Hello!
Apparently, even though of the errors described I am able to run amber to
construct the trajectories from simulations that ran on a cluster.
So apparently for now all good.
Thank you for your help :-)
-u
On Thu, Dec 15, 2022 at 5:09 PM Ursula Perez-Salas <ursulaps.uic.edu> wrote:
> Hello!
>
> I have a Mac OS 13 and I have now installed Amber22! However in the
> testing step ("make test.serial") I got several errors and failures -
>
> here is the summary:
>
> finished serial test suite for AmberTools at Mon Dec 12 11:01:48 CST 2022.
>
> 2396 file comparisons passed
> 8 file comparisons failed ( 1 of which can be ignored)
> 4 tests experienced errors
>
> I ran an additional test using this line suggested by Hai to someone else
> (I can't find the page where I read it!):
>
> "python3 -c "import sander"
>
> and the output was:
>
> Could not import the compiled Python-sander interface. Make sure you have
> the Python development libraries installed and that you have sourced
> amber.sh or amber.cshTraceback (most recent call last):
> File "", line 1, in
> File "/Applications/Amber/amber22/lib/python3.9/site-packages/sander/
> *init*.py", line 14, in
> from . import pysander as _pys
> ImportError: cannot import name 'pysander' from partially initialized
> module 'sander' (most likely due to a circular import)
> (/Applications/Amber/amber22/lib/python3.9/site-packages/sander/*init*.py)
>
> So the first question I have is: did I misplace or mishandled the line:
> "source /Applications/Amber/amber22/amber.sh"? I just simply added this
> command line to my local .zshrc and .zshr files. They read like this now:
>
> export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
> export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"
> export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
> export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
> source /Applications/Amber/amber22/amber.sh
>
> I closed terminal and then re-opened it, re-ran the test ("python3 -c
> "import sander") and the error persisted.
>
> Putting "source /Applications/Amber/amber22/amber.sh" may be indeed
> incorrect! If so, where should it go.
>
> I also installed development tools for python ("python3 -m pip install
> python-dev-tools --user --upgrade") and repeated the test ("python3 -c
> "import sander") but it continues to give me the same errors.
>
> In the error a reference to "sanders" led me to trying to install
> Python-sander? => "pip3 install python-timbl" but that resulted in errors
> as well:
>
> Collecting python-timbl
> Using cached python-timbl-2017.04.04.tar.gz (28 kB)
> Preparing metadata (setup.py) ... error
> error: subprocess-exited-with-error
>
> × python setup.py egg_info did not run successfully.
> │ exit code: 1
> ╰─> [6 lines of output]
> Traceback (most recent call last):
> File "", line 2, in
> File "", line 34, in
> File
> "/private/var/folders/zb/nhjs5chd7s78xshs8z_9f0h00000gn/T/pip-install-w15h3tb6/python-timbl_8218218eec1d40278de43acf720d7707/setup.py",
> line 7, in
> from itertools import ifilter
> ImportError: cannot import name 'ifilter' from 'itertools' (unknown
> location)
> [end of output]
>
> note: This error originates from a subprocess, and is likely not a problem
> with pip.
> error: metadata-generation-failed
>
> ...so maybe this is not the way to go....
>
> Attached the full log and diff -zipped- files from "make test.serial".
>
> Thank you in advance again,
>
> -ursula
>
>
>
>
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Received on Mon Dec 19 2022 - 18:00:02 PST
