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openworm/sibernetic

This is a C++/OpenCL implementation of the PCISPH algorithm supplemented with a set of biomechanics simulations related features applied to C. elegans locomotion

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Mar 10 11:18

pgleeson commented #176
Mar 10 10:28

pgleeson opened #177
Mar 09 09:42

woobin3069 commented #176
Mar 09 09:13

woobin3069 commented #176
Mar 08 03:14

mwatts15 commented #176
Mar 08 03:13

mwatts15 commented #176
Mar 08 01:27

woobin3069 opened #176
Feb 05 08:10

skhayrulin labeled #171
Feb 05 08:10

skhayrulin labeled #171
Dec 08 2020 09:37

md-121 commented #168
Nov 18 2020 12:28

waayst closed #175
Nov 18 2020 12:27

waayst commented #175
Nov 18 2020 09:36

waayst opened #175
Oct 23 2020 18:53

fix27 edited #174
Oct 23 2020 18:53

fix27 commented #174
Oct 23 2020 18:53

fix27 commented #174
Oct 23 2020 18:38

fix27 edited #174
Oct 23 2020 18:16

fix27 opened #174
Oct 17 2020 12:43

clausagerskov closed #173
Oct 17 2020 12:43

clausagerskov commented #173

a-palyanov

@a-palyanov

https://writelatex.s3.amazonaws.com/wjbrbfrmgwxn/uploads/9/5768735/1.png

I think it's a good idea to display the trace of the worm tail and center of mass when visualizing worm movement.

Stephen Larson

@slarson

@a-palyanov you can drag / drop images into gitter

This seems promising; i'm about to sleep now but will look in detail in the morning

a-palyanov

@a-palyanov

Thanks, Stephen!

Stephen Larson

@slarson

Very cool. Do you think it is possible to estimate the wavelength and frequency in those three viscosity conditions @a-palyanov ?

a-palyanov

@a-palyanov

Sure. It shouldn't take much time.

a-palyanov

@a-palyanov

For viscosity = 1.0e-04 frequency = 1.7 and wavelength = 0.8. For 2e-4 and 3e-4 frequency is the same (I didn't changed it) and wavelength is a bit larger because amplitude is lower.

Stephen Larson

@slarson

Interesting. Frequency of 1.7 is right on the money for swimming.

Wavelength looks more like crawling though...

Stephen Larson

@slarson

Hey there @a-palyanov

a-palyanov

@a-palyanov

Hi @slarson

Stephen Larson

@slarson

@skhayrulin — just pinging you in case you are around

First of all; we should probably set up a new session for next week to chat via hangouts

Do you think you can fix the webcam issue by then?

a-palyanov

@a-palyanov

It works already. Tried another usb slot

Stephen Larson

@slarson

Oh yes, shall we go back in?

a-palyanov

@a-palyanov

So we can return to hangout

David Simeroth

@davidsimeroth

Hello, everyone! I have a background in fluid dynamics and was wondering what I could help with

Sergey

@skhayrulin

Hi @davidsimeroth nice to hear from you! I think your expirience sold be useful in model validation and testing, if you have any Idea how we can check correctness of our methods (may be some physical tests, actually we have implemented couple but I think it's not enough) it would be great. If you're interest in that we can make hangout meeting where I'll make some introduction into sibenertic and methods inside it

Sergey

@skhayrulin

Sorry I have got a typo I meant your experience "should" be useful

Stephen Larson

@slarson

@pgleeson I know you are on travel. When should we start looking for good times to coordinate a meeting to update progress on c302 / Sibernetic with @a-palyanov and @skhayrulin (and any others like @davidsimeroth @tessbianchi )

Padraig Gleeson

@pgleeson

@slarson I'm back and things are much quieter from 12th July, so any time after that would be good with me.

Deepak Sharma

@dpkshrma

Hello! I just saw a tedx talk about this project.. and am highly intrigued by the complexity of the problem that its aiming to solve. Can anyone spare a minute to let me in and direct me to right place to get started? I am a software dev btw with decent experience in python, JS.

Stephen Larson

@slarson

Hi @/all — please fill out the poll here to sync between @pgleeson @skhayrulin @a-palyanov and myself on c302 stuff. @tessbianchi you are most welcome to join us in this to reconnect with your stuff as well: http://doodle.com/poll/vrt847hdn2bdwdut Others are welcome too, but this one will require some existing knowledge as we are going to want to get into some recent progress

Stephen Larson

@slarson

@DemoN1810 @a-palyanov @skhayrulin — Dimitriy here is a new volunteer for the project intereste to get involved. Can you guys find a time to chat. You are all in Russia :)

DemoN1810

@DemoN1810

Hello

Stephen Larson

@slarson

@skhayrulin @pgleeson Just made #113 to address the problem you were having

Stephen Larson

@slarson

@skhayrulin is the issue on #11 clear?

Sergey

@skhayrulin

@slarson yes looks like so

David Lung

@lungd

Hi, I've installed sibernetic on a machine and it is running correctly. I would like to connect to that machine (server) via ssh and forward the graphical output of the simulation to my development notebook. While I can start e.g. xclock or firefox remotely and see it locally I have problems with sibernetic.
The simulation is running but I don't see any output like the steps. Instead I get the following error:
X Error of failed request: BadValue (integer parameter out of range for operation)
Major opcode of failed request: 154 (GLX)
Minor opcode of failed request: 24 (X_GLXCreateNewContext)
Value in failed request: 0x0
Serial number of failed request: 37
Current serial number in output stream: 38

Server: ubuntu14.04. Notebook: 16.04
I use ssh -X.
X11Forwarding is set to yes in the sshd_config of the server.
Any suggestions?

Stephen Larson

@slarson

Found this, not sure if it helps: https://bbs.archlinux.org/viewtopic.php?id=195435

This too: https://askubuntu.com/questions/666615/upgrading-to-newest-nvidia-drivers-on-a-laptop-that-uses-optimus-ubuntu-15-04

@lungd suspecting a drivers issue locally; I would explore that.

David Lung

@lungd

Because sibernetic is working on the server (also on my notebook) if I run it locally I thought this issue could be related to sibernetic. But now I also think that the graphics driver is not installed correctly on the server because I get a very similar error with glxinfo over ssh

David Lung

@lungd

I just wanted to let you know that I have solved my problem by installing VirtualGL on the server and on my notebook. Now I can connect with "vglconnect -s USER@IP" and run sibernetic with "/opt/VirtualGL/bin/vglrun ./Release/Sibernetic -f worm"

Stephen Larson

@slarson

Brilliant! Congrats :thumbsup:

Stephen Larson

@slarson

@pgleeson mind if I post some of your recent progress in here?

Padraig Gleeson

@pgleeson

Sure, it was on my todo list, but if you want to cut & paste...

Stephen Larson

@slarson

Cool. From @pgleeson:

From my side I've finally got the c302-Sibernetic bridge cleaned up and it's been integrated into Sibernetic development branch.
I've run some large scale simulations with it: 2 seconds of simulation time, taking 10 hours and producing 90GB of data...

cc: @skhayrulin @lungd @a-palyanov

David Lung

@lungd

@pgleeson, nice. what was the frame rate?

David Lung

@lungd

Well, now I think that this was a stupid question :smile:
But can you tell me what frame rate you get with "./Release/Sibernetic -f worm"?

Padraig Gleeson

@pgleeson

@lungd I get about 8-9 FPS with standard worm based sibernetic with the GUI showing on my 20 processor Inter Xeon machine. The procs seem to be just half used, which I've not looked into... It goes from total step time of ~70 ms with graphics to ~50 ms without...

Elijah Balcwin

@befitsandpiper

hello

Chee Wai Lee

@cheelee

Hi Elijah! Everyone, this is Elijah Baldwin and he's interested to get started doing stuff with OpenWorm on neuro-network modeling and Sibernetic physical modeling simulation. It'd be great if we have something we could help him get started on. @pgleeson @a-palyanov @slarson