Updating

examples/parallel/KTH_PDC/lateral_inhibition/Dardel_runSnudda_lateral.job

@@ -2,7 +2,7 @@
 #SBATCH --partition=main
 #SBATCH -o log/runSnudda-%j-output.txt
 #SBATCH -e log/runSnudda-%j-error.txt
-#SBATCH -t 00:59:00
+#SBATCH -t 1:59:00
 #SBATCH -J Snudda
 #SBATCH -A naiss2023-5-231
 #SBATCH --nodes=2

examples/parallel/KTH_PDC/lateral_inhibition/Dardel_runSnudda_lateral.sh

@@ -3,7 +3,7 @@
 
 
 SNUDDA_DIR=$HOME/Snudda/snudda
-JOBDIR=networks/lateral_1
+JOBDIR=networks/lateral_2
 
 SIMSIZE=50000
 
@@ -41,7 +41,7 @@ else
 
     echo ">>> Init: "`date`
     # snudda init ${JOBDIR} --size ${SIMSIZE} --overwrite --randomseed 1234
-    python setup_lateral.py
+    python setup_lateral.py ${JOBDIR}
 
     if [ $? != 0 ]; then
 	echo "Something went wrong during init, aborting!"
@@ -98,11 +98,12 @@ else
 
     # Disable input generation at the moment
 
-    #echo ">>> Input: "`date`
-    # cp -a $SNUDDA_DIR/data/input_config/input-v10-scaled.json ${JOBDIR}/input.json
-    # cp -a $SNUDDA_DIR/data/input_config/external-input-dSTR-scaled-v4.json ${JOBDIR}/input.json
-
-    snudda input ${JOBDIR} --parallel --time 5 --input input.json
+    echo ">>> Ablate: "`date`
+    python ablate_network.py ${JOBDIR}
+
+    echo ">>> Input: "`date`
+    # snudda input ${JOBDIR} --parallel --time 5 --input input.json
+    snudda input ${JOBDIR} --parallel --time 5 --input input.json --networkFile ${JOBDIR}/network-synapses-minimal.hdf5
 
 
     #.. Shut down cluster

examples/parallel/KTH_PDC/lateral_inhibition/Dardel_simulate_lateral.job

@@ -67,4 +67,6 @@ srun -n 1 nrnivmodl -incflags "-lltdl=/usr/lib64/libltdl.so.7 -lreadline=/lib64/
 # srun -n $N_WORKERS $SNUDDA_DIR/examples/parallel/x86_64/special -mpi -python $SNUDDA_DIR/simulate/simulate.py $NETWORK_INFO_FILE $NETWORK_INPUT_FILE --disableGJ --time 3.5 --voltOut $NETWORK_VOLTAGE_FILE
 
 # GJ active
-srun -n $N_WORKERS $SNUDDA_DIR/examples/parallel/KTH_PDC/x86_64/special -mpi -python $SNUDDA_DIR/snudda/simulate/simulate.py $NETWORK_INFO_FILE $NETWORK_INPUT_FILE --time 5 --noVolt
+srun -n $N_WORKERS $SNUDDA_DIR/examples/parallel/KTH_PDC/x86_64/special -mpi -python $SNUDDA_DIR/snudda/simulate/simulate.py $NETWORK_INFO_FILE $NETWORK_INPUT_FILE --time 5
+
+# srun -n $N_WORKERS $SNUDDA_DIR/examples/parallel/KTH_PDC/x86_64/special -mpi -python $SNUDDA_DIR/snudda/simulate/simulate.py $NETWORK_INFO_FILE $NETWORK_INPUT_FILE --time 5 --noVolt

examples/parallel/KTH_PDC/lateral_inhibition/setup_lateral.py

@@ -1,9 +1,20 @@
 import os
+import sys
 import numpy as np
-network_path = "networks/lateral_1"
+
+if len(sys.argv) > 1:
+    network_path = sys.argv[1]
+else:
+    sys.exit("No network path specified!")
+    network_path="networks/lateral_1"
+
+# network_path = "networks/lateral_1"
 # snudda_data = "$HOME/BasalGangliaData/data"
 snudda_data = "../../../../../BasalGangliaData/data/"
 
+print(f"Network_path = {network_path}, snudda data = {snudda_data}")
+
+
 duration=5
 
 # import pdb
@@ -12,8 +23,8 @@
 # from snudda import SnuddaInit -- this works on local machine, but not on dardel
 import snudda.init
 
-n_DSPN = 30000
-n_ISPN = 30000
+n_DSPN = 50000
+n_ISPN = 50000
 n_FS = 0
 n_LTS = 0
 n_ChIN = 0
@@ -27,11 +38,11 @@
 
 # The centre of the cube is [0.00475, 0.004, 0.00775]. num_neurons is optional
 si.add_population_unit_density(structure_name="Striatum", neuron_types=["dSPN", "iSPN"], 
-                               unit_centre=np.array([0.00475, 0.004, 0.00775]) -np.array([0,50e-6,150e-6]),
-                               probability_function="(d < 200e-6)*1", num_neurons=200)
+                               unit_centre=np.array([0.00475, 0.004, 0.00775]) -np.array([0,50e-6,50e-6]),
+                               probability_function="(d < 250e-6)*1", num_neurons=1000)
 si.add_population_unit_density(structure_name="Striatum", neuron_types=["dSPN", "iSPN"], 
-                               unit_centre=np.array([0.00475, 0.004, 0.00775]) -np.array([150e-6,0,0]),
-                               probability_function="(d < 200e-6) * 1", num_neurons=200)
+                               unit_centre=np.array([0.00475, 0.004, 0.00775]) -np.array([50e-6,0,0]),
+                               probability_function="(d < 250e-6) * 1", num_neurons=1000)
 
 print("Writing json")