analysis for dt=0.025
Config | Run time | Relative | _ |
---|---|---|---|
nmlcc-super | 1.14 sim.s/bio.s | fastest | 5 trials |
nmlcc | 1.33 sim.s/bio.s | 16.598% slower | 5 trials |
neuron | 5.84 sim.s/bio.s | 411.810% slower | 5 trials |
Run setup-env.sh to create a environment with versioned simulators
Required dependencies
java
(for pyNeuroML)cargo
(for nmlcc)
Sources:
Todo
- Run on Juwels
Intel Xeon Platinum 8168
node - Compile with vectorization
- Install RUST
ssh juwels
jutil env activate -p cslns
mkdir -p $SCRATCH/$USER
cd $SCRATCH/$USER
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
source "$HOME/.cargo/env"
git clone 'https://github.com/llandsmeer/nmlcc' \
--branch='feat/sm-merge-nonuniform' \
--recursive
cd nmlcc
cargo install --path .
nmlcc --version
https://docs.arbor-sim.org/en/latest/install/build_install.html
module load Python/3.9.6 GCC/11.2.0 CMake/3.21.1
pyprefix=`python3 -c 'import site; print(site.getusersitepackages())'`
cd $SCRATCH/$USER
git clone --recursive https://github.com/arbor-sim/arbor
cd arbor
mkdir build
cd build
cmake .. \
-DARB_VECTORIZE=ON \
-DARB_ARCH=native \
-DARB_WITH_PYTHON=on \
-DCMAKE_BUILD_TYPE=release \
-DARB_USE_BUNDLED_LIBS=ON \
-DARB_PYTHON_LIB_PATH="${pyprefix}" \
-DCMAKE_INSTALL_PREFIX=$HOME/.local
make -j 64
make install
python3 -c 'import arbor; print(arbor); print(arbor.config())'
cd $SCRATCH/$USER
git clone https://github.com/llandsmeer/Layer5Comparison
cd Layer5Comparison
pip3 install pandas neuron
srun --account slns --partition batch --mem 80G --time 20:00:00 --pty bash
export PATH="$HOME/.local/bin:$PATH"
rm -fr generated
./run-all.sh
# y