Output fails when running with duration higher than 2000

Question

Output fails when running with duration higher than 2000

Opened this issue a year ago · 6 comments

If this issue is intended to be a bug report, please fill out the following:

Expected behavior
Using 0.9.3 image in docker, but whenever I try to run the simulation with command run.cmd -d 2000 or more, it fails.

here is an example:

2023-04-22 02:25:06 >> --------------------------------------------------------------
2023-04-22 02:25:06 >> Command exited with -9: python sibernetic_c302.py
2023-04-22 02:25:06 -duration 2200.0
2023-04-22 02:25:06 -dt 0.005
2023-04-22 02:25:06 -dtNrn 0.05
2023-04-22 02:25:06 -logstep 100
2023-04-22 02:25:06 -device=CPU
2023-04-22 02:25:06 -configuration worm_crawl_half_resolution
2023-04-22 02:25:06 -reference FW
2023-04-22 02:25:06 -c302params C2
2023-04-22 02:25:06 -datareader UpdatedSpreadsheetDataReader2
2023-04-22 02:25:06 -outDir simulations
2023-04-22 02:25:06 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2023-04-22 02:25:06
2023-04-22 02:25:06 Exiting as the last command failed

Actual behavior

Steps to reproduce the behavior

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Requirements are clearly specified
Links to relevant "getting started" documentation
Tagged as "beginner"
Tagged with language skill needed to complete
Level of difficulty:
- Trivial = Changing one-line of code somewhere.
- Standalone = Changes & Development do not affect other components of project. Tasks can be on a critical path, but probably should not be.
- Simple = from 2 hours work to maybe a week’s work (Thinking + Coding)

Answer 1 · 2023-04-28T17:03:55.000Z

Thanks for reporting @LucianSheen. I've not had problems running the docker file myself recently, but admittedly I've not run it for very long simulations. I'll try again locally and see if I can reproduce. Just to clarify, did you rebuild the image from the master branch or use the dockerhub version?

Answer 2 · 2023-04-28T17:10:31.000Z

Hello Padraig, Thanks for the email, and I built the image using github repo(tried the both master branch and 0.9.3 and they both showed me this issue) I'll try the dockerhub version and will let you know, too. Best, Lucian

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On Fri, 28 Apr 2023 at 18:04, Padraig Gleeson ***@***.***> wrote: Thanks for reporting @LucianSheen <https://github.com/LucianSheen>. I've not had problems running the docker file myself recently, but admittedly I've not run it for very long simulations. I'll try again locally and see if I can reproduce. Just to clarify, did you rebuild the image from the master branch or use the dockerhub version? — Reply to this email directly, view it on GitHub <#332 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7G37LVXGCRW3U5SWONBBNTXDP2ANANCNFSM6AAAAAAXKYA7DI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

Answer 3 · 2023-05-05T17:23:49.000Z

So I've been trying to test this out. The 5 second run of the Docker image worked fine on my Linux machine, but took 10 hours. It has 20 processers and 64GB ram and after it finished the swap memory had been used, so I suspect it took up quite a bit of memory while running.

A simulation of 0.5 seconds on my more modest laptop (Mac M2) failed with a similar error to you. I suspect then that it's running out of memory in the image and failing. What OS/specs are your machine?

Unfortunately I suspect it will require quite a powerful machine to run the full thing, unless Sibernetic (or the Python interface) can be optimised more...

Answer 4 · 2023-05-05T18:14:11.000Z

Hello Padraig, I was running the simulation in Windows 10 with my desktop, which has got amd 3900x, 32gb ram, gtx 1070. I was suspecting the same because I failed with the docker pulled image, although I haven’t tried in Linux, but thank you so much for the update!

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On Fri, 5 May 2023 at 18:24, Padraig Gleeson ***@***.***> wrote: So I've been trying to test this out. The 5 second run of the Docker image worked fine on my Linux machine, but took 10 hours. It has 20 processers and 64GB ram and after it finished the swap memory had been used, so I suspect it took up quite a bit of memory while running. A simulation of 0.5 seconds on my more modest laptop (Mac M2) failed with a similar error to you. I suspect then that it's running out of memory in the image and failing. What OS/specs are your machine? Unfortunately I suspect it will require quite a powerful machine to run the full thing, unless Sibernetic (or the Python interface) can be optimised more... — Reply to this email directly, view it on GitHub <#332 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7G37LU6MEEE5VTKIZE26M3XEUZTBANCNFSM6AAAAAAXKYA7DI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

Answer 5 · 2023-09-19T19:54:12.000Z

Hello Padraig! I have been also working with robot project as well, and it seems like wormpy.py in WormHost lacks of some codes. In worm_run.py , which will run the robot, it has got: wormpy.get_segment_angles(segment) but there's no such function get_segment_angles in wormpy.py I tried to add: def get_segment_angles(segment): return _wormpy.get_segment_angles(segment) get_segment_angles = _wormpy.get_segment_angles but it seems _wormpy.pyd doesn't have get_segment_angles either. Do I need to calculate the angle per segments? if so, it would be great to get help for how to do this. Best, Lucain

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On Fri, 5 May 2023 at 19:13, Lucian Shin ***@***.***> wrote: Hello Padraig, I was running the simulation in Windows 10 with my desktop, which has got amd 3900x, 32gb ram, gtx 1070. I was suspecting the same because I failed with the docker pulled image, although I haven’t tried in Linux, but thank you so much for the update! On Fri, 5 May 2023 at 18:24, Padraig Gleeson ***@***.***> wrote: > So I've been trying to test this out. The 5 second run of the Docker > image worked fine on my Linux machine, but took 10 hours. It has 20 > processers and 64GB ram and after it finished the swap memory had been > used, so I suspect it took up quite a bit of memory while running. > > A simulation of 0.5 seconds on my more modest laptop (Mac M2) failed with > a similar error to you. I suspect then that it's running out of memory in > the image and failing. What OS/specs are your machine? > > Unfortunately I suspect it will require quite a powerful machine to run > the full thing, unless Sibernetic (or the Python interface) can be > optimised more... > > — > Reply to this email directly, view it on GitHub > <#332 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/A7G37LU6MEEE5VTKIZE26M3XEUZTBANCNFSM6AAAAAAXKYA7DI> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> >

Answer 6 · 2023-09-21T16:08:02.000Z

Hi @LucianSheen. I've not been involved with that code, but I see @portegys over there has helped you out with some answers.

BTW, there is a new Python visualisation/replay tool for the Boyle Berri Cohen model at https://github.com/OpenSourceBrain/CelegansNeuromechanicalGaitModulation.

See also https://github.com/openworm/CE_locomotion