Simulator.py throws error when finding output directory

[Deepika-Parthasarathy]

(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]

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

[timrudge]

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 <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. > > — > Reply to this email directly, view it on GitHub > <#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]

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]

@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]

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.

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]

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]

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]

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 #36 (comment).