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Friedemann Zenke
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Merge branch 'release-v0.7'
Merges release branch into master for full release of Auryn v0.7.
2 parents 4db7bf5 + f1ac5a3 commit 75c6e8c

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‎.gitignore

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*.[oa]
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*.l[oa]
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*/.libs
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# Ignore docs
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docs/*
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# Ignore development files
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dev/*
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# Ignore stuff in the build dirs except the makefiles
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build/*
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!build/lcncluster/Makefile
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!build/lcnsunc1/Makefile
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!build/home/Makefile
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!build/debug/Makefile
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!build/tug/Makefile
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# http://www.gnu.org/software/automake
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Makefile.in
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Makefile
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# # http://www.gnu.org/software/autoconf
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/autom4te.cache
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/aclocal.m4
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/compile
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/configure
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/depcomp
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/install-sh
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/missing
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/stamp-h1
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config*
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.deps
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libtool
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ltmain.sh
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m4/libtool.m4
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m4/ltoptions.m4
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m4/ltsugar.m4
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m4/ltversion.m4
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m4/lt~obsolete.m4
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# Ignore stuff in the build dir
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build/*
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cscope.out
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tags
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# travis build file
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.travis.yml

‎.travis.yml

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language: cpp
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compiler:
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- gcc
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before_install:
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- sudo add-apt-repository ppa:boost-latest/ppa -y
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- sudo add-apt-repository ppa:dns/gnu -y
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- sudo add-apt-repository ppa:yjwong/cmake -y
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- sudo apt-get update -qq -y
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- sudo apt-get -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" install build-essential libtool m4 --force-yes
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- sudo apt-get install libboost1.54-all-dev mpich2 libmpich2-dev libcr-dev -y
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- sudo apt-get install cmake cmake-data -y
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script:
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- CFLAGS="${CFLAGS:--O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic}" ; export CFLAGS ;
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- CXXFLAGS="${CXXFLAGS:--O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic}" ; export CXXFLAGS ;
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- LDFLAGS="${LDFLAGS:--Wl,-z,relro}";export LDFLAGS ;
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- cmake -DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON && make
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notifications:
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email:
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recipients:
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- [email protected]
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- [email protected]
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on_success: change
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on_failure: always

‎CMakeLists.txt

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cmake_minimum_required (VERSION 2.6)
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project (Auryn)
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# The version number.
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set (Auryn_VERSION_MAJOR 0)
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set (Auryn_VERSION_MINOR 6)
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# Important GCC Compiler flags for Auryn's performance
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native -ffast-math")
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")
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# Display flags (for debugging only)
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# message("CMAKE_CXX_FLAGS_DEBUG is ${CMAKE_CXX_FLAGS_DEBUG}")
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# message("CMAKE_CXX_FLAGS_RELEASE is ${CMAKE_CXX_FLAGS_RELEASE}")
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# Required external MPI libraries
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FIND_PACKAGE(MPI REQUIRED)
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# Required Boost libraries
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SET(BOOST_MIN_VERSION "1.41.0")
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FIND_PACKAGE(Boost ${BOOST_MIN_VERSION} REQUIRED COMPONENTS mpi serialization program_options date_time)
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INCLUDE_DIRECTORIES( ${MPI_CXX_INCLUDE_PATH} )
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INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS} )
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INCLUDE_DIRECTORIES(src)
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ADD_SUBDIRECTORY(src)
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ADD_SUBDIRECTORY(examples)
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ADD_SUBDIRECTORY(tools)
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‎build/Makefile.include

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‎build/debug/Makefile

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‎build/home/Makefile

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‎doc/auryn_logo_small.png

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‎examples/CMakeLists.txt

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ADD_EXECUTABLE( sim_background sim_background.cpp )
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TARGET_LINK_LIBRARIES( sim_background auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_bg_lowpass sim_bg_lowpass.cpp )
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TARGET_LINK_LIBRARIES( sim_bg_lowpass auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_bg_static sim_bg_static.cpp )
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TARGET_LINK_LIBRARIES( sim_bg_static auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_brunel2k sim_brunel2k.cpp )
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TARGET_LINK_LIBRARIES( sim_brunel2k auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_brunel2k_pl sim_brunel2k_pl.cpp )
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TARGET_LINK_LIBRARIES( sim_brunel2k_pl auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_coba_benchmark sim_coba_benchmark.cpp )
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TARGET_LINK_LIBRARIES( sim_coba_benchmark auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_dense sim_dense.cpp )
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TARGET_LINK_LIBRARIES( sim_dense auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_epsp sim_epsp.cpp )
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TARGET_LINK_LIBRARIES( sim_epsp auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_epsp_stp sim_epsp_stp.cpp )
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TARGET_LINK_LIBRARIES( sim_epsp_stp auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_isp_big sim_isp_big.cpp )
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TARGET_LINK_LIBRARIES( sim_isp_big auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_isp_orig sim_isp_orig.cpp )
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TARGET_LINK_LIBRARIES( sim_isp_orig auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_poisson sim_poisson.cpp )
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TARGET_LINK_LIBRARIES( sim_poisson auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
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ADD_EXECUTABLE( sim_coba_binmon sim_coba_binmon.cpp )
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TARGET_LINK_LIBRARIES( sim_coba_binmon auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )

‎examples/sim_coba_benchmark.cpp

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@@ -134,6 +134,9 @@ int main(int ac,char *av[]) {
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TIFGroup * neurons_e = new TIFGroup( ne);
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TIFGroup * neurons_i = new TIFGroup( ni);
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137+
neurons_e->set_refractory_period(5.0e-3); // minimal ISI 5.1ms
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neurons_i->set_refractory_period(5.0e-3);
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neurons_e->set_state("bg_current",2e-2); // corresponding to 200pF for C=200pF and tau=20ms
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neurons_i->set_state("bg_current",2e-2);
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if ( !fwmat_ii.empty() ) con_ii->load_from_complete_file(fwmat_ii);
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if ( !fast ) {
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logger->msg("Use --fast option to turn off IO for benchmarking!", WARNING);
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msg = "Setting up monitors ...";
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logger->msg(msg,PROGRESS,true);
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stringstream filename;
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filename << outputfile << "e.ras";
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SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, filename.str().c_str() );
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// filename.str("");
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// filename.clear();
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// filename << outputfile << "e.dras";
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// DelayedSpikeMonitor * dsmon_e = new DelayedSpikeMonitor( neurons_e, filename.str().c_str() );
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filename.str("");
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filename.clear();
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filename << outputfile << "i.ras";
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SpikeMonitor * smon_i = new SpikeMonitor( neurons_i, filename.str().c_str() );
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filename.str("");
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filename << outputfile << "e.mem";
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StateMonitor * smon_mem = new StateMonitor( neurons_e, 7, "mem", filename.str() ,dt );
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filename.str("");
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filename << outputfile << "e.ampa";
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StateMonitor * smon_ampa = new StateMonitor( neurons_e, 7, "g_ampa", filename.str() );
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filename.str("");
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filename << outputfile << "e.gaba";
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StateMonitor * smon_gaba = new StateMonitor( neurons_e, 7, "g_gaba", filename.str() );
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}
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RateChecker * chk = new RateChecker( neurons_e , -0.1 , 1000. , 100e-3);
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logger->msg("Running sanity check ...",PROGRESS,true);
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con_ee->sanity_check();
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con_ei->sanity_check();
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con_ie->sanity_check();
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con_ii->sanity_check();
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// RateChecker * chk = new RateChecker( neurons_e , -0.1 , 1000. , 100e-3);
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logger->msg("Simulating ..." ,PROGRESS,true);
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if (!sys->run(simtime,true))

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