MDsrv with MDAnalysis

[sperezconesa]

Hello,
How can I install MDsvr with MDAnalysis instead of MDtraj?
Thank you in advanced!
Best,
Sergio

[j0kaso]

Hey Sergio,

the currently easiest way is to comment it out in the setup.py and install it from the git repo. It runs perfectly fine without mdtraj but with MDAnalysis, just the installation raises an issue (need to update that - thanks for the reminder!).

I hope that helps you!
Cheers,
Johanna

[sperezconesa]

If I comment out mdtraj in setup.py, I can install it. But then I don't get the import option in the web-gui file menu...

[sperezconesa]

If install with mdtraj (although it is a version commenting out all subroutines that use hardware acceleration) I do get that option.

[j0kaso]

okay, this sounds strange and should not happen. MDsrv checks internally if mdtraj or MDAnalysis is installed and if they are, it takes their functionalities to get the utmost possible functions to handle trajectories.
Can you send me more info about your environment, versions, installations protocol/history?

[sperezconesa]

Now that I can properly install things on my raspberry pi I can come back to this thread. I have installed MDAnalysis as you suggested in the other thread. I still have the problem that if I install with MDAnalysis I don't have the import option. The import appears on the commandline.
The installation environment has the following versions:

Package         Version                       Location                
--------------- ----------------------------- ------------------------
biopython       1.76                          
click           7.1.2                         
cycler          0.10.0                        
Cython          0.29.17                       
decorator       4.4.2                         
Flask           1.1.2                         
GridDataFormats 0.5.0                         
gsd             2.1.1                         
itsdangerous    1.1.0                         
Jinja2          2.11.2                        
joblib          0.14.1                        
kiwisolver      1.2.0                         
MarkupSafe      1.1.1                         
matplotlib      3.2.1                         
MDAnalysis      0.20.1                        
MDsrv           0.3.5.post1+11.g6a08002.dirty /home/sperez/mdsrv/mdsrv
mmtf-python     1.1.2                         
mock            4.0.2                         
msgpack         1.0.0                         
networkx        2.4                           
numpy           1.18.3                        
pip             20.0.2                        
pyparsing       2.4.7                         
python-dateutil 2.8.1                         
scipy           1.4.1                         
setuptools      46.1.3                        
six             1.14.0                        
Werkzeug        1.0.1                         
wheel           0.34.2                
python 3.7.3

I installed it with a new environment. I cloned the mdsrv repository I changed it mda as you said in the previous thread. Then installed it with:

pip install -e . 
pip install mdanalysis

Is there anything else I can help out with?

[j0kaso]

Thanks! 🙏
Is this also on the raspberry?
Aso, can you check again what python version is used? (e.g. in /var/log/apache2/error.log)

I hope I find time on the weekend to look into it 🤞

[sperezconesa]

Yes, this is on the raspberry.

[Thu Apr 30 21:15:43.689815 2020] [mpm_event:notice] [pid 471:tid 1995809296] AH00489: Apache/2.4.38 (Raspbian) mod_wsgi/4.6.5 Python/3.7 configured -- resuming normal operations
[Thu Apr 30 21:15:43.689991 2020] [core:notice] [pid 471:tid 1995809296] AH00094: Command line: '/usr/sbin/apache2'
[Thu Apr 30 21:26:44.200288 2020] [mpm_event:notice] [pid 471:tid 1995809296] AH00491: caught SIGTERM, shutting down
[Thu Apr 30 21:26:44.850696 2020] [mpm_event:notice] [pid 1092:tid 1995932176] AH00489: Apache/2.4.38 (Raspbian) mod_wsgi/4.6.5 Python/3.7 configured -- resuming normal operations
[Thu Apr 30 21:26:44.851112 2020] [core:notice] [pid 1092:tid 1995932176] AH00094: Command line: '/usr/sbin/apache2'

Thanks a lot for helping me! Don't worry if you don't have time, there is no hurry.

[sperezconesa]

Any luck with this? Is there anything else I can help you with? By the way, I understand this probably low on your priorities (which makes sense).