Use local installations for benchmarking

Makefile

@@ -1,3 +1,13 @@
+# These are the directories that contain everything we need after 'make setup'
+# is completed.  We assume that 'matlab' is available on the PATH.
+export INCLUDEPATH := $(shell pwd)/libraries/include/
+export LIBPATH := $(shell pwd)/libraries/lib/
+export BINPATH := $(shell pwd)/libraries/bin/
+export JAVAPATH := $(shell pwd)/libraries/share/
+export DEBUGBINPATH := $(shell pwd)/libraries/debug/bin/
+export DEBUGINCLUDEPATH := $(shell pwd)/libraries/debug/include/
+export DEBUGLIBPATH := $(shell pwd)/libraries/debug/lib/
+
 # Locate the python bin.
 PYTHON_BIN := $(shell which python3.3)
 ifndef PYTHON_BIN
@@ -38,52 +48,10 @@ COPY := False
 USER := ""
 PASSWORD := ""
 
-################################################################################################
-# How to use:                                                                                  #
-# Specify the environment variables in this file or set these variables from the command line. #
-# All environment path variables should end with a slash.                                      #
-# Note that four settings need to be changed for this to work.                                 #
-# 1) SHOGUN_PATH                                                                               #
-# 2) PYTHONPATH                                                                                #
-# 3) WEKA_CLASSPATH                                                                            #
-# 4) MATLAB_BIN                                                                                #
-################################################################################################
-
-# Set the environment variable for the mlpack executables.
-
-ifdef $(shell which mlpack_knn)
-	export MLPACK_BIN=$(shell dirname $(firstword $(shell which mlpack_knn)))/
-else
-	export MLPACK_BIN=""
-endif
-
-# Set the environment variable for the mlpack executables.
-export MLPACK_BIN_DEBUG=$(MLPACK_BIN)
-
-# Export the MLPACK_PATH environment variable.
-export MLPACK_PATH=$(shell dirname $(MLPACK_BIN))/
+# Set the environment variable for the compiled mlpack executables.
 export MLPACK_BIN_SRC=methods/mlpack/src/build/
 export MLPACK_BIN_DEBUG_SRC=methods/mlpack/src/build/
 
-# Set the environment variable for the matlab executable.
-# You can use the following command to search the 'matlab' file everytime:
-# export MATLAB_BIN=$(shell find / -name matlab  -print 2>/dev/null -quit)
-export MATLAB_BIN=""
-
-# Export the MATLABPATH environment variable.
-export MATLABPATH=$(shell pwd)/methods/matlab/
-
-# Export the WEKA_CLASSPATH environment variable.
-# You can use the following command to search the 'weka.jar' file everytime:
-# export WEKA_CLASSPATH=".:$(shell find / -name weka.jar  -print 2>/dev/null -quit)"
-export WEKA_CLASSPATH=".:/Users/marcus/Downloads/weka-3-6-11/weka.jar"
-
-# Export the SHOGUN_PATH environment variable.
-export SHOGUN_PATH=""
-
-# Export the PYTHONPATH environment variable.
-export PYTHONPATH=""
-
 # Set the environment variable for the the ms_print executable.
 export MS_PRINT_BIN=$(shell which ms_print)
 
@@ -92,12 +60,14 @@ export VALGRIND_BIN=$(shell which valgrind)
 
 # Export the path to the FLANN library.
 export FLANN_PATH=methods/flann/
-
 # Export the path to the ANN library.
 export ANN_PATH=methods/ann/
 
-# Export the path to the HLearn library.
-export HLEARN_PATH=""
+# Set LD_LIBRARY_PATH correctly.
+export LD_LIBRARY_PATH=$(shell echo $(LIBPATH))
+# Set PYTHONPATH correctly.
+PYVERSION=$(shell python3 -c 'import sys; print("python" + sys.version[0:3])')
+export PYTHONPATH=$(shell printenv PYTHONPATH):$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/dist-packages:$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/site-packages
 
 # Color settings.
 NO_COLOR=\033[0m
@@ -200,11 +170,14 @@ endif
 
 .scripts:
 	# Compile the java files for the weka methods.
-	javac -cp $(shell echo $(WEKA_CLASSPATH)) -d methods/weka methods/weka/src/*.java
+	javac -cp $(shell echo $(JAVAPATH)/weka.jar) -d methods/weka methods/weka/src/*.java
 	# Compile the ann scripts.
-	g++ -O0 -std=c++11 methods/ann/src/allknn.cpp -o methods/ann/allknn -I$(MLPACK_PATH)/include -I$(ANN_PATH)/include -L$(MLPACK_PATH)/lib -L$(ANN_PATH)/lib -lANN -lmlpack -lboost_program_options
+	g++ -O0 -std=c++11 methods/ann/src/allknn.cpp -o methods/ann/allknn -I$(INCLUDEPATH) -L$(LIBPATH) -lANN -lmlpack -lboost_program_options
 	# Compile the FLANN scripts.
-	g++ -O0 -std=c++11 methods/flann/src/allknn.cpp -o methods/flann/allknn -I$(MLPACK_PATH)/include -I$(FLANN_PATH)/include -L$(MLPACK_PATH)/lib -L$(FLANN_PATH)/lib -lmlpack -lboost_program_options
+	g++ -O0 -std=c++11 methods/flann/src/allknn.cpp -o methods/flann/allknn -I$(INCLUDEPATH) -L$(LIBPATH) -lmlpack -lboost_program_options -llz4
+	# Compile the mlpack scripts.  (Can't do this until ANN is released or a
+	# git version of mlpack is used.)
+	#cd methods/mlpack/src/ && ./build_scripts.sh
 
 .setup:
 	cd libraries/ && ./download_packages.sh && ./install_all.sh

README.md

@@ -35,6 +35,7 @@ Benchmarks are run with the `make` command.
 * `make run`        -- Perform the benchmark.
 * `make memory`     -- Get memory profiling information.
 * `make test`       -- Test the configuration file. Check for correct syntax and then try to open files referred in the configuration file.
+* `make setup`      -- Download and set up all of the libraries to compare against.
 * `make scripts`    -- Make additional scripts.
 
 

libraries/ann_install.sh

@@ -5,28 +5,22 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One ann*.tar.gz file should be located in this directory containing the
+# One ann.tar.gz file should be located in this directory containing the
 # source code of the desired mlpack version.
-tars=`ls ann*.tar.gz | wc -l`;
+tars=`ls ann.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No ann source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one ann source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source ann.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf ann/
 mkdir ann/
-tar -xzpf ann*.tar.gz --strip-components=1 -C ann/
+tar -xzpf ann.tar.gz --strip-components=1 -C ann/
 
 cd ann/
-make linux-g++
+CXXFLAGS=-fPIC make linux-g++
 cp -r include/* ../include/
 cp -r bin/* ../bin/
 cp -r lib/* ../lib/

libraries/annoy_install.sh

@@ -5,25 +5,20 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One annoy*.tar.gz file should be located in this directory.
-tars=`ls annoy*.tar.gz | wc -l`;
+# One annoy.tar.gz file should be located in this directory.
+tars=`ls annoy.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No annoy source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one annoy source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source annoy.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf annoy/
 mkdir annoy/
-tar -xzpf annoy*.tar.gz --strip-components=1 -C annoy/
+tar -xzpf annoy.tar.gz --strip-components=1 -C annoy/
 
 cd annoy/
 python3 setup.py build
-python3 setup.py install --prefix=../../ -O2
+PYVER=`python3 -c 'import sys; print("python" + sys.version[0:3])'`;
+PYTHONPATH=../lib/$PYVER/site-packages/ python3 setup.py install --prefix=../ -O2

libraries/flann_install.sh

@@ -5,25 +5,19 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One flann*.tar.gz file should be located in this directory containing the
+# One flann.tar.gz file should be located in this directory containing the
 # source code of the desired mlpack version.
-tars=`ls flann*.tar.gz | wc -l`;
+tars=`ls flann.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No flann source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one flann source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source flann.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf flann/
 mkdir flann/
-tar -xzpf flann*.tar.gz --strip-components=1 -C flann/
+tar -xzpf flann.tar.gz --strip-components=1 -C flann/
 
 cd flann/
 mkdir build/

libraries/hlearn_install.sh

@@ -5,43 +5,31 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One HLearn*.tar.gz file should be located in this directory.  Also since
+# One HLearn.tar.gz file should be located in this directory.  Also since
 # HLearn depends on subhask, a subhask*.tar.gz file should also be located in
 # this directory.
-tars=`ls HLearn*.tar.gz | wc -l`;
+tars=`ls HLearn.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No HLearn source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one HLearn source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source HLearn.tar.gz found in libraries/!"
   exit 1
 fi
 
-subhasktars=`ls subhask*.tar.gz | wc -l`;
+subhasktars=`ls subhask.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No subhask source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one subhask source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source subhask.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf hlearn/
 mkdir hlearn/
-tar -xzpf HLearn*.tar.gz --strip-components=1 -C hlearn/
+tar -xzpf HLearn.tar.gz --strip-components=1 -C hlearn/
 
 rm -rf subhask/
 mkdir subhask/
-tar -xvzpf subhask*.tar.gz --strip-components=1 -C subhask/
+tar -xvzpf subhask.tar.gz --strip-components=1 -C subhask/
 
 cd hlearn/
 cabal sandbox init

libraries/matlab_install.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 # This does not install MATLAB but instead simply checks for its presence.
-if [ ! -f /opt/matlab/bin/matlab ];
+if [ ! -f `which matlab` ];
 then
   echo "MATLAB not found!"
   exit 1

libraries/mlpack_install.sh

@@ -5,28 +5,29 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One mlpack*.tar.gz file should be located in this directory containing the
+# One mlpack.tar.gz file should be located in this directory containing the
 # source code of the desired mlpack version.
-tars=`ls mlpack*.tar.gz | wc -l`;
+tars=`ls mlpack.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No mlpack source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one mlpack source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source mlpack.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf mlpack/
 mkdir mlpack/
-tar -xzpf mlpack*.tar.gz --strip-components=1 -C mlpack/
+tar -xzpf mlpack.tar.gz --strip-components=1 -C mlpack/
 
 cd mlpack/
 mkdir build/
 cd build/
 cmake -DCMAKE_INSTALL_PREFIX=../../ -DBUILD_TESTS=OFF ../
 make install
+
+# Also install debug version.
+cd ..
+mkdir build-debug/
+cd build-debug/
+cmake -DDEBUG=ON -DCMAKE_INSTALL_PREFIX=../../debug/ -DBUILD_TEST=OFF ../
+make install

libraries/mlpy_install.sh

@@ -5,25 +5,19 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One mlpy*.tar.gz file should be located in this directory.
-tars=`ls mlpy*.tar.gz | wc -l`;
+# One mlpy.tar.gz file should be located in this directory.
+tars=`ls mlpy.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No mlpy source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one mlpy source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source mlpy.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf mlpy/
 mkdir mlpy/
-tar -xzpf mlpy*.tar.gz --strip-components=1 -C mlpy/
+tar -xzpf mlpy.tar.gz --strip-components=1 -C mlpy/
 
 cd mlpy/
 python3 setup.py build
-python3 setup.py install --prefix=../../ -O2
+python3 setup.py install --prefix=../ -O2

libraries/scikit_install.sh

@@ -5,25 +5,19 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One scikit*.tar.gz file should be located in this directory.
-tars=`ls scikit*.tar.gz | wc -l`;
+# One scikit.tar.gz file should be located in this directory.
+tars=`ls scikit.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No scikit source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one scikit source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source scikit.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf scikit/
 mkdir scikit/
-tar -xzpf scikit*.tar.gz --strip-components=1 -C scikit/
+tar -xzpf scikit.tar.gz --strip-components=1 -C scikit/
 
 cd scikit/
 python3 setup.py build
-python3 setup.py install --prefix=../../ -O2
+python3 setup.py install --prefix=../ -O2

libraries/shogun_install.sh

@@ -5,24 +5,18 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One shogun*.tar.gz file should be located in this directory.
-tars=`ls shogun*.tar.gz | wc -l`;
+# One shogun.tar.gz file should be located in this directory.
+tars=`ls shogun.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No shogun source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one shogun source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source shogun.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf shogun/
 mkdir shogun/
-tar -xzpf shogun*.tar.gz --strip-components=1 -C shogun/
+tar -xzpf shogun.tar.gz --strip-components=1 -C shogun/
 
 cd shogun/
 mkdir build/