Please try
export
PYTHONPATH=$PYTHONPATH:$AMBERHOME/lib/python3.8/site-packages/pdb4amber-1.7.dev0-py3.8.egg/
and try "pdb4amber -h" again.
Reason: for the latest setuptools, it moves "pdb4amber" folder from
*lib/python3.8/site-packages/
*to
*lib/python3.8/site-packages/pdb4amber-1.7.dev0-py3.8.egg/*
I have no clue how to fix it yet. But adding
$AMBERHOME/lib/python3.8/site-packages/pdb4amber-1.7.dev0-py3.8.egg/
to your PYTHONPATH will
resolve the problem.
Cheers
Hai
On Wed, Oct 7, 2020 at 9:52 AM <bgostyns.cbmm.lodz.pl> wrote:
> Hello, everyone!
>
>
> I've recently tried to compile and run Amber20 and AmberTools20 on my
> Ubuntu 20.04.
>
> After solving some initial problems, such as installing Cuda 10.2 next
> to Cuda 11.0 and downgrading my GNU compilers to version 8.4 I was
> finally able to compile and install the binaries.
>
> Unfortunately, it turned out that there's absolute no possibillity of
> using pdb4amber program or sourcing the amber.sh file.
>
> My cmake options are:
>
> -DCMAKE_INSTALL_PREFIX=$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
>
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>
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Received on Wed Oct 07 2020 - 15:00:02 PDT
