/*
* This is where we actually parse the memory map lines.
*/
static int mem_map_add_string(target_context_t *tc,
const char *desc)
{
mem_region_t *mr = NULL;
char *ptr = NULL, *s = NULL, *tok;
int i = 0;
mr = region_new();
/* strtok_r modifies its first argument, so we duplicate
'desc' before using it */
for (s = xstrdup(desc);
#ifndef WIN32
(tok = strtok_r(ptr ? NULL : s, " \t\n", &ptr));
#else
(tok = strtok(ptr ? NULL : s, " \t\n"));
#endif
/* nada */) {
#ifdef WIN32
ptr = (ptr ? ptr : s) + strlen (tok) + 1;
#endif
/* order of tokens is fixed */
switch (i++) {
case 0:
if (parse_addrs(mr, tok) < 0)
goto failure;
break;
case 1:
mr->type = region_type(tok);
if (mr->type == MEMTYPE_INVALID)
goto failure;
break;
case 2:
/* name is always valid */
mr->name = xstrdup(tok);
break;
default:
/* there can be any number of options */
if (parse_opt(mr, tok) < 0)
goto failure;
}
}
if (i < 3)
goto failure;
mem_map_add(tc, mr);
free(s);
return 0;
failure:
if (tok)
bad_desc(desc, desc + (tok - s));
else
bad_desc(desc, desc + strlen(desc));
free(mr);
free(s);
return -1;
}
int monte_load_linux_initrd(struct monte_boot_t *boot,
const void *buffer, long size) {
long initrd_addr;
void *ramdisk_data;
struct monte_region_t *region;
/*--- XXX Disgusting hack ---------------------------------------------
* We can't tell how big memory is very easily from user space.
* /proc/meminfo is close but a pain to read. In stead we just
* stat /proc/kcore. This seems easiest and comes closest to the
* correct answer. What a mess.
*-------------------------------------------------------------------*/
struct stat buf;
if (stat("/proc/kcore", &buf) == -1) {
buf.st_size = 32*1024*1024; /* a random guess if /proc isn't mounted.*/
}
initrd_addr = ((buf.st_size/4)*3) & PAGE_MASK;
/* Next problem: We don't know how big this ram disk image is a
* head of time so just start loading a page at a time :P */
region = region_new(boot, (void *) initrd_addr);
ramdisk_data = region_size(region, size);
memcpy(ramdisk_data, buffer, size);
printf("monte: initial ramdisk: %8ld bytes at %p\n",
size, (void *)initrd_addr);
/* Put the right bits in RAM so the kernel will find the initrd */
#if defined(__i386__)
boot->setup->ramdisk = initrd_addr;
boot->setup->ramdisk_size = size;
#elif defined(__alpha__)
region = region_new(boot, (void *) __pa(boot->param.entrypoint - 0x6000));
ramdisk_data = region_size(region, PAGE_SIZE);
ramdisk_data += 0x100;
((long*)ramdisk_data)[0] = __va(initrd_addr);
((long*)ramdisk_data)[1] = size;
#else
#error No initrd argument placement code for this architecture.
#endif
return 0;
}
static int
calculate_highlight_region (Window wp, Region *rp)
{
if ((wp != cur_wp
&& !get_variable_bool ("highlight-nonselected-windows"))
|| get_buffer_mark (get_window_bp (wp)) == NULL
|| !get_buffer_mark_active (get_window_bp (wp)))
return false;
*rp = region_new (window_o (wp), get_marker_o (get_buffer_mark (get_window_bp (wp))));
return true;
}
region_table_t *parse_regions(char *input_regions, int as_positions, const char *url, const char *species, const char *version) {
region_table_t *regions_table = new_region_table_from_ws(url, species, version);
char *saveptr, *token;
size_t token_len;
int num_regions;
char **regions_data = split(input_regions, ",", &num_regions);
region_t *regions[num_regions];
for (int i = 0; i < num_regions; i++) {
// Set chromosome
token = strtok_r(regions_data[i], ":", &saveptr);
token_len = strlen(token);
char *chromosome = strndup(token, token_len);
// Set start position
token = strtok_r(NULL, "-", &saveptr);
size_t start_position, end_position;
start_position = (token != NULL) ? atol(token) : 1;
// Set end position
token = strtok_r(NULL, "-", &saveptr);
if (token != NULL) {
end_position = atol(token);
} else {
if (as_positions) {
end_position = start_position;
} else {
end_position = UINT_MAX;
}
}
regions[i] = region_new(chromosome, start_position, end_position, NULL, NULL);
LOG_DEBUG_F("region '%s:%u-%u'\n", regions[i]->chromosome, regions[i]->start_position, regions[i]->end_position);
}
insert_regions(regions, num_regions, regions_table);
finish_region_table_loading(regions_table);
for (int i = 0; i < num_regions; i++) {
free(regions_data[i]);
free(regions[i]);
}
free(regions_data);
return regions_table;
}
int monte_load_linux_command_line(struct monte_boot_t *boot, char *cmdline) {
struct monte_region_t *region;
char *cmd_line;
/* Setup the kernel command line */
region = region_new(boot, (void *) MONTE_CMDLINE_BEGIN);
cmd_line = region_size(region, PAGE_SIZE);
boot->setup->cmd_line_ptr = MONTE_CMDLINE_BEGIN;
boot->setup->cmd_magic = CMDLINE_MAGIC;
boot->setup->cmd_offset = MONTE_CMDLINE_BEGIN - MONTE_SETUP_BEGIN;
strcpy(cmd_line, cmdline);
printf("monte: command line : \"%s\"\n", cmdline);
return 0;
}
int monte_load_linux_command_line(struct monte_boot_t *boot, char *cmdline) {
struct monte_region_t *region;
char *cmd_line;
/* Setup the kernel command line */
/* On alpha, the command line sits in the zero page at address
* ?0a000 which is in the region before the kernel entry
* point... Also, one page should be enough for it.*/
region = region_new(boot, (void *) __pa(boot->param.entrypoint - 0x6000));
cmd_line = region_size(region, PAGE_SIZE);
strcpy(cmd_line, cmdline);
printf("monte: command line : \"%s\"\n", cmdline);
return 0;
}
// Picks a language and perform string initialization based on the chosen language.
void nov_region_init(const char *language)
{
ASSERT(language != NULL, "Crash in nov_region_init() due to empty parameters being passed. This should not happen!");
// Detect supported languages.
region_new();
region_scan();
bool b = region_set_language(language);
if(b) {
game_log_write( str_printf( NULL, "Language successfully set to %s", _chr(region_get_language()) ) );
}
localized_init();
}
static
int load_elf_image(struct monte_boot_t *boot, const void *buffer, long size) {
int i;
Elf64_Ehdr *ehdr;
Elf64_Phdr *phdr;
struct monte_region_t *region;
void *kernimage;
/* Super simple ELF loader that makes gobs of assumptions that
* won't be valid anywhere except Linux ELF kernel images */
ehdr = (Elf64_Ehdr *) buffer;
if (memcmp(ehdr->e_ident, ELFMAG, SELFMAG) != 0) {
fprintf(stderr, "not an ELF file.\n");
return -1;
}
if (ehdr->e_ident[EI_CLASS] != ELFCLASS64) {
fprintf(stderr, "ELF object is not an ELF64 object.\n");
return -1;
}
phdr = (Elf64_Phdr *)(buffer + ehdr->e_phoff);
for (i=0; i < ehdr->e_phnum; i++) {
/* Load a program section */
/* Setup a region for this thing */
region = region_new(boot, (void*)__pa(phdr[i].p_vaddr));
kernimage = region_size(region, phdr[i].p_memsz+(1024*PAGE_SIZE));
/* Load data and zero the rest (BSS) */
printf("monte: kernel code : %8ld bytes at %p\n",
phdr[i].p_filesz, (void*) __pa(phdr[i].p_vaddr));
memcpy(kernimage, buffer + phdr[i].p_offset, phdr[i].p_filesz);
memset(kernimage + phdr[i].p_filesz, 0,
phdr[i].p_memsz - phdr[i].p_filesz);
}
boot->param.entrypoint = ehdr->e_entry;
printf("monte: entry point : %p\n", (void*)boot->param.entrypoint);
return 0;
}
region_table_t *parse_regions_from_gff_file(char *filename, const char *url, const char *species, const char *version) {
gff_file_t *file = gff_open(filename);
if (file == NULL) {
return NULL;
}
region_table_t *regions_table = new_region_table_from_ws(url, species, version);
int ret_code = 0;
size_t max_batches = 20, batch_size = 2000;
list_t *read_list = (list_t*) malloc (sizeof(list_t));
list_init("batches", 1, max_batches, read_list);
#pragma omp parallel sections
{
// The producer reads the GFF file
#pragma omp section
{
LOG_DEBUG_F("Thread %d reads the GFF file\n", omp_get_thread_num());
ret_code = gff_read_batches(read_list, batch_size, file);
list_decr_writers(read_list);
if (ret_code) {
LOG_FATAL_F("Error while reading GFF file %s (%d)\n", filename, ret_code);
}
}
// The consumer inserts regions in the structure
#pragma omp section
{
list_item_t *item = NULL;
gff_batch_t *batch;
gff_record_t *record;
region_t *regions_batch[REGIONS_CHUNKSIZE];
int avail_regions = 0;
while ( item = list_remove_item(read_list) ) {
batch = item->data_p;
// For each record in the batch, generate a new region
for (int i = 0; i < batch->records->size; i++) {
record = batch->records->items[i];
region_t *region = region_new(strndup(record->sequence, record->sequence_len),
record->start, record->end,
record->strand ? strndup(&record->strand, 1) : NULL,
record->feature ? strndup(record->feature, record->feature_len) : NULL);
LOG_DEBUG_F("region '%s:%u-%u'\n", region->chromosome, region->start_position, region->end_position);
regions_batch[avail_regions++] = region;
// Save when the recommended size is reached
if (avail_regions == REGIONS_CHUNKSIZE) {
insert_regions(regions_batch, avail_regions, regions_table);
for (int i = 0; i < avail_regions; i++) {
free(regions_batch[i]);
}
avail_regions = 0;
}
}
gff_batch_free(batch);
list_item_free(item);
}
// Save the remaining regions that did not fill a batch
if (avail_regions > 0) {
insert_regions(regions_batch, avail_regions, regions_table);
for (int i = 0; i < avail_regions; i++) {
free(regions_batch[i]);
}
avail_regions = 0;
}
}
}
finish_region_table_loading(regions_table);
list_free_deep(read_list, NULL);
gff_close(file, 1);
return regions_table;
}
int monte_load_linux_kernel(struct monte_boot_t *boot,
const void *buffer, long size){
void *setup_data, *kernel_data;
struct monte_region_t *region;
struct kernel_setup_t *stmp;
stmp = (struct kernel_setup_t *)buffer;
/* Sanity check */
/* Check for the kernel setup signature */
if (stmp->boot_flag != BS_SIG_VAL) {
fprintf(stderr, "monte: Boot signature not found.\n");
return -1;
}
/* Sanity check number of sectors */
if (stmp->setup_sects > MAX_SETUP_SECTS) {
fprintf(stderr, "monte: number of setup sectors too large: %d"
" (max %d)\n",(int) stmp->setup_sects, MAX_SETUP_SECTS);
return -1;
}
/* Check for that setup signature. */
if (strncmp(stmp->signature, SETUP_SIG_VAL,
strlen(SETUP_SIG_VAL)) != 0) {
fprintf(stderr, "monte: Kernel image setup signature not found.\n");
return -1;
}
/* Setup the region for the setup code */
region = region_new(boot, (void *)MONTE_SETUP_BEGIN);
setup_data = region_size(region, (stmp->setup_sects+1)*512);
boot->setup = setup_data;
memcpy(setup_data, buffer, (stmp->setup_sects+1)*512);
printf("monte: kernel setup : %8d bytes at %p\n",
((int) stmp->setup_sects)*512, (void*)MONTE_SETUP_BEGIN);
buffer += (stmp->setup_sects+1)*512; /* update buffer pointers */
size -= (stmp->setup_sects+1)*512;
/* The number of kernel "paragraphs" is getting overflowed by
* todays kernels. Ignore it and just load the rest of the data
* we have. */
region = region_new(boot, (void*)boot->setup->start);
kernel_data = region_size(region, size);
memcpy(kernel_data, buffer, size);
printf("monte: kernel code : %8d bytes at %p\n",
(int) size, (void *) boot->setup->start);
if (boot->param.flags & MONTE_PROTECTED) {
if (save_old_setup(boot)) return -1;
boot->param.entrypoint = boot->setup->start;
} else
boot->param.entrypoint = 0x90200000; /* Real mode 9020:0000 */
/* XXXXX FIX ME XXXXXX THIS IS A HACK!!! XXXXXX */
if (boot->param.entrypoint == 0) {
printf("monte: Forcing entry point to 0x100000\n");
boot->param.entrypoint = 0x100000;
}
/* XXXXX FIX ME XXXXXX THIS IS A HACK!!! XXXXXX */
boot->setup->loader = 0x50; /* Set the loader type. */
boot->setup->ramdisk = 0;
boot->setup->ramdisk_size = 0;
boot->setup->cmd_magic = 0;
boot->setup->cmd_offset = 0;
return 0;
}
/*
* Flash map is a string like "2x16K/l,6x16K,63x128K", where "2x16K"
* means "two blocks of size 16 Kbytes each", and the "/l" is a flag
* meaning "locked" (used for boot blocks which can't be programmed
* without special intervention). Possible size suffixes are none
* (bytes), "K" (kilobytes), and "M" (megabytes). Parse with a little
* state machine, and add the blocks as a mem_region_t chain that's a
* child of the given one.
*/
int flash_parse_map(mem_region_t *mr, const char *map)
{
enum state { S_NBLOCKS, S_SIZE, S_FLAGS, S_END } state = S_NBLOCKS;
mem_region_t *cur = mr;
int nblocks = 0;
tsize_t size = 0;
taddr_t vma, lma;
unsigned flags = 0;
const char *p;
assert(mr);
vma = mr->vma;
lma = mr->lma;
assert(map);
/* clear out prior flash blocks */
region_destroy(mr->children);
mr->children = NULL;
p = map;
goto loop;
do {
++p;
loop:
if (isspace(*p))
continue;
switch (state) {
case S_NBLOCKS:
if (isdigit(*p)) {
nblocks = (nblocks * 10) + (*p - '0');
} else if (*p == 'x') {
state = S_SIZE;
} else {
bad_map(map, p);
goto failure;
}
break;
case S_SIZE:
switch (*p) {
case '0': case '1': case '2': case '3':
case '4': case '5': case '6': case '7':
case '8': case '9':
size = (size * 10) + (*p - '0');
break;
case 'K':
size *= 1024;
break;
case 'M':
size *= (1024 * 1024);
break;
case '/':
state = S_FLAGS;
break;
case ',': case '\0':
state = S_END;
break;
default:
bad_map(map, p);
goto failure;
}
break;
case S_FLAGS:
switch (*p) {
case 'l':
flags |= MRF_LOCKED;
break;
case ',': case '\0':
state = S_END;
break;
default:
bad_map(map, p);
goto failure;
}
break;
default:
assert(0);
}
if (state == S_END) {
/*
* Create one mem_region_t for each flash
* block, and link them into a chain.
*/
while (nblocks--) {
mem_region_t *tmp = region_new();
tmp->name = xstrdup("(anonymous flash block)");
tmp->type = MEMTYPE_FLASH;
tmp->size = size;
tmp->flags = flags;
tmp->bufsize = mr->bufsize;
tmp->vma = vma;
vma += size;
tmp->lma = lma;
lma += size;
if (cur == mr) {
mr->children = tmp;
cur = tmp;
} else {
cur->next = tmp;
cur = tmp;
}
}
if(flags != 0) mr->flags |= flags;
state = S_NBLOCKS;
nblocks = 0;
size = 0;
flags = 0;
}
} while (*p);
return 0;
failure:
region_destroy(mr->children);
mr->children = NULL;
return -1;
}