CADET Build in Ubuntu, in Anaconda base env: cadet-python error: glibc incompatible

CADET Troubleshooting
1

Hello all,

I built CADET on my Linux machine (see “Prerequisites and OS details” at the bottom), and followed it up with the Anaconda instructions mentioned in the tutorial.

However, upon trying to install cadet-python in Anaconda’s (base) environment, I get the error given below (under “Error”).

Do you have any suggestions/ recommendations?

Thanks in advance!
Soumitra.

CMake Files
CMakeError.txt (5.2 KB)
CMakeOutput.txt (49.6 KB)

Error:

(base) soumi@Neptune:~$ conda install -c immudzen cadet-python Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |

Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package → Available versionsThe following specifications were found to be incompatible with your system:

  • feature:/linux-64::__glibc==2.31=0
  • feature:|@/linux-64::__glibc==2.31=0

Your installed version is: 2.31

Prerequisites and OS details:

Ubuntu 20.04.2 LTS (codename = focal)
libhdf5-dev: 1.10.4+repack-11ubuntu1
cmake: 3.16.3-1ubuntu1
clang: 1:10.0-50~exp1
intel-mkl: 2020.0.166-1

1 Like
2

Hi Soumitra,

The problem seems to be because of mixing packages between Anaconda’s defaults and conda-forge channels. You can fix this by removing one of these (it’s better to remove defaults).

conda config --show channels
conda config --remove channels <channel-name>

After this point, I’d recommend cleaning your environment, removing/reinstalling packages from the deleted channel. You can see all the installed packages (and channel) with conda list. This should solve your problem, but I recommend following the next few steps as well.

Firstly, let’s ensure that conda is updated.

conda update conda

Secondly, it’s best practice to NOT use the base conda environment for your work. Typical workflow is to create a new environment for each project. This way dependency conflicts are mostly avoided. Using dedicated environments, you don’t have to worry about cleaning your base environment.

conda create -n cadet     ## Creates an env called cadet
conda activate cadet
conda install -c immudzen cadet-python

If the problem still persists, we might try setting python=3.7, and just a full reinstall of anaconda which seems to have helped some users. Do let us know if this works :grinning_face_with_smiling_eyes:

Related links:

3 Likes
3

Thanks Jayghosh.

The original issue is resolved! However, another has cropped up which I don’t seem to be able to fix.

I built CADET, installed Anaconda, created a virtual environment and within that installed cadet-python - successfully.

However, when I run a test script (the tutorial script) from iPython, it gives me an error upon ‘model.run’:

PermissionError: [Errno 13] Permission denied: '/home/soumi/cadet_root/build/src/cadet-cli'

When I try to see the permissions, I do seem to have all permissions:

In [1]: ls
build-tools/  cadet-cli/  libcadet/  tools/

In [2]: ls -l
total 16
drwxrwxrwx 3 soumi soumi 4096 Jul 21 15:24 build-tools/
drwxrwxrwx 3 soumi soumi 4096 Jul 21 15:25 cadet-cli/
drwxrwxrwx 3 soumi soumi 4096 Jul 21 15:25 libcadet/
drwxrwxrwx 3 soumi soumi 4096 Jul 21 15:25 tools/

In [4]: cd cadet-cli/
/home/soumi/cadet_root/build/src/cadet-cli

In [5]: ls
cadet-cli*  CMakeFiles/  cmake_install.cmake  Makefile

In [6]: ls -l
total 552
-rwxrwxrwx 1 soumi soumi 543448 Jul 21 15:25 cadet-cli*
drwxrwxrwx 3 soumi soumi   4096 Jul 21 15:23 CMakeFiles/
-rw-rw-rw- 1 soumi soumi   2369 Jul 21 15:23 cmake_install.cmake
-rw-rw-rw- 1 soumi soumi  12053 Jul 21 15:23 Makefile

I’m currently trying to figure this one out. Any help would be much appreciated! :slight_smile:

Thanks,

4

I believe the issue is that you’re pointing to the cadet-cli/ folder instead of the executable inside it.

Try pointing to /home/soumi/cadet_root/build/src/cadet-cli/cadet-cli

Cheers!

1 Like
5

Whoops! My mistake. Everything is now fine.

Thanks so much for your help!