On Thu, Apr 15, 2021 at 11:25 PM 石谷沁 <guqin.shi.qilu-pharma.com> wrote:
> Hi David, thanks for the reply.
>
> > If you try a fresh install of AmberTools20 using cmake, I think you
> should get a functioning pytraj.
>
> With cmake instead of cmake3 on CentOS 7 for AmberTools20? I am trying to
> clarify if the key is re-installing AmberTool20 or the key is re-building
> AmberTool20 separately with cmake...
>
>
>
> > (Of course, if you are not planning to use pytraj, you can ignore the
> > failure....)
>
>
> I used to use cpptraj a lot...not sure if it utilizes the function of
> pytraj....
>
>
pytraj is actually a python version of cpptraj (using libcpptraj under the
hood). So don't worry about pytraj if you don't use Python.
Your installation procedure seems fine to me, and I don't have any clue
"why". Final shot: what's your setuptools version in miniconda?
$AMBERHOME/miniconda/bin/python -c 'import setuptools as s;
print(s.__version__)'
I do see the issue of pytraj with python 3.8 and a relatively new
setuptools version:
https://github.com/Amber-MD/pdb4amber/issues/85
The above issue is for pdb4amber but you can try similar thing with pytraj:
https://github.com/Amber-MD/pdb4amber/issues/85#issuecomment-723529395
I am sorry for the trouble without any clear solution.
Hai
>
> Thanks,
> Guqin
>
> -----邮件原件-----
> 发件人: David A Case [mailto:david.case.rutgers.edu]
> 发送时间: 2021年4月15日 20:23
> 收件人: AMBER Mailing List <amber.ambermd.org>
> 主题: [ambermd.org代发]Re: [AMBER] "No module named pytraj" during make test
> step
>
> On Thu, Apr 15, 2021, 石谷沁 wrote:
> >
> >I’m here again…so I successfully installed the serial AMBER packages.
> >
> >make test.serial works well except for 1 error on pytraj test.
> >
> >The traceback showed that program correctly used the python3.8 in
> >miniconda (which was installed automatically during AMBER build)
> >
> >Below is the full message. Does it related to other python packages of
> >the Linux platform?
> >
> >ModuleNotFoundError: No module named 'pytraj'
>
> > To supplement, python was installed via Miniconda. I followed the
> > prompts during build and make.
>
> This problem comes up a lot. As best I can tell, "older" miniconda python
> installations are missing something that is needed to build pytraj. The
> current install procedure (in AmberTools20) seems to be working.
>
> I'm cc-ing to Hai in case he has any way of debugging this problem. The
> build scripts don't fail (although there may be some error message hidden
> in there), but the pytraj module is not found.
>
> If you try a fresh install of AmberTools20 using cmake, I think you should
> get a functioning pytraj.
>
> (Of course, if you are not planning to use pytraj, you can ignore the
> failure....)
>
> ...good luck....dac
>
>
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Received on Thu Apr 15 2021 - 22:00:02 PDT
