Merge pull request #428 from Hjorthmedh/neuromod_redux2

Neuromod redux2

examples/parallel/KTH_PDC/neuromodulation/dspn_DA_bath/Dardel_setup_neuromodulation_network.py

@@ -0,0 +1,25 @@
+import os
+from snudda.input.input_tuning import InputTuning
+
+# Create a separate dir for Neuromodulation Basal Ganglia Data while tuning
+snudda_data = os.getenv("SNUDDA_DATA")
+
+network_path = os.path.join("..", "networks", "dspn_DA_bath")
+
+print(f"Creating network in {network_path}")
+
+input_tuning = InputTuning(network_path, snudda_data=snudda_data)
+
+neurons_path = os.path.join("$DATA", "neurons", "striatum")
+
+input_tuning.setup_network(neurons_path=neurons_path, 
+                           num_replicas=1,
+                           neuron_types="dspn",
+                           reaction_diffusion_file="reaction_diffusion_D1_bath.json",
+                           network_random_seed=1234)
+input_tuning = None
+
+
+from snudda import Snudda
+snd = Snudda(network_path=network_path)
+snd.setup_input(input_config="input.json")

examples/parallel/KTH_PDC/neuromodulation/dspn_DA_bath/Dardel_setup_neuromodulation_network.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+# This is to prevent NEURON from trying to open display 
+unset DISPLAY
+
+export SNUDDA_DATA="$HOME/BasalGangliaData/data"
+
+JOBDIR=../networks/dspn_DA_bath
+
+
+echo "Running Dardel_setup_neuromodulation_network: $JOBDIR"
+
+echo "SLURM_PROCID = $SLURM_PROCID"
+
+if [ "$SLURM_PROCID" -gt 0 ]; then
+    mock_string="Not main process"
+else
+    echo "Running"
+    python Dardel_setup_neuromodulation_network.py
+fi

examples/parallel/KTH_PDC/neuromodulation/dspn_DA_bath/Dardel_simulate_dspn_DA_bath.job

@@ -0,0 +1,71 @@
+#!/bin/bash -l
+#SBATCH --partition=main
+#SBATCH -o log/Simulate-%j-output.txt
+#SBATCH -e log/Simulate-%j-error.txt
+#SBATCH -t 0:59:00
+#SBATCH --time-min=0:59:00
+#SBATCH -J Simulate
+#SBATCH -A naiss2024-5-306
+#SBATCH --nodes=1
+#SBATCH --tasks-per-node=51
+#SBATCH --mail-type=ALL
+
+ulimit -s unlimited
+module load snic-env
+
+source $HOME/Snudda/snudda_env/bin/activate
+SNUDDA_DIR=/cfs/klemming/home/"${USER:0:1}"/$USER/Snudda
+
+export SNUDDA_DATA="/cfs/klemming/home/${USER:0:1}/$USER/BasalGangliaData/data"
+
+# Create the network
+
+export N_WORKERS=$SLURM_NTASKS
+
+# This will stop NEURON from failing with "can't open DISPLAY"
+unset DISPLAY
+
+NETWORK_DIR=../networks/dspn_modulation
+echo "Calling Dardel_setup_neuromodulation_network.sh"
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+srun -n 1 -N 1 --exact --overlap --mem=0 Dardel_setup_neuromodulation_network.sh
+
+
+NETWORK_INFO_FILE=$NETWORK_DIR/network-synapses.hdf5
+NETWORK_INPUT_FILE=$NETWORK_DIR/input-spikes.hdf5
+
+echo "Network dir: "$NETWORK_DIR
+
+export PATH=$SNUDDA_DIR/snudda_env/bin/:$PATH
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CRAY_LD_LIBRARY_PATH
+export PYTHONPATH=$SNUDDA_DIR/snudda_env/lib/python3.11/
+
+export CXX=CC
+export CC=cc
+export FC=ftn
+export MPICC=cc
+export MPICXX=CC
+
+CC --version
+
+pushd $SNUDDA_DIR/examples/parallel/KTH_PDC/neuromodulation
+
+rm mechanisms
+ln -s $SNUDDA_DATA/neurons/mechanisms/ mechanisms
+
+rm -r x86_64
+
+echo "About to run nrnivmodl"
+which nrnivmodl
+
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+srun -n 1 nrnivmodl -incflags "-lltdl=/usr/lib64/libltdl.so.7 -lreadline=/lib64/libreadline.so.7 -lncurses=/lib64/libncurses.so.6.1" -loadflags "-DLTDL_LIBRARY=/usr/lib64/libltdl.so.7 -DREADLINE_LIBRARY=/lib64/libreadline.so.7 -DNCURSES_LIBRARY=/lib64/libncurses.so.6.1" mechanisms/
+
+popd
+
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+srun -n $N_WORKERS $SNUDDA_DIR/examples/parallel/KTH_PDC/neuromodulation/x86_64/special -mpi -python $SNUDDA_DIR/snudda/simulate/simulate.py dummy_file dummy_file --simulation_config dspn_bath_experiment_config.json
+
+
+
+

examples/parallel/KTH_PDC/neuromodulation/dspn_DA_bath/dspn_bath_experiment_config.json

@@ -0,0 +1,27 @@
+{
+    "network_file": "../networks/dspn_DA_bath/network-synapses.hdf5",
+    "input_file": "../networks/dspn_DA_bath/input-spikes.hdf5",
+    "output_file": "../networks/dspn_DA_bath/simulation/dspn-output.hdf5",
+    "log_file": "../networks/dspn_DA_bath/log/network-simulation-log.txt",
+    "sample_dt": 0.01,
+    "time": 5,
+    "record_all_soma": true,
+
+    "rxd_enable_extracellular": false,
+    "bath_application": {
+        "DA": {
+            "time": [0, 1.99, 2, 3, 3.01, 10],
+            "concentration": [0, 0, 60e-6, 60e-6, 0, 0]
+        }
+    },
+
+    "record_density_mechanism": {
+	"kir_ms.modulation_factor": {
+	    "neuron_id": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50],
+	    "section_id": [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3],
+	    "section_x": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
+	}
+    },
+    "record_rxd_species_concentration_all_compartments": [["PKAc", [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]], ["DA", [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]]]
+
+}

examples/parallel/KTH_PDC/neuromodulation/dspn_DA_bath/input.json

@@ -0,0 +1,24 @@
+{
+    "dspn": {
+	"cortical": {
+	    "generator": "poisson",
+	    "start": [0.5, 2, 3.5],
+	    "end": [1.5, 3, 4.5],
+	    "frequency": [10, 10, 10],
+	    "parameter_file": "tmglut_DA_parameters.json",
+	    "mod_file": "tmGlut"
+	},
+
+	"GABA": {
+	    "generator": "poisson",
+	    "type": "GABA",
+	    "start": [0.5, 2, 3.5],
+	    "end": [1.5, 3, 4.5],
+	    "frequency": [5, 5, 5],
+	    "num_inputs": 100,
+	    "conductance": 5e-10,
+	    "mod_file": "tmGabaA",
+	    "parameter_file": "$DATA/synapses/striatum/PlanertFitting-DD-tmgaba-fit.json"
+	}
+    }
+}