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Fixed documentation link (dev-mpi) #82

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Oct 18, 2023
Merged

Fixed documentation link (dev-mpi) #82

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d02298a
aligned hpc benchmark script
gmtiddia Oct 17, 2023
ef8beee
fixed link
gmtiddia Oct 17, 2023
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -15,7 +15,7 @@ To get started with NEST GPU, please see the [NEST GPU Documentation](https://ne
NEST GPU is an open source software licensed under the [GNU General Public Lincese version 2](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html).

## Installing NEST GPU
To install NEST GPU see the [NEST GPU Installation Intructions](https://nest-gpu.readthedocs.io/en/latest/installation/installation.html) on our Documentation.
To install NEST GPU see the [NEST GPU Installation Intructions](https://nest-gpu.readthedocs.io/en/latest/installation/index.html) on our Documentation.

## Citing NEST GPU
If you use NEST GPU in your work, please cite the publications in our [publication list](https://nest-gpu.readthedocs.io/en/latest/publications.html).
52 changes: 27 additions & 25 deletions python/hpc_benchmark/hpc_benchmark.py
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Expand Up @@ -102,39 +102,41 @@
mpi_id = ngpu.HostId()
mpi_np = ngpu.HostNum()

def rank_print(message):
"""Prints message and attaches MPI rank"""
print(f"MPI RANK {mpi_id}: {message}")

rank_print("Simulation with {} MPI processes".format(mpi_np))


###############################################################################
# Parameter section
# Define all relevant parameters: changes should be made here


params = {
'scale': 1., # scaling factor of the network size
# total network size = scale*11250 neurons
'seed': args.seed, # seed for random number generation
'simtime': 250., # total simulation time in ms
'presimtime': 50., # simulation time until reaching equilibrium
'dt': 0.1, # simulation step
'stdp': False, # enable plastic connections [feature not properlyly implemented yet!]
'record_spikes': True, # switch to record spikes of excitatory
# neurons to file
'show_plot': False, # switch to show plot at the end of simulation
# disabled by default for benchmarking
'scale': 1., # scaling factor of the network size
# total network size = scale*11250 neurons
'seed': args.seed, # seed for random number generation
'simtime': 250., # total simulation time in ms
'presimtime': 50., # simulation time until reaching equilibrium
'dt': 0.1, # simulation step
'stdp': False, # enable plastic connections [feature not properlyly implemented yet!]
'record_spikes': False, # switch to record spikes of excitatory
# neurons to file
'show_plot': False, # switch to show plot at the end of simulation
# disabled by default for benchmarking
'raster_plot': False, # when record_spikes=True, depicts a raster plot
'path_name': args.path, # path where all files will have to be written
'log_file': 'log', # naming scheme for the log files
'path_name': args.path, # path where all files will have to be written
'log_file': 'log', # naming scheme for the log files
'use_all_to_all': False, # Connect using all to all rule
'check_conns': False, # Get ConnectionId objects after build. VERY SLOW!
'use_dc_input': False, # Use DC input instead of Poisson generators
'check_conns': False, # Get ConnectionId objects after build. VERY SLOW!
'use_dc_input': False, # Use DC input instead of Poisson generators
'verbose_log': False, # Enable verbose output per MPI process
}


def rank_print(message):
"""Prints message and attaches MPI rank"""
if params['verbose_log']:
print(f"MPI RANK {mpi_id}: {message}")

rank_print("Simulation with {} MPI processes".format(mpi_np))


def lambertwm1(x):
"""Wrapper for LambertWm1 function"""
# Using scipy to mimic the gsl_sf_lambert_Wm1 function.
Expand Down Expand Up @@ -312,7 +314,7 @@ def build_network():
syn_dict_ex = {'weight': JE_pA, 'delay': brunel_params['delay']}

if mpi_id==0:
print("Synaptic weights: JE={}; JI={}".format(JE_pA, JE_pA*brunel_params['g']))
rank_print("Synaptic weights: JE={}; JI={}".format(JE_pA, JE_pA*brunel_params['g']))

if not params["use_dc_input"]:
rank_print('Connecting stimulus generators.')
Expand Down Expand Up @@ -474,12 +476,12 @@ def run_simulation():
json.dump(info_dict, f, indent=4)

def my_connect(source, target, conn_dict, syn_dict):
print("MY id {} LOCAL Source {} {} | Target {} {}".format(mpi_id, source.i0, source.n, target.i0, target.n))
rank_print("MY id {} LOCAL Source {} {} | Target {} {}".format(mpi_id, source.i0, source.n, target.i0, target.n))
ngpu.Connect(source, target, conn_dict, syn_dict)


def my_remoteconnect(source_host, source, target_host, target, conn_dict, syn_dict):
print("MY id {} REMOTE Source {} {} {} | Target {} {} {}".format(mpi_id, source_host, source.i0, source.n, target_host, target.i0, target.n))
rank_print("MY id {} REMOTE Source {} {} {} | Target {} {} {}".format(mpi_id, source_host, source.i0, source.n, target_host, target.i0, target.n))
ngpu.RemoteConnect(source_host, source, target_host, target, conn_dict, syn_dict)


Expand Down