MDsrv on raspberry pi

[sperezconesa]

Hello,
I am trying to use MDsrv on a raspberry pi server. Since the raspberry pi has ARM architecture it cannot use all of mdtrajs features since a lot of them are hardware accelerated. Does MDsrv use mdtraj extensively or just to load structures, which should work on the pi? In addition, is there a version or some posibility to use MDAnalysis rather than mdtraj which might be more compatible.
Thank you very much for your help,
Sergio

[j0kaso]

Hey Sergio,

you can just use MDAnalysis, we used mdtraj as a lighter version but MDAnalysis is now quite powerful and covers mostly all file formats. And yes, we only use it to read the coordinates.
I could make it work (last year) to run on a raspberry but would be great if you feedback how it is working for you!

Cheers,
Johanna

[sperezconesa]

I commented-out a few functions in mdtraj and installed it. I've been able to install MDAnalysis. I will try to see if it works fine and keep you posted.

[sperezconesa]

Hello,
I am getting this error:

[Thu Apr 23 11:41:00.698469 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620] mod_wsgi (pid=1406): Exception occurred processing WSGI script '/var/www/mdsrv/mdsrv.wsgi'.
[Thu Apr 23 11:41:00.698547 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620] Traceback (most recent call last):
[Thu Apr 23 11:41:00.698617 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]   File "/var/www/mdsrv/mdsrv.wsgi", line 28, in <module>
[Thu Apr 23 11:41:00.698759 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]     from mdsrv import app as application
[Thu Apr 23 11:41:00.698797 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]   File "/home/sperez/mdsrv/mdsrv/__init__.py", line 8, in <module>
[Thu Apr 23 11:41:00.698851 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]     from .mdsrv import *
[Thu Apr 23 11:41:00.698881 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]   File "/home/sperez/mdsrv/mdsrv/mdsrv.py", line 23, in <module>
[Thu Apr 23 11:41:00.698934 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]     from .trajectory import *
[Thu Apr 23 11:41:00.698964 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]   File "/home/sperez/mdsrv/mdsrv/trajectory.py", line 10, in <module>
[Thu Apr 23 11:41:00.699020 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]     import numpy as np
[Thu Apr 23 11:41:00.699050 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/numpy/__init__.py", line 140, in <module>
[Thu Apr 23 11:41:00.699106 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620]     from . import _distributor_init
[Thu Apr 23 11:41:00.699170 2020] [wsgi:error] [pid 1406] [remote 192.168.0.100:52620] ImportError: cannot import name _distributor_init

Can anyone help me?

[sperezconesa]

By the way, running mdsrv just on the terminal works fine.

[j0kaso]

hm, that looks like a numpy error - could you check if that is individually working? (and while you're on it, it's also good, as a backup, to check if MDAnalysis is working or missing some dependencies ;-))

[sperezconesa]

On the commandline, mdsrv works fine so MDAnalysis must be fine. Numpy can be imported on the commandline too and I have tried doing some simple calculations and they look fine...
The command:

from numpy import _distributor_init

works fine too.

[j0kaso]

just for clarification, you can start the MDsrv from the command line & visualize & run simulations from there but have problems with the deployment?

Can you also check if you have different numpy versions installed? might be a dependency problem still... But strange...

MDAnalysis can still have some dependency problems which do not arise when you just import it (bug on their side). That's why I recommend trying to import MDAnalysis and e.g. check the version of it. When that works, this is of course not the problem (quite often so far it was the main problem that's why I posted it also here).

[sperezconesa]

On the commandline I can visualize simulations by calling mdsvr. So it must be the deployment.

MDAnalysis seems to be able to load trajectories fine in the commandline.

I will workout the numpy versions problem, I am not sure how to check this. I am using a virtual-environment which I thought would take care of this.

[sperezconesa]

In the environment and on the system I have numpy 1.18.3. Perhaps the problem is that it is using python2 which I have also installed.

[j0kaso]

oh yes, python2 can be an issue! MDAnalysis only works with python3, so a mixup could result in not being able to run it. Still strange with having the virtual env.

[sperezconesa]

It seems that it was using the systems's python binary which is python2. I don't know why it was picking it up. I made some changes and I don't know how, I fixed it.

[j0kaso]

okay, that sounds great! I totally forgot to mention, for the deployment, you have to set your virtual environment correctly (in the wsgi file) - maybe there an error occurred too.

Of note - how is it running on your raspberry?

[sperezconesa]

I haven't tried much because I am getting an error when loading a trajectory. This is using mdtraj with commented stuff. I import a .gro file and then onto it I import an .xtc. But when I hit the play button I get this error:

[Mon Apr 27 09:01:09.058109 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889] ERROR:mdsrv.mdsrv:Exception on /traj/frame/0/examplepath/step0.xtc [POST]
[Mon Apr 27 09:01:09.058247 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889] Traceback (most recent call last):
[Mon Apr 27 09:01:09.058283 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/flask/app.py", line 2447, in wsgi_app
[Mon Apr 27 09:01:09.058320 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     response = self.full_dispatch_request()
[Mon Apr 27 09:01:09.058352 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/flask/app.py", line 1952, in full_dispatch_request
[Mon Apr 27 09:01:09.058385 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     rv = self.handle_user_exception(e)
[Mon Apr 27 09:01:09.058417 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/flask/app.py", line 1821, in handle_user_exception
[Mon Apr 27 09:01:09.058453 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     reraise(exc_type, exc_value, tb)
[Mon Apr 27 09:01:09.058484 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request
[Mon Apr 27 09:01:09.058516 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     rv = self.dispatch_request()
[Mon Apr 27 09:01:09.058550 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request
[Mon Apr 27 09:01:09.058584 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     return self.view_functions[rule.endpoint](**req.view_args)
[Mon Apr 27 09:01:09.058616 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/mdsrv/mdsrv.py", line 91, in decorated
[Mon Apr 27 09:01:09.058649 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     return f( *args, **kwargs )
[Mon Apr 27 09:01:09.058681 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/mdsrv/mdsrv.py", line 139, in wrapped_function
[Mon Apr 27 09:01:09.058714 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     resp = make_response( f( *args, **kwargs ) )
[Mon Apr 27 09:01:09.058746 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/mdsrv/mdsrv.py", line 299, in traj_frame
[Mon Apr 27 09:01:09.058778 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     return TRAJ_CACHE.get( path, struc_path ).get_frame_string(
[Mon Apr 27 09:01:09.058831 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/mdsrv/trajectory.py", line 122, in get
[Mon Apr 27 09:01:09.058958 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     self.add( path, pathList, struc_path )
[Mon Apr 27 09:01:09.058992 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/mdsrv/trajectory.py", line 104, in add
[Mon Apr 27 09:01:09.059026 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     self.cache[ path ] = TrajectoryCollection( pathList, struc_path )
[Mon Apr 27 09:01:09.059060 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]   File "/home/sperez/mdsrv_env/lib/python3.7/site-packages/mdsrv/trajectory.py", line 200, in __init__
[Mon Apr 27 09:01:09.059093 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889]     self.box = self.parts[ 0 ].box
[Mon Apr 27 09:01:09.059124 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889] AttributeError: 'NoneType' object has no attribute 'box'
[Mon Apr 27 09:01:09.061606 2020] [wsgi:error] [pid 2381] [remote 192.168.0.100:51889] Exception AttributeError: "'NoneType' object has no attribute '__del__'" in <bound method TrajectoryCollection.__del__ of <mdsrv.trajectory.TrajectoryCollection object at 0x68f06c30>> ignore

I am not sure if have commented out too many thing of mdtraj (this is the reason I am trying to use mdanalysis which is not hardware accelerated).

[j0kaso]

To comment mdtraj out, you can just set

try:
    import mdtraj as md
    from mdtraj.formats import *
    importarray[0] = True
    importarray[2] = True

both to False .

I guess the trajectory is fine (MDsrv out of raspberry is running it - or you took one from the example directory) & also MDAnalysis is working from python (e.g. MDAnalysis.__version__ )?

If that's all fine (plz check!), give me your installation protocol/environment, aso, so I can try to reproduce the error on my Raspberry.

[sperezconesa]

In which file is this? I don't see it in setup.py.
(Nevermind I found it. Somedays I can't even grep right)