On Thu, Sep 25, 2025, Jiang, Wei via AMBER wrote:
>Hi, I am trying to re-install Amber24 on an Nvidia A100 cluster. Last
>December run_cmake worked fine and I got Amber24 installed
>successfully. But now with the identical code I see the following error
>when running run_cmake. It looks like miniconda is installing something
>incompatible with the existing software environment. This did not happen
>before. Can anybody advise how to avoid it?
Thank you for the report.
It would be helpful to know exactly what commands you used, and what
OS and compiler environment you are using.
It looks like you are trying to install "Amber24" from a year or so ago.
The current versions are AmberTools25 and a re-packaged "Amber24". You
might try downloading the latest versions to see if that would help. Note
that the updated Amber24 (which extracts into the directory tree headed by
"pmemd24_src") has no need for python or miniconda, and should not
encounter the errors you report.
It's hard to tell if AmberTools25 (which does download miniconda) would
encounter these problems; no one else has reported this problem, which is why
we would like to know more about your OS environment.
That said, it looks like the whole thing is related to cython-0.29 somehow.
I don't understand what is going on, since the AmberTools25 code that
is distributed has already been cythonized, and should have no reason to
look for a particular version of cython. It is certainly possible that
there is an error in the miniconda install options that is just now causing
problems.
Others on the list, better versed in miniconda and python/cython, may be
able to offer better insights.
...hope this helps....dac
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Received on Thu Sep 25 2025 - 13:30:02 PDT
