Thank you David for your reply.
1) The log files to see failures and errors are attached.
Looking at the end of the log file I have:
Finished serial test suite for Amber 22 at Mon Dec 12 11:03:52 CST 2022.
176 file comparisons passed
1 file comparisons failed ( 1 of which can be ignored)
0 tests experienced errors
Test log file saved as
/Applications/Amber/amber22/logs/test_amber_serial/2022-12-12_11-01-49.log
Test diffs file saved as
/Applications/Amber/amber22/logs/test_amber_serial/2022-12-12_11-01-49.diff
which is different from what I got after it was done...here is the output
after running "make test.serial":
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
??
2) Next point to clarify: what compilers I am using...
First, I only modified the run_make file with the small addition: "import
warnings" at the beginning of the run_make script. Everything else in the
script is unchanged.
Here are the versions I have for compilers:
% clang --version
Homebrew clang version 15.0.6
Target: arm64-apple-darwin22.2.0
Thread model: posix
InstalledDir: /opt/homebrew/opt/llvm/bin
% gfortran --version
GNU Fortran (Homebrew GCC 12.2.0) 12.2.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
% gcc --version
Apple clang version 14.0.0 (clang-1400.0.29.202)
Target: arm64-apple-darwin22.2.0
Thread model: posix
InstalledDir:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
my $PATH:
/Applications/Amber/amber22/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/llvm/bin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/ATSAS/bin
my local environment file: .z
export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
export PATH="/usr/local/opt/llvm/bin:$PATH"export
PATH="/opt/homebrew/opt/llvm/bin:$PATH"
export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
source /Applications/Amber/amber22/amber.sh
(maybe I should remove the "source /Applications/Amber/amber22/amber.sh"?)
Should this "source /Applications/Amber/amber22/amber.sh" I ran this line
on the terminal instead but the errors persist (see below)
3) Errors persists.
i) typing in a terminal:
source /Applications/Amber/amber22/amber.sh
ii) followed by:
python3 -c "import sander"
output:
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 "<string>", line 1, in <module>
File
"/Applications/Amber/amber22/lib/python3.9/site-packages/sander/__init__.py",
line 14, in <module>
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)
iii) ls -l /Applications/Amber/amber22/lib/python3.9/site-packages/sander
output:
total 144
-rw-r--r--. 1 ursulaps staff 12453 Apr 8 2022 __init__.py
drwxr-xr-x. 4 ursulaps staff 128 Dec 12 11:08 __pycache__
-rwxr-xr-x. 1 ursulaps staff 53552 Dec 8 20:27
pysander.cpython-39-darwin.so
4) The files for the test.serial are attached
Thank you!
-u
On Fri, Dec 16, 2022 at 7:56 AM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Dec 15, 2022, Ursula Perez-Salas via AMBER wrote:
> >
> >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
>
> You should look at the log files to see what failures and errors there are.
> Post more specific info here. It would also help to know what compilers
> you
> are using (especially what Fortran compiler, if you are setting CLANG as
> the
> compiler in the run_cmake script.)
>
> >
> >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"
>
> Just type this in a terminal:
>
> source /Applications/Amber/amber22/amber.sh
>
> then try this:
>
> python -c "import sander"
>
> This is probably not going to work, but will elminate problems arising
> from any possible mistakes in your startup files.
>
>
> >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)
>
> I hope the python gurus on the list can offer some insight here. You might
> report the result of the following command
>
> ls -l /Applications/Amber/amber22/lib/python3.9/site-packages/sander
>
> ...thanks...dac
>
>
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Received on Fri Dec 16 2022 - 09:00:02 PST
