Re: [AMBER] FixCondaShebang persists

From: Stephan Schott <>
Date: Thu, 14 Oct 2021 18:02:37 +0200

Hi again,
.David I had a mishap with the updater within cmake. It was not running the
updater properly (maybe some permission issues?), but after running the
python updater by hand, everything seems to be working on my side :D, sorry
for the confusion.

.German please make sure to start from a clean build directory, and with a
fully updated amber source tree. You can execute ./update_amber --update in
the root dir and make sure you get the patch up until update.10. It should
do the trick.


El jue, 14 oct 2021 a las 17:44, David A Case (<>)

> On Thu, Oct 14, 2021, Stephan Schott wrote:
> >I had this issue some time ago, so I gave it a try now to see if I can
> >replicate it. I also had trouble with pip, and it seems that the conda
> >update (line 152 of UseMiniconda.cmake) causes pip to be removed (at least
> >under Linux). Then, as pip is never explicitly requested, it is never
> >installed again, and makes pip to be missing. Now, the issue there is that
> >if cmake fails to update the shebang of amber.pip, it apparently also
> fails
> >to update the shebang of other python scripts. Can someone else try to
> >replicate this independently? I think forcing pip to be installed could be
> >a quick solution, but maybe someone has an idea why the conda update
> causes
> >the uninstall on the first place.
> I still can't seem to reproduce this here. On my ubuntu 20.04 system,
> there
> is no $AMBERHOME/miniconda/bin/pip, so the symlink to $AMBERHOME/bin is
> never made, and the FixShebang script doesn't try to do anything with the
> (missing) $AMBERHOME/bin/amber.pip file. But the other python
> scripts all seem to be correctly fixed.
> The behavior in the paragraph above is what the code looks like it should
> be
> doing, and what was intended. One thing to try would be to uncomment line
> 36 in cmake/FixCondaShebang/FixCondaShebang.cmake. This will indicate what
> order all these fixes are done in, which might somehow not be be that same
> on all machines. Or, if amber.pip is present in the list, try to figure
> out why that is. One could also add a check on the existence of ${FILE}
> inside the loop starting at line 42, so that configuretime_file_replace()
> won't try to work on a non-existent file, and hence won't fail.
> Since you are able to get things to fail, you might be able to track down
> the
> problem.
> But my further question is this: does any workflow really make use of
> $AMBERHOME/bin/{amber.conda,amber.ipython,amber.jupyter}? I have a feeling
> that the answer might be "no", and we could just skip this whole process
> entirely.
> ...thanks...dac
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Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Thu Oct 14 2021 - 09:30:02 PDT
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