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nest.rules
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nest.rules
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ruleorder: run_nest_reproduction > run_nest_model
rule install_nest:
output:
expand('{nest_folder}/instl/bin/nest_vars.sh',nest_folder=NEST_SRC_DIR)
params:
nest_dir=NEST_SRC_DIR,
shell:
"""
cd {params.nest_dir}
mkdir -p bld
mkdir -p instl
cd bld
cmake3 -DCMAKE_INSTALL_PREFIX:PATH={params.nest_dir}/instl -Dwith-python3=ON {params.nest_dir} -Dwith-mpi=ON
make -j8
make install
"""
rule collect_data:
input:
spikes=expand("{folder}/{{experiment}}/{{rep}}/{{mem_or_spk}}-{{gid,(1001|1002)}}-{threads}.{{ext,(dat|gdf)}}",folder=NEST_DATA_DIR,threads=range(NUM_THREADS)),
output:
spikes=expand("{folder}/{{experiment}}/{{rep}}/{{mem_or_spk}}-{{gid,(1001|1002)}}.{{ext,(dat|gdf)}}",folder=NEST_DATA_DIR),
shell:
"""
cat {input} > {output}
sort -k2,2 -k1,1 -V {output} -o {output}
"""
rule run_nest_model:
output:
weights= "{folder}/{{experiment}}/{{rep}}/connectivity.json".format(folder=NEST_DATA_DIR),
spikes=expand("{folder}/{{experiment}}/{{rep}}/spikes-1001-{threads}.gdf",folder=NEST_DATA_DIR,threads=range(NUM_THREADS)),
membrane_potential=expand("{folder}/{{experiment}}/{{rep}}/membrane_potential-1002-{threads}.dat",folder=NEST_DATA_DIR,threads=range(NUM_THREADS)),
input:
model='{folder}/model.py'.format(folder=NEST_CODE_DIR),
conf='{folder}/experiments/{{experiment}}.yaml'.format(folder=NEST_CODE_DIR),
nest=rules.install_nest.output
threads: NUM_THREADS
log: 'logs/nest_{experiment}_{rep}.log'
#benchmark: "benchmarks/nest_{{experiment}}_{threads}.log".format(threads=NUM_THREADS)
shell:
"""
source {{input.nest}}
python3 {folder}/model.py -c {{input.conf}} -r {{wildcards.rep}} -n {{threads}} &>{{log}}
""".format(folder=NEST_CODE_DIR)
rule run_nest_reproduction:
input:
model='{folder}/model.py'.format(folder=NEST_CODE_DIR),
nest=rules.install_nest.output,
repro= expand('{folder}/bitwise_reproduction/{{rep}}/connectivity.json',folder=IZHI_DATA_DIR),
stim=rules.original_bitwise_reproduction.output.stim,
init=rules.original_bitwise_reproduction.output.init,
conf='{folder}/experiments/{{experiment}}_reproduction.yaml'.format(folder=NEST_CODE_DIR)
output:
mem=expand('{folder}/{{experiment}}_reproduction/{{rep}}/membrane_potential-1002-{threads}.dat',folder=NEST_DATA_DIR,threads=range(NUM_THREADS)),
spikes=expand("{folder}/{{experiment}}_reproduction/{{rep}}/spikes-1001-{threads}.gdf",folder=NEST_DATA_DIR,threads=range(NUM_THREADS)),
weights=expand("{folder}/{{experiment}}_reproduction/{{rep}}/connectivity.json",folder=NEST_DATA_DIR)
priority:1
threads: NUM_THREADS
#benchmark: "benchmarks/nest_{{experiment}}_reproduction_{threads}.log".format(threads=NUM_THREADS)
log: 'logs/nest_{experiment}_reproduction_{rep}.log'
shell:
"""
source {{input.nest}}
python3 {folder}/model.py -c {{input.conf}} -r {{wildcards.rep}} -n {{threads}} &>{{log}}
""".format(folder=NEST_CODE_DIR)
rule find_groups_nest_random:
threads: 48
input:
connectivity="{folder}/{experiment}/random/{r}/connectivity_random.json",
conf='{nest_folder}/experiments/{{experiment}}.yaml'.format(nest_folder=NEST_CODE_DIR),
output:
groups="{folder}/{experiment}/random/{r}/groups_nest_random.json",
stats="{folder}/{experiment}/random/{r}/stats.json"
priority: 50
shell:
"""
source {rules.install_nest.output}
python3 code/analysis/find_polychronous_groups_nest.py -i {input.connectivity} -n 48 -c {input.conf} -o {output.groups} -s {output.stats} || true
"""
rule find_groups_nest_random_EE:
threads: 48
input:
connectivity="{folder}/{experiment}/random/{r}/connectivity_random_EE.json",
conf='{nest_folder}/experiments/{{experiment}}.yaml'.format(nest_folder=NEST_CODE_DIR),
output:
groups="{folder}/{experiment}/random/{r}/groups_nest_random_EE.json",
stats="{folder}/{experiment}/random/{r}/stats.json"
priority: 50
shell:
"""
source {rules.install_nest.output}
python3 code/analysis/find_polychronous_groups_nest.py -i {input.connectivity} -n 48 -c {input.conf} -o {output.groups} -s {output.stats} || true
"""
rule find_groups_nest:
threads: 48
input:
connectivity="{folder}/{experiment}/{rep}/connectivity.json",
conf='{nest_folder}/experiments/{{experiment}}.yaml'.format(nest_folder=NEST_CODE_DIR),
output:
groups="{folder}/{experiment}/{rep}/groups_nest.json",
stats="{folder}/{experiment}/{rep}/stats.json"
log: 'logs/{folder}/find_groups_nest_{experiment}_{rep}.log'
priority: 50
shell:
"""
source {rules.install_nest.output}
python3 code/analysis/find_polychronous_groups_nest.py -i {input.connectivity} -n 48 -c {input.conf} -o {output.groups} -s {output.stats} || true
"""
rule compare_STDP:
output:
weights="{folder}/{{experiment}}/stdp_window.json".format(folder=NEST_DATA_DIR),
sim="{folder}/{{experiment}}/stdp_simulation.json".format(folder=NEST_DATA_DIR),
input:
model='{folder}/stdp_window.py'.format(folder=ANA_DIR),
conf='{folder}/experiments/{{experiment}}.yaml'.format(folder=NEST_CODE_DIR),
nest=rules.install_nest.output
threads: NUM_THREADS
log: 'logs/nest_{experiment}.log'
shell:
"""
source {input.nest}
python {input.model} -c {input.conf} -o {output.weights} -p {output.sim} &>{log}
"""
rule plot_neuron_dyn:
input:
program='{folder}/plot_neuron_dynamics.py'.format(folder=ANA_DIR),
nest=rules.install_nest.output
output:
plot="{folder}/neuron_dynamics.pdf".format(folder=FIG_DIR),
shell:
"""
source {input.nest}
python {input.program} -o {output.plot}
"""