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Requirements

- git 
- cmake
- CLION

For configuring the project

1. Open VCELL Solvers complete project inside CLION.
2. Open CLION go to `File > settings > Build, Execution, Deployement > Toolchains > +`  
    Let it detect everything automatically `CMake`, `Make`, `C Complier`, `C++ Compiler` and `Debugger`
3. Configure CMake `File > settings > Build, Execution, Deployement > CMake > +`
    - Build type as `Default`
    - Give `CMake options`
        For all solvers

        ```
        -DCMAKE_PREFIX_PATH="/usr/lib/x86_64-linux-gnu/"
        -DOPTION_TARGET_MESSAGING=OFF
        -DOPTION_TARGET_PARALLEL=OFF
        -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF
        -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF
        -DOPTION_TARGET_SMOLDYN_SOLVER=ON
        -DOPTION_TARGET_FV_SOLVER=ON
        -DOPTION_TARGET_STOCHASTIC_SOLVER=ON
        -DOPTION_TARGET_NFSIM_SOLVER=ON
        -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF
        -DOPTION_TARGET_SUNDIALS_SOLVER=ON
        -DOPTION_TARGET_HY3S_SOLVERS=OFF
        ```
    - Generation path `build/bin`
    - Apply all these changes, that builds every solver in `bin` directory. The `Run/Debug Configurations` should be populated automatically for all solvers.

Debugging Solvers

NOTE: All solvers are command line apps, which are invoked by VCELL_Rel/VCELL_Alpha internally.

  1. Debugging and setting up environment variables through CLION

For FiniteVolume_X64

  1. We need .fvinput and _link files to run FinitVolumne_X64 solver as Command Line app. These can be generated by running VCELL_Rel or VCELL_Alpha once (we don't need to wait for the simulation to finish, just cancel it after it says "Running Simulation").
  2. On CLION, open Run/Debug Configurations and select Edit Configurations. From the list of configurations select CMAKE Application > FiniteVolume_X64
  3. Go to Program arguments and enter <VCELL home>/simdata/temp/SimID_<simulation_ID>_0.fvinput Example: /home/akhil/.vcell/simdata/temp/SimID_1812661980_0_.fvinput
  4. Go to Working directory and enter <VCELL home>/simdata
  5. Set up Environment variables as LD_LIBRARY_PATH=<VCELL home>/simdata/temp/<simulation_ID>_link Example: LD_LIBRARY_PATH=/home/akhil/.vcell/simdata/temp/1812661980_link

To get <VCELL_home> and path details from VCell_Rel/VCELL_Alpha. Go to Help > Vcell Properties... > General Properties