Hi Hai,
To supplement, I installed Amber20 and AmberTool20 on CentOS 7.
I installed and sourced devtoolset-8 according to
http://ambermd.org/InstCentOS.php to make sure all gnu compilers are with the same version.
I built Amber20 and AmberTool20 together with cmake3 according to
https://ambermd.org/pmwiki/index.php/Main/CMake-Quick-Start
Make install seems fine.
Make test.serial gave the aforementioned error on pytraj.
Thanks,
Guqin
-----邮件原件-----
发件人: 石谷沁
发送时间: 2021年4月16日 11:03
收件人: AMBER Mailing List <amber.ambermd.org>
主题: 答复: [ambermd.org代发]Re: [AMBER] "No module named pytraj" during make test step
Hi Hai and David,
Thanks for checking upon my questions.
cd $AMBERHOME/lib/python3.8/site-packages/
Only 1 directory related to pytraj: pytraj-2.0.5-py3.8-linux-x86_64.egg
echo $PYTHONPATH
/home/gqshi/amber20/lib/python3.8/site-packages:/opt/rh/devtoolset-8/root/usr/lib64/python2.7/site-packages:/opt/rh/devtoolset-8/root/usr/lib/python2.7/site-packages
I sourced /opt/rh/devtoolset-8/ in ~/.bashrc for AMBER build and make install.
Hope these help...Let me know you need more info?
Thank you a lot!
-Guqin
-----邮件原件-----
发件人: Hai Nguyen [mailto:nhai.qn.gmail.com]
发送时间: 2021年4月16日 2:39
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 Wed, Apr 14, 2021 at 9:33 PM 石谷沁 <guqin.shi.qilu-pharma.com> wrote:
> Dear Amber Community,
>
> I’m here again…so I successfully installed the serial AMBER packages.
>
>
> make test.serial works well except for 1 error on pytraj test.
>
>
Hi, do you see `pytraj` in $AMBERHOME/lib/python3.8/site-packages/
What's the output of `echo $PYTHONPATH`?
Hai
> 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?
>
> Thank you for the help!!
> -Guqin
>
> ======================================================================
> ================================================
> Testing serial pytraj
> /home/gqshi/amber20//miniconda/bin/python test.py Traceback (most
> recent call last):
> File "test.py", line 2, in <module>
> import pytraj as pt
> ModuleNotFoundError: No module named 'pytraj'
> test.pytraj: Program error
> ===============================test session starts
> =======================================
> platform linux -- Python 3.8.5, pytest-6.2.3, py-1.10.0, pluggy-0.13.1
> -- /home/gqshi/amber20//miniconda/bin/python
> cachedir: .pytest_cache
> rootdir: /home/gqshi/amber20/AmberTools collected 0 items / 1 error
>
> =========================================ERRORS
> ===================================================================
> _____________________ ERROR collecting
> src/pytraj/tests/test_energy/test_sander_energies.py
> __________________ ImportError while importing test module
> '/home/gqshi/amber20/AmberTools/src/pytraj/tests/test_energy/test_sander_energies.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> ../../../miniconda/lib/python3.8/importlib/__init__.py:127: in
> import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> ../../src/pytraj/tests/test_energy/test_sander_energies.py:4: in <module>
> import pytraj as pt
> E ModuleNotFoundError: No module named 'pytraj'
> ================================== short test summary info
> ======================================================
> ERROR ../../src/pytraj/tests/test_energy/test_sander_energies.py
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> Interrupted: 1 error during collection
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ======================================== 1 error in 0.07s
> =================================================
>
>
>
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***********Business Email Disclaimer**************
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Received on Thu Apr 15 2021 - 21:00:02 PDT
