can also do import rdkit.Chem and import rdkit without issue, so I'm not entirely sure what's going on here.

[JacksonBurns]

Does it run if you just downgrade rdkit?

Also how did you get that readout of the dependencies for rdkit? That's really helpful

[sevyharris]

Does it run if you just downgrade rdkit?

Also how did you get that readout of the dependencies for rdkit? That's really helpful

I'll give that a try!

I got the dependencies readout by using conda list to check my exact build version of rdkit, then heading over to conda-forge's rdkit page: https://anaconda.org/conda-forge/rdkit/files

There's an info button you can press for each version of the files that shows the dependencies used to build the file, so you just click the one that matches your build version from conda list

^here I just circled a random info button, not the version I have installed

[github-actions]

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