update problems

[smar966]

Hi,
I've just updated the htmd as requested wjile running some analysis notebooks, and now these notebook are not running.
I've already tried to re-install it with 'conda install -c acellera -c psi4 htmd', and still not working.
What should I do?

Thanks in advance

[stefdoerr]

Could you please post the error? Otherwise it's hard to guess what went wrong.

[smar966]

/home/sergio/miniconda3/compiler_compat/ld: cannot find -lpthread
/home/sergio/miniconda3/compiler_compat/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Traceback (most recent call last):
File "/home/sergio/miniconda3/bin/jupyter-notebook", line 7, in
from notebook.notebookapp import main
File "/home/sergio/miniconda3/lib/python3.6/site-packages/notebook/notebookapp.py", line 46, in
from zmq.eventloop import ioloop
File "/home/sergio/miniconda3/lib/python3.6/site-packages/zmq/init.py", line 47, in
from zmq import backend
File "/home/sergio/miniconda3/lib/python3.6/site-packages/zmq/backend/init.py", line 40, in
reraise(*exc_info)
File "/home/sergio/miniconda3/lib/python3.6/site-packages/zmq/utils/sixcerpt.py", line 34, in reraise
raise value
File "/home/sergio/miniconda3/lib/python3.6/site-packages/zmq/backend/init.py", line 27, in
_ns = select_backend(first)
File "/home/sergio/miniconda3/lib/python3.6/site-packages/zmq/backend/select.py", line 27, in select_backend
mod = import(name, fromlist=public_api)
File "/home/sergio/miniconda3/lib/python3.6/site-packages/zmq/backend/cython/init.py", line 6, in
from . import (constants, error, message, context,
ImportError: libsodium.so.23: cannot open shared object file: No such file or directory

[stefdoerr]

This is not related to HTMD. This is related to the zmq package which is not used by HTMD. So it seems like your conda installation possibly broke after updating other packages not related to HTMD.

My best suggestion is to reinstall the whole miniconda. Trying to fix broken packages in conda is a lose-lose game.

[smar966]

OK, I'll try to do that.
Thanks

[stefdoerr]

Generally I'd suggest against updating stuff in conda or at least keeping in mind the risks. I would say from my experience that around 50% of the time something breaks if you update. I either create a new environment which is faster or reinstall conda from scratch.

[stefdoerr]

@j3mdamas maybe we should stop suggesting to people to update to the latest HTMD version and just say there is a new version available without giving the update command? Then at least it's not our responsibility when conda breaks.

[smar966]

The command for the updating was given and I used it. But still got into these troubles.
And it's actually the second time something like this happens

[stefdoerr]

Yes, I agree that's why I'm suggesting we should remove the command suggestion from the news post. It's not really an issue of HTMD, conda sometimes decides to update other packages with HTMD which then break for random reasons. I know it's a decent bit of time and trouble reinstalling all the packages, I'm sorry.

[smar966]

Thanks for your feedback, though!

[stefdoerr]

I'll leave this open to remember to remove the update message from HTMD.

[j3mdamas]

@j3mdamas maybe we should stop suggesting to people to update to the latest HTMD version and just say there is a new version available without giving the update command? Then at least it's not our responsibility when conda breaks.

I agree. I've already removed from the news. It's also displayed when there's a newer version. What do you think we should recommend? New environment creation? New conda installation?

I would propose the following text (adapted from the current one):

print('New {} HTMD version ({}{}) is available. You are currently on ({}).'
      'There are several methods to update:'
      '    - Run: `conda update htmd -c acellera -c psi4` (NOT RECOMMENDED)'
      '    - Create a new conda python environment from scratch and run `conda install htmd -c acellera -c psi4`'
      '    - Create a brand new conda installation and run `conda install htmd -c acellera -c psi4`'
      'Note: A new Python version may also be needed if the current Python version is no longer supported'.format(verstring, latest, pydeps, currver))

What do you think?

[stefdoerr]

Yes, remove the python version message though since we don't recommend updating anyway. Also maybe you should put the update option last.

Also you could give directly the command for making the env like:

- Create a new conda HTMD environment with `conda create -n htmd{} htmd={} -c acellera -c psi4`
- Create a brand new conda installation and run `conda install htmd -c acellera -c psi4`'
- Run: `conda update htmd -c acellera -c psi4` (NOT RECOMMENDED)'

which would become conda create -n htmd1.3.15 htmd=1.3.15 -c acellera -c psi4

[j3mdamas]

Thanks, looks good.