mfahdaz / Cosim_NestDesktop_Insite

Integration of NEST Desktop, Insite pipeline and Modular Science - Multiscale Co-simulation.

 

Modular Science: Multi-scale Co-simulation

Status

Multi-scale Co-simulation - TVB-NEST-usecase1

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About   |   Technologies   |   Getting Started   |   License   |   Author   |   Acknowledgement

About

TODO: add usecase 1 descr.

Technologies

The following tools were used in this project:

• Python
• CMake
• C++
• Makefile

Getting Started

The framework and usecase can be installed and launched on:

• Local systems: e.g. a virtual machine (VM) on a laptop. We support the useage of Virtualbox and Vagrant.
• HPC systems: currently supported on the JUWELS and JUSUF clusters at the Jülich Supercomputing Centre.

The intended platform to deploy the MSC framework with this co-simulation usecase are HPC systems. They allow independant scaling of the components and efficient simulations. Deploying it on a laptop aids testing and development.

Installation

Please check HERE for installation details.

How to run

The framework and usecase can be installed and launched on:

• Local systems:

  • go to run_usecase/local directory and run this script from there e.g.

  $ sh ./cosim_launch_local_dev.sh
  

  • On the VM (see Installation guide above) you will find two scripts in /home/vagrant/multiscale-cosim:

    vagrant@ubuntu-focal:~multiscale-cosim$ source Cosim_NestDesktop_Insite.source
    vagrant@ubuntu-focal:~multiscale-cosim$ ./run_on_loacl.sh
    

• HPC systems: To execute the usecase on HPC systems, go to run_usecase/hpc directory. The usecase can be deployed and executed within an interactive session or could also be submitted as a SLURM job.

  • Interactive session: first allocate the required resources by specifying the cluster partition and account e.g:

    $ salloc --partition=<partition> --nodes=2 --account=<account>
    

    Then, run this script from there e.g.:

    $ sh ./cosim_launch_hpc_sbatch.sh
    

  • SLURM job: To submit the usecase as a slurm job, run this script e.g.:

    $ sh ./run_usecase_sbatch.sh
    

    NOTE It will create a directory named as slurm_logs at the same location where the execution script is run, to capture the outputs and errors from the SLURM.

  Simulation Results: The simulation results, logs, and the resource usage stats can be found in directory Cosimulation_outputs created by Modular Science during the execution at the same location where the execution script is run.

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License

This project is under license from Apache License, Version 2.0. For more details, see the LICENSE file.

Made by Multiscale Co-simulation team.

Acknowledgement

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 785907 (HBP SGA2), from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (HBP SGA3) and from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3)

 

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