arbor-sim
arbor

Repository

# clone repository
git clone git@github.com:eth-cscs/nestmc-proto.git
cd nestmc-proto/

# setup environment
# on a desktop system this is probably not required
# on a cluster this is usually required to make sure that an appropriate
# compiler is chosen.
module load gcc
module load cmake
export CC=`which gcc`
export CXX=`which g++`

# build main project (out-of-tree)
mkdir build
cd build
cmake <path to CMakeLists.txt>
make -j

# test
cd tests
./test.exe
export CXX=mpicxx
export CC=mpicc
cmake <path to CMakeLists.txt> -DWITH_MPI=ON
source <path to TBB installation>/tbbvars.sh
cmake <path to CMakeLists.txt> -DWITH_TBB=ON
# load the gnu environment for compiling the application
module load PrgEnv-gnu
# gcc 5.x does not work with the version of TBB installed on Cray
# requires at least version 4.4 of TBB
module swap gcc/4.9.3
# load the intel programming module
# on Cray systems this automatically sets `TBB_ROOT` environment variable
module load intel
module load cmake
export CXX=`which CC`
export CC=`which cc`

# multithreading only
cmake <path to CMakeLists.txt> -DWITH_TBB=ON -DSYSTEM_CRAY=ON

# multithreading and MPI
cmake <path to CMakeLists.txt> -DWITH_TBB=ON -DWITH_MPI=ON -DSYSTEM_CRAY=ON
# First build a 'normal' non KNL version of the software

# Load your environment (see section 6 for detailed example)
export CC=`which gcc`; export CXX=`which g++`

# Make directory , do the configuration and build
mkdir build
cd build
cmake <path to CMakeLists.txt> -DCMAKE_BUILD_TYPE=release
make -j8

# set path and test that you can see modcc
export PATH=`pwd`/bin:$PATH
which modcc
# clone the repository and set up the submodules
git clone https://github.com/eth-cscs/nestmc-proto.git
cd nestmc-proto

# make a path for out of source build
mkdir build_knl
cd build_knl

# run cmake with all the magic flags
export CC=`which icc`
export CXX=`which icpc`
cmake <path to CMakeLists.txt> -DCMAKE_BUILD_TYPE=release -DWITH_TBB=ON -DWITH_PROFILING=ON -DVECTORIZE_TARGET=KNL -DUSE_OPTIMIZED_KERNELS=ON
make -j
cd tests
./test.exe
cd ..
cd miniapp

# a small run to check that everything works
./miniapp.exe -n 1000 -s 200 -t 20 -p 0

# a larger run for generating meaningful benchmarks
./miniapp.exe -n 2000 -s 2000 -t 100 -p 0
              ---------------------------------------
             |       small       |       large       |
-------------|-------------------|-------------------|
total        |  0.791     100.0  | 38.593     100.0  |
  stepping   |  0.738      93.3  | 36.978      95.8  |
    matrix   |  0.406      51.3  |  6.034      15.6  |
      solve  |  0.308      38.9  |  4.534      11.7  |
      setup  |  0.082      10.4  |  1.260       3.3  |
      other  |  0.016       2.0  |  0.240       0.6  |
    state    |  0.194      24.5  | 23.235      60.2  |
      expsyn |  0.158      20.0  | 22.679      58.8  |
      hh     |  0.014       1.7  |  0.215       0.6  |
      pas    |  0.003       0.4  |  0.053       0.1  |
      other  |  0.019       2.4  |  0.287       0.7  |
    current  |  0.107      13.5  |  7.106      18.4  |
      expsyn |  0.047       5.9  |  6.118      15.9  |
      pas    |  0.028       3.5  |  0.476       1.2  |
      hh     |  0.006       0.7  |  0.096       0.2  |
      other  |  0.026       3.3  |  0.415       1.1  |
    events   |  0.005       0.6  |  0.125       0.3  |
    sampling |  0.003       0.4  |  0.051       0.1  |
    other    |  0.024       3.0  |  0.428       1.1  |
  other      |  0.053       6.7  |  1.614       4.2  |
-----------------------------------------------------
module load cmake
module load intel-ics
module load openmpi_ics/2.0.0
module load gcc/6.1.0