Merge branch 'release-v0.7'

Merges release branch into master for full release of Auryn v0.7.

.gitignore

@@ -3,41 +3,10 @@
 *.[oa]
 *.l[oa]
 */.libs
+
 # Ignore docs
 docs/*
-# Ignore development files
-dev/*
-# Ignore stuff in the build dirs except the makefiles
-build/*
-!build/lcncluster/Makefile
-!build/lcnsunc1/Makefile
-!build/home/Makefile
-!build/debug/Makefile
-!build/tug/Makefile
 
-# http://www.gnu.org/software/automake
-Makefile.in
-Makefile
-# # http://www.gnu.org/software/autoconf
-/autom4te.cache
-/aclocal.m4
-/compile
-/configure
-/depcomp
-/install-sh
-/missing
-/stamp-h1
-config*
-.deps
-libtool
-ltmain.sh
-m4/libtool.m4
-m4/ltoptions.m4
-m4/ltsugar.m4
-m4/ltversion.m4
-m4/lt~obsolete.m4
+# Ignore stuff in the build dir
+build/*
 
-cscope.out
-tags
-# travis build file
-.travis.yml

.travis.yml

@@ -0,0 +1,24 @@
+language: cpp
+compiler:
+    - gcc
+before_install:
+    - sudo add-apt-repository ppa:boost-latest/ppa -y
+    - sudo add-apt-repository ppa:dns/gnu -y
+    - sudo add-apt-repository ppa:yjwong/cmake -y
+    - sudo apt-get update -qq -y
+    - sudo apt-get -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" install  build-essential libtool m4  --force-yes
+    - sudo apt-get install libboost1.54-all-dev mpich2 libmpich2-dev libcr-dev -y
+    - sudo apt-get install cmake cmake-data -y
+script: 
+    - CFLAGS="${CFLAGS:--O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic}" ; export CFLAGS ;
+    - CXXFLAGS="${CXXFLAGS:--O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic}" ; export CXXFLAGS ;
+    - LDFLAGS="${LDFLAGS:--Wl,-z,relro}";export LDFLAGS ;
+    - 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
+
+notifications:
+    email:
+        recipients: 
+            - ankursinha@fedoraproject.org
+            - fzenke@stanford.edu
+        on_success: change
+        on_failure: always

CMakeLists.txt

@@ -0,0 +1,30 @@
+cmake_minimum_required (VERSION 2.6)
+project (Auryn)
+
+# The version number.
+set (Auryn_VERSION_MAJOR 0)
+set (Auryn_VERSION_MINOR 6)
+
+# Important GCC Compiler flags for Auryn's performance
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native -ffast-math")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")
+
+# Display flags (for debugging only)
+# message("CMAKE_CXX_FLAGS_DEBUG is ${CMAKE_CXX_FLAGS_DEBUG}")
+# message("CMAKE_CXX_FLAGS_RELEASE is ${CMAKE_CXX_FLAGS_RELEASE}")
+
+# Required external MPI libraries 
+FIND_PACKAGE(MPI REQUIRED)
+
+# Required Boost libraries 
+SET(BOOST_MIN_VERSION "1.41.0")
+FIND_PACKAGE(Boost ${BOOST_MIN_VERSION} REQUIRED COMPONENTS mpi serialization program_options date_time)
+
+INCLUDE_DIRECTORIES( ${MPI_CXX_INCLUDE_PATH} )
+INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS} )
+INCLUDE_DIRECTORIES(src)
+
+ADD_SUBDIRECTORY(src)
+ADD_SUBDIRECTORY(examples)
+ADD_SUBDIRECTORY(tools)
+

examples/CMakeLists.txt

@@ -0,0 +1,38 @@
+ADD_EXECUTABLE( sim_background sim_background.cpp )
+TARGET_LINK_LIBRARIES( sim_background auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_bg_lowpass sim_bg_lowpass.cpp )
+TARGET_LINK_LIBRARIES( sim_bg_lowpass auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_bg_static sim_bg_static.cpp )
+TARGET_LINK_LIBRARIES( sim_bg_static auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_brunel2k sim_brunel2k.cpp )
+TARGET_LINK_LIBRARIES( sim_brunel2k auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_brunel2k_pl sim_brunel2k_pl.cpp )
+TARGET_LINK_LIBRARIES( sim_brunel2k_pl auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_coba_benchmark sim_coba_benchmark.cpp )
+TARGET_LINK_LIBRARIES( sim_coba_benchmark auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_dense sim_dense.cpp )
+TARGET_LINK_LIBRARIES( sim_dense auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_epsp sim_epsp.cpp )
+TARGET_LINK_LIBRARIES( sim_epsp auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_epsp_stp sim_epsp_stp.cpp )
+TARGET_LINK_LIBRARIES( sim_epsp_stp auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_isp_big sim_isp_big.cpp )
+TARGET_LINK_LIBRARIES( sim_isp_big auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_isp_orig sim_isp_orig.cpp )
+TARGET_LINK_LIBRARIES( sim_isp_orig auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_poisson sim_poisson.cpp )
+TARGET_LINK_LIBRARIES( sim_poisson auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+
+ADD_EXECUTABLE( sim_coba_binmon sim_coba_binmon.cpp )
+TARGET_LINK_LIBRARIES( sim_coba_binmon auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )

examples/sim_coba_benchmark.cpp

@@ -134,6 +134,9 @@ int main(int ac,char *av[]) {
 	TIFGroup * neurons_e = new TIFGroup( ne);
 	TIFGroup * neurons_i = new TIFGroup( ni);
 
+	neurons_e->set_refractory_period(5.0e-3); // minimal ISI 5.1ms
+	neurons_i->set_refractory_period(5.0e-3);
+
 	neurons_e->set_state("bg_current",2e-2); // corresponding to 200pF for C=200pF and tau=20ms
 	neurons_i->set_state("bg_current",2e-2);
 
@@ -161,45 +164,25 @@ int main(int ac,char *av[]) {
 	if ( !fwmat_ii.empty() ) con_ii->load_from_complete_file(fwmat_ii);
 
 
+
 	if ( !fast ) {
+		logger->msg("Use --fast option to turn off IO for benchmarking!", WARNING);
+
 		msg = "Setting up monitors ...";
 		logger->msg(msg,PROGRESS,true);
 
 		stringstream filename;
 		filename << outputfile << "e.ras";
 		SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, filename.str().c_str() );
 
-		// filename.str("");
-		// filename.clear();
-		// filename << outputfile << "e.dras";
-		// DelayedSpikeMonitor * dsmon_e = new DelayedSpikeMonitor( neurons_e, filename.str().c_str() );
-
 		filename.str("");
 		filename.clear();
 		filename << outputfile << "i.ras";
 		SpikeMonitor * smon_i = new SpikeMonitor( neurons_i, filename.str().c_str() );
-
-		filename.str("");
-		filename << outputfile << "e.mem";
-		StateMonitor * smon_mem = new StateMonitor( neurons_e, 7, "mem", filename.str() ,dt ); 
-
-		filename.str("");
-		filename << outputfile << "e.ampa";
-		StateMonitor * smon_ampa = new StateMonitor( neurons_e, 7, "g_ampa", filename.str() );
-
-		filename.str("");
-		filename << outputfile << "e.gaba";
-		StateMonitor * smon_gaba = new StateMonitor( neurons_e, 7, "g_gaba", filename.str() );
 	}
 
 
-	RateChecker * chk = new RateChecker( neurons_e , -0.1 , 1000. , 100e-3);
-
-	logger->msg("Running sanity check ...",PROGRESS,true);
-	con_ee->sanity_check();
-	con_ei->sanity_check();
-	con_ie->sanity_check();
-	con_ii->sanity_check();
+	// RateChecker * chk = new RateChecker( neurons_e , -0.1 , 1000. , 100e-3);
 
 	logger->msg("Simulating ..." ,PROGRESS,true);
 	if (!sys->run(simtime,true))