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 Thu Dec 15 2022 - 15:30:02 PST
