Longest Palindromic Subsequence Multithread in C - c

I'm trying to learn how to multithread with c, and thought that the longest palindromic subsequence problem would be a good place to start.
The idea is that we run two threads and compare their results to find the answer. One thread deals with "odd" subsequences, the other with "even" ones.
Although the code below seems to work, my question is: where in the program should I check for multi-threading errors? It is very new to me so I just need to know what parts may be prone to the issues that multi-threading brings.
#include <stdio.h>
#include <stdlib.h>
#include <pthread.h>
struct str{
char* seq;
int len;
};
void *odd(void* arg){
struct str index = *(struct str*)arg;
int maxAns = 1;
for(int i = 1; i < index.len; i++){
int low = i - 1;
int high = i + 1;
int currMax = 1;
while(low >= 0 && high < index.len && index.seq[low] == index.seq[high]){
low--;
high++;
currMax=currMax+2;
}
if(currMax > maxAns){
maxAns = currMax;
}
}
int* res = malloc(sizeof(int));
*res = maxAns;
free(arg);
return (void*)res;
}
void *even(void* arg){
struct str index = *(struct str*)arg;
int maxAns = 0;
for(int i = 0; i < index.len; i++){
int low = i;
int high = i + 1;
int currMax = 0;
while(low >= 0 && high < index.len && index.seq[low] == index.seq[high]){
low--;
high++;
currMax=currMax+2;
}
if(currMax > maxAns){
maxAns = currMax;
}
}
int* res = malloc(sizeof(int));
*res = maxAns;
free(arg);
return (void*)res;
}
int main(void){
char seq0[] = "aaasaaasadaadsdafa";
int len = sizeof(seq0)/sizeof(seq0[0])-1;
struct str* s0 = malloc(sizeof(struct str));
struct str* s1 = malloc(sizeof(struct str));
s0->seq = (char*)seq0;
s1->seq = (char*)seq0;
s0->len = len;
s1->len = len;
pthread_t t0;
pthread_t t1;
int* res0;
int* res1;
if (pthread_create(&t0, NULL, &odd, s0)!=0){
return 0;
}
if (pthread_create(&t1, NULL, &even, s1)!=0){
return 00;
}
if(pthread_join(t0, (void**)&res0)!=0){
return 1;
}
if(pthread_join(t1, (void**)&res1)!=0){
return 11;
}
if(*res0 > *res1){
printf("%d\n", *res0);
}else{
printf("%d\n", *res1);
}
free(s0);
free(s1);
return 0;
}

Related

variable sized object may not be initialized

I am getting the error variable sized object may not be initialized and I don't understand why.
Could someone show me how to fix this line?
int arr[size] = (int *)(augs->one);
Here is my code:
#include <stdio.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/wait.h>
#include <stdlib.h>
#include <pthread.h>
#include <assert.h>
int count = 0;
int cmpfunc(const void *a, const void *b) {
return (*(int*)a - *(int*)b);
}
struct structure {
int two;
int *one;
};
void *sort(void *augments) {
struct structure *augs = (struct structure*)augments;
int i = 0;
int size = 1;
size = augs->two;
int arr[size] = (int *)(augs->one);
//int *arr = (int *)data;
//printf("sizeof:%d\n", sizeof(arr));
qsort(arr, size, sizeof(int), cmpfunc);
printf("finaloutput:\n");
for (i = 0; i < size; i++) {
printf("%d ", arr[i]);
}
printf("\n");
return NULL;
}
int main(int argc, char *argv[]) {
FILE *myFile;
myFile = fopen("data.txt", "r");
// number of lines in file
char charicter;
for (charicter = getc(myFile); charicter != EOF; charicter = getc(myFile)) {
if (charicter == '\n') {
count++;
}
}
printf("count is %d\n", count);
int numberArray[count];
int i = 0;
if ((myFile = fopen("data.txt", "r"))) {
while ((fscanf(myFile, "%d", &numberArray[i]) != EOF)) {
++i;
}
fclose(myFile);
}
assert(argv[1] != NULL);
int num = atoi(argv[1]); //num equals number input
int arrayarray[num - 1][(count / num)];
int idx;
for (i = 0; i < (count); i++) {
printf("numberarray[%d]= %d\n", i, numberArray[i] /*[0],numberArray[i][1]*/);
}
for (i = 1; i < num + 1; i++) {
for (idx = 0; idx < (count / num); idx++) {
arrayarray[i - 1][idx] = numberArray[i * idx];
}
}
///*
for (i = 0; i < ((count / num)); i++) {
printf("arrayarray[0]=%d\n", arrayarray[0][i]);
}
//*/
int lastarray[((count / num) + (count % num))];
for (idx = 0; idx < ((count / num) + (count % num)); idx++) {
lastarray[idx] = numberArray[idx + ((count / num) * (num - 1))];
}
for (i = 0; i < ((((count / num) + (count % num)))); i++) {
printf("lastaray[%d]=%d\n", i, lastarray[i]);
}
//*******************
pthread_t thread_id_arr[num];
for (i = 0; i < num; i++) {
pthread_t tid;
struct structure *augs;
if (i != (num - 1)) {
augs = malloc(sizeof(struct structure) + sizeof(int) + sizeof(int) * num);
(*augs).one = arrayarray[i];
(*augs).two = (count / num);
pthread_create(&tid, NULL, sort, augs);
} else {
(*augs).one = lastarray;
(*augs).two = (count / num) + (count % num);
pthread_create(&tid, NULL, sort, augs);
//pthread_create(&tid, NULL, sort, (void*)lastarray);
}
thread_id_arr[i] = tid;
}
for (i = 0; i < num; i++) {
pthread_join(thread_id_arr[i], NULL);
}
return 0;
}
As others pointed out, you can't initialize a Variable Length Array with a pointer, like you are doing. However, you don't actually need a VLA at all. Use this instead :
int *arr = augs -> one;
You want to act directly on the array that is passed into the thread, not make a copy of it.
That being said, I see another problem. In the loop that spawns the sorting threads, you are not allocating a new args on the last loop iteration, it reuses the allocated args from the previous iteration, which can cause disaster for the 2nd-to-last thread. You need to move the malloc() call above the if.
Also, the malloc() is allocating more memory than your threads actually use. You only need to allocate enough memory for just the struct by itself, not for any integers following the struct.
Also, when each thread is done using the allocated args that it is given, it needs to free() the args to avoid leaking memory.

Difference in behavior between clang and gcc?

I'm writing a C function to simulate a cache given an address trace. The function works as expected when compiled on my mac using gcc (really clang). gcc --version on my mac returns this:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.1.0 (clang-802.0.42)
When I compile the same program on linux using gcc, the returns are way off, and eC & hC in my program (cache eviction counter and hit counter) are in the hundreds of thousands, when they should be below 10. When typing gcc --version on the linux machine, it returns this:
gcc (Ubuntu 4.9.3-8ubuntu2~14.04) 4.9.3
Here is the program:
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <limits.h>
#include <getopt.h>
#include "cachelab.h"
typedef struct{
int v;
int t;
int LRU;
} block;
typedef struct{
block *blocks;
} set;
typedef struct{
set *sets;
} cache;
void simulate(int s, int E, int b, char* file, int* hC, int* mC, int* eC)
{
int numSets = (1 << s);
char operation;
int address;
int size;
int curTag;
int curSet;
int maxLRU = 0;
int curLRU = 0;
int check = 0;
cache c;
set *sets = malloc(sizeof(set) * numSets);
c.sets = sets;
int i = 0;
while(i < numSets)
{
c.sets[i].blocks = malloc(sizeof(block) * E);
for (int j = 0; j < E; j++)
{
c.sets[i].blocks[j].v = 0;
c.sets[i].blocks[j].t = INT_MIN;
c.sets[i].blocks[j].LRU = 0;
}
i++;
}
FILE *f = fopen(file, "r");
while(fscanf(f," %c %x,%d", &operation, &address, &size) != EOF)
{
check = 0;
curTag = ((unsigned int) address) >> (s+b);
curSet = (address >> b) & ((1 << s) - 1);
for (int i = 0; i < E; i++)
{
c.sets[curSet].blocks[i].LRU++;
if(c.sets[curSet].blocks[i].LRU >= maxLRU)
{
maxLRU = c.sets[curSet].blocks[i].LRU;
curLRU = i;
}
if(curTag == c.sets[curSet].blocks[i].t)
{
*hC = *hC + 1;
if (operation == 'M')
{
*hC = *hC + 1;
}
c.sets[curSet].blocks[i].LRU = 0;
check = 1;
}
}
if(check == 0)
{
for(int i = 0; i < E; i++)
{
if(c.sets[curSet].blocks[i].v == 0)
{
*mC = *mC + 1;
if (operation == 'M')
{
*hC = *hC + 1;
}
c.sets[curSet].blocks[i].v = 1;
c.sets[curSet].blocks[i].LRU = 0;
c.sets[curSet].blocks[i].t = curTag;
check = 1;
break;
}
}
}
if(check == 0)
{
*eC = *eC + 1;
*mC = *mC + 1;
if (operation == 'M')
{
*hC = *hC + 1;
}
c.sets[curSet].blocks[curLRU].t = curTag;
c.sets[curSet].blocks[curLRU].v = 1;
c.sets[curSet].blocks[curLRU].LRU = 0;
}
}
}
int main(int argc, char** argv)
{
int hitCount, missCount, evictionCount;
int s, E, b;
char *file;
char opt;
while((opt = getopt(argc,argv,"v:h:s:E:b:t:")) != -1)
{
switch(opt){
case 'v':
break;
case 'h':
break;
case 's':
s = atoi(optarg);
break;
case 'E':
E = atoi(optarg);
break;
case 'b':
b = atoi(optarg);
break;
case 't':
file = optarg;
break;
default:
exit(1);
}
}
simulate(s, E, b, file, &hitCount, &missCount, &evictionCount);
printSummary(hitCount, missCount, evictionCount);
return 0;
}
EDIT:
I understand that this is due to a difference between clang and gcc. Does anyone have any information about how I can go about fixing this discrepancy?
Here is cachelab.c:
/*
* cachelab.c - Cache Lab helper functions
*/
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include "cachelab.h"
#include <time.h>
trans_func_t func_list[MAX_TRANS_FUNCS];
int func_counter = 0;
/*
* printSummary - Summarize the cache simulation statistics. Student cache simulators
* must call this function in order to be properly autograded.
*/
void printSummary(int hits, int misses, int evictions)
{
printf("hits:%d misses:%d evictions:%d\n", hits, misses, evictions);
FILE* output_fp = fopen(".csim_results", "w");
assert(output_fp);
fprintf(output_fp, "%d %d %d\n", hits, misses, evictions);
fclose(output_fp);
}
/*
* initMatrix - Initialize the given matrix
*/
void initMatrix(int M, int N, int A[N][M], int B[M][N])
{
int i, j;
srand(time(NULL));
for (i = 0; i < N; i++){
for (j = 0; j < M; j++){
// A[i][j] = i+j; /* The matrix created this way is symmetric */
A[i][j]=rand();
B[j][i]=rand();
}
}
}
void randMatrix(int M, int N, int A[N][M]) {
int i, j;
srand(time(NULL));
for (i = 0; i < N; i++){
for (j = 0; j < M; j++){
// A[i][j] = i+j; /* The matrix created this way is symmetric */
A[i][j]=rand();
}
}
}
/*
* correctTrans - baseline transpose function used to evaluate correctness
*/
void correctTrans(int M, int N, int A[N][M], int B[M][N])
{
int i, j, tmp;
for (i = 0; i < N; i++){
for (j = 0; j < M; j++){
tmp = A[i][j];
B[j][i] = tmp;
}
}
}
/*
* registerTransFunction - Add the given trans function into your list
* of functions to be tested
*/
void registerTransFunction(void (*trans)(int M, int N, int[N][M], int[M][N]),
char* desc)
{
func_list[func_counter].func_ptr = trans;
func_list[func_counter].description = desc;
func_list[func_counter].correct = 0;
func_list[func_counter].num_hits = 0;
func_list[func_counter].num_misses = 0;
func_list[func_counter].num_evictions =0;
func_counter++;
}
You forgot to initialize the counters and flags so they start at undefined values. The following lines:
int hitCount, missCount, evictionCount;
int s, E, b;
should be:
int hitCount = 0, missCount = 0, evictionCount = 0;
int s = 0, E = 0, b = 0;
It just happens that the initial values happen to be lower on the mac so you're not getting correct results on the mac either (at least not guaranteed since the initial value is undefined).

Segmentation fault when accessing elements of pointer

#include <stdio.h>
#include <stdlib.h>
#include "frac_heap.h"
#define ARRAYSIZE 10
#define ENDOFARRAY 999
fraction heap[ARRAYSIZE] = {0};
block freeBlocks[ARRAYSIZE] = {0};
int startingBlock = 0;
int nextFree = 0;
fraction* fracPointers[][ARRAYSIZE] = {0};
block* blockPointers[][ARRAYSIZE] = {0};
void init_Heap(){
int x;
for(x = 0; x < ARRAYSIZE; x ++){
block *currBlock = &freeBlocks[x];
currBlock->isFree = 1;
fraction *fractionPointer = &heap[x];
if(x<ARRAYSIZE - 1){
fractionPointer->denominator = x+1;
}
else if(x == ARRAYSIZE - 1){
fractionPointer->denominator = ENDOFARRAY;
}
}
}
void dump_heap(){
int x;
for(x = 0; x < ARRAYSIZE; x ++){
fraction* tempFrac = &heap[x];
printf("%d\t%d\t%d\n",tempFrac->sign, tempFrac->numerator, tempFrac->denominator);
}
}
fraction* new_frac(){
fraction* testFraction = &heap[0];
if(testFraction->numerator == 0 && testFraction ->denominator==0){
printf("Before return");
return testFraction;
}
}
int main(){
init_Heap();
dump_heap();
fraction *p1;
p1 = new_frac();
p1->sign = -1;
p1->numerator = 2;
p1->denominator = 3;
dump_heap();
}
I get segmentation faults when trying to call new_frac(). At this point im just testing the code and I realize that testfraction wont always be = &heap[0];. However, I thought I was able to access parts of the struct that I am point to with '->'?
After editing it some more, it seems to only segfault when it reaches testFraction->denominator. If I only check for the denominator it still segfaults, but it works fine with just the numerator.
The issue is that not all code paths through new_frac() actually return a value. You then proceed to assign through this potentially uninitialized pointer:
p1 = new_frac();
p1->sign = -1;
p1->numerator = 2;
p1->denominator = 3;

Strange occurence in genetic algorithm implementation

#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#define SIZE 8
#define POP 8
int answers[SIZE] = {5,3,1,7,4,6,0,2};
int getRand(int mod){
if (mod==0) return 0;
else return random()%mod;
}
void printArray(int array[]){
int i;
for(i=0; i<SIZE-1; i++) printf("(%i,%i),",i,array[i]);
printf("(%i,%i)",SIZE-1,array[SIZE-1]);
printf("\n");
}
int getWeight(int array[]){
int weight = 28;
int queen;
for(queen=0;queen<SIZE;queen++){ //for each queen
int nextqueen;
for(nextqueen=queen+1;nextqueen<SIZE;nextqueen++){ //for each of the other queens (nextqueen = queen to avoid counting pairs twice)
if(array[queen] == array[nextqueen] || abs(queen-nextqueen)==abs(array[queen]-array[nextqueen])){ //if conflict
weight--;
}
}
}
return weight;
}
void geneticAlgorithm(){
int population[POP][SIZE];
int children[POP][SIZE];
int weightProb[] = {};
int wpl = 0; //weightProb[] length
float mutProb = 0.05;
int done = 0;
int i;
for(i=0;i<POP;i++) for(int j=0;j<SIZE;j++) population[i][j] = getRand(SIZE);
while(done == 0){
for(i=0;i<POP;i++){
if(getWeight(children[i]) == 28){
printf("solution: ");
printArray(children[i]);
done = 1;
}
}
for(i=0;i<wpl;i++) weightProb[i] = (int)NULL; //clear weightprob
wpl=0;
//weighted probability distribution
for(i=0;i<POP;i++){
int w = getWeight(population[i]);
for(int j=0;j<w;j++){
weightProb[wpl] = i; //fill array with member number w times
wpl++;
}
}
//reproduce
for(i=0;i<POP;i+=2){
int par1 = weightProb[getRand(wpl)];
int par2 = weightProb[getRand(wpl)];
int split = getRand(SIZE);
//crossover
for(int j=0;j<split;j++){
children[i][j] = population[par1][j];
children[i+1][j] = population[par2][j];
}
for(int j=split;j<SIZE;j++){
children[i][j] = population[par2][j];
children[i+1][j] = population[par1][j];
}
//mutation
if(getRand(1000000)<=mutProb*1000000){
int child=getRand(2);
if(child == 0) children[i][getRand(SIZE)] = getRand(SIZE);
else children[i+1][getRand(SIZE)] = getRand(SIZE);
}
}
for(i=0;i<POP;i++) for(int j=0;j<SIZE;j++) population[i][j] = children[i][j];
wpl = 0;
}
}
int main(int argc, const char * argv[]){
srandom((unsigned int)time(NULL)); //seed random
geneticAlgorithm();
return 0;
}
when filling weightProb[], the population randomly changes.
i've debugged using print statements and it stops when wpl++ is commented out, but that is required
(wpl is the length of the weightProb array).
how is this happening?
This declaration:
int weightProb[] = {};
declares an empty array. This means each time you write to an element you write out of bounds of the array, and bad things will happen.

Dynamic array in struct calloc or pointers failing, C

I'm attempting to complete an assignment on sparse matrices in C. I have a sparse matrix held as a list of values and coordinates and am converting it to Yale format.
I have run into a strange memory allocation issue that no one seems to have seen before. My code is:
yale* convertMatrix(matrix_list* input){
int matrix_elements = input->elements;
int matrix_rows = input->m;
yale* yale = (struct y*)calloc(1, sizeof(yale));
int* A = (int*)calloc(matrix_elements, sizeof(int));
int* IA = (int*)calloc(matrix_rows + 1, sizeof(int));
int* JA = (int*)calloc(matrix_elements, sizeof(int));
printf("%d elements\n",matrix_elements);
yale->A = A; // Value
yale->IA = IA; // Row (X)
yale->JA = JA; // Column (Y)
yale->elements = matrix_elements;
yale->m = matrix_rows;
yale->n = input->n;
list* tmp_list = input->first;
for(int i = 0, j = 0, tmp_y = 0; i < matrix_elements && tmp_list!=NULL; i++){
printf("Input Value: %d \n",tmp_list->point.value);
A[i] = tmp_list->point.value;
// Initialise the first row
if(i == 0) IA[0] = tmp_list->point.x;
else{
// Add a new row index
if(tmp_y != tmp_list->point.x){
j++;
IA[j] = i;
tmp_y = tmp_list->point.x;
}
}
JA[i] = tmp_list->point.y;
tmp_list = tmp_list->next;
}
for(int i = 0; i < matrix_elements; i++)
printf("%d,",yale->A[i]);
printf("\n");
for(int i = 0; i < matrix_rows + 1; i++)
printf("%d,",yale->IA[i]);
printf("\n");
for(int i = 0; i < matrix_elements; i++)
printf("%d,",yale->JA[i]);
return yale;
}
And here is the struct for yale:
typedef struct y{
int n;
int m;
int elements;
int *IA;
int *JA;
int *A;
} yale;
But the program segfaults at the first relevant printf on the first iteration of the loop.
printf("%d,",yale->A[i]);
I'm positive:
matrix_elements is an integer (9 in my test case)
matrix_rows is an integer
A / IA / JA are all filled with correct values (if you swap yale->A for A in the printf, it works fine).
Directly callocing the array to the struct pointers doesn't affect the result.
Mallocing, callocing, not typecasting, all no effect.
Thanks to Xcode and gdb I can also see that at the point of the segfault. The structure pointers do NOT seem to point to the arrays
I suggest you run your code under Valgrind. This should report the buffer overflow error. (A buffer overflow is where you write past the end of an array).
I also recommend you write some unit tests for your code. They can be very helpful detecting bugs. In particular, I suggest you write a test with a 3x3 input matrix with a value in every position. Check that the values you get out are what you expect.
To get it compiled, I need to prepend this to the snippet:
#include <stdlib.h>
#include <stdio.h>
typedef struct y{
int n;
int m;
int elements;
int *IA;
int *JA;
int *A;
} yale;
typedef struct list {
struct list *next;
struct point { int x,y,value; } point;
} list;
typedef struct matrix_list {
int elements;
int m;
int n;
struct list *first;
int *point;
} matrix_list;
UPDATE: I transformed the program into something more readable (IMHO). I don't have the faintest idea what the IA and JA are supposed to do, but the below fragment should be equivalent to the OP.
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
struct y {
unsigned int n;
unsigned int m;
unsigned int elements;
unsigned int *IA;
unsigned int *JA;
int *A;
} ;
struct list {
struct list *next;
struct point { unsigned int x,y; int value; } point;
} ;
struct matrix_list {
unsigned int elements;
unsigned int m;
unsigned int n;
struct list *first;
} ;
struct y *convertMatrix(struct matrix_list* input)
{
unsigned int matrix_elements = input->elements;
unsigned int matrix_rows = input->m;
unsigned int ii,jj,tmp_y;
struct y *yale ;
struct list *tmp_list ;
yale = calloc(1, sizeof *yale);
assert (yale != NULL);
printf("%u elements\n",matrix_elements);
yale->A = calloc(matrix_elements, sizeof *yale->A);
assert (yale->A != NULL);
yale->IA = calloc(matrix_rows + 1, sizeof *yale->IA);
assert (yale->IA != NULL);
yale->JA = calloc(matrix_elements, sizeof *yale->JA);
assert (yale->JA != NULL);
yale->elements = matrix_elements;
yale->m = matrix_rows;
yale->n = input->n;
// Initialise the first row, set start condition
// FIXME: this ignores the empty list or size=0 cases
yale->IA[0] = tmp_y = input->first->point.x;
ii = jj = 0;
for(tmp_list = input->first ;tmp_list; tmp_list = tmp_list->next) {
printf("Input Value: %d \n",tmp_list->point.value);
yale->A[ii] = tmp_list->point.value;
// Add a new row index
if(tmp_y != tmp_list->point.x){
jj++;
yale->IA[jj] = ii;
tmp_y = tmp_list->point.x;
}
yale->JA[ii] = tmp_list->point.y;
if (++ii >= matrix_elements ) break;
}
for(int i = 0; i < matrix_elements; i++)
printf("%d,",yale->A[i]);
printf("\n");
for(int i = 0; i < matrix_rows + 1; i++)
printf("%u,",yale->IA[i]);
printf("\n");
for(int i = 0; i < matrix_elements; i++)
printf("%u,",yale->JA[i]);
return yale;
}
Note: I moved the (ii == 0) {} condition out of the loop, and replaced the one-letter indices by there two-letter equivalents. Also: all the indices are unsigned (as they should be)

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