Ember installation issues

[Gautham Krishnan]

Hello,

I have been facing some issues related to the errors in the attached build log following the installation instructions for ember on  https://github.com/speth/ember. I had set up the conda environment based on the environment.yaml file and the subsequent scons build failed with these errors. I would greatly appreciate any guidance to resolve this issue and install ember.

P.S. I also tried editing the enviroment.yaml file to reflect the dependencies listed on https://speth.github.io/ember-doc/sphinx/html/installation.html. This mainly included using some of the listed older dependency versions, and resulted in build appearing successful but the subsequent scons install failed with the error in the attached install.log.

Regards,
Gautham

[Ray Speth]

Hi,

Can you share the list of packages installed in your Conda environment (run conda list with the environment activated), and the contents of the config.log generated by build process? I just tested the build process and the environment.yaml provided still works for me, even though quite a few of the dependencies have had significant new versions.

Regards,
Ray

​

[gkr...@gmail.com]

Hi,

Please find attached the conda list of packages and the config.log. I hope this helps reveal the issue.

Regards,

Gautham

[Ray Speth]

Hi,

I figured out why it was working on my local machine — I had a different (older) copy of SUNDIALS installed that was being used instead of the one from the Conda environment.

I’ve just pushed a commit to the Ember repo that should fix the compatibility issues with SUNDIALS 7.x.

I also ran into an issue with getting consistent versions of the Cantera Python module and shared library installed, which was a problem for the Conda packages for Cantera 3.0. If you run into this, you may need to specify matching builds of each. For example, if the build is different among the packages shown by conda list | grep cantera, e.g.

cantera 3.0.1 py313h4beef36_12 conda-forge libcantera 3.0.1 h4beef36_12 conda-forge libcantera-devel 3.0.1 h4beef36_12 conda-forge

does not show the same build (here, h4beef36_12) for all packages, you can install a consistent version by running:
conda install libcantera=3.0.1=h4beef36_12 where the build specified in this command is the one matching the Python package (minus the part specifying the Python version). This part shouldn’t be an issue once I get around to migrating Ember to Cantera 3.1.

Regards,
Ray

​

[gkr...@gmail.com]

Hi Ray,

I pulled the latest commit from the repo, recreated the conda env and went through the build and install process, all associated logs attached. I believe from these that build worked but install still fails. Do you have a better idea from the logs why this might be?

I had also tried specifying the specific Cantera versions you mentioned in the last message but this did not seem to resolve the install error.

Regards,

Gautham

[Ray Speth]

Hi Gautham,

It looks like this error is due to a recent(ish) change in how setuptools names wheel files. I've pushed an updated version that should resolve the problem.

Regards,

Ray

[gkr...@gmail.com]

Good Morning, Ray

Thank you! I attempted a fresh build/install using the latest commit. I believe both install and build succeed now, attached are the logs for reference. However, something about the installation seems broken. When I try to import ember in python I find the following error:

import ember as eb
Traceback (most recent call last):
  File "<python-input-0>", line 1, in <module>
    import ember as eb
  File "~/miniconda3/envs/ember-build/lib/python3.13/site-packages/ember/__init__.py", line 4, in <module>
    from ._ember import *
ImportError: ~/miniconda3/envs/ember-build/lib/python3.13/site-packages/ember/_ember.cpython-313-x86_64-linux-gnu.so: undefined symbol: _ZN7Cantera9Transport9setThermoERNS_11ThermoPhaseE

Would you know if theres something about the environment or installation that still needs to be fixed to use the package?

Regards,
Gautham

[Ray Speth]

Hi Gautham,

That looks like an issue with conflicting versions of Cantera — the member function mentioned (after demangling the C++ symbol name) is Transport::setThermo(ThermoPhase&) which was removed in Cantera 3.1. It is not called directly from Ember. My best guess is that your compilation process picked up header files for Cantera 3.0 rather than Cantera 3.1, where the latter is the version installed in your Conda environment. It might be that Ember wasn’t fully recompiled after updating the Cantera version, or you have another copy of Cantera 3.0 installed somewhere that the compiler is picking up (e.g. /usr/local/include).

One thing you can try is a fresh build of Ember, deleting all build artifacts, by running rm -rf build .sconf_temp from the Ember source directory before running scons build again.

Does the scons test step work correctly, before installation?

Regards,
Ray

​

[gkr...@gmail.com]

Hi Ray,

Thank you for that hint. I cleared up all the old install files and tried a fresh build. Now, I got build and install to run and in python when I import ember, I do not run into the same error I had reported. However, I did notice that the environment is not fully getting set up correctly, as when running an example I can see that matplotlib and h5py were not installed. I could however get past that issue via manually installing those.

Regards,

Gautham

P.S. The scons test step before install does not work correctly, it throws the error that gtest/gtest.h is not found as indicated in the associated log i attached in my last email.