run Package

model_driver

class tvb.rateML.run.model_driver.Driver_Execute(ds)[source]

Bases: Driver_Setup

cf(array)[source]
compare_with_ref(tavg0)[source]
gpu_mem_info()[source]
make_gpu_data(data)[source]
make_kernel(source_file, warp_size, args, lineinfo=False, nh='nh')[source]
nbytes(data)[source]
plot_output(tavg)[source]
release_gpumem(gpu_data)[source]
run_all()[source]
run_simulation()[source]
set_CUDA_ref_model_dir()[source]
set_CUDAmodel_dir()[source]
write_output(tavg, bold)[source]
class tvb.rateML.run.model_driver.Driver_Setup[source]

Bases: object

checkargbounds()[source]
gpu_device_info()[source]

Get GPU device information TODO use this information to give user GPU setting suggestions

logdata()[source]
parse_args()[source]
setup_params(n0, n1)[source]

This code generates the parameters ranges that need to be set

tvb_connectivity(tvbnodes)[source]

model_driver_bold

class tvb.rateML.run.model_driver_bold.Driver_Execute(ds)[source]

Bases: Driver_Setup

cf(array)[source]
compare_with_ref(tavg0)[source]
gpu_mem_info()[source]
make_gpu_data(data)[source]
make_kernel(source_file, warp_size, args, lineinfo=False, nh='nh')[source]
nbytes(data)[source]
plot_output(tavg)[source]
release_gpumem(gpu_data)[source]
run_all()[source]
run_simulation()[source]
set_CUDA_ref_model_dir()[source]
set_CUDAmodel_dir()[source]
write_output(tavg, bold)[source]
class tvb.rateML.run.model_driver_bold.Driver_Setup[source]

Bases: object

checkargbounds()[source]
gpu_device_info()[source]

Get GPU device information TODO use this information to give user GPU setting suggestions

logdata()[source]
parse_args()[source]
setup_params(n0, n1)[source]

This code generates the parameters ranges that need to be set

tvb_connectivity(tvbnodes)[source]

model_driver_heun

model_driver_zerlaut

This is the partly rateML generated and partly manual implementation of the Zerlaut [1] HPC GPU model driver for exploration of the paramters : global_coupling, b_e, E_L_e, E_L_i and T as in [2]. A Jyputer notebook can be found here: https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Public_3Species_TVBAdEx_EITN_FallSchool/Human/Different_brain_states_simulated_in_the_human_brain.ipynb

[1] Zerlaut, Yann, Sandrine Chemla, Frederic Chavane, and Alain Destexhe. “Modeling Mesoscopic Cortical Dynamics Using a Mean-Field Model of Conductance-Based Networks of Adaptive Exponential Integrate-and-Fire Neurons.” Journal of Computational Neuroscience 44, no. 1 (February 1, 2018): 45–61. https://doi.org/10.1007/s10827-017-0668-2.

[2] A comprehensive neural simulation of slow-wave sleep and highly responsive wakefulness dynamics Jennifer S. Goldman, Lionel Kusch, Bahar Hazal Yalçinkaya, Damien Depannemaecker, Trang-Anh E. Nghiem, Viktor Jirsa, Alain Destexhe bioRxiv 2021.08.31.458365; doi: https://doi.org/10.1101/2021.08.31.458365

class tvb.rateML.run.model_driver_zerlaut.Driver_Execute(ds)[source]

Bases: Driver_Setup

cf(array)[source]
compare_with_ref(tavg0)[source]
gpu_mem_info()[source]
make_gpu_data(data)[source]
make_kernel(source_file, warp_size, args, lineinfo=False, nh='nh')[source]
nbytes(data)[source]
plot_output(tavg)[source]
release_gpumem(gpu_data)[source]
run_all()[source]
run_simulation()[source]
set_CUDA_ref_model_dir()[source]
set_CUDAmodel_dir()[source]
write_output(tavg)[source]
class tvb.rateML.run.model_driver_zerlaut.Driver_Setup[source]

Bases: object

checkargbounds()[source]
gpu_device_info()[source]

Get GPU device information TODO use this information to give user GPU setting suggestions

logdata()[source]
parse_args()[source]
setup_params(n0, n1, n2, n3, n4)[source]

This code generates the parameters ranges that need to be set

tvb_connectivity(tvbnodes)[source]

regular_run

class tvb.rateML.run.regular_run.regularRun(sim_length, g, s, dt, period, omega=60, filename='connectivity_zerlaut_68.zip')[source]

Bases: object

simulate_python(modelExec)[source]
tvb_connectivity(filename)[source]
tvb_python_model(modelExec)[source]