Problems installing HTMD

[lblaabjerg]

Hi,

I am having some problems installing HTMD (specifically version 2.0.5). I am installing in a fresh Miniconda environment with Python 3.7.

If I run conda install htmd=2.0.5 -c acellera -c conda-forge it gets stuck trying to solve the environment (have tried waiting for ~20 min):

(thermonet) [lasbla@s96n41 ThermoNet]$ conda install htmd=2.0.5 -c acellera -c conda-forge 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: \

If I run conda install htmd=2.0.5 -c acellera I get the following error:

(thermonet) [lasbla@s96n41 ThermoNet]$ conda install htmd=2.0.5 -c acellera 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==2.17=0
• feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17

[stefdoerr]

Why do you want to install an old version of HTMD? (and python 3.7 which reaches end of life in 6 months from now?)

[lblaabjerg]

Hi Stefan. Thank you for the quick reply. I am trying to reproduce the results in this paper: https://github.com/gersteinlab/ThermoNet.

[stefdoerr]

Try 2.0.8. It's the latest version we released for python 3.7 and it should not have significant changes to 2.0.5

[stefdoerr]

Oh actually I now read the full question. You indeed should have waited for 20+ minutes :laughing: That's conda for you. The much faster alternative is using mamba

conda create -n myenv
conda activate myenv
conda install python=3.7 mamba -c conda-forge
mamba install htmd=2.0.8 -c acellera -c conda-forge

Conda dependency resolver is total trash. Installing and using mamba instead will get the package installed in a minute

[lblaabjerg]

Thanks! Interesting. I see that Mamba is indeed much faster. I now get the error:

(thermonet) [lasbla@s96n41 ThermoNet]$ mamba install htmd=2.0.8 -c acellera -c conda-forge

Looking for: ['htmd=2.0.8']

acellera/noarch 2.7kB @ 8.0kB/s 0.3s acellera/linux-64 58.0kB @ 115.6kB/s 0.5s pkgs/r/noarch 1.3MB @ 1.9MB/s 0.4s pkgs/main/noarch 818.5kB @ 842.4kB/s 0.2s pkgs/r/linux-64 1.4MB @ 1.3MB/s 0.6s pkgs/main/linux-64 5.0MB @ 4.2MB/s 1.2s conda-forge/noarch 10.6MB @ 4.1MB/s 2.7s conda-forge/linux-64 28.4MB @ 4.0MB/s 7.2s

Pinned packages:

• python 3.7.*

Encountered problems while solving:

• package htmd-2.0.8-py37_0 requires htmd-deps 2.0.8, but none of the providers can be installed

Installed Python version is 3.7.12.

[stefdoerr]

This is very weird because I can see htmd-deps 2.0.8 for python 3.7 existing... Is there any chance you could move to python 3.8?

[lblaabjerg]

Hmm. I don't think that is possible because of dependency issues with the Tensorflow version used in ThermoNet (https://github.com/gersteinlab/ThermoNet).

I also tried installing HTMD 1.22 but then get the error:

Looking for: ['htmd=1.22']

conda-forge/linux-64 Using cache conda-forge/noarch Using cache pkgs/main/noarch No change pkgs/r/linux-64 No change pkgs/main/linux-64 No change pkgs/r/noarch No change acellera/noarch No change acellera/linux-64 No change

Pinned packages:

• python 3.7.*

Encountered problems while solving:

• nothing provides ambermini >=16.16.0 needed by htmd-deps-1.22.3-py37_0

[stefdoerr]

The more back you go, the more issues you will have with dependencies. Try 2.0.6. It worked with python 3.7 for me

[lblaabjerg]

It works, thanks a lot for your help Stefan!

[stefdoerr]

You are welcome :)