NU-MineBench-3.0.1.patch

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..a77143f
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,121 @@
+*~
+*.o
+*.a
+*.la
+
+*.lo
+*.log
+*.status
+
+
+AFI/afi
+
+Apriori/omp_apriori
+
+BIRCH/birch
+
+Bayesian/bayes/src/bcdb
+Bayesian/bayes/src/bci
+Bayesian/bayes/src/bcx
+Bayesian/bayes/src/corr
+Bayesian/matrix/src/invert
+Bayesian/matrix/src/solve
+Bayesian/matrix/src/transp
+Bayesian/table/src/dom
+Bayesian/table/src/opc
+Bayesian/table/src/t1inn
+Bayesian/table/src/tbal
+Bayesian/table/src/tjoin
+Bayesian/table/src/tmerge
+Bayesian/table/src/tnorm
+Bayesian/table/src/tsplit
+Bayesian/table/src/uvins
+Bayesian/table/src/xmat
+
+ECLAT/eclat
+
+HOP/para_hop
+
+KMeans/example
+
+PLSA/parasw
+
+ParETI/pareti
+
+RSEARCH/Makefile
+RSEARCH/squid/Makefile
+RSEARCH/squid/Testsuite/Makefile
+RSEARCH/squid/squid.h
+RSEARCH/squid/squidconf.h
+RSEARCH/makernamat
+RSEARCH/rsearch
+RSEARCH/squid/afetch
+RSEARCH/squid/alistat
+RSEARCH/squid/compalign
+RSEARCH/squid/compstruct
+RSEARCH/squid/revcomp
+RSEARCH/squid/seqsplit
+RSEARCH/squid/seqstat
+RSEARCH/squid/sfetch
+RSEARCH/squid/shuffle
+RSEARCH/squid/sindex
+RSEARCH/squid/sreformat
+RSEARCH/squid/translate
+RSEARCH/squid/version.h
+RSEARCH/squid/weight
+
+
+Recursive_Weak/rw
+Recursive_Weak_pp/rwpp
+
+SEMPHY/programs/NJ/NJ
+SEMPHY/programs/checkCov/checkCov
+SEMPHY/programs/distanceBasedSeqs2TreeSA/distanceBasedSeqs2TreeSA
+SEMPHY/programs/distanceEstimation/distanceEstimation
+SEMPHY/programs/randGamma/randGamma
+SEMPHY/programs/rate4site/rate4site
+SEMPHY/programs/readSeq/readSeq
+SEMPHY/programs/semphy/semphy
+SEMPHY/programs/simulateSequance/simulateSequnce
+SEMPHY/programs/treeUtil/makeSureAllBranchesAreLargerThanEpsilon
+SEMPHY/programs/treeUtil/sametree
+SEMPHY/programs/treeUtil/shortenTree
+
+SNP/pnl.snp/PNL/**/.libs
+SNP/pnl.snp/PNL/**/.deps
+SNP/pnl.snp/PNL/Makefile
+SNP/pnl.snp/PNL/c_pgmtk/Makefile
+SNP/pnl.snp/PNL/c_pgmtk/**/Makefile
+SNP/pnl.snp/PNL/cxcore/Makefile
+SNP/pnl.snp/PNL/cxcore/**/Makefile
+SNP/pnl.snp/PNL/high/Makefile
+SNP/pnl.snp/PNL/high/**/Makefile
+SNP/pnl.snp/PNL/doc/Makefile
+SNP/pnl.snp/PNL/trs/Makefile
+SNP/pnl.snp/PNL/trs/**/Makefile
+
+SNP/pnl.snp/PNL/c_pgmtk/examples/ex_inf_learn_dbn/src/inf_learn_dbn
+SNP/pnl.snp/PNL/c_pgmtk/examples/ex_param/Src/ex_param
+SNP/pnl.snp/PNL/c_pgmtk/examples/gibbs/Src/gibbs
+SNP/pnl.snp/PNL/c_pgmtk/examples/inf_learn_bnet/Src/inf_learn_bnet
+SNP/pnl.snp/PNL/c_pgmtk/examples/learn_param/src/learn_param
+SNP/pnl.snp/PNL/c_pgmtk/examples/linux_test/test_run
+SNP/pnl.snp/PNL/c_pgmtk/examples/mixture_gaussian_bnet/Src/mixture_gaussian_bnet
+SNP/pnl.snp/PNL/c_pgmtk/examples/parPNLTest/src/parPNLTest
+SNP/pnl.snp/PNL/c_pgmtk/examples/testLIMID/src/TestLIMID
+SNP/pnl.snp/PNL/c_pgmtk/examples/testSL/testSEM
+SNP/pnl.snp/PNL/c_pgmtk/examples/testSL/testSL
+SNP/pnl.snp/PNL/c_pgmtk/examples/testSL/testSL_DBN
+SNP/pnl.snp/PNL/c_pgmtk/examples/testSoftMax/src/TestSoftMax
+SNP/pnl.snp/PNL/c_pgmtk/examples/trial/Src/trial
+SNP/pnl.snp/PNL/c_pgmtk/examples/use_matrix/src/use_matrix
+SNP/pnl.snp/PNL/high/examples/example
+SNP/pnl.snp/PNL/libtool
+SNP/pnl.snp/snp/snp
+
+SVM-RFE/svm_mkl
+
+ScalParC/scalparc
+
+Utility_Mining/para_tran_utility/utility_mine
+Utility_Mining/tran_utility/utility_mine
\ No newline at end of file
diff --git a/Apriori/Database.C b/Apriori/Database.C
index 4919c0a..f1882d8 100644
--- a/Apriori/Database.C
+++ b/Apriori/Database.C
@@ -91,7 +91,8 @@ int Database_readfrom(char *infile, int * &items, int * & offsets, int pid, int
 
    seconds(t_io_1); 
    Dbase_file = fopen(infile,"r");
-   if (Dbase_file < 0){
+   if (Dbase_file == NULL){
+      perror(infile);
       printf("Error couldn't open file %s\n", infile);
       exit(-1);
    }
@@ -165,6 +166,7 @@ int Database_readfrom(char *infile, int * &items, int * & offsets, int pid, int
    }
 
    free(buffer);
+   fclose(Dbase_file);
    return max_trans_sz;
 }
 
diff --git a/Apriori/Makefile b/Apriori/Makefile
index 650e256..d0cf552 100644
--- a/Apriori/Makefile
+++ b/Apriori/Makefile
@@ -2,8 +2,8 @@ CXX     = g++
 OMPFLAG = -fopenmp
 
 OPTS	= -g -O2 -DBALT 
-CFLAGS  = $(OPTS) $(OMPFLAG)
-LIBS    = -lm 
+CFLAGS  = $(OPTS) $(OMPFLAG) $(shell pkg-config --cflags copper-eval)
+LIBS    = -lm $(shell pkg-config --libs --static copper-eval)
 
 HEADERS = Itemset.h \
           ListItemset.h \
diff --git a/Apriori/omp_apriori.C b/Apriori/omp_apriori.C
index 36e8504..8efaf45 100644
--- a/Apriori/omp_apriori.C
+++ b/Apriori/omp_apriori.C
@@ -11,6 +11,7 @@
 #include <sys/types.h>
 #include <math.h>
 #include <string.h>
+#include <copper-eval.h>
 
 #include "Itemset.h"
 #include "ListItemset.h"
@@ -560,6 +561,19 @@ void clean_up(){
 
 int main(int argc, char **argv)
 {
+   if (copper_eval_init()) {
+      perror("copper_eval_init");
+      exit(1);
+   }
+
+   unsigned long jobs = 100;
+   const char* env_jobs = getenv("JOBS");
+   if (env_jobs != NULL) {
+    jobs = atoi(env_jobs);
+   }
+   unsigned long job;
+   for (job = 0; job < jobs; job++) {
+
    char sumfile[100];
    
    parse_args(argc, argv);
@@ -591,6 +605,12 @@ int main(int argc, char **argv)
    fflush(stdout);
    clean_up();
    fclose(summary);
+
+   copper_eval_iteration(job, 0);
+   }
+   if (copper_eval_finish()) {
+      perror("copper_eval_finish");
+   }
    exit(0);
 }
 
diff --git a/HOP/Makefile b/HOP/Makefile
index 811b201..4501e00 100644
--- a/HOP/Makefile
+++ b/HOP/Makefile
@@ -2,8 +2,8 @@
 CXX     = g++
 OMPFLAG = -fopenmp
 
-CFLAGS = -O -g -Wno-write-strings $(OMPFLAG)
-LIB    = -lm
+CFLAGS = -O -g -Wno-write-strings $(OMPFLAG) $(shell pkg-config --cflags copper-eval)
+LIB    = -lm $(shell pkg-config --libs --static copper-eval)
 
 SRCS   = para_hop.c      \
          para_hop_kd.c   \
diff --git a/HOP/para_hop.c b/HOP/para_hop.c
index d13124d..3e0e4b9 100644
--- a/HOP/para_hop.c
+++ b/HOP/para_hop.c
@@ -24,6 +24,8 @@ http://www.sns.ias.edu/~eisenste/hop/hop_doc.html */
 #include "para_kd.h"
 #include "smooth.h"
 
+#include <copper-eval.h>
+
 static int _debug;
 int nthreads,*start_index,num_particles,*local_num_p, *local_buf_size;
 float **samples_set, **median_seg, **local_median_seg;
@@ -108,6 +110,18 @@ int main(int argc, char *argv[])
 	strcpy(achFile,"output_hop");
 	inputfile = NULL;
         double t1, t2,timing_io_read, total_time, timing[NUM_STAGES];
+
+        if (copper_eval_init()) {
+          perror("copper_eval_init");
+          exit(1);
+        }
+        unsigned long jobs = 400;
+        const char* env_jobs = getenv("JOBS");
+        if (env_jobs != NULL) {
+          jobs = atoi(env_jobs);
+        }
+        unsigned long job;
+        for (job = 0; job < jobs; job++) {
 	
         for (j=0;j<3;++j) fPeriod[j] = 1.0;
 	nMerge = 4;
@@ -214,6 +228,7 @@ if (pid==0)
                 kd->bnd.fMax[j]=local_bnd[i].fMax[j];
             }
         }
+        fclose(fp);
 }/*end of parallelization*/	
 
 seconds(t1);
@@ -343,6 +358,11 @@ printf("number of groups = %d\n", smx->nGroups);
 	kdFinish(kd);
 	INFORM("All Done!");
 */
+    copper_eval_iteration(job, 0);
+    }
+    if (copper_eval_finish()) {
+      perror("copper_eval_finish");
+    }
 	return 0;
 }
 
diff --git a/KMeans/Makefile b/KMeans/Makefile
index a27f287..5abed63 100644
--- a/KMeans/Makefile
+++ b/KMeans/Makefile
@@ -8,8 +8,8 @@ DFLAGS      =
 
 OPTFLAGS    = -O2
 INCFLAGS    =
-CFLAGS      = $(OPTFLAGS) $(DFLAGS) $(INCFLAGS)
-LDFLAGS     = -lm
+CFLAGS      = $(OPTFLAGS) $(DFLAGS) $(INCFLAGS) $(shell pkg-config --cflags copper-eval)
+LDFLAGS     = -lm $(shell pkg-config --libs --static copper-eval)
 
 H_FILES     = fuzzy_kmeans.h
 
diff --git a/KMeans/example.c b/KMeans/example.c
index 76253ae..6876126 100644
--- a/KMeans/example.c
+++ b/KMeans/example.c
@@ -30,6 +30,7 @@
 #include <unistd.h>
 #include <fcntl.h>
 #include <omp.h>
+#include <copper-eval.h>
 
 #include "fuzzy_kmeans.h"
 
@@ -140,6 +141,18 @@ int main(int argc, char **argv) {
 
     if (filename == 0) usage(argv[0]);
 
+    if (copper_eval_init()) {
+      perror("copper_eval_init");
+      exit(1);
+    }
+    unsigned long jobs = 100;
+    const char* env_jobs = getenv("JOBS");
+    if (env_jobs != NULL) {
+      jobs = atoi(env_jobs);
+    }
+    unsigned long job;
+    for (job = 0; job < jobs; job++) {
+
 /*
     if (perform_fuzzy_kmeans == 1)
         is_perform_valid = 1;
@@ -393,6 +406,12 @@ int main(int argc, char **argv) {
     free(cluster_centres);
     free(buf);
 
+    copper_eval_iteration(job, 0);
+    }
+    if (copper_eval_finish()) {
+      perror("copper_eval_finish");
+    }
+
     return(0);
 }
 
diff --git a/PLSA/Makefile b/PLSA/Makefile
index f61b2c8..edbed16 100644
--- a/PLSA/Makefile
+++ b/PLSA/Makefile
@@ -2,7 +2,7 @@
 CCOMPILE   = gcc
 CPPCOMPILE = g++
 
-COMPILEOPTION = -g -Wno-write-strings
+COMPILEOPTION = -g -Wno-write-strings -fopenmp
 INCLUDEDIR =
 LIBHOME = 
 LINK = $(CPPCOMPILE)
@@ -13,7 +13,7 @@ OBJS = wtime.o ParseFile.o ParallelSWAlgorithm.o ParaSWProcessorSet.o ParaSWProb
 OUTPUT = ./parasw
 ################OPTION END################
 $(OUTPUT):$(OBJS)
-	$(LINK) $(OBJS) $(LINKOPTION) -o $(OUTPUT) $(LIBS) $(LIBDIRS) 
+	$(LINK) $(OBJS) $(LINKOPTION) -o $(OUTPUT) $(LIBS) $(LIBDIRS) -fopenmp
 
 clean: 
 	rm -f $(OBJS) $(OUTPUT)
diff --git a/SEMPHY/programs/rate4site/rate4siteOptions.cpp b/SEMPHY/programs/rate4site/rate4siteOptions.cpp
index 1ea03bf..cf127a7 100644
--- a/SEMPHY/programs/rate4site/rate4siteOptions.cpp
+++ b/SEMPHY/programs/rate4site/rate4siteOptions.cpp
@@ -3,6 +3,7 @@
 #include "rate4siteOptions.h"
 #include "errorMsg.h"
 #include <iostream>
+#include <unistd.h>
 using namespace std;
 
 rate4siteOptions::rate4siteOptions(int& argc, char *argv[]):
diff --git a/SNP/pnl.snp/snp/Makefile b/SNP/pnl.snp/snp/Makefile
index 69ee033..76ec5b0 100644
--- a/SNP/pnl.snp/snp/Makefile
+++ b/SNP/pnl.snp/snp/Makefile
@@ -1,5 +1,5 @@
 # CXX = icpc -openmp
-CXX = g++ -fopenmp
+CXX = g++ -fopenmp -fpermissive
 
 all: snp
 
diff --git a/SVM-RFE/Makefile b/SVM-RFE/Makefile
index 90c8fde..f411de7 100644
--- a/SVM-RFE/Makefile
+++ b/SVM-RFE/Makefile
@@ -2,14 +2,14 @@
 ################OPTION###################
 CCOMPILE = gcc
 CPPCOMPILE = g++
-COMPILEOPTION = -g -fopenmp -D_OPT
+COMPILEOPTION = -g -fopenmp -D_OPT $(shell pkg-config --cflags copper-eval)
 # INCLUDEDIR = -I/opt/intel/vtune/analyzer/include -I/opt/intel/mkl721/include
 INCLUDEDIR = -I.
 LIBHOME = 
 LINK = g++
 LINKOPTION = -g -fopenmp -o ./svm_mkl
 LIBS =  /opt/intel/mkl721/lib/32/libmkl_ia32.a
-LIBS =  
+LIBS = $(shell pkg-config --libs --static copper-eval)
 LIBDIRS =  
 OBJS = wtime.o svm.o svm_rfe.o svm_rfe_test.o
 OUTPUT = ./svm_mkl
diff --git a/SVM-RFE/svm_rfe.cpp b/SVM-RFE/svm_rfe.cpp
index 272a216..9349ec7 100644
--- a/SVM-RFE/svm_rfe.cpp
+++ b/SVM-RFE/svm_rfe.cpp
@@ -7,6 +7,7 @@
 #include <math.h>
 #include <string>
 #include <iostream>
+#include <copper-eval.h>
 
 #include "svm_rfe.h"
 
@@ -1343,6 +1344,7 @@ bool Svm_RFE::svm_rfe_engine(struct svm_problem prob,struct svm_parameter param,
 	}	
 	else
 	{
+		int count = 0;
 		while (nIteration --)	// Test use, eric, 5/14/2004
 		{	
 			int temp= weights.size();		
@@ -1401,6 +1403,7 @@ bool Svm_RFE::svm_rfe_engine(struct svm_problem prob,struct svm_parameter param,
 			end_t = clock();
 			total += (double)(end_t-start_t)/CLOCKS_PER_SEC;
 #endif
+			copper_eval_iteration(count++, 0);
 		}
 	}	
 	
diff --git a/SVM-RFE/svm_rfe_test.cpp b/SVM-RFE/svm_rfe_test.cpp
index da0bbae..f13fe62 100644
--- a/SVM-RFE/svm_rfe_test.cpp
+++ b/SVM-RFE/svm_rfe_test.cpp
@@ -5,6 +5,7 @@
 #include <iostream>
 #include <fstream>
 #include "time.h"
+#include <copper-eval.h>
 
 #include "svm_rfe.h"
 #define Malloc(type,n) (type *)malloc((n)*sizeof(type))
@@ -49,6 +50,11 @@ int cmdline_parse(int argc, char* argv[]);
 
 int main(int argc, char* argv[])
 {
+	if (copper_eval_init()) {
+		perror("copper_eval_init");
+		exit(1);
+	}
+
 	int i, j;	
 	clock_t start0, end0;
 	double sum0;	
@@ -109,6 +115,10 @@ int main(int argc, char* argv[])
 	}
 	fprank.close();
 
+	if (copper_eval_finish()) {
+		perror("copper_eval_finish");
+	}
+
 	return 0;
 }
 
diff --git a/ScalParC/Makefile b/ScalParC/Makefile
index a539bfd..7a54452 100644
--- a/ScalParC/Makefile
+++ b/ScalParC/Makefile
@@ -1,12 +1,12 @@
 # CC = icc -openmp
 CC = gcc -fopenmp
 
-CFLAGS = -g $(INCLUDE_DIR) 
+CFLAGS = -g $(INCLUDE_DIR) $(shell pkg-config --cflags copper-eval)
 LINKFLAGS = 
 
 INCLUDE_DIR = -I. 
 
-LIBS = -lm
+LIBS = -lm $(shell pkg-config --libs --static copper-eval)
 TARGET = scalparc
 OBJ  = drive.o getdata.o parsort.o parclass.o
 
diff --git a/ScalParC/drive.c b/ScalParC/drive.c
index 7678d5a..56312f9 100644
--- a/ScalParC/drive.c
+++ b/ScalParC/drive.c
@@ -3,6 +3,7 @@
 #include <string.h>
 #include <math.h>
 #include <time.h>
+#include <copper-eval.h>
 
 #define MAIN_FILE
 #include "pclass.h"
@@ -17,6 +18,18 @@ struct timeval tp;
   
 int main(int argc, char *argv[])
 {
+  if (copper_eval_init()) {
+    perror("copper_eval_init");
+    exit(1);
+  }
+  unsigned long jobs = 400;
+  const char* env_jobs = getenv("JOBS");
+  if (env_jobs != NULL) {
+    jobs = atoi(env_jobs);
+  }
+  unsigned long job;
+  for (job = 0; job < jobs; job++) {
+
   FILE *fp_data;
   char datafile[FILE_NAME_LEN], file_name[FILE_NAME_LEN];
   int i,j,k;
@@ -97,4 +110,9 @@ int main(int argc, char *argv[])
   printf("Total execution time with %d processoers: %f\n",nthreads, te-ts); 
   printf("I/O time = %f\n", max);
   printf("Computation time =%f\n", te-ts - max);
+  copper_eval_iteration(job, 0);
+  }
+  if (copper_eval_finish()) {
+    perror("copper_eval_finish");
+  }
 }
diff --git a/Utility_Mining/para_tran_utility/Makefile b/Utility_Mining/para_tran_utility/Makefile
index 9091e92..0390f28 100644
--- a/Utility_Mining/para_tran_utility/Makefile
+++ b/Utility_Mining/para_tran_utility/Makefile
@@ -1,11 +1,11 @@
 # CXX  =  icpc -openmp
 CXX  =  g++ -fopenmp
 
-CFLAGS  = -O2 -g
+CFLAGS  = -O2 -g $(shell pkg-config --cflags copper-eval)
 OBJS	= ListItemset.o
 OBJS2   = Database.o Itemset.o HashTree.o
 OPTS	= -DBALT -DOPTIMAL 
-LIBS = -lm 
+LIBS = -lm $(shell pkg-config --libs --static copper-eval)
 
 TARGET  = utility_mine 
 
diff --git a/Utility_Mining/para_tran_utility/utility.cc b/Utility_Mining/para_tran_utility/utility.cc
index 6173ce2..6bb723e 100644
--- a/Utility_Mining/para_tran_utility/utility.cc
+++ b/Utility_Mining/para_tran_utility/utility.cc
@@ -15,6 +15,7 @@
 #include <unistd.h>
 #include <memory.h>
 #include <fcntl.h>
+#include <copper-eval.h>
 
 #include "Itemset.h"
 #include "ListItemset.h"
@@ -530,6 +531,18 @@ void clean_up(){
 
 int main(int argc, char **argv)
 {
+    if (copper_eval_init()) {
+      perror("copper_eval_init");
+      exit(1);
+    }
+    unsigned long jobs = 100;
+    const char* env_jobs = getenv("JOBS");
+    if (env_jobs != NULL) {
+      jobs = atoi(env_jobs);
+    }
+    unsigned long job;
+    for (job = 0; job < jobs; job++) {
+
     int profit_file;
     summary = fopen("out", "a+");
     int lb, ub, pid, blk,indx, i, k, j, m, n, *buf, numitem, tid;
@@ -682,6 +695,12 @@ seconds(t3);
 //     close_DCB(DCB);
      clean_up();
 
+     copper_eval_iteration(job, 0);
+     }
+     if (copper_eval_finish()) {
+        perror("copper_eval_finish");
+     }
+
      return(0);
 }
 
diff --git a/compilenotes.txt b/compilenotes.txt
index ef0e403..3695ba8 100644
--- a/compilenotes.txt
+++ b/compilenotes.txt
@@ -107,10 +107,10 @@
 
 -- SNP --
 	cd SNP/pnl.snp/PNL 
-	run commands "./configure CC=gcc CXX=g++"
+	run commands "./configure CC=gcc CXX=g++ CXXFLAGS=-fpermissive"
 	run "make"
        	cd ../snp 
-	edit Makefile to set CXX to g++ and run command "make"
+	edit Makefile to append "-fpermissive" to CXX and run command "make"
 	This will produce executable named "snp".
 
 	For icc 7.1 and 8.1