Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors

[ursulap]

Hello!

I have a Mac OS 13 and I have now installed Amber22 (through step: "make install" - addressed in my previous post #1618 - thanks for helping out there!). 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

2022-12-12_10-28-41.log.zip

2022-12-12_10-28-41.log.zip)

[hainm]

Hi

Please repost your question to AMBER mailing list. This github repo has very low traffic.

[hainm]

http://ambermd.org/MailingLists.php

[ursulap]

Hi I have emailed 3 times to [email protected] with the simple subject "amber" or "subscribe" or blank "" and that is it and I have not received any confirmation... hence I am not in the list yet and hence I can not post this issue.
-ursula
ps. in the meantime I checked the archive and I didn't find the solution to the issue above.. Looking forward to being able to have amber properly running :)
-ursula

[hainm]

Hi I have emailed 3 times to [email protected] with the simple subject "amber" or "subscribe" or blank "" and that is it and I have not received any confirmation... hence I am not in the list yet and hence I can not post this issue. -ursula ps. in the meantime I checked the archive and I didn't find the solution to the issue above.. Looking forward to being able to have amber properly running :) -ursula

hi @ursulap, I suggest to check your spam filter in your email. Unfortunately posting question here won't help since (again), it's for pytraj and this repo has very low traffic.