Merge branch 'release-v0.8.0' for beta release

Conflicts:
	examples/sim_coba_binmon.cpp
	tools/aube.cpp

.gitignore

@@ -4,6 +4,9 @@
 *.l[oa]
 */.libs
 
+*.pyc
+
+
 # Ignore docs
 docs/*
 

.travis.yml

@@ -8,7 +8,7 @@ install:
     - sudo apt-get install -y -qq libboost-all-dev openmpi-bin libopenmpi-dev 
     - sudo apt-get install -y -qq cmake 
 script: 
-    - mkdir build && cd build && cmake ../ -DCMAKE_BUILD_TYPE=Release && make
+    - cd build/release && cmake ../../ -DCMAKE_BUILD_TYPE=Release && make && cd ../../test && ./run_tests.sh
 
 notifications:
     email:

CMakeLists.txt

@@ -3,10 +3,10 @@ project (Auryn)
 
 # The version number.
 set (Auryn_VERSION_MAJOR 0)
-set (Auryn_VERSION_MINOR 6)
+set (Auryn_VERSION_MINOR 7)
 
 # Important GCC Compiler flags for Auryn's performance
-set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native -ffast-math")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native -ffast-math -pipe")
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")
 
 # Display flags (for debugging only)
@@ -18,7 +18,11 @@ 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)
+FIND_PACKAGE(Boost ${BOOST_MIN_VERSION} REQUIRED COMPONENTS mpi serialization program_options date_time unit_test_framework)
+
+# Recommended: Doxygen
+FIND_PACKAGE(Doxygen)
+
 
 INCLUDE_DIRECTORIES( ${MPI_CXX_INCLUDE_PATH} )
 INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS} )
@@ -28,3 +32,5 @@ ADD_SUBDIRECTORY(src)
 ADD_SUBDIRECTORY(examples)
 ADD_SUBDIRECTORY(tools)
 
+# Unit tests
+ADD_SUBDIRECTORY(test/src)

README.md

@@ -17,9 +17,8 @@ To download and compile the examples try:
 
 ```
 sudo apt-get install cmake git build-essential libboost-all-dev
-git clone https://github.com/fzenke/auryn.git && cd auryn 
-mkdir build && cd build
-cmake ../ -DCMAKE_BUILD_TYPE=Release && make
+git clone https://github.com/fzenke/auryn.git && cd auryn/build/release
+./bootstrap.sh && make
 ```
 
 Documentation & Installation/Use
@@ -60,6 +59,6 @@ Bibtex:
 ```
 
 
-Copyright 2014-2015 Friedemann Zenke.
+Copyright 2014-2016 Friedemann Zenke.
 Copying and distribution of this file, with or without modification, are
 permitted provided the copyright notice and this notice are preserved.

build/debug/bootstrap.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cmake ../../ -DCMAKE_BUILD_TYPE=Debug && make
+

build/profiling/bootstrap.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cmake ../../ -DCMAKE_CXX_FLAGS=-pg -DCMAKE_BUILD_TYPE=Release && make 
+

build/release/bootstrap.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cmake ../../ -DCMAKE_BUILD_TYPE=Release 
+

build/release/plot_benchmark_results.gnu

@@ -0,0 +1,41 @@
+#!/usr/bin/gnuplot
+
+set out 'benchmark_results.pdf'
+set term pdf size 7.0, 2.4
+
+unset key
+
+set border 3 
+set xtics nomirror out
+set ytics nomirror out
+set xtics rotate # by -45
+
+set boxwidth 0.8
+
+
+
+set boxwidth 1.0
+set style histogram errorbars gap 1.0 lw 1
+set style data histograms
+# set style fill solid border -1
+
+# set yrange [0:]
+
+revname(x) = sprintf("%s",x[1:6])
+
+set multiplot layout 1,3
+
+set label 1 at screen 0.001, screen 0.1 'Commit:' left
+set title 'Vogels \& Abbott benchmark'
+set ylabel 'Wall time (s)'
+plot 'benchmark_results.dat' using  3:4:xticlabels(revname(strcol(2))) lc -1
+
+unset ylabel 
+unset label 1
+
+
+set title 'Zenke et al. benchmark, single'
+plot 'benchmark_results.dat' using  5:6:xticlabels(revname(strcol(2))) lc -1
+set title 'Zenke et al. benchmark, parallel'
+plot 'benchmark_results.dat' using  7:8:xticlabels(revname(strcol(2))) lc -1
+unset multiplot

build/release/run_benchmark.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+# Compile code
+make clean
+./bootstrap.sh && make 
+sleep 2
+
+# Benchmark parameters
+SIMTIME=100
+STATRUNS="1 2 3 4 5"
+HOSTNAME=`hostname`
+DATE=`date +"%Y-%m-%d"`
+REVISION=`git log --pretty=oneline -1 | cut -d " " -f 1`
+TMPDIR=`mktemp -d`
+
+# Function declaration
+function fun_benchmark() 
+{
+	echo $1
+	> $TMPDIR/times.dat
+	for VARIABLE in $STATRUNS; do
+		$1
+		cat $TMPDIR/elapsed.dat >> $TMPDIR/times.dat
+	done
+
+	awk '{ for (i=1;i<=NF;i++) { sum[i] += 1.0*$i; sum2[i] += 1.0*$i*$i; } } \
+		END { for (i=1;i<=NF;i++) { mean = 1.*sum[i]/NR; var  = 1.*sum2[i]/NR-mean*mean; std = sqrt(var + 1.0/12); \
+		   printf "%f  %f\t",mean,std } printf "\n" }' $TMPDIR/times.dat > $TMPDIR/result.dat
+
+	FUNCTION_RESULT=`cat $TMPDIR/result.dat`
+	cp $TMPDIR/result.dat last_benchmark_result.dat
+}
+
+
+# Vogels-Abbott benchmark, single core
+CMD_BENCHMARK1="examples/sim_coba_benchmark --fast --simtime $SIMTIME --dir $TMPDIR"
+fun_benchmark "$CMD_BENCHMARK1"
+RESULT_BENCHMARK1=$FUNCTION_RESULT
+
+# Zenke plasticity benchmark, single core
+CMD_BENCHMARK2="examples/sim_background --fast --tau 10 --simtime $SIMTIME --dir $TMPDIR"
+fun_benchmark "$CMD_BENCHMARK2"
+RESULT_BENCHMARK2=$FUNCTION_RESULT
+
+# Zenke plasticity benchmark, two cores
+CMD_BENCHMARK3="mpirun -n 2 examples/sim_background --fast --tau 10 --simtime $SIMTIME --dir $TMPDIR"
+fun_benchmark "$CMD_BENCHMARK3"
+RESULT_BENCHMARK3=$FUNCTION_RESULT
+
+
+# Writ result to file
+echo "$HOSTNAME $REVISION $RESULT_BENCHMARK1 $RESULT_BENCHMARK2 $RESULT_BENCHMARK3 $DATE" >> benchmark_results.dat
+
+# Clean up
+rm -r $TMPDIR

src/Doxyfile → doc/Doxyfile

@@ -31,7 +31,7 @@ PROJECT_NAME           = Auryn
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 0.7
+PROJECT_NUMBER         = $(AURYNVERSIONSTRING)
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description for a project that appears at the top of each page and should give viewer a quick idea about the purpose of the project. Keep the description short.
 
@@ -42,14 +42,14 @@ PROJECT_BRIEF          = "Plastic Spiking Neural Network Simulator"
 # exceed 55 pixels and the maximum width should not exceed 200 pixels.
 # Doxygen will copy the logo to the output directory.
 
-PROJECT_LOGO           = ../doc/auryn_logo_small.png
+PROJECT_LOGO           = ./auryn_logo_small.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = ../doc
+OUTPUT_DIRECTORY       = .
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -598,7 +598,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  =
+INPUT                  = ../src ../examples/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is

examples/CMakeLists.txt

@@ -1,38 +1,8 @@
-ADD_EXECUTABLE( sim_background sim_background.cpp )
-TARGET_LINK_LIBRARIES( sim_background auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+file( GLOB SIM_SOURCES *.cpp )
+foreach( sourcepath ${SIM_SOURCES} )
+	get_filename_component( sourcefile ${sourcepath} NAME )
+	string( REPLACE ".cpp" "" simname ${sourcefile} )
+	add_executable( ${simname} ${sourcefile} )
+	target_link_libraries( ${simname} auryn ${MPI_C_LIBRARIES} ${Boost_LIBRARIES} )
+endforeach( sourcepath ${SIM_SOURCES} )
 
-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} )