Merge pull request #406 from Hjorthmedh/init_redux

Init redux

examples/notebooks/README.md

@@ -12,6 +12,7 @@ Here is a collection of Jupyter Notebooks, some of the workflows are split over
 * [example_of_neuron_rotations](example_of_neuron_rotations.ipynb) shows how to rotate neurons based on position.
 * [bend_morphologies](bend_morphologies.ipynb) shows how to make the neurons bend the axons and dendrites at the edge of the mesh, to keep them constrained to the volume.
 * [connect_structures_example](connect_structures_example.ipynb) shows how to create neuron projections between volumes when no-axon data is available ([parallel version](connect_structures_example_parallel.ipynb)). There is also an [alternative version](connect_structures_example_projection_detection.ipynb) that places axon voxels randomly within the projection zone and then applies touch detection.
+* [composite axon example](ProjectionExample/composite_axon_projections.ipynb) shows how to create neuron projections between (or within) volumes using separate axon morphologies (.swc-files).
 * [virtual_neurons](VirtualNeurons/VirtualNeurons.ipynb) shows how to only simulate the core of a volume of neurons, by turning the outer neurons to virtual neurons that spike at predetermined times. This is useful to avoid edge effects in your simulations.
 
 ## Input creation
@@ -38,4 +39,4 @@ Here is a collection of Jupyter Notebooks, some of the workflows are split over
 
 ## Additional notebooks
 * [Paired current injection](validation/synapses/network_pair_pulse_simulation.ipynb) in a simulated network
-* [Neuromodulation examples](https://github.com/jofrony/Neuromodulation-software/tree/main/examples) in a network
+* [Neuromodulation examples](https://github.com/jofrony/Neuromodulation-software/tree/main/examples) in a network

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_cortical_signal_dspn-clustered.job

@@ -0,0 +1,133 @@
+#!/bin/bash -l
+#SBATCH --partition=main
+#SBATCH -o log/InputTuning-%j-output.txt
+#SBATCH -e log/InputTuning-%j-error.txt
+#SBATCH -t 1:59:00
+#SBATCH --time-min=1:59:00
+#SBATCH -J InputTuning
+#SBATCH -A naiss2023-5-231
+#SBATCH --nodes=12
+#SBATCH --tasks-per-node=128
+#SBATCH --mem-per-cpu=930M
+#SBATCH --mail-type=ALL
+
+export SNUDDA_TUNE_NEURON="dspn"
+export SEED_LIST="[10,20,30,40,50]"
+export INPUT_TYPE="cortical-clustered"
+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_${INPUT_FREQ}Hz
+
+# This is used for NEURON
+export N_WORKERS=$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_input_tuning_signal.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 --seed_list $SEED_LIST
+
+

examples/parallel/KTH_PDC/input_tuning/Dardel_run_input_tuning_cortical_signal_dspn-correlated.job

@@ -0,0 +1,134 @@
+#!/bin/bash -l
+#SBATCH --partition=main
+#SBATCH -o log/InputTuning-%j-output.txt
+#SBATCH -e log/InputTuning-%j-error.txt
+#SBATCH -t 1:59:00
+#SBATCH --time-min=1:59:00
+#SBATCH -J InputTuning
+#SBATCH -A naiss2023-5-231
+#SBATCH --nodes=12
+#SBATCH --tasks-per-node=128
+#SBATCH --mem-per-cpu=930M
+#SBATCH --mail-type=ALL
+
+export SNUDDA_TUNE_NEURON="dspn"
+export SEED_LIST="[10,20,30,40,50]"
+export INPUT_TYPE="cortical-correlated"
+export INPUT_FREQ=10
+export INPUT_CORRELATION=0.5
+
+# 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_${INPUT_FREQ}Hz
+
+# This is used for NEURON
+export N_WORKERS=$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_input_tuning_signal.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 --seed_list $SEED_LIST
+
+