Merge pull request #405 from Hjorthmedh/region_mesh_redux

More flexible input generation from meta.json

examples/notebooks/README.md

@@ -19,8 +19,9 @@ Here is a collection of Jupyter Notebooks, some of the workflows are split over
 * [input_generation_example_2_frequency_vectors](input_generation_example_2_frequency_vectors.ipynb) define Poisson input with multiple start/stop times (uses [simple_network_creation](simple_network_creation.ipynb)).
 * [input_generation_example_3_correlation](input_generation_example_3_correlation.ipynb) finer control in input targeting (uses [population_unit_network](population_unit_network.ipynb))
 * [input_tuning_example](input_tuning_example.ipynb) explore what input number and frequency are good neurons, e.g to avoid depolarisation block.
-* [Adanced input tuning](../parallel/KTH_PDC/input_tuning/) using the Dardel super computer. Here both background and signal level are optimised.
+* [Advanced input tuning](../parallel/KTH_PDC/input_tuning/) using the Dardel super computer. Here both background and signal level are optimised, and the result is written to meta.json in BasalGangliaData.
 * [input_frequency](InputFrequency/InputFrequency.ipynb) time varying input frequency example
+* [basal_ganglia_data_input](Input-generation-using-BasalGangliaData.ipynb) builds upon the input tuned in BasalGangliaData.
 
 ## Striatum example
 * [striatum_example](striatum_example.ipynb) creates a small striatal network, increase number of neurons for the full version.

examples/notebooks/input_config/basal-ganglia-data-input.json

@@ -0,0 +1,40 @@
+{
+    "dSPN": {
+        "cortical:1" : {
+            "generator" : "poisson",
+            "start" : [1, 4],
+            "end" :   [3, 6],
+            "frequency" : [5, 5],
+            "populationUnitID" : 1
+        },
+
+        "cortical:2" : {
+            "generator" : "poisson",
+            "start" : [4],
+            "end" :   [6],
+            "frequency" : [10],
+            "populationUnitID" : 2
+        }       
+    },
+
+
+    "iSPN": {
+        "cortical:1" : {
+            "generator" : "poisson",
+            "start" : [1, 4],
+            "end" :   [3, 6],
+            "frequency" : [5, 5],
+            "populationUnitID" : 1          
+        },
+
+        "cortical:2" : {
+            "generator" : "poisson",
+            "start" : [4],
+            "end" :   [6],
+            "frequency" : [10],
+            "populationUnitID" : 2
+        }       
+    }
+
+
+}

examples/notebooks/input_tuning_example.ipynb

@@ -5,6 +5,10 @@
    "id": "heated-thousand",
    "metadata": {},
    "source": [
+    "__Update__\n",
+    "\n",
+    "__There is an more extensive and updated version of this using parallel computing [here](../parallel/KTH_PDC/input_tuning)__\n",
+    "\n",
     "Different morphologies of the same neuron type might require different activation to reach comparable firing frequency. InputScaling simulates a network of a neuron type with different number of inputs, and different frequency to infer what level of input is needed.\n",
     "\n",
     "Here we look at the input to ```neuron_types=\"fs\"```.\n",

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_cortical_signal_dspn.job

@@ -14,7 +14,7 @@
 export SNUDDA_TUNE_NEURON="dspn"
 export SEED_LIST="[10,20,30,40,50]"
 export INPUT_TYPE="cortical"
-export INPUT_FREQ=40
+export INPUT_FREQ=10
 
 # You need to point this as the directory where you created the network in
 #NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_cortical_signal_fs.job

@@ -2,8 +2,8 @@
 #SBATCH --partition=main
 #SBATCH -o log/InputTuning-%j-output.txt
 #SBATCH -e log/InputTuning-%j-error.txt
-#SBATCH -t 6:59:00
-#SBATCH --time-min=5:59:00
+#SBATCH -t 3:59:00
+#SBATCH --time-min=2:59:00
 #SBATCH -J InputTuning
 #SBATCH -A naiss2023-5-231
 #SBATCH --nodes=8-12
@@ -14,10 +14,11 @@
 export SNUDDA_TUNE_NEURON="fs"
 export SEED_LIST="[10,20,30,40,50]"
 export INPUT_TYPE="cortical"
+export INPUT_FREQ=10
 
 # You need to point this as the directory where you created the network in
 #NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k
-NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal
+NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal_${INPUT_FREQ}Hz
 
 # This is used for NEURON
 export N_WORKERS=$SLURM_NTASKS

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_cortical_signal_ispn.job

@@ -2,8 +2,8 @@
 #SBATCH --partition=main
 #SBATCH -o log/InputTuning-%j-output.txt
 #SBATCH -e log/InputTuning-%j-error.txt
-#SBATCH -t 8:59:00
-#SBATCH --time-min=7:59:00
+#SBATCH -t 3:59:00
+#SBATCH --time-min=2:59:00
 #SBATCH -J InputTuning
 #SBATCH -A naiss2023-5-231
 #SBATCH --nodes=8-12
@@ -14,10 +14,11 @@
 export SNUDDA_TUNE_NEURON="ispn"
 export SEED_LIST="[10,20,30,40,50]"
 export INPUT_TYPE="cortical"
+export INPUT_FREQ=10
 
 # You need to point this as the directory where you created the network in
 #NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k
-NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal
+NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal_${INPUT_FREQ}Hz
 
 # This is used for NEURON
 export N_WORKERS=$SLURM_NTASKS

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_thalamic_signal_dspn.job

@@ -14,7 +14,7 @@
 export SNUDDA_TUNE_NEURON="dspn"
 export SEED_LIST="[10,20,30,40,50]"
 export INPUT_TYPE="thalamic"
-export INPUT_FREQ=40
+export INPUT_FREQ=10
 
 # You need to point this as the directory where you created the network in
 #NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_thalamic_signal_fs.job

@@ -2,8 +2,8 @@
 #SBATCH --partition=main
 #SBATCH -o log/InputTuning-%j-output.txt
 #SBATCH -e log/InputTuning-%j-error.txt
-#SBATCH -t 6:59:00
-#SBATCH --time-min=5:59:00
+#SBATCH -t 3:59:00
+#SBATCH --time-min=1:59:00
 #SBATCH -J InputTuning
 #SBATCH -A naiss2023-5-231
 #SBATCH --nodes=8-12
@@ -14,10 +14,11 @@
 export SNUDDA_TUNE_NEURON="fs"
 export SEED_LIST="[10,20,30,40,50]"
 export INPUT_TYPE="thalamic"
+export INPUT_FREQ=10
 
 # You need to point this as the directory where you created the network in
 #NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k
-NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal
+NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal_${INPUT_FREQ}Hz
 
 # This is used for NEURON
 export N_WORKERS=$SLURM_NTASKS

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_thalamic_signal_ispn.job

@@ -2,8 +2,8 @@
 #SBATCH --partition=main
 #SBATCH -o log/InputTuning-%j-output.txt
 #SBATCH -e log/InputTuning-%j-error.txt
-#SBATCH -t 8:59:00
-#SBATCH --time-min=7:59:00
+#SBATCH -t 3:59:00
+#SBATCH --time-min=2:59:00
 #SBATCH -J InputTuning
 #SBATCH -A naiss2023-5-231
 #SBATCH --nodes=8-12
@@ -14,10 +14,11 @@
 export SNUDDA_TUNE_NEURON="ispn"
 export SEED_LIST="[10,20,30,40,50]"
 export INPUT_TYPE="thalamic"
+export INPUT_FREQ=10
 
 # You need to point this as the directory where you created the network in
 #NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k
-NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal
+NETWORK_DIR=networks/input_tuning_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}_signal_${INPUT_FREQ}Hz
 
 # This is used for NEURON
 export N_WORKERS=$SLURM_NTASKS

examples/parallel/KTH_PDC/input_tuning/Dardel_verify_cortical_dspn.job

@@ -0,0 +1,131 @@
+#!/bin/bash -l
+#SBATCH --partition=main
+#SBATCH -o log/InputTuning-%j-output.txt
+#SBATCH -e log/InputTuning-%j-error.txt
+#SBATCH -t 3:59:00
+#SBATCH --time-min=2:59:00
+#SBATCH -J InputTuning
+#SBATCH -A naiss2023-5-231
+#SBATCH --nodes=4
+#SBATCH --tasks-per-node=128
+#SBATCH --mem-per-cpu=930M
+#SBATCH --mail-type=ALL
+
+export SNUDDA_TUNE_NEURON="dspn"
+export INPUT_TYPE="cortical"
+
+# You need to point this as the directory where you created the network in
+#NETWORK_DIR=/cfs/klemming/home/${USER:0:1}/$USER/Snudda/examples/parallel/KTH_PDC/networks/test_10k
+NETWORK_DIR=networks/verify_input_${SNUDDA_TUNE_NEURON}_${INPUT_TYPE}
+
+# This is used for NEURON
+export N_WORKERS=$SLURM_NTASKS
+
+# export N_WORKERS=50
+# export IPNWORKERS=$N_WORKERS
+
+# This is used for ipyparallel and Snudda
+export IPNWORKERS=100
+
+# Clear old ipyparallel
+export IPYTHONDIR="/cfs/klemming/scratch/${USER:0:1}/$USER/.ipython"
+rm -r $IPYTHONDIR
+export IPYTHON_PROFILE=default
+
+module load snic-env
+source $HOME/Snudda/snudda_env/bin/activate
+SNUDDA_DIR=/cfs/klemming/home/"${USER:0:1}"/$USER/Snudda
+
+
+# If the BasalGangliaData directory exists, then use that for our data
+if [[ -d "/cfs/klemming/home/${USER:0:1}/$USER/BasalGangliaData/data" ]]; then
+    export SNUDDA_DATA="/cfs/klemming/home/${USER:0:1}/$USER/BasalGangliaData/data"
+    echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
+    rm mechanisms
+    ln -s $SNUDDA_DATA/neurons/mechanisms/ mechanisms
+else
+    echo "SNUDDA_DATA environment variable not changed (may be empty): $SNUDDA_DATA"
+    rm mechanisms
+    ln -s ../../../snudda/data/neurons/mechanisms/
+fi
+
+
+# Start ipyparallel
+#.. Start the ipcontroller
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+srun -n 1 -N 1 -c 2 --exact --overlap --mem=0 ./../ipcontroller_new.sh &
+
+
+echo ">>> waiting 60s for controller to start"
+sleep 60 
+
+#.. Read in CONTROLLERIP
+CONTROLLERIP=$(<controller_ip.txt)
+
+##.. Start the engines
+echo ">>> starting ${IPNWORKERS} engines "
+echo "SLURM_JOB_NUM_NODES={SLURM_JOB_NUM_NODES}"
+
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+srun -n ${IPNWORKERS} -c 2 -N ${SLURM_JOB_NUM_NODES} --exact --overlap --mem=0 ipengine \
+--location=${CONTROLLERIP} --profile=${IPYTHON_PROFILE} --mpi \
+--ipython-dir=${IPYTHONDIR}  --timeout=30.0 c.EngineFactory.max_heartbeat_misses=10  c.MPI.use='mpi4py' \
+1> ipe_${SLURM_JOBID}.out 2> ipe_${SLURM_JOBID}.err &
+
+
+echo ">>> waiting 60s for engines to start"
+sleep 30
+
+
+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/python3.9/
+
+# This will stop NEURON from failing with "can't open DISPLAY"
+unset DISPLAY
+
+# Do we need this magic?
+# export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+# srun -n 1 python test_script.py &> test_print.txt
+
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+
+# srun -n 1 python setup_input_tuning_background.py &> log/setup_network_log.txt
+srun -n 1 -N 1 --exact --overlap --mem=0 python setup_verify_input_tuning.py &> log/setup_network_log.txt
+
+
+# Quit ipyparallel
+
+python ../ipcontroller_shutdown.py
+
+
+##############
+
+rm -r x86_64
+
+export CXX=CC
+export CC=cc
+export FC=ftn
+export MPICC=cc
+export MPICXX=CC
+
+CC --version
+
+echo "About to run nrnivmodl"
+which nrnivmodl
+
+# srun -n nrnivmodl mechanisms/
+
+# Do we need this magic?
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+
+srun -n 1 nrnivmodl -incflags "-lltdl=/usr/lib64/libltdl.so.7 -lreadline=/lib64/libreadline.so.7 -lncurses=/lib64/libncurses.so.6.1" -loadflags "-DLTDL_LIBRARY=/usr/lib64/libltdl.so.7 -DREADLINE_LIBRARY=/lib64/libreadline.so.7 -DNCURSES_LIBRARY=/lib64/libncurses.so.6.1" mechanisms/
+
+# Do we need this magic?
+export FI_CXI_DEFAULT_VNI=$(od -vAn -N4 -tu < /dev/urandom)
+
+srun -n $N_WORKERS $SNUDDA_DIR/examples/parallel/KTH_PDC/input_tuning/x86_64/special -mpi -python $SNUDDA_DIR/snudda/input/input_tuning.py simulate $NETWORK_DIR 
+
+