https://github.com/bluebrain/neurox
A parallel & distributed asynchronous simulator of extended Hodgkin-Huxley neuron models
https://github.com/bluebrain/neurox
Last synced: about 1 year ago
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A parallel & distributed asynchronous simulator of extended Hodgkin-Huxley neuron models
- Host: GitHub
- URL: https://github.com/bluebrain/neurox
- Owner: BlueBrain
- License: bsd-3-clause
- Created: 2017-04-27T14:00:55.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2022-04-27T11:14:28.000Z (about 4 years ago)
- Last Synced: 2024-11-13T01:03:04.320Z (over 1 year ago)
- Language: C++
- Homepage:
- Size: 71.3 MB
- Stars: 3
- Watchers: 5
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# neurox
A scalable parallel & distributed asynchronous simulator of extended Hodgkin-Huxley neuron models
## Installation
Dependencies
- cmake 2.8.12+: www.cmake.org
- hpx 4+: https://hpx.crest.iu.edu/
- tclap 1.2.1+: http://tclap.sourceforge.net/
- libCoreNeuron: https://github.com/BlueBrain/coreneuron
- sundials CVODES 3.1.0+: https://computation.llnl.gov/projects/sundials/cvodes
- requires SUPERLUMT solver: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt
- requires KLU solver: http://faculty.cse.tamu.edu/davis/suitesparse.html
- hint: add `-DSUPERLUMP_ENABLE=ON -DKLU_ENABLE=ON` to the `cmake` command to enable support
## set-up
General compilation parameters:
```
export CC=mpicc
export CXX=mpicxx
export WORKSPACE_PATH=/home/username/Workspace
```
HPX compilation parameters:
```
export HPX_INSTALL_PATH=$WORKSPACE_PATH/hpx-install
export PKG_CONFIG_PATH=$HPX_INSTALL_PATH/lib/pkgconfig/:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=$HPX_INSTALL_PATH/lib:$LD_LIBRARY_PATH
export PATH=$HPX_INSTALL_PATH/bin:$PATH
```
neurox compilation parameters
```
export NEUROX_INSTALL_PATH=$WORKSPACE_PATH/neurox-install
export LD_LIBRARY_PATH=$NEUROX_INSTALL_PATH/lib:$LD_LIBRARY_PATH
export PATH=$NEUROX_INSTALL_PATH/bin:$PATH
```
## Compilation
```
cmake .. -DCMAKE_INSTALL_PREFIX=$NEUROX_INSTALL_PATH
```
*Note*: requires libcoreneuron installation with export of function pointers (`-DEXPORT_MECHS_FUNCTIONS`) and extra mechanisms path when applicable(`-DADDITIONAL_MECHPATH` and `-DADDITIONAL_MECHS`). To be on the safe side, we will also disable timing out of coreneuron after a certain period of inactivity (`-DDISABLE_NRN_TIMEOUT`) and OpenMP that may interfere with HPX scheduler (`-DCORENEURON_OPENMP`).
To allow header files to be exposed externally we activate the flag`ENABLE_DEV_FILES_INSTALLATION`. Vectorization is provided by setting the input data-structure as Array-Of-Structures or Structures-of-Arrays (`-DENABLE_SOA`). All other flags are optional and are added to speed-up compilation.
```
cmake .. -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=$NEUROX_INSTALL_PATH \
-DADDITIONAL_MECHPATH=$NEURODAMUS_LIB_PATH \
-DADDITIONAL_MECHS=$ADDITIONAL_MECHS_PATH \
-DEXPORT_MECHS_FUNCTIONS=ON \
-DCORENEURON_OPENMP=OFF \
-DDISABLE_NRN_TIMEOUT=ON\
-DENABLE_DEV_FILES_INSTALLATION=ON \
-DCMAKE_CXX_FLAGS="-std=c++11" \
\
-DENABLE_CUDA_MODULES=OFF \
-DENABLE_NET_RECEIVE_BUFFERING=OFF \
-DENABLE_OPENACC_INFO=OFF \
-DENABLE_REPORTINGLIB=OFF \
-DUNIT_TESTS=OFF \
-DFUNCTIONAL_TESTS=OFF \
-DCORENEURON_MAIN=OFF
```
## Execution
```
./neurox --help for execution parameters
./neurox -d -e for execution with minimum parameters
```
## Misc
- We follow the google coding style (https://google.github.io/styleguide/cppguide.html) and format. To automatically format the code recursively in all folders use `clang-format`.
```
find ./neurox -iname *.h -o -iname *.cc | xargs clang-format -i -style=Google
```
- To check for coding style errors, use `ccplint.py` (https://raw.githubusercontent.com/google/styleguide/gh-pages/cpplint/cpplint.py ). False positives can be ignored by putting `// NOLINT` at the end of the line or `// NOLINTNEXTLINE` in the previous line.
```
find ./neurox -iname *.h -o -iname *.cc | xargs cpplint.py
```
- Documentation follows the doxygen (www.doxygen.org) notation and can be exported with `make doc`;
- Developer note: to collect CPU hotspots with inter VTune (`amplxe-cl --help` for details):
```
amplxe-cl -collect hotspots -r r000hs srun -n 1 ./bin/neurox_exec -d /gpfs/bbp.cscs.ch/project/proj16/bmagalha/Circuits/PCP/1/coreneuron_input
```
## Citations
Please use following citation to reference this work:
B. R. C. Magalhães, T. Sterling, M. Hines, and F. Schürmann, “Asynchronous Branch-Parallel Simulation of Detailed Neuron Models,” Frontiers in Neuroinformatics, vol. 13, p. 54, 2019, doi: 10.3389/fninf.2019.00054.
## Funding
The work was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology. A portion of Michael Hines efforts was supported by NINDS grant R01NS11613.
## Copyright
Copyright (c) 2015-2022 Blue Brain Project/EPFL & Center for Research in Extreme Scale Technologies (CREST), Indiana University