Merge pull request #126 from Milkyway-at-home/mendel_auto_diff

Mendel auto diff

CMakeLists.txt

@@ -124,6 +124,14 @@ mark_as_advanced(INSTALL_BOINC)
 option(DOUBLEPREC
        "Build with double precision" ON)
 
+option(AUTODIFF
+       "Build with automatic differentiation" OFF)
+mark_as_advanced(AUTODIFF)
+
+option(AUTODIFF_LOG
+       "Calculate derivative information in logspace" OFF)
+mark_as_advanced(AUTODIFF_LOG)
+
 option(NVIDIA_OPENCL "Using Nvidia OpenCL" OFF)
 mark_as_advanced(NVIDIA_OPENCL)
 

cmake_modules/PrintInfo.cmake

@@ -29,14 +29,16 @@ endmacro()
 
 macro(print_build_options)
   message("   ----")
-  message("   Double precision:  ${DOUBLEPREC}")
-  message("   Separation:        ${SEPARATION}")
-  message("   N-Body:            ${NBODY}")
-  message("   OpenCL separation: ${SEPARATION_OPENCL}")
-  message("   OpenCL nbody:      ${NBODY_OPENCL}")
-  message("   Nbody graphics:    ${NBODY_GL}")
-  message("   Nbody use GL3W:    ${USE_GL3W}")
-  message("   BOINC application: ${BOINC_APPLICATION}")
+  message("   Double precision:      ${DOUBLEPREC}")
+  message("   Auto differentiation:  ${AUTODIFF}")
+  message("   Logspace Derivatives:  ${AUTODIFF_LOG}")
+  message("   Separation:            ${SEPARATION}")
+  message("   N-Body:                ${NBODY}")
+  message("   OpenCL separation:     ${SEPARATION_OPENCL}")
+  message("   OpenCL nbody:          ${NBODY_OPENCL}")
+  message("   Nbody graphics:        ${NBODY_GL}")
+  message("   Nbody use GL3W:        ${USE_GL3W}")
+  message("   BOINC application:     ${BOINC_APPLICATION}")
   message("   ----")
 endmacro()
 

get_test_likelihoods.py

@@ -0,0 +1,104 @@
+###########################################################
+#This code runs the model tests and records their results.#
+#         Useful for when they need to be updated.        #
+#          Needs get_test_likelihood.sh to work.          #
+###########################################################
+
+#Import necessary packages
+import os
+import os.path as pth
+
+#Set Pathways
+lua_pth = '~/milkywayathome_client/nbody/tests/RunTestUnits.lua'
+tmp_pth = '~/likelitemp.out'
+result_pth = '~/test_likelihoods.txt'
+
+#Define lists
+
+model_list = ["model_1","model_2","model_3","model_4","model_5","model_5_bounds_test","model_6","model_7","model_8","model_9","model_ninkovic","model_triaxial","model_newhist1","model_newhist2","model_newhist3","model_LMC","model_bar","model_LMC_bar"]
+body_list = ["100","1024","10000"]
+seed_list = ["670828913", "886885833", "715144259", "430281807", "543966758"]
+
+#model_list = ["model_1","model_2"]
+#body_list = ["100","1024"]
+#seed_list = ["670828913", "886885833"]
+
+empty_seed_array = []
+empty_body_array = []
+likelihoods = []
+for s in range(len(seed_list)):
+	empty_seed_array.append(' ')
+for t in range(len(body_list)):
+	exec("empty_body_array.append("+str(empty_seed_array)+")")
+for u in range(len(model_list)):
+	exec("likelihoods.append("+str(empty_body_array)+")")
+
+#Loop through all tests
+
+for i in range(len(model_list)):
+	for j in range(len(body_list)):
+		for k in range(len(seed_list)):
+			#Change seed in lua file
+			print("REWRITING LUA FILE................................")
+			temp = open('~/lua_temp.lua','w+')
+			lua_file = open(lua_pth,'r')
+			for line in lua_file:
+				if (line.startswith('local testSeed =')):
+					temp.write('local testSeed = testSeeds['+str(k+1)+']\n')
+				else:
+					temp.write(line)
+			lua_file.close()
+			temp.close()
+			os.system('rm '+lua_pth)
+			os.rename('~/lua_temp.lua',lua_pth)
+
+			#Run test and get likelihood
+			print("Running "+model_list[i]+"__"+body_list[j]+"_test: SEED = "+seed_list[k])
+			check = False
+			os.system("sh get_test_likelihoods.sh "+model_list[i]+" "+body_list[j])
+			tmp_file = open(tmp_pth, 'r')
+			test_num = 0
+			for line in tmp_file:
+				if (line.startswith('test ')):
+					test_num = int(line.replace('test ',''))
+				prefix = str(test_num)+": "
+				if (line.startswith(prefix+"<search_likelihood>")):
+					string = line.replace(prefix+"<search_likelihood>-",'')
+					like_score = float(string.replace('</search_likelihood>',''))
+					print("Likelihood = "+str(like_score))
+					likelihoods[i][j][k] = str(like_score)
+					check = True
+			if(not check):
+				assert False    #NO LIKELIHOOD FOUND!
+			tmp_file.close()
+			os.system('rm '+tmp_pth)
+
+
+#Write data
+results = open(result_pth,'w+')
+for i in range(len(model_list)):
+	results.write('   ["'+model_list[i]+'"] = {\n')
+	for j in range(len(body_list)):
+		results.write('      ["'+body_list[j]+'"] = {\n')
+		for k in range(len(seed_list)):
+			if (k+1 == len(seed_list)):
+				results.write('         ["'+seed_list[k]+'"] = '+str(likelihoods[i][j][k])+'\n')
+			else:
+				results.write('         ["'+seed_list[k]+'"] = '+str(likelihoods[i][j][k])+',\n')
+		if (j+1 == len(body_list)):
+			results.write('      }\n')
+		else:
+			results.write('      },\n\n')
+	if (i+1 == len(model_list)):
+		results.write('   }\n')
+	else:
+		results.write('   },\n\n')
+results.close()			
+
+
+
+
+
+
+
+

get_test_likelihoods.sh

@@ -0,0 +1,3 @@
+cd test_env/
+
+ctest -R $1__$2_test -VV > ~/likelitemp.out

make_run_v2.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+#/* Copyright (c) 2016 Siddhartha Shelton */
+
+rebuild=true
+run=true
+run_compare=false
+compare_only=false
+get_flag_list=false
+
+PathToMilkyWayAtHomeClientFolder='INSERT PATHWAY HERE'
+
+if $rebuild
+then
+    rm -r build
+    mkdir build
+    cd build
+    cmake  -DCMAKE_BUILD_TYPE=Release -DNBODY_DEV_OPTIONS=ON -DNBODY_GL=OFF -DBOINC_APPLICATION=ON -DSEPARATION=OFF -DDOUBLEPREC=ON -DNBODY_OPENMP=ON -DNBODY_OPENCL=OFF -DAUTODIFF=OFF -DAUTODIFF_LOG=OFF $PathToMilkyWayAtHomeClientFolder/milkywayathome_client/
+    make -j 
+fi
+
+cd $PathToMilkyWayAtHomeClientFolder/build/bin
+
+if $run 
+then
+    ./milkyway_nbody \
+    -f $PathToMilkyWayAtHomeClientFolder/milkywayathome_client/nbody/sample_workunits/for_developers.lua \
+    -o $PathToMilkyWayAtHomeClientFolder/test.out \
+    -z $PathToMilkyWayAtHomeClientFolder/test.hist \
+    -n 8 -b -w 1 -P -e 54231651\
+    -i 4.0 1.0 0.2 0.2 12.0 0.2 \
+
+fi
+
+if $run_compare
+then
+    ./milkyway_nbody \
+    -f $PathToMilkyWayAtHomeClientFolder/milkywayathome_client/nbody/sample_workunits/for_developers.lua \
+    -o $PathToMilkyWayAtHomeClientFolder/output.out \
+    -z $PathToMilkyWayAtHomeClientFolder/output.hist \
+    -h $PathToMilkyWayAtHomeClientFolder/test.hist \
+    -y $PathToMilkyWayAtHomeClientFolder/output.ad \
+    -n 8 -b -w 1 -P -e 54231651\
+    -p 4.0 1.0 0.2 0.2 12.0 0.2 \
+
+fi
+
+#SMU = 222,288.47 SOLAR MASSES
+
+#OPTIONS:
+#-s -> compare using only emd and cost component
+#-S -> use emd, cost, beta dispersion
+#-V -> use emd, cost, velocity dispersion
+#-D -> use emd, cost, beta dispersion and velocity dispersion
+if $compare_only 
+then
+    ./milkyway_nbody \
+    -h $PathToMilkyWayAtHomeClientFolder/test.hist \
+    -S $PathToMilkyWayAtHomeClientFolder/output.hist \
+
+fi
+
+
+# if you run:
+
+if $get_flag_list
+then
+    ./milkyway_nbody --help
+# it will show you what all the flags mean
+fi

milkyway/CMakeLists.txt

@@ -136,6 +136,8 @@ set(mw_lib_headers include/milkyway_config.h.in
                    include/milkyway_math_double.h
                    include/milkyway_math_float.h
                    include/milkyway_math_supplemental.h
+                   include/milkyway_math_autodiff.h
+                   include/milkyway_math_supplemental2.h
                    include/milkyway_util.h
                    include/milkyway_alloc.h
                    include/milkyway_boinc_util.h

milkyway/include/milkyway_config.h.in

@@ -23,6 +23,8 @@
 
 #cmakedefine01 BOINC_APPLICATION
 #cmakedefine01 DOUBLEPREC
+#cmakedefine01 AUTODIFF
+#cmakedefine01 AUTODIFF_LOG
 #cmakedefine01 MW_ENABLE_DEBUG
 
 #cmakedefine01 HAVE_EXP10

milkyway/include/milkyway_lua_marshal.h

@@ -145,8 +145,8 @@ int mw_lua_typecheck(lua_State* luaSt, int idx, int expectedType, const char* ty
 
 void handleNamedArgumentTable(lua_State* luaSt, const MWNamedArg* args, int table);
 
-int pushRealArray(lua_State* luaSt, const real* arr, int n);
-real* popRealArray(lua_State* luaSt, int* outN);
+int pushRealArray(lua_State* luaSt, const real_0* arr, int n);
+real_0* popRealArray(lua_State* luaSt, int* outN);
 
 int expectTable(lua_State* luaSt, int idx);
 

milkyway/include/milkyway_lua_math.h

@@ -22,6 +22,13 @@
 
 #include <lua.h>
 
+real* checkReal(lua_State* luaSt, int idx);
+real* toReal(lua_State* luaSt, int idx);
+real* expectReal(lua_State* luaSt, int idx);
+int pushReal(lua_State* luaSt, real realIn);
+int getReal(lua_State* luaSt, void* r);
+int setReal(lua_State* luaSt, void* r);
+
 void registerMilkywayMath(lua_State* luaSt);
 
 #endif /* _LUA_MILKYWAY_MATH_H_ */

milkyway/include/milkyway_math.h

@@ -55,6 +55,8 @@
 #endif
 
 #include "milkyway_math_supplemental.h"
+#include "milkyway_math_autodiff.h"
+#include "milkyway_math_supplemental2.h"
 #include "milkyway_vectors.h"