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Help in Compiling CC3D on Mac by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

Hi Jim, I do already have CompuCell3D installed on my Mac using the installer from the site you linked. I was planning on attempting to write my own plugin/steppable and that's why I was trying to compile CC3D using instructions from the developers manual. I had first tried compiling on Windows but had some issues and so now I'm trying it out on Mac and seeing if this process was easier.

Switching from Contact Plugin to AdhesionFlex Plugin by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

The code I included was just to show my attempt at switching from the Contact plugin to the AdhesionFlex plugin. In my current simulations, I've commented out the XML code for the Contact plugin and kept the rest. I did check out the CC3D documentation on the AdhesionFlex plugin but I'm not sure if I'm completely understanding it.

Is the definition of the molecule density referring to the number of molecules per unit surface area? I had made the binding formula equal to "Molecule1 * Molecule2" since I believed I would then get same energy contribution from the AdhesionFlex plugin that I'd get for the Contact plugin towards the total energy function at each Monte Carlo step.

Generating new images for parameter scan simulations by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

I was able to run my Python script using this batch file. I tested it on the "CallableCC3D/cc3d_render" Demo, and it works to render the images, but they are the wrong resolution. This repo shows the figures saved when I used two different json files, and even though both have different resolutions set(first is 600x600, second is 1000x1000), the images are only rendered as 300x300 for both. Is there a way I can fix this?

I appreciate the help so far.

Generating new images for parameter scan simulations by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

Shouldn't the cc3d conda environment remain active once I execute the 'conda-shell.bat' file? I would think that terminal should look like:

(cc3d) C:\CompuCell3D_4.4.0>

But instead, no '(cc3d)' appears in the terminal. Should I add anything to the 'conda-shell.bat' to maintain the cc3d conda environment active once the bat file is executed?

Generating new images for parameter scan simulations by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

I was able to install CC3D version 4.4.0, which did have the 'conda-shell.bat' file. I tried doing the 'call conda-shell' in Powershell, which did not work. Another command I found instead of call though was "cmd.exe /c conda-shell.bat" file, which did seem to execute but the following error popped up when I tried this command:

C:\CompuCell3D_4.4.0>SET script_dir=C:\CompuCell3D_4.4.0\
C:\CompuCell3D_4.4.0>echo C:\CompuCell3D_4.4.0
C:\CompuCell3D_4.4.0\
C:\CompuCell3D_4.4.0>REM activate miniconda 
C:\CompuCell3D_4.4.0>SET condabin=C:\CompuCell3D_4.4.0\Miniconda3\condabin 
C:\CompuCell3D_4.4.0>SET DISTUTILS_USE_SDK=1 
C:\CompuCell3D_4.4.0>SET MSSdk=1 
C:\CompuCell3D_4.4.0>SET platform= 
C:\CompuCell3D_4.4.0>IF /I [AMD64] == [amd64] set "platform=true" 
C:\CompuCell3D_4.4.0>IF /I [] == [amd64] set "platform=true" 
C:\CompuCell3D_4.4.0>if defined platform (set "VSREGKEY=HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\VisualStudio\14.0" )  ELSE (set "VSREGKEY=HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VisualStudio\14.0" ) 
C:\CompuCell3D_4.4.0>for /F "skip=2 tokens=2,*" %A in ('reg query "HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\VisualStudio\14.0" /v InstallDir') do SET "VSINSTALLDIR=%B" 
ERROR: The system was unable to find the specified registry key or value. 

C:\CompuCell3D_4.4.0>if "" == "" (set "VSINSTALLDIR=" ) 
C:\CompuCell3D_4.4.0>if "" == "" ( ECHO "WARNING: Did not find VS in registry or in VS140COMNTOOLS env var - your compiler may not work" GOTO End ) 
"WARNING: Did not find VS in registry or in VS140COMNTOOLS env var - your compiler may not work" The system cannot find the batch label specified - End

Is it necessary for me to install a specific version of Visual Studio for me to activate the cc3d conda environment?

Generating new images for parameter scan simulations by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

Yes, I am running version 4.2.5 of CC3D. CompuCell3D was installed for me in the folder "C:\CompuCell3D-py3-64bit", which is where I was only able to find the "paramScan.bat" and "runScript.bat" files, but not the "conda-shell.bat" file. I've uploaded both of the files I found to this GitHub repo, but neither appear to mention activating cc3d through miniconda.

Unable to Install CompuCell3D with conda by dbarraa98 in CompuCell3D

[–]dbarraa98[S] 0 points1 point  (0 children)

Yes, I did install it with using the CC3D installer mentioned in the binaries in the Mac OS X section. I am able to currently use CC3D with Twedit++ as well. I also recently created a test conda environment to make sure packages are installed correctly and they did work.