Missing Conda Channel

Cyberteams TRECIS
1

I’m trying to install Phonopy on Europa. Phonopy provides a Conda install, which I figured would be easier than a manual install. The installation command

conda install -c conda-forge phonopy

is met with the following message

UnavailableInvalidChannel: The channel is not accessible or is invalid.
channel name: conda_channel
channel url: file:///opt/intel/oneapi/conda_channel
error code: 404

You will need to adjust your conda configuration to proceed.
Use conda config --show channels to view your configuration’s current state,
and use conda config --show-sources to view config file locations.

As of conda 4.3, a valid channel must contain a noarch/repodata.json and
associated noarch/repodata.json.bz2 file, even if noarch/repodata.json is
empty. Use conda index /opt/intel/oneapi/conda_channel, or create noarch/repodata.json
and associated noarch/repodata.json.bz2.

The obvious fix seems to be: create the noarch directory and put an empty repodata.json file inside it. But this needs to happen in Conda directory, which I don’t have permission to edit (I’m using the minicoduna/4.9.2 module). There may be another fix that I’m not seeing that doesn’t require a change to the module.

Let me know if you have any ideas.
Thanks in advance,
Patrick

2

I ran into another issue when attempting a manual install. The command:

git clone https://github.com/phonopy/phonopy.git

Produces this error:

/usr/libexec/git-core/git-remote-https: symbol lookup error: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b

3

Hey Patrick,

Sorry for the delay. I’ve been in review panels all week and Supercomputing is next week and I’m just swamped.

I recommend starting with your own miniconda3 install

$ cd $SCRATCH && mkdir src && cd src
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh

If you’re only installing a bit of stuff, you can install miniconda to $HOME/miniconda3, else install it to $SCRATCH/miniconda3

I answer yes to allow the Miniconda3 installer to run conda init and then logout and log back in.

Finally, when I log back in, I also turn off auto activate of base and then let’s update conda to the latest version as well

$ conda config --set auto_activate_base false 
$ conda update -n base -c defaults conda

Now, let’s install phonopy in a conda environment.

$ conda create -n phonopy -c conda-forge
$ conda activate phonopy
$ conda install -c conda-forge phonopy

Finally, the libk5crypto error you have is probably do to having anaconda3 or something else in your python paths. I don’t get an error when I git clone either inside or outside of the above phonopy conda enviornment.

Best,
Chris

4

Hi Chris,

No worries. I actually relocated this project from Europa to Ganymede. Phonopy wasn’t happy with any of the conda modules available over there either, but Sol has been helping me configure a new one.

Incidentally, I suspect the libk5crypto thing on Europa came from a conflict with IntelPython. I always have the OneAPI environment active for VASP, but it brings a lot else with it.

Thanks,
Patrick