Hello, everyone!
I've recently tried to compile and run Amber20 and AmberTools20 on my
Ubuntu 20.04.
After solving some initial problems, such as installing Cuda 10.2 next
to Cuda 11.0 and downgrading my GNU compilers to version 8.4 I was
finally able to compile and install the binaries.
Unfortunately, it turned out that there's absolute no possibillity of
using pdb4amber program or sourcing the amber.sh file.
My cmake options are:
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20_src/amber20 \ (I
checked - for my issue it doesn't really matter wheter the installation
folder is inside or outside the source folder)
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.2
-DINSTALL_TESTS=TRUE \
-DFORCE_INTERNAL_LIBS=lapack \
-DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
-DPRINT_PACKAGING_REPORT=TRUE \
If there are more instances of this issue with other programs of
Amber20- I don't know, since pdb4amber is so basic that I haven't even
tried to check the other ones.
The output that I get when I try using it is:
> Traceback (most recent call last):
> File "/home/spmk/amber20_src/amber20/bin/pdb4amber", line 33, in
> <module>
> sys.exit(load_entry_point('pdb4amber==1.7.dev0', 'console_scripts',
> 'pdb4amber')())
> File "/home/spmk/amber20_src/amber20/bin/pdb4amber", line 22, in
> importlib_load_entry_point
> for entry_point in distribution(dist_name).entry_points
> File
> "/home/spmk/amber20_src/amber20/miniconda/lib/python3.8/importlib/metadata.py",
> line 504, in distribution
> return Distribution.from_name(distribution_name)
> File
> "/home/spmk/amber20_src/amber20/miniconda/lib/python3.8/importlib/metadata.py",
> line 177, in from_name
> raise PackageNotFoundError(name)
> importlib.metadata.PackageNotFoundError: pdb4amber
In the GitHub forum (link to the thread below)
https://github.com/Amber-MD/pdb4amber/issues/85
I found an indication that this may be related to the Python 3.8 I use
when compiling and they suggested downgrading setuptools to the 47.3.1
version, deleting all existing files and re-running the whole process of
instalation. Unfortunately - the situation repeated and it turned out
additionally that I don't have the /opt/amber20 folder.
As follows from the thread - the problem applies to other programs as
well, not only to the Amber20 suite ones.
Does any of you know how to handle the issue?
Thanks in advance and best regards!
Bartlomiej
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 07 2020 - 07:00:02 PDT
