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cellmodeller / CellModeller

GPU-accelerated multicellular modelling framework
http://cellmodeller.github.io/CellModeller/
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Simulator.py throws error when finding output directory #47

Open Deepika-Parthasarathy opened 1 year ago

Deepika-Parthasarathy commented 1 year ago

(celmod) dinky@DESKTOP-DGB9GV7:~/CellModeller$ python3 Scripts/batch.py Examples/ex1_simpleGrowth.py Select OpenCL platform: press 0 for <pyopencl.Platform 'Portable Computing Language' at 0x7f702676d008> Platform Number: 0 Select OpenCL device: press 0 for <pyopencl.Device 'pthread-Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz' on 'Portable Computing Language' at 0x5568594c50e0> Device Number: 0 Set up OpenCL context: Platform: Portable Computing Language Device: pthread-Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz Importing model ex1_simpleGrowth Traceback (most recent call last): File "/home/dinky/CellModeller/Scripts/batch.py", line 54, in <module> main() File "/home/dinky/CellModeller/Scripts/batch.py", line 50, in main simulate(moduleName, platnum, devnum) File "/home/dinky/CellModeller/Scripts/batch.py", line 16, in simulate sim = Simulator(modname, 0.025, clPlatformNum=platform, clDeviceNum=device, saveOutput=True) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 109, in __init__ self.setSaveOutput(saveOutput) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 117, in setSaveOutput self.init_data_output() File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 135, in init_data_output os.mkdir(self.outputDirPath) FileNotFoundError: [Errno 2] No such file or directory: 'data/ex1_simpleGrowth-23-08-16-11-38'

I got this error running both in batch mode and from the GUI when I toggle the 'save pickles' I understand it is unable to create a directory or find it. But I am not sure on how to go about debugging this. I am on ubuntu LTS 22.04 and I am using VScode for debugging. Thanks.

timrudge commented 1 year ago

Hi - you need to make the directory ~/cellmodeller/data before running. Let me know if that resolves the issue. Thanks, Tim

On Wed, 16 Aug 2023 at 16:45, Deepika-Parthasarathy < @.***> wrote:

(celmod) @.***:~/CellModeller$ python3 Scripts/batch.py Examples/ex1_simpleGrowth.py Select OpenCL platform: press 0 for <pyopencl.Platform 'Portable Computing Language' at 0x7f702676d008> Platform Number: 0 Select OpenCL device: press 0 for <pyopencl.Device 'pthread-Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz' on 'Portable Computing Language' at 0x5568594c50e0> Device Number: 0 Set up OpenCL context: Platform: Portable Computing Language Device: pthread-Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz Importing model ex1_simpleGrowth Traceback (most recent call last): File "/home/dinky/CellModeller/Scripts/batch.py", line 54, in main() File "/home/dinky/CellModeller/Scripts/batch.py", line 50, in main simulate(moduleName, platnum, devnum) File "/home/dinky/CellModeller/Scripts/batch.py", line 16, in simulate sim = Simulator(modname, 0.025, clPlatformNum=platform, clDeviceNum=device, saveOutput=True) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 109, in init self.setSaveOutput(saveOutput) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 117, in setSaveOutput self.init_data_output() File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 135, in init_data_output os.mkdir(self.outputDirPath) FileNotFoundError: [Errno 2] No such file or directory: 'data/ex1_simpleGrowth-23-08-16-11-38'

I got this error running both in batch mode and from the GUI when I toggle the 'save pickles' I understand it is unable to create a directory or find it. But I am not sure on how to go about debugging this. I am on ubuntu LTS 22.04 and I am using VScode for debugging. Thanks.

— Reply to this email directly, view it on GitHub https://github.com/cellmodeller/CellModeller/issues/47, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABWAWAKAHONVWEGUBTTW2PLXVTTINANCNFSM6AAAAAA3SXSMRU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

timrudge commented 1 year ago

Wait sorry my mistake, try running from your ~/cellmodeller directory

On Wed, 16 Aug 2023 at 16:49, Tim Rudge @.***> wrote:

Hi - you need to make the directory ~/cellmodeller/data before running. Let me know if that resolves the issue. Thanks, Tim

On Wed, 16 Aug 2023 at 16:45, Deepika-Parthasarathy < @.***> wrote:

(celmod) @.***:~/CellModeller$ python3 Scripts/batch.py Examples/ex1_simpleGrowth.py Select OpenCL platform: press 0 for <pyopencl.Platform 'Portable Computing Language' at 0x7f702676d008> Platform Number: 0 Select OpenCL device: press 0 for <pyopencl.Device 'pthread-Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz' on 'Portable Computing Language' at 0x5568594c50e0> Device Number: 0 Set up OpenCL context: Platform: Portable Computing Language Device: pthread-Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz Importing model ex1_simpleGrowth Traceback (most recent call last): File "/home/dinky/CellModeller/Scripts/batch.py", line 54, in main() File "/home/dinky/CellModeller/Scripts/batch.py", line 50, in main simulate(moduleName, platnum, devnum) File "/home/dinky/CellModeller/Scripts/batch.py", line 16, in simulate sim = Simulator(modname, 0.025, clPlatformNum=platform, clDeviceNum=device, saveOutput=True) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 109, in init self.setSaveOutput(saveOutput) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 117, in setSaveOutput self.init_data_output() File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 135, in init_data_output os.mkdir(self.outputDirPath) FileNotFoundError: [Errno 2] No such file or directory: 'data/ex1_simpleGrowth-23-08-16-11-38'

I got this error running both in batch mode and from the GUI when I toggle the 'save pickles' I understand it is unable to create a directory or find it. But I am not sure on how to go about debugging this. I am on ubuntu LTS 22.04 and I am using VScode for debugging. Thanks.

— Reply to this email directly, view it on GitHub https://github.com/cellmodeller/CellModeller/issues/47, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABWAWAKAHONVWEGUBTTW2PLXVTTINANCNFSM6AAAAAA3SXSMRU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Deepika-Parthasarathy commented 1 year ago

cellmodeller/data directory was created early on (as per the user guidelines) There exist two directories:

  1. CellModeller (cloned from git hub)
  2. cellmodeller (directory created to store data in the home directory) I tried running the GUI from both and outside of both directories. It throws the same FileNotFoundError Traceback (most recent call last): File "/home/dinky/CellModeller/CellModeller/GUI/PyGLCMViewer.py", line 128, in toggleSavePickles self.sim.setSaveOutput(save) File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 117, in setSaveOutput self.init_data_output() File "/home/dinky/CellModeller/CellModeller/Simulator.py", line 135, in init_data_output os.mkdir(self.outputDirPath) FileNotFoundError: [Errno 2] No such file or directory: 'data/ex1_simpleGrowth-23-08-16-12-28' saveOutput True
avimanyu786 commented 1 year ago

@Deepika-Parthasarathy Are you trying to run it on CPU? You can try the docker containers. They would work for both CPU and GPU. For CPU, you can run a cellmodeller container without having to add any GPU options and it should run fine.

Here's the relevant documentation on our wiki for the docker method:

https://github.com/cellmodeller/CellModeller/wiki/Installation#alternate-method-docker-containers

Deepika-Parthasarathy commented 1 year ago

Hey Avimanyu, I followed those instructions, and was able to deploy the container. I haven't worked with docker before but I get errors with accessing packages I thought I had downloaded. Here is the snippet.

image

I am not sure of what is to be done. I tried sudo apt install but that doesn't work? I am wondering if it has something to do with the -v /tmp/.X11-unix:/tmp/.X11-unix argument? I can use some guidance with this.

avimanyu786 commented 1 year ago

I see. Could you retry a new container again by adding --device=/dev/dri ? /tmp/.X11-unix:/tmp/.X11-unix is what allows running the cellmodeller graphics.

It would be great if you could also share your system specifications for understanding the issue better.

Deepika-Parthasarathy commented 1 year ago

okay. Here goes I am working on windows 11. I have got Ubuntu 22.04 installed on WSL. I have been trying to run cellmodeller on this. I hope this would be helpful.

avimanyu786 commented 1 year ago

The Docker containers were built for Linux and haven't quite been tested on WSL. Since you are using Windows, you can refer to this tutorial: https://gist.github.com/waterfleas/f539dd69634cd65596641ca2c6df980b as mentioned earlier in https://github.com/cellmodeller/CellModeller/issues/36#issuecomment-989469169.