-
Notifications
You must be signed in to change notification settings - Fork 1
tillschumann/thesis
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
NEST: - Install NEST with hdf5 load module implementation - Checkout Mike2 branch from nest repo https://github.com/tillschumann/nest-simulator.git - Adapt library pathes in the first lines in build-nest.sh (inside) the set ones are valid for bbpbg1.cscs.ch - Adapt NEST file path and build folder - Build NEST using script: build-nest.sh - NEST is installation is now placed in INSTALL_PATH (from build-nest.sh script) - To use NEST, all necessary paths can be loaded via: 'source INSTALL_PATH/bin/nest_vars.sh' How to run a nest simulation: nest script.sli (resp. srun nest script.sli) script.sli contains the full simulatoin workflow. (http://www.nest-simulator.org/neural_simulations/) How to use neuron and synapse load module see thesis. NEST Models: https://github.com/tillschumann/models Needed changes: Adapt nest install path in slurm scripts (eventually adapt batch script to given cluster) Info: Sli script and execute script is nessecary. Because nest parameter is still changing, look at newest update. to adapt script to it. Currently it is 1per300mouse In the sli file the location of the circuit has to be adapted if it changes. Further the number of neurons is hardcoded inside. Before running make sure specified output folder is existing. GenBrain: Info: Generate Ciruit with long range and short range connectivity - See manual for Csaba Tools: - Paraview Used to visulize voxelized densities in 3D space The data can be loaded from MHD files. MHD files can be generated via BBP viz tools are my python scripts Python scripts for analysis during thesis: https://github.com/tillschumann/thesis.git located in subfolder: scripts: Merging of gdf spike files written by nest spikedetector - mergeSpikeDetectors.py Input: path, number of spiking neurons Output: neurons.npy spikes.npy Info: Set number of spiking neurons too high and run the script. The last number which is displayed is the correct one. If the number is too low the run aboards. Visualize own written trace files (ex. traceFile_000.csv) - viewTraceFile.py Input: path to file, number of shown ranks Output: matplotlib windows Info: You can see scatter plots, showing the ranks on the y axis and iterations on the x axis. The color shows the measured timing in seconds Plotting nest memory consumption based on "Spiking network simulation code for petascale computers" - calc_Mem_consumption_Circuit.py - calc_Mem_consumption_Nest.py Easy voxelizing scripts to visualize point neurons with paraview. Scripts only creates raw data. mhd has to be added by hand. - voxelizeSpikingNeurons.py - voxelizeTargetNeurons.py Info: ex. mhd file content: ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = 0 0 0 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 100 100 100 DimSize = 133 81 115 ElementType = MET_INT ElementDataFile = filename.raw Create spiking plots from neurons.npy spikes.npy files - spiking.py Info: Specify input path on line 82 and 83. Included functions like cut, sort, compare, dotplot can be used to interact with data Visualizing tools from bbp viz team: git: ssh://schumann@bbpcode.epfl.ch/viz/Fivox branch: origin/allen_loader Example usage written in doc/UserGuide.md in repo Circuit analysis repo (an example): Used to perform easy statistical analysis on the big dataset - https://github.com/tillschumann/STATS_SYN.git H5SynapseLoader.h Class to load synapses (extracted from NEST synapse load module) NESTNodeSynapse.* Class to store synapse information in memory main.cpp Applying easy math operation to all synapses iterativly Used Cluster: - bbplviz bbpviz1.cscs.ch - BGQ bbpbg1.cscs.ch - bbpviz bbplviz1.cscs.ch - juqueen juqueen.fz-juelich.de
About
No description, website, or topics provided.
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published