void test_gc_build_structure(MM *mm, Obj handle_start) {
Obj handle_prev = handle_start;
Obj hdl;
uint64 suma;
int i;
for (i = 1; i <= 1000; i++) {
Obj handle_current = mm_alloc(mm, 2);
mm_set(handle_current, 0, MK_IMMEDIATE(i));
mm_set(handle_prev, 1, handle_current);
handle_prev = handle_current;
}
mm_set(handle_prev, 1, MK_IMMEDIATE(9999));
{
suma = 0;
hdl = handle_start;
while (hdl & OBJ_FLAG_HANDLE) {
suma += OBJ_HANDLE_TO_PTR(hdl)[0];
hdl = OBJ_HANDLE_TO_PTR(hdl)[1];
}
assert(IMM_VALUE(suma) == 500544);
}
hdl = handle_start;
for (i = 1; i <= 10; i++) {
hdl = OBJ_HANDLE_TO_PTR(hdl)[1];
}
mm_set(handle_prev, 1, OBJ_HANDLE_TO_PTR(hdl)[1]);
mm_set(hdl, 1, MK_IMMEDIATE(18));
}
void bd_set_transitions(BDPhyloHmm *bdphmm) {
int state;
HMM *hmm = bdphmm->phmm->hmm;
TreeNode *tree = bdphmm->phmm->mods[0]->tree;
/* set transition probs based on mu, nu, and phi */
for (state = 1; state < hmm->nstates; state++) {
if (state == tree->nnodes)
mm_set(hmm->transition_matrix, 0, state, bdphmm->nu * (1-bdphmm->phi));
else
mm_set(hmm->transition_matrix, 0, state, bdphmm->nu * bdphmm->phi /
(hmm->nstates-2));
mm_set(hmm->transition_matrix, state, 0, bdphmm->mu);
mm_set(hmm->transition_matrix, state, state, 1-bdphmm->mu);
}
mm_set(hmm->transition_matrix, 0, 0, 1-bdphmm->nu);
/* begin transitions */
vec_set(hmm->begin_transitions, 0,
bdphmm->mu/(bdphmm->mu + bdphmm->nu));
for (state = 1; state < hmm->nstates; state++) {
if (state == tree->nnodes)
vec_set(hmm->begin_transitions, state, bdphmm->nu * (1-bdphmm->phi)/
(bdphmm->mu + bdphmm->nu));
else
vec_set(hmm->begin_transitions, state, bdphmm->nu * bdphmm->phi /
((bdphmm->mu + bdphmm->nu) * (hmm->nstates-2)));
}
hmm_reset(hmm);
}
// QUESTION: Why are we not calculating the string length automatically?
void ns_wipe(chr_t *s, size_t len) {
#ifdef MAGMA_PEDANTIC
if (!s) log_pedantic("Attempting to wipe a NULL string pointer.");
#endif
if (s && len) mm_set(s, 0, len);
}
/**
* @brief Zero out a block of memory.
* @note Uses the 'optimize (0)' and 'noinline' function attributes to prevent compiler optimization from removing logic it might consider unnecessary.
* @param block the block of memory to be zeroed.
* @param len the number of zero bytes to write to memory.
* @see http://gcc.gnu.org/onlinedocs/gcc-4.4.4/gcc/Function-Attributes.html
*/
void *mm_wipe(void *block, size_t len) {
#ifdef MAGMA_PEDANTIC
if (!block) {
log_pedantic("Attempting to wipe a NULL block pointer.");
}
#endif
if (block && len) {
mm_set(block, 0, len);
}
return block;
}
/**
*
* @brief Allocate a chunk of memory with the system allocator and zero-wipe it.
* @note Uses the 'malloc' function attribute to indicate any non-NULL return value is not an alias for any other valid pointer.
* @note The buffer length must be non-zero.
* @see http://gcc.gnu.org/onlinedocs/gcc-4.4.4/gcc/Function-Attributes.html
* @param len the amount of memory to allocate.
* @return a valid pointer to the allocated memory on success, or NULL on error.
*/
void *mm_alloc(size_t len) {
void *result;
if (!len) {
log_pedantic("Attempted to allocate a zero length string.");
return NULL;
} else if ((result = malloc(len))) {
mm_set(result, 0, len);
} else {
log_pedantic("Unable to allocate a block of %zu bytes.", len);
}
return result;
}
bool_t check_string_print(void) {
uint64_t total;
bool_t result = true;
stringer_t *strings[14];
mm_set(strings, 0, sizeof(strings));
strings[0] = st_print(NULLER_T | CONTIGUOUS | HEAP, "%.*s", st_length_int(constant), st_char_get(constant));
strings[1] = st_print(NULLER_T | JOINTED | HEAP, "%.*s", st_length_int(strings[0]), st_char_get(strings[0]));
strings[2] = st_print(BLOCK_T | CONTIGUOUS | HEAP, "%.*s", st_length_int(strings[1]), st_char_get(strings[1]));
strings[3] = st_print(BLOCK_T | JOINTED | HEAP, "%.*s", st_length_int(strings[2]), st_char_get(strings[2]));
strings[4] = st_print(MANAGED_T | CONTIGUOUS | HEAP, "%.*s", st_length_int(strings[3]), st_char_get(strings[3]));
strings[5] = st_print(MANAGED_T | JOINTED | HEAP, "%.*s", st_length_int(strings[4]), st_char_get(strings[4]));
strings[6] = st_print(MAPPED_T | JOINTED | HEAP, "%.*s", st_length_int(strings[5]), st_char_get(strings[5]));
strings[7] = st_print(NULLER_T | CONTIGUOUS | SECURE, "%.*s", st_length_int(strings[6]), st_char_get(strings[6]));
strings[8] = st_print(NULLER_T | JOINTED | SECURE, "%.*s", st_length_int(strings[7]), st_char_get(strings[7]));
strings[9] = st_print(BLOCK_T | CONTIGUOUS | SECURE, "%.*s", st_length_int(strings[8]), st_char_get(strings[8]));
strings[10] = st_print(BLOCK_T | JOINTED | SECURE, "%.*s", st_length_int(strings[9]), st_char_get(strings[9]));
strings[11] = st_print(MANAGED_T | CONTIGUOUS | SECURE, "%.*s", st_length_int(strings[10]), st_char_get(strings[10]));
strings[12] = st_print(MANAGED_T | JOINTED | SECURE, "%.*s", st_length_int(strings[11]), st_char_get(strings[11]));
strings[13] = st_print(MAPPED_T | JOINTED | SECURE, "%.*s", st_length_int(strings[12]), st_char_get(strings[12]));
for (int i = 0; i < 14 && strings[i]; i++) {
for (unsigned int j = total = 0; strings[i] && j < st_length_get(strings[i]); j++) {
total += *(st_char_get(strings[i]) + j);
}
if (total != 5366) {
result = false;
}
}
log_print("%28.28s = %s", "print", result ? "passed" : "failed");
for (int i = 0; i < 14; i++) {
if (strings[i])
st_free(strings[i]);
}
return result;
}
void test_gc(void) {
printf("-- test mm_gc\n");
MM _mm;
MM *mm = &_mm;
mm_init(mm, mm_stack_pointer_orig());
Obj handle_start = mm_alloc(mm, 2);
mm_set(handle_start, 0, MK_IMMEDIATE(44));
test_gc_build_structure(mm, handle_start);
mm_gc(mm);
{
uint64 suma = 0;
Obj hdl = handle_start;
while (hdl & OBJ_FLAG_HANDLE) {
suma += OBJ_HANDLE_TO_PTR(hdl)[0];
hdl = OBJ_HANDLE_TO_PTR(hdl)[1];
}
assert(IMM_VALUE(suma) == 99);
}
test_gc_build_structure(mm, handle_start);
mm_gc(mm);
{
uint64 suma = 0;
Obj hdl = handle_start;
while (hdl & OBJ_FLAG_HANDLE) {
suma += OBJ_HANDLE_TO_PTR(hdl)[0];
hdl = OBJ_HANDLE_TO_PTR(hdl)[1];
}
assert(IMM_VALUE(suma) == 99);
}
mm_free_blocks(mm);
}
void start(uint32_t* modulep, void* physbase, void* physfree)
{
int i;
struct smap_t {
uint64_t base, length;
uint32_t type;
}__attribute__((packed)) *smap;
// initially Mark all pages used
mm_set(freePage,MEM_SIZE);
while(modulep[0] != 0x9001) modulep += modulep[1]+2;
for(smap = (struct smap_t*)(modulep+2); smap < (struct smap_t*)((char*)modulep+modulep[1]+2*4); ++smap) {
if (smap->type == 1 /* memory */ && smap->length != 0) {
// Mark the memory available in the free list
pmmngr_init_region(smap->base, smap->length);
}
}
/* we need to mark the kernel memory as used kernel starts from 200000 and end at 220000 */
/* so we will mark the memory till 400000 as used however we can keep it till 220000 as well */
pmmngr_uninit_region((uint64_t)0,(uint64_t)0x400000); // mark all kernel memory as used
/* we need to map the kernel memory to the page table */
// initialize the page table
set_page_table(&Page_Table);
uint64_t *addr = (uint64_t*)physbase;
/* we need to map the kernel memory to the page table */
for(addr = (uint64_t*)physbase; addr<=(uint64_t*)physfree; addr++)
{
vmmngr_map_page(addr,(uint64_t *)((uint64_t)addr + KERNEL_VIRTUAL_BASE),&Page_Table);
}
/* Map the Video memory This will map to single page 80*25*2 < 1 page */
vmmngr_map_page((uint64_t *)0xb8000,(uint64_t*)VIDEO_VIRTUAL_MEMORY,&Page_Table);
// printf("Video Memory has been marked in virtual address space\n");
/* pass the pml4e value to cr3 register */
kernel_pml4e = (uint64_t *)ALIGN_DOWN((uint64_t)Page_Table.root);
write_cr3(&Page_Table);
init_video();
/********************************* KERNEL CREATION ********************************/
struct task_struct *pcb0 = (struct task_struct *)kmalloc(sizeof(struct task_struct)); //kernel
pcb0->pml4e =(uint64_t)kernel_pml4e; // kernel's page table
pcb0->pid = 0; // I'm kernel init process so pid 0
pcb0->iswait = 0; //not waiting for any one
pcb0->stack =(uint64_t *)stack; //my stack is already created by prof :)
process_count = 0; //at this point we don't have any other process in ready_queue so go ahead and create one and update this
sleeping_process_count = 0; // at this point no body is sleeping
// initialize processes queue
for(i=0;i<100;i++) {
zombie_queue[i] = 0; // no process is zombie
}
foreground_process = 3; // process with this pid will be foreground process
// put them in the ready queue
ready_queue[0] =(uint64_t ) pcb0; //kernel
/*
char fname[] = "bin/hello";
malloc_pcb(fname);
char fname1[] = "bin/world";
malloc_pcb(fname1);
char fname2[] = "bin/proc3";
malloc_pcb(fname2);
char fname3[] = "bin/proc4";
malloc_pcb(fname3);
*/
/*************************************** Please change here fname ******************/
char fname4[] = "bin/printf";
malloc_pcb(fname4);
idt_install();
__asm__("sti");
//init_context_switch();
asm volatile("mov $0x2b,%ax");
asm volatile("ltr %ax");
tarfs_init();
while(1);
}
bool_t check_string_merge(void) {
uint64_t total;
bool_t result = true;
stringer_t *strings[16];
mm_set(strings, 0, sizeof(strings));
strings[0] = st_alloc_opts(PLACER_T | JOINTED | HEAP | FOREIGNDATA, 0);
st_data_set(strings[0], st_data_get(string_check_constant));
st_length_set(strings[0], st_length_get(string_check_constant));
strings[1] = st_merge_opts(NULLER_T | CONTIGUOUS | HEAP, "s", strings[0]);
strings[2] = st_merge_opts(NULLER_T | JOINTED | HEAP, "s", strings[1]);
strings[3] = st_merge_opts(BLOCK_T | CONTIGUOUS | HEAP, "s", strings[2]);
strings[4] = st_merge_opts(BLOCK_T | JOINTED | HEAP, "s", strings[3]);
strings[5] = st_merge_opts(MANAGED_T | CONTIGUOUS | HEAP, "s", strings[4]);
strings[6] = st_merge_opts(MANAGED_T | JOINTED | HEAP, "s", strings[5]);
strings[7] = st_merge_opts(MAPPED_T | JOINTED | HEAP, "s", strings[6]);
strings[8] = st_merge_opts(NULLER_T | CONTIGUOUS | SECURE, "s", strings[7]);
strings[9] = st_merge_opts(NULLER_T | JOINTED | SECURE, "s", strings[8]);
strings[10] = st_merge_opts(BLOCK_T | CONTIGUOUS | SECURE, "s", strings[9]);
strings[11] = st_merge_opts(BLOCK_T | JOINTED | SECURE, "s", strings[10]);
strings[12] = st_merge_opts(MANAGED_T | CONTIGUOUS | SECURE, "s", strings[11]);
strings[13] = st_merge_opts(MANAGED_T | JOINTED | SECURE, "s", strings[12]);
strings[14] = st_merge_opts(MAPPED_T | JOINTED | SECURE, "s", strings[13]);
for (int i = 0; i < 15 && strings[i]; i++) {
for (unsigned int j = total = 0; strings[i] && j < st_length_get(strings[i]); j++) {
total += *(st_char_get(strings[i]) + j);
}
if (total != 5366) {
result = false;
}
}
if (result) {
strings[15] = st_merge_opts(MANAGED_T | JOINTED | HEAP, "snsnsnsnsnsnsnsnsnsnsnsnsnsnsnsn", string_check_constant, "\n", strings[0], "\n", strings[1], "\n", strings[2], "\n",
strings[3], "\n", strings[4], "\n", strings[5], "\n", strings[6], "\n", strings[7], "\n", strings[8], "\n", strings[9], "\n", strings[10], "\n", strings[11],
"\n", strings[12], "\n", strings[13], "\n", strings[14], "\n");
for (unsigned int i = total = 0; strings[15] && i < st_length_get(strings[15]); i++) {
total += *(st_char_get(strings[15]) + i);
}
if (total != (5376UL * 16)) {
result = false;
}
}
for (int i = 0; i < 16; i++) {
st_cleanup(strings[i]);
}
return result;
}
bool_t check_string_merge(void) {
uint64_t total;
bool_t result = true;
stringer_t *strings[16];
mm_set(strings, 0, sizeof(strings));
strings[0] = st_alloc(PLACER_T | JOINTED | HEAP, 0);
st_placer_set(strings[0], st_data_get(constant), st_length_get(constant));
strings[1] = st_merge(NULLER_T | CONTIGUOUS | HEAP, "s", strings[0]);
strings[2] = st_merge(NULLER_T | JOINTED | HEAP, "s", strings[1]);
strings[3] = st_merge(BLOCK_T | CONTIGUOUS | HEAP, "s", strings[2]);
strings[4] = st_merge(BLOCK_T | JOINTED | HEAP, "s", strings[3]);
strings[5] = st_merge(MANAGED_T | CONTIGUOUS | HEAP, "s", strings[4]);
strings[6] = st_merge(MANAGED_T | JOINTED | HEAP, "s", strings[5]);
strings[7] = st_merge(MAPPED_T | JOINTED | HEAP, "s", strings[6]);
strings[8] = st_merge(NULLER_T | CONTIGUOUS | SECURE, "s", strings[7]);
strings[9] = st_merge(NULLER_T | JOINTED | SECURE, "s", strings[8]);
strings[10] = st_merge(BLOCK_T | CONTIGUOUS | SECURE, "s", strings[9]);
strings[11] = st_merge(BLOCK_T | JOINTED | SECURE, "s", strings[10]);
strings[12] = st_merge(MANAGED_T | CONTIGUOUS | SECURE, "s", strings[11]);
strings[13] = st_merge(MANAGED_T | JOINTED | SECURE, "s", strings[12]);
strings[14] = st_merge(MAPPED_T | JOINTED | SECURE, "s", strings[13]);
for (int i = 0; i < 15 && strings[i]; i++) {
for (unsigned int j = total = 0; strings[i] && j < st_length_get(strings[i]); j++) {
total += *(st_char_get(strings[i]) + j);
}
if (total != 5366) {
result = false;
}
}
if (result) {
strings[15] = st_merge(MANAGED_T | JOINTED | HEAP, "snsnsnsnsnsnsnsnsnsnsnsnsnsnsnsn", constant, "\n", strings[0], "\n", strings[1], "\n", strings[2], "\n",
strings[3], "\n", strings[4], "\n", strings[5], "\n", strings[6], "\n", strings[7], "\n", strings[8], "\n", strings[9], "\n", strings[10], "\n", strings[11],
"\n", strings[12], "\n", strings[13], "\n", strings[14], "\n");
for (unsigned int i = total = 0; strings[15] && i < st_length_get(strings[15]); i++) {
total += *(st_char_get(strings[15]) + i);
}
if (total != (5376lu * 16lu)) {
result = false;
}
}
log_print("%28.28s = %s", "merged", result ? "passed" : "failed");
for (int i = 0; i < 16; i++) {
if (strings[i])
st_free(strings[i]);
}
return result;
}