.. _conf_run_hippo_pre: Configure and run a rat hippocampus CA1 region using preconfigured HBP model and data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This use case allows a user to configure and launch a simulation on HBP HPAC infrastructure using `Unicore API `__. =============== Run Simulations =============== |run_simulation| In the **Section 1)** you can configure: - ``Population``: Population of cells to be loaded by the simulator. - ``Duration``: Time length of stimulus duration, given in milliseconds(ms) - ``View Simulations``: From here you can see all the history of simulations (explained in page `View Simulations <#view-simulations>`_) In the **Section 2)** you can configure: - Using the buttons |edit_buttons| you can ``add``, ``edit`` or ``remove`` new stimulus/report (You can also double-click on the timeline to add or edit) - ``Stimulations`` configuration: - *Population*: Name of a population to receive the stimulation - *Delay*: Time when the stimulus commences, given in milliseconds(ms) - *Duration*: Time length of stimulus duration, given in milliseconds(ms) - *Pattern*: Type of stimulus to inject - *Synapses per cell*: The number of synapses to create - *Lambda*: Configure the random distribution - *Weight*: The strength of the created synapses |edit_stimulus| - ``Reports`` - *Population*: Defines the population from where the data will be reported. - *StartTime*: Time to start reporting(ms) - *EndTime*: Time to stop reporting(ms) - *Compartments*: Which compartment(s) to report [Soma = compartment, Soma + Dendrites = AllCompartments] - *ReportOn*: What to report [Voltage, Calcium Concentration, Current Summation (for LFP)] - *dt*: The frequency of reporting in milliseconds(ms) - *Format*: Defines the report output format [Binary (.bbp), ASCII, HDF5] |edit_report| In the **Section 3)** you can modify the **connection** between populations on the circuit specifying: - *Source:* This target defines presynaptic cells - *Destination:* This target defines postsynaptic cells - *Delay (ms):* A delay after which the modifications are applied - *Weight:* A scaling factor to adjust the synaptic strength (default = 1) - *MinisFreq:* The Poisson mean rate for spontaneous synaptic activity - *Synapse Configuration:* Snippets of hoc code to manipulate additional synaptic parameters |connection_manipulation| - If you want to modify a synpase just click *configure* and a pop-up will appear |synapse_configurator| In the **Section 4)** you can modify the **projection** going to the circuit - *Weight:* A scaling factor to adjust the synaptic strength (default = 1) - *Minis Projection:* Generate inputs based on spontaneous synaptic activity - *Frequency (Hz):* Frequency of the spontaneous synaptic activity - *Spike Replay Projection:* Generate inputs based on a given distribution - *Target:* From which cells the projection is coming - *Frequency (Hz):* The input mean rate - *Stimulus Type:* Type of distribution (default = Poisson) |projection_manipulation| - If you want to modify a projection just click *configure* and a pop-up will appear |projection_edition| - Launching a simulation will open a form to configure the parameters before executing the jobs on the supercomputer - *Title*: The title of the job - *Computer*: Which supercomputer will run the simulation. - *Project*: (optional) If you want to specify under which project the simulation should be run - *Nodes*: The amount of nodes that will be allocated and used for the simulation - *Run Time*: The maximum time before timeout (in seconds). - *CPUs Per Node*: Number of CPUs that are going to be used for the simulation. - *Total Processors*: The total amount (nodes * cpus). - *Preview BlueConfig*: This will open a new tab with the complete configuration that is going to be sent |run_simulation_form| -------------- ================ View Simulations ================ |view_simulation| In the **Section 1)** you are able to: - ``Filter`` by *Title*, *Status*, *Supercomputer*, *Project* - ``Import Simulation`` providing the full path to simulation folder on that HPC - ``Launch Simulation``: this goes back to *Configure and Launch simuation* page In the **Section 2)** you are able to: - ``Check status`` of Simulation and Analysis steps: - ready |done| - queue |sync| - aborted |block| - failed |error| - ``View`` the details page of the simulation. - ``Analyse`` will open a form to configure the parameters before executing the analysis on the supercomputer - *Title*: Title of the job - *Report*: Report created by the simulation - *Raster / Traces*: (Basic Analysis) Type of analysis to run - *Whole Population*: Population cells - *Cells GIDs*: Specify single GID and/or ranges of GIDs - *Random Cells*: Amount of random cells (from the report) to analyze |run_analysis_form| - *LFP*: (Advanced Analysis) Type of analysis to run - *Population*: Population cells - *Plots*: Type of plots to get as a result of the LFP calculation - *Duration*: Start and End duration of the LFP calculation - *Points*: Either write or upload a file with points to calculate LFP |run_lfp_analysis_form| - ``Delete`` the simulation -------------- ================== Simulation Details ================== |simulation_details| In the **Section 1)** you are able to see: - ``Simulation`` with the following information - *Name* - *ID* - *Status* - *Submission Date* In the **Section 2)** you are able to see: - *Analysis*: Plots of the analysis will be shown here - *BlueConfig*: The configuration that was sent to run the simulation - *Files*: List of files that the simulation produced - *Technical Logs*: - *Unicore Logs* - *Stderr*: Logs of the simulation - *Stdout*: Output information of the simulation The ``Analysis`` section shows the different analyses the user has run |simulation_details_analysis| .. |run_simulation| image:: images/run_simulation.png .. |edit_buttons| image:: images/edit_buttons.png .. |edit_stimulus| image:: images/edit_stimulus.png .. |edit_report| image:: images/edit_report.png .. |connection_manipulation| image:: images/connection_manipulation.png .. |synapse_configurator| image:: images/synapse_configurator.png .. |projection_manipulation| image:: images/projection_manipulation.png .. |projection_edition| image:: images/projection_edition.png .. |run_simulation_form| image:: images/run_simulation_form.png .. |view_simulation| image:: images/view_simulation.png .. |done| image:: images/done.png .. |sync| image:: images/sync.png .. |block| image:: images/block.png .. |error| image:: images/error.png .. |run_analysis_form| image:: images/run_analysis_form.png .. |run_lfp_analysis_form| image:: images/run_lfp_analysis_form.png .. |simulation_details| image:: images/simulation_details.png .. |simulation_details_analysis| image:: images/simulation_details_analysis.png