static int
check_package_conflict(const char *pkgname, void *v)
{
struct package_conflict *conflict = v;
package_t pkg;
plist_t *p;
FILE *f;
int rv;
if (conflict->skip_pkgname != NULL &&
strcmp(conflict->skip_pkgname, pkgname) == 0)
return 0;
rv = 0;
f = fopen_contents(pkgname, "r");
read_plist(&pkg, f);
(void)fclose(f);
for (p = pkg.head; p; p = p->next) {
if (p->type != PLIST_PKGCFL)
continue;
if (pkg_match(p->name, conflict->pkgname) == 1) {
*(conflict->conflicting_pkgname) = xstrdup(pkgname);
*(conflict->conflicting_pattern) = xstrdup(p->name);
rv = 1 /* nonzero, stop iterating */;
break;
}
}
free_plist(&pkg);
return rv;
}
static
void linear_delete(Mindex mdx, Term t)
{
Plist curr, prev;
prev = NULL;
curr = mdx->linear_first;
while (curr != NULL && curr->v != t) {
prev = curr;
curr = curr->next;
}
if (curr == NULL) {
fprint_term(stderr, t);
fprintf(stderr, "\n");
fatal_error("mindex_delete (linear), term not found.");
}
else {
if (prev != NULL)
prev->next = curr->next;
else
mdx->linear_first = curr->next;
if (curr == mdx->linear_last)
mdx->linear_last = prev;
free_plist(curr);
}
} /* linear_delete */
static int
add_depends_of(const char *pkgname, void *cookie)
{
FILE *fp;
plist_t *p;
package_t plist;
char *path;
path = pkgdb_pkg_file(pkgname, CONTENTS_FNAME);
if ((fp = fopen(path, "r")) == NULL)
errx(EXIT_FAILURE, "Cannot read %s of package %s",
CONTENTS_FNAME, pkgname);
free(path);
read_plist(&plist, fp);
fclose(fp);
for (p = plist.head; p; p = p->next) {
if (p->type == PLIST_PKGDEP)
add_required_by(p->name, pkgname);
}
free_plist(&plist);
return 0;
}
/* PUBLIC */
void zap_plist_of_terms(Plist lst)
{
Plist p = lst;
while (p != NULL) {
Plist p2 = p;
p = p->next;
zap_term(p2->v);
free_plist(p2);
}
} /* zap_plist_of_terms */
/* PUBLIC */
void zap_formula_list(Plist lst)
{
Plist p = lst;
while (p != NULL) {
Plist p2 = p;
p = p->next;
zap_formula(p2->v);
free_plist(p2);
}
} /* zap_formula_list */
int main(int argc, char *argv[]){
plist_info plist;
int snapshot;
char filename_in[256];
char filename_out[256];
SID_init(&argc,&argv,NULL,NULL);
/**********************/
/* Parse command line */
/**********************/
if(argc!=2){
fprintf(stderr,"\n syntax: %s gadget_file\n",argv[0]);
fprintf(stderr," ------\n\n");
return(ERROR_SYNTAX);
}
else{
strcpy(filename_in, argv[1]);
snapshot=atoi(argv[2]);
strcpy(filename_out,argv[3]);
strcat(filename_out,".csv");
}
SID_log("Converting GADGET file to .csv...",SID_LOG_OPEN|SID_LOG_TIMER,filename_in,filename_out);
/****************************************/
/* Read GADGET file into data structure */
/****************************************/
init_plist(&plist,NULL,GADGET_LENGTH,GADGET_MASS,GADGET_VELOCITY);
SID_log("Reading GADGET file {%s}...",SID_LOG_OPEN|SID_LOG_TIMER,filename_in);
read_gadget_binary(filename_in,snapshot,&plist,READ_GADGET_DEFAULT);
SID_log("Done.",SID_LOG_CLOSE);
/********************/
/* Write ascii file */
/********************/
SID_log("Writing .csv file {%s}...",SID_LOG_OPEN|SID_LOG_TIMER,filename_out);
write_gadget_csv(filename_out,&plist);
SID_log("Done.",SID_LOG_CLOSE);
/************/
/* Clean-up */
/************/
free_plist(&plist);
SID_log("Done.",SID_LOG_CLOSE);
return(ERROR_NONE);
}
static int
create_from_installed(const char *ipkg, const char *pkg, const char *suf)
{
FILE *fp;
Package plist;
char homedir[MAXPATHLEN], log_dir[FILENAME_MAX];
snprintf(log_dir, sizeof(log_dir), "%s/%s", LOG_DIR, ipkg);
if (!fexists(log_dir)) {
warnx("can't find package '%s' installed!", ipkg);
return FALSE;
}
getcwd(homedir, sizeof(homedir));
if (chdir(log_dir) == FAIL) {
warnx("can't change directory to '%s'!", log_dir);
return FALSE;
}
/* Suck in the contents list */
plist.head = plist.tail = NULL;
fp = fopen(CONTENTS_FNAME, "r");
if (!fp) {
warnx("unable to open %s file", CONTENTS_FNAME);
return FALSE;
}
read_plist(&plist, fp);
fclose(fp);
Install = isfile(INSTALL_FNAME) ? (char *)INSTALL_FNAME : NULL;
PostInstall = isfile(POST_INSTALL_FNAME) ?
(char *)POST_INSTALL_FNAME : NULL;
DeInstall = isfile(DEINSTALL_FNAME) ? (char *)DEINSTALL_FNAME : NULL;
PostDeInstall = isfile(POST_DEINSTALL_FNAME) ?
(char *)POST_DEINSTALL_FNAME : NULL;
Require = isfile(REQUIRE_FNAME) ? (char *)REQUIRE_FNAME : NULL;
Display = isfile(DISPLAY_FNAME) ? (char *)DISPLAY_FNAME : NULL;
Mtree = isfile(MTREE_FNAME) ? (char *)MTREE_FNAME : NULL;
make_dist(homedir, pkg, suf, &plist);
free_plist(&plist);
if (chdir(homedir) == FAIL) {
warnx("can't change directory to '%s'!", homedir);
return FALSE;
}
return TRUE;
}
static
Plist get_sos_limit_pickers(Plist pickers)
{
if (pickers == NULL)
return NULL;
else {
Plist rest = get_sos_limit_pickers(pickers->next);
Picker p = pickers->v;
if (p->use_for_sos_limit) {
pickers->next = rest;
return(pickers);
}
else {
free_plist(pickers);
return rest;
}
}
} /* get_sos_limit_pickers */
static int
create_from_installed_recursive(const char *pkg, const char *suf)
{
FILE *fp;
Package plist;
PackingList p;
char tmp[PATH_MAX];
int rval;
if (!create_from_installed(InstalledPkg, pkg, suf))
return FALSE;
snprintf(tmp, sizeof(tmp), "%s/%s/%s", LOG_DIR, InstalledPkg, CONTENTS_FNAME);
if (!fexists(tmp)) {
warnx("can't find package '%s' installed!", InstalledPkg);
return FALSE;
}
/* Suck in the contents list */
plist.head = plist.tail = NULL;
fp = fopen(tmp, "r");
if (!fp) {
warnx("unable to open %s file", tmp);
return FALSE;
}
read_plist(&plist, fp);
fclose(fp);
rval = TRUE;
for (p = plist.head; p ; p = p->next) {
if (p->type != PLIST_PKGDEP)
continue;
if (Verbose)
printf("Creating package %s\n", p->name);
if (!create_from_installed(p->name, p->name, suf)) {
rval = FALSE;
break;
}
}
free_plist(&plist);
return rval;
}
int main(int argc, char *argv[]) {
SID_Init(&argc, &argv, NULL);
// Parse command line
select_gadget_volume_params_info select_gadget_volume_params;
int snapshot;
int n_files_out;
int select_mode;
char filename_in_root[SID_MAX_FILENAME_LENGTH];
char filename_out_root[SID_MAX_FILENAME_LENGTH];
GBPREAL cen_select[3];
GBPREAL select_size;
strcpy(filename_in_root, argv[1]);
snapshot = atoi(argv[2]);
select_gadget_volume_params.cen[0] = (GBPREAL)atof(argv[3]);
select_gadget_volume_params.cen[1] = (GBPREAL)atof(argv[4]);
select_gadget_volume_params.cen[2] = (GBPREAL)atof(argv[5]);
select_gadget_volume_params.size = (GBPREAL)atof(argv[6]);
strcpy(filename_out_root, argv[7]);
n_files_out = atoi(argv[8]);
select_mode = atoi(argv[9]);
// Check that the selection mode is valid and set function pointer
int (*select_function)(
gadget_read_info * fp_gadget, void *params, size_t i_particle, size_t i_particle_type, int i_type, GBPREAL *pos, GBPREAL *vel, size_t ID_i);
if(select_mode == 1)
select_function = select_gadget_cube;
else if(select_mode == 2) {
select_function = select_gadget_sphere;
select_gadget_volume_params.size2 = pow(select_gadget_volume_params.size, 2.);
} else
SID_exit_error("Invalid selection mode (%d) given.", SID_ERROR_SYNTAX, select_mode);
SID_log("Excising volume from Gadget binary file {%s;snapshot=%d}...", SID_LOG_OPEN | SID_LOG_TIMER, filename_in_root, snapshot);
// Initialize the plist data structure
plist_info plist;
select_gadget_volume_params.plist = &plist;
init_plist(&plist, NULL, GADGET_LENGTH, GADGET_MASS, GADGET_VELOCITY);
// Read the header and determine the input file-format
gadget_read_info fp_gadget;
int flag_filefound = init_gadget_read(filename_in_root, snapshot, &fp_gadget);
int flag_multifile = fp_gadget.flag_multifile;
int flag_file_type = fp_gadget.flag_file_type;
gadget_header_info header = fp_gadget.header;
if(!flag_filefound)
SID_exit_error("File not found.", SID_ERROR_LOGIC);
select_gadget_volume_params.box_size = fp_gadget.header.box_size;
// Count the particles
size_t n_particles_type_local[N_GADGET_TYPE];
size_t n_particles_type[N_GADGET_TYPE];
int flag_long_IDs;
process_gadget_file("Counting particles in selection...",
filename_in_root,
snapshot,
select_function,
process_gadget_file_fctn_null,
&select_gadget_volume_params,
n_particles_type_local,
n_particles_type,
&flag_long_IDs,
PROCESS_GADGET_BINARY_DEFAULT);
// Allocate RAM for the particles
allocate_gadget_particles(&plist, n_particles_type_local, n_particles_type, flag_long_IDs);
// Read the particles
process_gadget_file("Performing read/select/write...",
filename_in_root,
snapshot,
select_function,
store_gadget_particles,
&select_gadget_volume_params,
NULL,
NULL,
&flag_long_IDs,
PROCESS_GADGET_BINARY_DEFAULT);
// Write the snapshot
char filename_out[SID_MAX_FILENAME_LENGTH];
sprintf(filename_out, "%s_%03d", filename_out_root, snapshot);
write_gadget_binary_new(&plist, filename_out, n_files_out, WRITE_GADGET_BINARY_DEFAULT);
// Clean-up
free_plist(&plist);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
int
pkg_perform(const char *pkg)
{
char *cp;
FILE *pkg_in;
package_t plist;
const char *full_pkg, *suffix;
char *allocated_pkg;
int retval;
/* Break the package name into base and desired suffix (if any) */
if ((cp = strrchr(pkg, '.')) != NULL) {
allocated_pkg = xmalloc(cp - pkg + 1);
memcpy(allocated_pkg, pkg, cp - pkg);
allocated_pkg[cp - pkg] = '\0';
suffix = cp + 1;
full_pkg = pkg;
pkg = allocated_pkg;
} else {
allocated_pkg = NULL;
full_pkg = pkg;
suffix = "tgz";
}
/* Preliminary setup */
sanity_check();
if (Verbose && !PlistOnly)
printf("Creating package %s\n", pkg);
get_dash_string(&Comment);
get_dash_string(&Desc);
if (IS_STDIN(Contents))
pkg_in = stdin;
else {
pkg_in = fopen(Contents, "r");
if (!pkg_in)
errx(2, "unable to open contents file '%s' for input", Contents);
}
plist.head = plist.tail = NULL;
/* Stick the dependencies, if any, at the top */
if (Pkgdeps)
register_depends(&plist, Pkgdeps, 0);
/*
* Put the build dependencies after the dependencies.
* This works due to the evaluation order in pkg_add.
*/
if (BuildPkgdeps)
register_depends(&plist, BuildPkgdeps, 1);
/* Put the conflicts directly after the dependencies, if any */
if (Pkgcfl) {
if (Verbose && !PlistOnly)
printf("Registering conflicts:");
while (Pkgcfl) {
cp = strsep(&Pkgcfl, " \t\n");
if (*cp) {
add_plist(&plist, PLIST_PKGCFL, cp);
if (Verbose && !PlistOnly)
printf(" %s", cp);
}
}
if (Verbose && !PlistOnly)
printf(".\n");
}
/* Slurp in the packing list */
append_plist(&plist, pkg_in);
if (pkg_in != stdin)
fclose(pkg_in);
/* Prefix should override the packing list */
if (Prefix) {
delete_plist(&plist, FALSE, PLIST_CWD, NULL);
add_plist_top(&plist, PLIST_CWD, Prefix);
}
/*
* Run down the list and see if we've named it, if not stick in a name
* at the top.
*/
if (find_plist(&plist, PLIST_NAME) == NULL) {
add_plist_top(&plist, PLIST_NAME, basename_of(pkg));
}
/* Make first "real contents" pass over it */
check_list(&plist, basename_of(pkg));
/*
* We're just here for to dump out a revised plist for the FreeBSD ports
* hack. It's not a real create in progress.
*/
if (PlistOnly) {
write_plist(&plist, stdout, realprefix);
retval = TRUE;
} else {
#ifdef BOOTSTRAP
warnx("Package building is not supported in bootstrap mode");
retval = FALSE;
#else
retval = pkg_build(pkg, full_pkg, suffix, &plist);
#endif
}
/* Cleanup */
free(Comment);
free(Desc);
free_plist(&plist);
free(allocated_pkg);
return retval;
}
int main(int argc, char *argv[]) {
SID_Init(&argc, &argv, NULL);
// Parse command line
select_gadget_ids_params_info params;
int snapshot;
int halo_index;
int halo_type;
int n_files_out;
int select_mode;
char filename_SSimPL_root[SID_MAX_FILENAME_LENGTH];
char filename_halo_version[SID_MAX_FILENAME_LENGTH];
char filename_in_root[SID_MAX_FILENAME_LENGTH];
char filename_out_root[SID_MAX_FILENAME_LENGTH];
GBPREAL cen_select[3];
GBPREAL select_size;
strcpy(filename_SSimPL_root, argv[1]);
strcpy(filename_halo_version, argv[2]);
snapshot = atoi(argv[3]);
halo_index = atoi(argv[4]);
halo_type = atoi(argv[5]);
strcpy(filename_out_root, argv[6]);
n_files_out = atoi(argv[7]);
SID_log("Writing halo particles to ascii file {%s;snapshot=%d;halo_index=%d}...",
SID_LOG_OPEN | SID_LOG_TIMER,
filename_SSimPL_root,
snapshot,
halo_index);
// Initialize the plist data structure
plist_info plist;
params.plist = &plist;
init_plist(&plist, NULL, GADGET_LENGTH, GADGET_MASS, GADGET_VELOCITY);
// Read the halo ID list. Generate sort indicies and copy the
// list to a duplicate array. Make sure this is the one added
// to params. Pass this to write_gadget_ascii below, so that
// the particles get written in the same order that they are
// in the halo catalog.
char filename_halos[SID_MAX_FILENAME_LENGTH];
if(halo_type == 0)
sprintf(filename_halos, "%s/halos/%s_%03d.catalog_groups", filename_SSimPL_root, filename_halo_version, snapshot);
else
sprintf(filename_halos, "%s/halos/%s_%03d.catalog_subgroups", filename_SSimPL_root, filename_halo_version, snapshot);
FILE * fp_groups = fopen(filename_halos, "r");
int n_groups;
int offset_size;
int halo_length;
size_t halo_offset;
SID_fread_verify(&n_groups, sizeof(int), 1, fp_groups);
SID_fread_verify(&offset_size, sizeof(int), 1, fp_groups);
fseeko(fp_groups, (off_t)(2 * sizeof(int) + halo_index * sizeof(int)), SEEK_SET);
SID_fread_verify(&halo_length, sizeof(int), 1, fp_groups);
fseeko(fp_groups, (off_t)(2 * sizeof(int) + n_groups * sizeof(int) + halo_index * offset_size), SEEK_SET);
if(offset_size == sizeof(int)) {
int halo_offset_i;
SID_fread_verify(&halo_offset_i, offset_size, 1, fp_groups);
halo_offset = (size_t)halo_offset_i;
} else
SID_fread_verify(&halo_offset, offset_size, 1, fp_groups);
fclose(fp_groups);
char filename_ids[SID_MAX_FILENAME_LENGTH];
sprintf(filename_ids, "%s/halos/%s_%03d.catalog_particles", filename_SSimPL_root, filename_halo_version, snapshot);
FILE * fp_ids = fopen(filename_ids, "r");
int id_byte_size;
size_t n_ids;
SID_fread_verify(&id_byte_size, sizeof(int), 1, fp_ids);
SID_log("%d %d-byte IDs to be read (offset=%d)", SID_LOG_COMMENT, halo_length, id_byte_size, halo_offset);
if(id_byte_size == sizeof(int)) {
int n_ids_i;
SID_fread_verify(&n_ids_i, sizeof(int), 1, fp_ids);
n_ids = (size_t)n_ids_i;
} else
SID_fread_verify(&n_ids, sizeof(size_t), 1, fp_ids);
fseeko(fp_ids, (off_t)(sizeof(int) + id_byte_size + halo_offset * id_byte_size), SEEK_SET);
params.n_ids = halo_length;
params.id_list = (size_t *)SID_malloc(sizeof(size_t) * halo_length);
size_t *id_list_unsorted = (size_t *)SID_malloc(sizeof(size_t) * halo_length);
int flag_long_ids = GBP_TRUE;
if(id_byte_size == sizeof(int)) {
flag_long_ids = GBP_FALSE;
int *id_list_i = (int *)SID_malloc(sizeof(int) * halo_length);
SID_fread_verify(id_list_i, id_byte_size, halo_length, fp_ids);
for(int i_p = 0; i_p < halo_length; i_p++)
id_list_unsorted[i_p] = (size_t)id_list_i[i_p];
SID_free(SID_FARG id_list_i);
} else
SID_fread_verify(id_list_unsorted, id_byte_size, halo_length, fp_ids);
fclose(fp_ids);
memcpy(params.id_list, id_list_unsorted, sizeof(size_t) * halo_length);
merge_sort(params.id_list, halo_length, NULL, SID_SIZE_T, SORT_INPLACE_ONLY, SORT_COMPUTE_INPLACE);
// Count the particles
size_t n_particles_type_local[N_GADGET_TYPE];
size_t n_particles_type[N_GADGET_TYPE];
int flag_long_IDs;
sprintf(filename_in_root, "%s/snapshots/snapshot", filename_SSimPL_root);
process_gadget_file("Counting particles in selection...",
filename_in_root,
snapshot,
select_gadget_all,
process_gadget_file_fctn_null,
¶ms,
n_particles_type_local,
n_particles_type,
&flag_long_IDs,
PROCESS_GADGET_BINARY_DEFAULT);
// Allocate RAM for the particles
allocate_gadget_particles(&plist, n_particles_type_local, n_particles_type, flag_long_IDs);
// Read the particles
process_gadget_file("Performing read...",
filename_in_root,
snapshot,
select_gadget_all,
store_gadget_particles,
¶ms,
NULL,
NULL,
&flag_long_IDs,
PROCESS_GADGET_BINARY_DEFAULT);
// Write the snapshot
if(SID.I_am_Master) {
char filename_out[SID_MAX_FILENAME_LENGTH];
sprintf(filename_out, "%s_%03d_%08d.ascii", filename_out_root, snapshot, halo_index);
FILE *fp = fopen(filename_out, "w");
fprintf(fp, "#Columns:\n");
fprintf(fp, "# 1) Gadget particle type\n");
fprintf(fp, "# 2) x [Mpc/h]\n");
fprintf(fp, "# 3) y [Mpc/h]\n");
fprintf(fp, "# 4) z [Mpc/h]\n");
fprintf(fp, "# 5) v_x [km/s]\n");
fprintf(fp, "# 6) v_y [km/s]\n");
fprintf(fp, "# 7) v_z [km/s]\n");
fprintf(fp, "# 8) id\n");
int i_species = GADGET_TYPE_DARK;
size_t n_p = ((size_t *)ADaPS_fetch(plist.data, "n_%s", plist.species[i_species]))[0];
GBPREAL *x = (GBPREAL *)ADaPS_fetch(plist.data, "x_%s", plist.species[i_species]);
GBPREAL *y = (GBPREAL *)ADaPS_fetch(plist.data, "y_%s", plist.species[i_species]);
GBPREAL *z = (GBPREAL *)ADaPS_fetch(plist.data, "z_%s", plist.species[i_species]);
GBPREAL *vx = (GBPREAL *)ADaPS_fetch(plist.data, "vx_%s", plist.species[i_species]);
GBPREAL *vy = (GBPREAL *)ADaPS_fetch(plist.data, "vy_%s", plist.species[i_species]);
GBPREAL *vz = (GBPREAL *)ADaPS_fetch(plist.data, "vz_%s", plist.species[i_species]);
size_t * id = (size_t *)ADaPS_fetch(plist.data, "id_%s", plist.species[i_species]);
size_t * id_indices = NULL;
SID_log("Sorting IDs...", SID_LOG_OPEN);
merge_sort(id, n_p, &id_indices, SID_SIZE_T, SORT_COMPUTE_INDEX, SORT_COMPUTE_NOT_INPLACE);
SID_log("Done.", SID_LOG_CLOSE);
SID_log("Writing particles...", SID_LOG_OPEN);
pcounter_info pcounter;
SID_Init_pcounter(&pcounter, halo_length, 10);
int n_unfound = 0;
for(int i_p = 0; i_p < halo_length; i_p++) {
size_t k_p = id_indices[find_index(id, id_list_unsorted[i_p], n_p, id_indices)];
if(id[k_p] != id_list_unsorted[i_p])
n_unfound++;
else
fprintf(fp,
"%1d %11.4e %11.4e %11.4e %11.4e %11.4e %11.4e %7zd\n",
i_species,
(double)(x[k_p]),
(double)(y[k_p]),
(double)(z[k_p]),
(double)(vx[k_p]),
(double)(vy[k_p]),
(double)(vz[k_p]),
id[k_p]);
SID_check_pcounter(&pcounter, i_p);
}
fclose(fp);
if(n_unfound != 0)
SID_log("(%d unfound)...", SID_LOG_CONTINUE, n_unfound);
SID_log("Done.", SID_LOG_CLOSE);
SID_free(SID_FARG id_indices);
}
// Clean-up
SID_free(SID_FARG id_list_unsorted);
SID_free(SID_FARG params.id_list);
free_plist(&plist);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
/*
* This is seriously ugly code following. Written very fast!
* [And subsequently made even worse.. Sigh! This code was just born
* to be hacked, I guess.. :) -jkh]
*/
static int
pkg_do(char *pkg)
{
Package Plist;
char pkg_fullname[FILENAME_MAX];
char playpen[FILENAME_MAX];
char extract_contents[FILENAME_MAX];
char *extract;
const char *where_to;
FILE *cfile;
int code;
PackingList p;
struct stat sb;
int inPlace, conflictsfound, errcode;
/* support for separate pre/post install scripts */
int new_m = 0;
char pre_script[FILENAME_MAX] = INSTALL_FNAME;
char post_script[FILENAME_MAX];
char pre_arg[FILENAME_MAX], post_arg[FILENAME_MAX];
char *conflict[2];
char **matched;
int fd;
conflictsfound = 0;
code = 0;
zapLogDir = 0;
LogDir[0] = '\0';
strcpy(playpen, FirstPen);
inPlace = 0;
memset(&Plist, '\0', sizeof(Plist));
/* Are we coming in for a second pass, everything already extracted? */
if (!pkg) {
fgets(playpen, FILENAME_MAX, stdin);
playpen[strlen(playpen) - 1] = '\0'; /* pesky newline! */
if (chdir(playpen) == FAIL) {
warnx("pkg_add in SLAVE mode can't chdir to %s", playpen);
return 1;
}
read_plist(&Plist, stdin);
where_to = playpen;
}
/* Nope - do it now */
else {
/* Is it an ftp://foo.bar.baz/file.t[bg]z specification? */
if (isURL(pkg)) {
if (!(where_to = fileGetURL(NULL, pkg, KeepPackage))) {
warnx("unable to fetch '%s' by URL", pkg);
return 1;
}
strcpy(pkg_fullname, pkg);
cfile = fopen(CONTENTS_FNAME, "r");
if (!cfile) {
warnx(
"unable to open table of contents file '%s' - not a package?",
CONTENTS_FNAME);
goto bomb;
}
read_plist(&Plist, cfile);
fclose(cfile);
}
else {
strcpy(pkg_fullname, pkg); /*
* Copy for sanity's sake,
* could remove pkg_fullname
*/
if (strcmp(pkg, "-")) {
if (stat(pkg_fullname, &sb) == FAIL) {
warnx("can't stat package file '%s'", pkg_fullname);
goto bomb;
}
sprintf(extract_contents, "--fast-read %s", CONTENTS_FNAME);
extract = extract_contents;
}
else {
extract = NULL;
sb.st_size = 100000; /* Make up a plausible average size */
}
if (!(where_to = make_playpen(playpen, sb.st_size * 4)))
errx(1, "unable to make playpen for %lld bytes", (long long)sb.st_size * 4);
/* Since we can call ourselves recursively, keep notes on where we came from */
if (!getenv("_TOP"))
setenv("_TOP", where_to, 1);
if (unpack(pkg_fullname, extract)) {
warnx(
"unable to extract table of contents file from '%s' - not a package?",
pkg_fullname);
goto bomb;
}
cfile = fopen(CONTENTS_FNAME, "r");
if (!cfile) {
warnx(
"unable to open table of contents file '%s' - not a package?",
CONTENTS_FNAME);
goto bomb;
}
read_plist(&Plist, cfile);
fclose(cfile);
/* Extract directly rather than moving? Oh goodie! */
if (find_plist_option(&Plist, "extract-in-place")) {
if (Verbose)
printf("Doing in-place extraction for %s\n", pkg_fullname);
p = find_plist(&Plist, PLIST_CWD);
if (p) {
if (!isdir(p->name) && !Fake) {
if (Verbose)
printf("Desired prefix of %s does not exist, creating..\n", p->name);
vsystem("/bin/mkdir -p %s", p->name);
if (chdir(p->name) == -1) {
warn("unable to change directory to '%s'", p->name);
goto bomb;
}
}
where_to = p->name;
inPlace = 1;
}
else {
warnx(
"no prefix specified in '%s' - this is a bad package!",
pkg_fullname);
goto bomb;
}
}
/*
* Apply a crude heuristic to see how much space the package will
* take up once it's unpacked. I've noticed that most packages
* compress an average of 75%, so multiply by 4 for good measure.
*/
if (!extract && !inPlace && min_free(playpen) < sb.st_size * 4) {
warnx("projected size of %lld exceeds available free space.\n"
"Please set your PKG_TMPDIR variable to point to a location with more\n"
"free space and try again", (long long)sb.st_size * 4);
warnx("not extracting %s\ninto %s, sorry!",
pkg_fullname, where_to);
goto bomb;
}
/* If this is a direct extract and we didn't want it, stop now */
if (inPlace && Fake)
goto success;
/* Finally unpack the whole mess. If extract is null we
already + did so so don't bother doing it again. */
if (extract && unpack(pkg_fullname, NULL)) {
warnx("unable to extract '%s'!", pkg_fullname);
goto bomb;
}
}
/* Check for sanity and dependencies */
if (sanity_check(pkg))
goto bomb;
/* If we're running in MASTER mode, just output the plist and return */
if (AddMode == MASTER) {
printf("%s\n", where_playpen());
write_plist(&Plist, stdout);
return 0;
}
}
/*
* If we have a prefix, delete the first one we see and add this
* one in place of it.
*/
if (Prefix) {
delete_plist(&Plist, FALSE, PLIST_CWD, NULL);
add_plist_top(&Plist, PLIST_CWD, Prefix);
}
setenv(PKG_PREFIX_VNAME, (p = find_plist(&Plist, PLIST_CWD)) ? p->name : ".", 1);
/* Protect against old packages with bogus @name and origin fields */
if (Plist.name == NULL)
Plist.name = "anonymous";
if (Plist.origin == NULL)
Plist.origin = "anonymous/anonymous";
/*
* See if we're already registered either with the same name (the same
* version) or some other version with the same origin.
*/
if ((isinstalledpkg(Plist.name) > 0 ||
matchbyorigin(Plist.origin, NULL) != NULL) && !Force) {
warnx("package '%s' or its older version already installed%s",
Plist.name, FailOnAlreadyInstalled ? "" : " (ignored)");
code = FailOnAlreadyInstalled != FALSE;
goto success; /* close enough for government work */
}
/* Now check the packing list for conflicts */
if (!IgnoreDeps){
for (p = Plist.head; p != NULL; p = p->next) {
if (p->type == PLIST_CONFLICTS) {
int i;
conflict[0] = strdup(p->name);
conflict[1] = NULL;
matched = matchinstalled(MATCH_GLOB, conflict, &errcode);
free(conflict[0]);
if (errcode == 0 && matched != NULL)
for (i = 0; matched[i] != NULL; i++)
if (isinstalledpkg(matched[i]) > 0) {
warnx("package '%s' conflicts with %s", Plist.name,
matched[i]);
conflictsfound = 1;
}
continue;
}
}
if(conflictsfound) {
if(!Force) {
warnx("please use pkg_delete first to remove conflicting package(s) or -f to force installation");
code = 1;
goto bomb;
} else
warnx("-f specified; proceeding anyway");
}
#if ENSURE_THAT_ALL_REQUIREMENTS_ARE_MET
/*
* Before attempting to do the slave mode bit, ensure that we've
* downloaded & processed everything we need.
* It's possible that we haven't already installed all of our
* dependencies if the dependency list was misgenerated due to
* other dynamic dependencies or if a dependency was added to a
* package without all REQUIRED_BY packages being regenerated.
*/
for (p = pkg ? Plist.head : NULL; p; p = p->next) {
const char *ext;
char *deporigin;
if (p->type != PLIST_PKGDEP)
continue;
deporigin = (p->next->type == PLIST_DEPORIGIN) ? p->next->name : NULL;
if (isinstalledpkg(p->name) <= 0 &&
!(deporigin != NULL && matchbyorigin(deporigin, NULL) != NULL)) {
char subpkg[FILENAME_MAX], *sep;
strlcpy(subpkg, pkg, sizeof subpkg);
if ((sep = strrchr(subpkg, '/')) != NULL) {
*sep = '\0';
if ((sep = strrchr(subpkg, '/')) != NULL) {
*sep = '\0';
strlcat(subpkg, "/All/", sizeof subpkg);
strlcat(subpkg, p->name, sizeof subpkg);
if ((ext = strrchr(pkg, '.')) == NULL) {
if (getenv("PACKAGESUFFIX"))
ext = getenv("PACKAGESUFFIX");
else
ext = ".tbz";
}
strlcat(subpkg, ext, sizeof subpkg);
pkg_do(subpkg);
}
}
}
}
#endif
/* Now check the packing list for dependencies */
for (p = Plist.head; p ; p = p->next) {
char *deporigin;
if (p->type != PLIST_PKGDEP)
continue;
deporigin = (p->next->type == PLIST_DEPORIGIN) ? p->next->name : NULL;
if (Verbose) {
printf("Package '%s' depends on '%s'", Plist.name, p->name);
if (deporigin != NULL)
printf(" with '%s' origin", deporigin);
printf(".\n");
}
if (isinstalledpkg(p->name) <= 0 &&
!(deporigin != NULL && matchbyorigin(deporigin, NULL) != NULL)) {
char path[FILENAME_MAX];
const char *cp = NULL;
if (!Fake) {
char prefixArg[2 + MAXPATHLEN]; /* "-P" + Prefix */
if (PrefixRecursive) {
strlcpy(prefixArg, "-P", sizeof(prefixArg));
strlcat(prefixArg, Prefix, sizeof(prefixArg));
}
if (!isURL(pkg) && !getenv("PKG_ADD_BASE")) {
const char *ext;
ext = strrchr(pkg_fullname, '.');
if (ext == NULL) {
if (getenv("PACKAGESUFFIX")) {
ext = getenv("PACKAGESUFFIX");
} else {
ext = ".tbz";
}
}
snprintf(path, FILENAME_MAX, "%s/%s%s", getenv("_TOP"), p->name, ext);
if (fexists(path))
cp = path;
else
cp = fileFindByPath(pkg, p->name);
if (cp) {
if (Verbose)
printf("Loading it from %s.\n", cp);
if (vsystem("%s %s %s '%s'", PkgAddCmd, Verbose ? "-v " : "", PrefixRecursive ? prefixArg : "", cp)) {
warnx("autoload of dependency '%s' failed%s",
cp, Force ? " (proceeding anyway)" : "!");
if (!Force)
++code;
}
}
else {
warnx("could not find package %s %s",
p->name, Force ? " (proceeding anyway)" : "!");
if (!Force)
++code;
}
}
else if ((cp = fileGetURL(pkg, p->name, KeepPackage)) != NULL) {
if (Verbose)
printf("Finished loading %s via a URL\n", p->name);
if (!fexists("+CONTENTS")) {
warnx("autoloaded package %s has no +CONTENTS file?",
p->name);
if (!Force)
++code;
}
else if (vsystem("(pwd; /bin/cat +CONTENTS) | %s %s %s %s -S", PkgAddCmd, Verbose ? "-v" : "", PrefixRecursive ? prefixArg : "", KeepPackage ? "-K" : "")) {
warnx("pkg_add of dependency '%s' failed%s",
p->name, Force ? " (proceeding anyway)" : "!");
if (!Force)
++code;
}
else if (Verbose)
printf("\t'%s' loaded successfully.\n", p->name);
/* Nuke the temporary playpen */
leave_playpen();
}
}
else {
if (Verbose)
printf("and was not found%s.\n", Force ? " (proceeding anyway)" : "");
else
printf("Package dependency %s for %s not found%s\n", p->name, pkg,
Force ? " (proceeding anyway)" : "!");
if (!Force)
++code;
}
}
else if (Verbose)
printf(" - already installed.\n");
}
} /* if (!IgnoreDeps) */
if (code != 0)
goto bomb;
/* Look for the requirements file */
if ((fd = open(REQUIRE_FNAME, O_RDWR)) != -1) {
fstat(fd, &sb);
fchmod(fd, sb.st_mode | S_IXALL); /* be sure, chmod a+x */
close(fd);
if (Verbose)
printf("Running requirements file first for %s..\n", Plist.name);
if (!Fake && vsystem("./%s %s INSTALL", REQUIRE_FNAME, Plist.name)) {
warnx("package %s fails requirements %s", pkg_fullname,
Force ? "installing anyway" : "- not installed");
if (!Force) {
code = 1;
goto success; /* close enough for government work */
}
}
}
/*
* Test whether to use the old method of passing tokens to installation
* scripts, and set appropriate variables..
*/
if (fexists(POST_INSTALL_FNAME)) {
new_m = 1;
sprintf(post_script, "%s", POST_INSTALL_FNAME);
pre_arg[0] = '\0';
post_arg[0] = '\0';
} else {
if (fexists(INSTALL_FNAME)) {
sprintf(post_script, "%s", INSTALL_FNAME);
sprintf(pre_arg, "PRE-INSTALL");
sprintf(post_arg, "POST-INSTALL");
}
}
/* If we're really installing, and have an installation file, run it */
if (!NoInstall && (fd = open(pre_script, O_RDWR)) != -1) {
fstat(fd, &sb);
fchmod(fd, sb.st_mode | S_IXALL); /* be sure, chmod a+x */
close(fd);
if (Verbose)
printf("Running pre-install for %s..\n", Plist.name);
if (!Fake && vsystem("./%s %s %s", pre_script, Plist.name, pre_arg)) {
warnx("install script returned error status");
unlink(pre_script);
code = 1;
goto success; /* nothing to uninstall yet */
}
}
/* Now finally extract the entire show if we're not going direct */
if (!inPlace && !Fake)
extract_plist(".", &Plist);
if (!Fake && fexists(MTREE_FNAME)) {
if (Verbose)
printf("Running mtree for %s..\n", Plist.name);
p = find_plist(&Plist, PLIST_CWD);
if (Verbose)
printf("mtree -U -f %s -d -e -p %s >%s\n", MTREE_FNAME, p ? p->name : "/", _PATH_DEVNULL);
if (!Fake) {
if (vsystem("/usr/sbin/mtree -U -f %s -d -e -p %s >%s", MTREE_FNAME, p ? p->name : "/", _PATH_DEVNULL))
warnx("mtree returned a non-zero status - continuing");
}
}
/* Run the installation script one last time? */
if (!NoInstall && (fd = open(post_script, O_RDWR)) != -1) {
fstat(fd, &sb);
fchmod(fd, sb.st_mode | S_IXALL); /* be sure, chmod a+x */
close(fd);
if (Verbose)
printf("Running post-install for %s..\n", Plist.name);
if (!Fake && vsystem("./%s %s %s", post_script, Plist.name, post_arg)) {
warnx("install script returned error status");
unlink(post_script);
code = 1;
goto fail;
}
}
/* Time to record the deed? */
if (!NoRecord && !Fake) {
char contents[FILENAME_MAX];
char **depnames = NULL, **deporigins = NULL, ***depmatches;
int i, dep_count = 0;
FILE *contfile;
if (getuid() != 0)
warnx("not running as root - trying to record install anyway");
sprintf(LogDir, "%s/%s", LOG_DIR, Plist.name);
zapLogDir = 1;
if (Verbose)
printf("Attempting to record package into %s..\n", LogDir);
if (make_hierarchy(LogDir, FALSE)) {
warnx("can't record package into '%s', you're on your own!",
LogDir);
bzero(LogDir, FILENAME_MAX);
code = 1;
goto success; /* close enough for government work */
}
/* Make sure pkg_info can read the entry */
fd = open(LogDir, O_RDWR);
fstat(fd, &sb);
fchmod(fd, sb.st_mode | S_IRALL | S_IXALL); /* be sure, chmod a+rx */
close(fd);
move_file(".", DESC_FNAME, LogDir);
move_file(".", COMMENT_FNAME, LogDir);
if (fexists(INSTALL_FNAME))
move_file(".", INSTALL_FNAME, LogDir);
if (fexists(POST_INSTALL_FNAME))
move_file(".", POST_INSTALL_FNAME, LogDir);
if (fexists(DEINSTALL_FNAME))
move_file(".", DEINSTALL_FNAME, LogDir);
if (fexists(POST_DEINSTALL_FNAME))
move_file(".", POST_DEINSTALL_FNAME, LogDir);
if (fexists(REQUIRE_FNAME))
move_file(".", REQUIRE_FNAME, LogDir);
if (fexists(DISPLAY_FNAME))
move_file(".", DISPLAY_FNAME, LogDir);
if (fexists(MTREE_FNAME))
move_file(".", MTREE_FNAME, LogDir);
sprintf(contents, "%s/%s", LogDir, CONTENTS_FNAME);
contfile = fopen(contents, "w");
if (!contfile) {
warnx("can't open new contents file '%s'! can't register pkg",
contents);
goto success; /* can't log, but still keep pkg */
}
write_plist(&Plist, contfile);
fclose(contfile);
for (p = Plist.head; p ; p = p->next) {
char *deporigin;
if (p->type != PLIST_PKGDEP)
continue;
deporigin = (p->next->type == PLIST_DEPORIGIN) ? p->next->name :
NULL;
if (Verbose) {
printf("Trying to record dependency on package '%s'", p->name);
if (deporigin != NULL)
printf(" with '%s' origin", deporigin);
printf(".\n");
}
if (deporigin) {
/* Defer to origin lookup */
depnames = realloc(depnames, (dep_count + 1) * sizeof(*depnames));
depnames[dep_count] = p->name;
deporigins = realloc(deporigins, (dep_count + 2) * sizeof(*deporigins));
deporigins[dep_count] = deporigin;
deporigins[dep_count + 1] = NULL;
dep_count++;
} else {
/* No origin recorded, try to register on literal package name */
sprintf(contents, "%s/%s/%s", LOG_DIR, p->name,
REQUIRED_BY_FNAME);
contfile = fopen(contents, "a");
if (!contfile) {
warnx("can't open dependency file '%s'!\n"
"dependency registration is incomplete", contents);
} else {
fprintf(contfile, "%s\n", Plist.name);
if (fclose(contfile) == EOF) {
warnx("cannot properly close file %s", contents);
}
}
}
}
if (dep_count > 0) {
depmatches = matchallbyorigin((const char **)deporigins, NULL);
free(deporigins);
if (!IgnoreDeps && depmatches) {
for (i = 0; i < dep_count; i++) {
if (depmatches[i]) {
int j;
char **tmp = depmatches[i];
for (j = 0; tmp[j] != NULL; j++) {
/* Origin looked up */
sprintf(contents, "%s/%s/%s", LOG_DIR, tmp[j],
REQUIRED_BY_FNAME);
if (depnames[i] && strcmp(depnames[i], tmp[j]) != 0)
warnx("warning: package '%s' requires '%s', but '%s' "
"is installed", Plist.name, depnames[i], tmp[j]);
contfile = fopen(contents, "a");
if (!contfile) {
warnx("can't open dependency file '%s'!\n"
"dependency registration is incomplete", contents);
} else {
fprintf(contfile, "%s\n", Plist.name);
if (fclose(contfile) == EOF)
warnx("cannot properly close file %s", contents);
}
}
} else if (depnames[i]) {
/* No package present with this origin, try literal package name */
sprintf(contents, "%s/%s/%s", LOG_DIR, depnames[i],
REQUIRED_BY_FNAME);
contfile = fopen(contents, "a");
if (!contfile) {
warnx("can't open dependency file '%s'!\n"
"dependency registration is incomplete", contents);
} else {
fprintf(contfile, "%s\n", Plist.name);
if (fclose(contfile) == EOF) {
warnx("cannot properly close file %s", contents);
}
}
}
}
}
}
if (Verbose)
printf("Package %s registered in %s\n", Plist.name, LogDir);
}
if ((p = find_plist(&Plist, PLIST_DISPLAY)) != NULL) {
FILE *fp;
char buf[BUFSIZ];
snprintf(buf, sizeof buf, "%s/%s", LogDir, p->name);
fp = fopen(buf, "r");
if (fp) {
putc('\n', stdout);
while (fgets(buf, sizeof(buf), fp))
fputs(buf, stdout);
putc('\n', stdout);
(void) fclose(fp);
} else {
if (!Fake) {
warnx("cannot open %s as display file", buf);
}
}
}
goto success;
bomb:
code = 1;
goto success;
fail:
/* Nuke the whole (installed) show, XXX but don't clean directories */
if (!Fake)
delete_package(FALSE, FALSE, &Plist);
success:
/* delete the packing list contents */
free_plist(&Plist);
leave_playpen();
return code;
}
int
pkg_perform(char **pkgs)
{
static const char *home;
char *pkg = *pkgs; /* Only one arg to create */
char *cp;
FILE *pkg_in, *fp;
Package plist;
int len;
const char *suf;
/* Preliminary setup */
if (InstalledPkg == NULL)
sanity_check();
if (Verbose && !PlistOnly)
printf("Creating package %s\n", pkg);
/* chop suffix off if already specified, remembering if we want to compress */
len = strlen(pkg);
if (len > 4) {
if (!strcmp(&pkg[len - 4], ".tbz")) {
Zipper = BZIP2;
pkg[len - 4] = '\0';
}
else if (!strcmp(&pkg[len - 4], ".tgz")) {
Zipper = GZIP;
pkg[len - 4] = '\0';
}
else if (!strcmp(&pkg[len - 4], ".txz")) {
Zipper = XZ;
pkg[len - 4] = '\0';
}
else if (!strcmp(&pkg[len - 4], ".tar")) {
Zipper = NONE;
pkg[len - 4] = '\0';
}
}
if (Zipper == BZIP2) {
suf = "tbz";
setenv("BZIP2", "--best", 0);
} else if (Zipper == GZIP) {
suf = "tgz";
setenv("GZIP", "-9", 0);
} else if (Zipper == XZ) {
suf = "txz";
} else
suf = "tar";
if (InstalledPkg != NULL) {
char *pkgglob[] = { InstalledPkg, NULL };
char **matched, **pkgs;
int i, error;
pkgs = pkgglob;
if (MatchType != MATCH_EXACT) {
matched = matchinstalled(MatchType, pkgs, &error);
if (!error && matched != NULL)
pkgs = matched;
else if (MatchType != MATCH_GLOB)
errx(1, "no packages match pattern");
}
/*
* Is there is only one installed package matching the pattern,
* we need to respect the optional pkg-filename parameter. If,
* however, the pattern matches several packages, this parameter
* makes no sense and is ignored.
*/
if (pkgs[1] == NULL) {
if (pkg == InstalledPkg)
pkg = *pkgs;
InstalledPkg = *pkgs;
if (!Recursive)
return (create_from_installed(InstalledPkg, pkg, suf));
return (create_from_installed_recursive(pkg, suf));
}
for (i = 0; pkgs[i] != NULL; i++) {
InstalledPkg = pkg = pkgs[i];
if (!Recursive)
create_from_installed(pkg, pkg, suf);
else
create_from_installed_recursive(pkg, suf);
}
return TRUE;
}
get_dash_string(&Comment);
get_dash_string(&Desc);
if (!strcmp(Contents, "-"))
pkg_in = stdin;
else {
pkg_in = fopen(Contents, "r");
if (!pkg_in) {
cleanup(0);
errx(2, "%s: unable to open contents file '%s' for input",
__func__, Contents);
}
}
plist.head = plist.tail = NULL;
/* Stick the dependencies, if any, at the top */
if (Pkgdeps) {
char **deps, *deporigin;
int i;
int ndeps = 0;
if (Verbose && !PlistOnly)
printf("Registering depends:");
/* Count number of dependencies */
for (cp = Pkgdeps; cp != NULL && *cp != '\0';
cp = strpbrk(++cp, " \t\n")) {
ndeps++;
}
if (ndeps != 0) {
/* Create easy to use NULL-terminated list */
deps = alloca(sizeof(*deps) * ndeps + 1);
if (deps == NULL) {
errx(2, "%s: alloca() failed", __func__);
/* Not reached */
}
for (i = 0; Pkgdeps;) {
cp = strsep(&Pkgdeps, " \t\n");
if (*cp) {
deps[i] = cp;
i++;
}
}
ndeps = i;
deps[ndeps] = NULL;
sortdeps(deps);
for (i = 0; i < ndeps; i++) {
deporigin = strchr(deps[i], ':');
if (deporigin != NULL) {
*deporigin = '\0';
add_plist_top(&plist, PLIST_DEPORIGIN, ++deporigin);
}
add_plist_top(&plist, PLIST_PKGDEP, deps[i]);
if (Verbose && !PlistOnly)
printf(" %s", deps[i]);
}
}
if (Verbose && !PlistOnly)
printf(".\n");
}
/* Put the conflicts directly after the dependencies, if any */
if (Conflicts) {
if (Verbose && !PlistOnly)
printf("Registering conflicts:");
while (Conflicts) {
cp = strsep(&Conflicts, " \t\n");
if (*cp) {
add_plist(&plist, PLIST_CONFLICTS, cp);
if (Verbose && !PlistOnly)
printf(" %s", cp);
}
}
if (Verbose && !PlistOnly)
printf(".\n");
}
/* If a SrcDir override is set, add it now */
if (SrcDir) {
if (Verbose && !PlistOnly)
printf("Using SrcDir value of %s\n", SrcDir);
add_plist(&plist, PLIST_SRC, SrcDir);
}
/* Slurp in the packing list */
read_plist(&plist, pkg_in);
/* Prefix should add an @cwd to the packing list */
if (Prefix) {
char resolved_prefix[PATH_MAX];
if (realpath(Prefix, resolved_prefix) == NULL)
err(EXIT_FAILURE, "couldn't resolve path for prefix: %s", Prefix);
add_plist_top(&plist, PLIST_CWD, resolved_prefix);
}
/* Add the origin if asked, at the top */
if (Origin)
add_plist_top(&plist, PLIST_ORIGIN, Origin);
/*
* Run down the list and see if we've named it, if not stick in a name
* at the top.
*/
if (find_plist(&plist, PLIST_NAME) == NULL)
add_plist_top(&plist, PLIST_NAME, basename(pkg));
if (asprintf(&cp, "PKG_FORMAT_REVISION:%d.%d", PLIST_FMT_VER_MAJOR,
PLIST_FMT_VER_MINOR) == -1) {
errx(2, "%s: asprintf() failed", __func__);
}
add_plist_top(&plist, PLIST_COMMENT, cp);
free(cp);
/*
* We're just here for to dump out a revised plist for the FreeBSD ports
* hack. It's not a real create in progress.
*/
if (PlistOnly) {
check_list(home, &plist);
write_plist(&plist, stdout);
exit(0);
}
/* Make a directory to stomp around in */
home = make_playpen(PlayPen, 0);
signal(SIGINT, cleanup);
signal(SIGHUP, cleanup);
/* Make first "real contents" pass over it */
check_list(home, &plist);
(void) umask(022); /*
* Make sure gen'ed directories, files don't have
* group or other write bits.
*/
/* copy_plist(home, &plist); */
/* mark_plist(&plist); */
/* Now put the release specific items in */
if (!Prefix) {
add_plist(&plist, PLIST_CWD, ".");
}
write_file(COMMENT_FNAME, Comment);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, COMMENT_FNAME);
add_cksum(&plist, plist.tail, COMMENT_FNAME);
write_file(DESC_FNAME, Desc);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, DESC_FNAME);
add_cksum(&plist, plist.tail, DESC_FNAME);
if (Install) {
copy_file(home, Install, INSTALL_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, INSTALL_FNAME);
add_cksum(&plist, plist.tail, INSTALL_FNAME);
}
if (PostInstall) {
copy_file(home, PostInstall, POST_INSTALL_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, POST_INSTALL_FNAME);
add_cksum(&plist, plist.tail, POST_INSTALL_FNAME);
}
if (DeInstall) {
copy_file(home, DeInstall, DEINSTALL_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, DEINSTALL_FNAME);
add_cksum(&plist, plist.tail, DEINSTALL_FNAME);
}
if (PostDeInstall) {
copy_file(home, PostDeInstall, POST_DEINSTALL_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, POST_DEINSTALL_FNAME);
add_cksum(&plist, plist.tail, POST_DEINSTALL_FNAME);
}
if (Require) {
copy_file(home, Require, REQUIRE_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, REQUIRE_FNAME);
add_cksum(&plist, plist.tail, REQUIRE_FNAME);
}
if (Display) {
copy_file(home, Display, DISPLAY_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, DISPLAY_FNAME);
add_cksum(&plist, plist.tail, DISPLAY_FNAME);
add_plist(&plist, PLIST_DISPLAY, DISPLAY_FNAME);
}
if (Mtree) {
copy_file(home, Mtree, MTREE_FNAME);
add_plist(&plist, PLIST_IGNORE, NULL);
add_plist(&plist, PLIST_FILE, MTREE_FNAME);
add_cksum(&plist, plist.tail, MTREE_FNAME);
add_plist(&plist, PLIST_MTREE, MTREE_FNAME);
}
/* Finally, write out the packing list */
fp = fopen(CONTENTS_FNAME, "w");
if (!fp) {
cleanup(0);
errx(2, "%s: can't open file %s for writing",
__func__, CONTENTS_FNAME);
}
write_plist(&plist, fp);
if (fclose(fp)) {
cleanup(0);
errx(2, "%s: error while closing %s",
__func__, CONTENTS_FNAME);
}
/* And stick it into a tar ball */
make_dist(home, pkg, suf, &plist);
/* Cleanup */
free(Comment);
free(Desc);
free_plist(&plist);
leave_playpen();
return TRUE; /* Success */
}
int main(int argc, char *argv[]){
int n_species;
int n_load;
int n_used;
int flag_used[N_GADGET_TYPE];
char species_name[256];
double h_Hubble;
double n_spec;
double redshift;
int i_species;
char n_string[64];
int n[3];
double L[3];
FILE *fp_1D;
FILE *fp_2D;
cosmo_info *cosmo;
field_info *field[N_GADGET_TYPE];
field_info *field_norm[N_GADGET_TYPE];
plist_info plist_header;
plist_info plist;
FILE *fp;
int i_temp;
int n_temp;
double *k_temp;
double *kmin_temp;
double *kmax_temp;
double *P_temp;
size_t *n_mode_temp;
double *sigma_P_temp;
double *shot_noise_temp;
double *dP_temp;
int snapshot_number;
int i_compute;
int distribution_scheme;
double k_min_1D;
double k_max_1D;
double k_min_2D;
double k_max_2D;
int n_k_1D;
int n_k_2D;
double *k_1D;
double *P_k_1D;
double *dP_k_1D;
int *n_modes_1D;
double *P_k_2D;
double *dP_k_2D;
int *n_modes_2D;
int n_groups=1;
double dk_1D;
double dk_2D;
char *grid_identifier;
// Initialization -- MPI etc.
SID_init(&argc,&argv,NULL,NULL);
// Parse arguments
int grid_size;
char filename_in_root[MAX_FILENAME_LENGTH];
char filename_out_root[MAX_FILENAME_LENGTH];
strcpy(filename_in_root, argv[1]);
snapshot_number=(int)atoi(argv[2]);
strcpy(filename_out_root, argv[3]);
grid_size =(int)atoi(argv[4]);
if(!strcmp(argv[5],"ngp") || !strcmp(argv[5],"NGP"))
distribution_scheme=MAP2GRID_DIST_NGP;
else if(!strcmp(argv[5],"cic") || !strcmp(argv[5],"CIC"))
distribution_scheme=MAP2GRID_DIST_CIC;
else if(!strcmp(argv[5],"tsc") || !strcmp(argv[5],"TSC"))
distribution_scheme=MAP2GRID_DIST_TSC;
else if(!strcmp(argv[5],"d12") || !strcmp(argv[5],"D12"))
distribution_scheme=MAP2GRID_DIST_DWT12;
else if(!strcmp(argv[5],"d20") || !strcmp(argv[5],"D20"))
distribution_scheme=MAP2GRID_DIST_DWT20;
else
SID_trap_error("Invalid distribution scheme {%s} specified.",ERROR_SYNTAX,argv[5]);
SID_log("Smoothing Gadget file {%s;snapshot=#%d} to a %dx%dx%d grid with %s kernel...",SID_LOG_OPEN|SID_LOG_TIMER,
filename_in_root,snapshot_number,grid_size,grid_size,grid_size,argv[5]);
// Initialization -- fetch header info
SID_log("Reading Gadget header...",SID_LOG_OPEN);
gadget_read_info fp_gadget;
int flag_filefound=init_gadget_read(filename_in_root,snapshot_number,&fp_gadget);
int flag_multifile=fp_gadget.flag_multifile;
int flag_file_type=fp_gadget.flag_file_type;
gadget_header_info header =fp_gadget.header;
double box_size =(double)(header.box_size);
size_t *n_all =(size_t *)SID_calloc(sizeof(size_t)*N_GADGET_TYPE);
size_t n_total;
if(flag_filefound){
if(SID.I_am_Master){
FILE *fp_in;
char filename[MAX_FILENAME_LENGTH];
int block_length_open;
int block_length_close;
set_gadget_filename(&fp_gadget,0,filename);
fp_in=fopen(filename,"r");
fread_verify(&block_length_open, sizeof(int),1,fp_in);
fread_verify(&header, sizeof(gadget_header_info),1,fp_in);
fread_verify(&block_length_close,sizeof(int),1,fp_in);
fclose(fp_in);
if(block_length_open!=block_length_close)
SID_trap_error("Block lengths don't match (ie. %d!=%d).",ERROR_LOGIC,block_length_open,block_length_close);
}
SID_Bcast(&header,sizeof(gadget_header_info),MASTER_RANK,SID.COMM_WORLD);
redshift=header.redshift;
h_Hubble=header.h_Hubble;
box_size=header.box_size;
if(SID.n_proc>1)
n_load=1;
else
n_load=header.n_files;
for(i_species=0,n_total=0,n_used=0;i_species<N_GADGET_TYPE;i_species++){
n_all[i_species]=(size_t)header.n_all_lo_word[i_species]+((size_t)header.n_all_hi_word[i_species])<<32;
n_total+=n_all[i_species];
if(n_all[i_species]>0){
n_used++;
flag_used[i_species]=TRUE;
}
else
flag_used[i_species]=FALSE;
}
// Initialize cosmology
double box_size =((double *)ADaPS_fetch(plist.data,"box_size"))[0];
double h_Hubble =((double *)ADaPS_fetch(plist.data,"h_Hubble"))[0];
double redshift =((double *)ADaPS_fetch(plist.data,"redshift"))[0];
double expansion_factor=((double *)ADaPS_fetch(plist.data,"expansion_factor"))[0];
double Omega_M =((double *)ADaPS_fetch(plist.data,"Omega_M"))[0];
double Omega_Lambda =((double *)ADaPS_fetch(plist.data,"Omega_Lambda"))[0];
double Omega_k =1.-Omega_Lambda-Omega_M;
double Omega_b=0.; // not needed, so doesn't matter
double f_gas =Omega_b/Omega_M;
double sigma_8=0.; // not needed, so doesn't matter
double n_spec =0.; // not needed, so doesn't matter
char cosmo_name[16];
sprintf(cosmo_name,"Gadget file's");
init_cosmo(&cosmo,
cosmo_name,
Omega_Lambda,
Omega_M,
Omega_k,
Omega_b,
f_gas,
h_Hubble,
sigma_8,
n_spec);
}
SID_log("Done.",SID_LOG_CLOSE);
grid_identifier=(char *)SID_calloc(GRID_IDENTIFIER_SIZE*sizeof(char));
// Only process if there are >0 particles present
if(n_used>0){
// Loop over ithe real-space and 3 redshift-space frames
int i_write;
int i_run;
int n_run;
int n_grids_total;
n_grids_total=4; // For now, hard-wire real-space density and velocity grids only
n_run=1; // For now, hard-wire real-space calculation only
for(i_run=0,i_write=0;i_run<n_run;i_run++){
// Read catalog
int n_grid;
char i_run_identifier[8];
switch(i_run){
case 0:
SID_log("Processing real-space ...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"r");
n_grid=4;
break;
case 1:
SID_log("Processing v_x redshift space...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"x");
n_grid=1;
break;
case 2:
SID_log("Processing v_y redshift space...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"y");
n_grid=1;
break;
case 3:
SID_log("Processing v_z redsift space...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"z");
n_grid=1;
break;
}
// For each i_run case, loop over the fields we want to produce
int i_grid;
for(i_grid=0;i_grid<n_grid;i_grid++){
char i_grid_identifier[8];
switch(i_grid){
case 0:
SID_log("Processing density grid ...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"rho");
break;
case 1:
SID_log("Processing v_x velocity grid...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"v_x");
break;
case 2:
SID_log("Processing v_y velocity grid...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"v_y");
break;
case 3:
SID_log("Processing v_z velocity grid...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"v_z");
break;
}
// Initialize the field that will hold the grid
int n[]={grid_size,grid_size,grid_size};
double L[]={box_size, box_size, box_size};
int i_init;
for(i_species=0;i_species<N_GADGET_TYPE;i_species++){
if(flag_used[i_species]){
field[i_species] =(field_info *)SID_malloc(sizeof(field_info));
field_norm[i_species]=(field_info *)SID_malloc(sizeof(field_info));
init_field(3,n,L,field[i_species]);
init_field(3,n,L,field_norm[i_species]);
i_init=i_species;
}
else{
field[i_species] =NULL;
field_norm[i_species]=NULL;
}
}
// Loop over all the files that this rank will read
int i_load;
for(i_load=0;i_load<n_load;i_load++){
if(n_load>1)
SID_log("Processing file No. %d of %d...",SID_LOG_OPEN|SID_LOG_TIMER,i_load+1,n_load);
// Initialization -- read gadget file
GBPREAL mass_array[N_GADGET_TYPE];
init_plist(&plist,&((field[i_init])->slab),GADGET_LENGTH,GADGET_MASS,GADGET_VELOCITY);
char filename_root[MAX_FILENAME_LENGTH];
read_gadget_binary_local(filename_in_root,
snapshot_number,
i_run,
i_load,
n_load,
mass_array,
&(field[i_init]->slab),
cosmo,
&plist);
// Generate power spectra
for(i_species=0;i_species<plist.n_species;i_species++){
// Determine how many particles of species i_species there are
if(n_all[i_species]>0){
// Fetch the needed information
size_t n_particles;
size_t n_particles_local;
int flag_alloc_m;
GBPREAL *x_particles_local;
GBPREAL *y_particles_local;
GBPREAL *z_particles_local;
GBPREAL *vx_particles_local;
GBPREAL *vy_particles_local;
GBPREAL *vz_particles_local;
GBPREAL *m_particles_local;
GBPREAL *v_particles_local;
GBPREAL *w_particles_local;
n_particles =((size_t *)ADaPS_fetch(plist.data,"n_all_%s",plist.species[i_species]))[0];
n_particles_local=((size_t *)ADaPS_fetch(plist.data,"n_%s", plist.species[i_species]))[0];
x_particles_local= (GBPREAL *)ADaPS_fetch(plist.data,"x_%s", plist.species[i_species]);
y_particles_local= (GBPREAL *)ADaPS_fetch(plist.data,"y_%s", plist.species[i_species]);
z_particles_local= (GBPREAL *)ADaPS_fetch(plist.data,"z_%s", plist.species[i_species]);
vx_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"vx_%s", plist.species[i_species]);
vy_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"vy_%s", plist.species[i_species]);
vz_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"vz_%s", plist.species[i_species]);
if(ADaPS_exist(plist.data,"M_%s",plist.species[i_species])){
flag_alloc_m=FALSE;
m_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"M_%s",plist.species[i_species]);
}
else{
flag_alloc_m=TRUE;
m_particles_local=(GBPREAL *)SID_malloc(n_particles_local*sizeof(GBPREAL));
int i_particle;
for(i_particle=0;i_particle<n_particles_local;i_particle++)
m_particles_local[i_particle]=mass_array[i_species];
}
// Decide the map_to_grid() mode
int mode;
if(n_load==1)
mode=MAP2GRID_MODE_DEFAULT;
else if(i_load==0 || n_load==1)
mode=MAP2GRID_MODE_DEFAULT|MAP2GRID_MODE_NONORM;
else if(i_load==(n_load-1))
mode=MAP2GRID_MODE_NOCLEAN;
else
mode=MAP2GRID_MODE_NOCLEAN|MAP2GRID_MODE_NONORM;
// Set the array that will weight the grid
field_info *field_i;
field_info *field_norm_i;
double factor;
switch(i_grid){
case 0:
v_particles_local=m_particles_local;
w_particles_local=NULL;
field_i =field[i_species];
field_norm_i =NULL;
mode|=MAP2GRID_MODE_APPLYFACTOR;
factor=pow((double)grid_size/box_size,3.);
break;
case 1:
v_particles_local=vx_particles_local;
w_particles_local=m_particles_local;
field_i =field[i_species];
field_norm_i =field_norm[i_species];
factor=1.;
break;
case 2:
v_particles_local=vy_particles_local;
w_particles_local=m_particles_local;
field_i =field[i_species];
field_norm_i =field_norm[i_species];
factor=1.;
break;
case 3:
v_particles_local=vz_particles_local;
w_particles_local=m_particles_local;
field_i =field[i_species];
field_norm_i =field_norm[i_species];
factor=1.;
break;
}
// Generate grid
map_to_grid(n_particles_local,
x_particles_local,
y_particles_local,
z_particles_local,
v_particles_local,
w_particles_local,
cosmo,
redshift,
distribution_scheme,
factor,
field_i,
field_norm_i,
mode);
if(flag_alloc_m)
SID_free(SID_FARG m_particles_local);
}
}
// Clean-up
free_plist(&plist);
if(n_load>1)
SID_log("Done.",SID_LOG_CLOSE);
} // loop over i_load
// Write results to disk
char filename_out_species[MAX_FILENAME_LENGTH];
init_plist(&plist,NULL,GADGET_LENGTH,GADGET_MASS,GADGET_VELOCITY);
for(i_species=0;i_species<plist.n_species;i_species++){
if(flag_used[i_species]){
sprintf(grid_identifier,"%s_%s_%s",i_grid_identifier,i_run_identifier,plist.species[i_species]);
sprintf(filename_out_species,"%s_%s",filename_out_root,plist.species[i_species]);
write_grid(field[i_species],
filename_out_species,
i_write,
n_grids_total,
distribution_scheme,
grid_identifier,
header.box_size);
free_field(field[i_species]);
free_field(field_norm[i_species]);
SID_free(SID_FARG field[i_species]);
SID_free(SID_FARG field_norm[i_species]);
i_write++;
}
}
// Clean-up
free_plist(&plist);
SID_log("Done.",SID_LOG_CLOSE);
} // loop over i_grid
SID_log("Done.",SID_LOG_CLOSE);
} // loop over i_run
} // if n_used>0
// Clean-up
free_cosmo(&cosmo);
SID_free(SID_FARG grid_identifier);
SID_free(SID_FARG n_all);
SID_log("Done.",SID_LOG_CLOSE);
SID_exit(ERROR_NONE);
}
int main(int argc, char *argv[]) {
int snapshot;
char filename_out[256];
char filename_smooth[256];
char filename_snapshot[256];
char * species_name;
double h_Hubble;
plist_info plist;
size_t i_particle;
int i_species;
int j_species;
int i_rank;
size_t n_particles;
GBPREAL * x_array;
GBPREAL * y_array;
GBPREAL * z_array;
GBPREAL * r_smooth_array;
GBPREAL * rho_array;
GBPREAL * sigma_v_array;
FILE * fp_out;
SID_Init(&argc, &argv, NULL);
strcpy(filename_snapshot, argv[1]);
snapshot = atoi(argv[2]);
strcpy(filename_smooth, argv[3]);
strcpy(filename_out, argv[4]);
SID_log("Creating ascii file {%s} from smmoth files {%s} and snapshot {%s}...",
SID_LOG_OPEN | SID_LOG_TIMER,
filename_out,
filename_smooth,
filename_snapshot);
// Read snapshot files
init_plist(&plist, NULL, GADGET_LENGTH, GADGET_MASS, GADGET_VELOCITY);
read_gadget_binary(filename_snapshot, snapshot, &plist, READ_GADGET_DEFAULT);
read_smooth(&plist, filename_smooth, 0, SMOOTH_DEFAULT);
h_Hubble = ((double *)ADaPS_fetch(plist.data, "h_Hubble"))[0];
// Loop over each species
for(i_species = 0, j_species = 0; i_species < N_GADGET_TYPE; i_species++) {
species_name = plist.species[i_species];
if(ADaPS_exist(plist.data, "n_all_%s", species_name))
n_particles = ((size_t *)ADaPS_fetch(plist.data, "n_all_%s", species_name))[0];
else
n_particles = 0;
// If at least one rank has particles for this species ...
if(n_particles > 0) {
SID_log("Writting %s particles...", SID_LOG_OPEN, species_name);
// ... then fetch arrays ...
n_particles = ((size_t *)ADaPS_fetch(plist.data, "n_%s", species_name))[0];
x_array = (GBPREAL *)ADaPS_fetch(plist.data, "x_%s", species_name);
y_array = (GBPREAL *)ADaPS_fetch(plist.data, "y_%s", species_name);
z_array = (GBPREAL *)ADaPS_fetch(plist.data, "z_%s", species_name);
if(ADaPS_exist(plist.data, "r_smooth_%s", species_name))
r_smooth_array = (GBPREAL *)ADaPS_fetch(plist.data, "r_smooth_%s", species_name);
else
r_smooth_array = NULL;
if(ADaPS_exist(plist.data, "rho_%s", species_name))
rho_array = (GBPREAL *)ADaPS_fetch(plist.data, "rho_%s", species_name);
else
rho_array = NULL;
if(ADaPS_exist(plist.data, "sigma_v_%s", species_name))
sigma_v_array = (GBPREAL *)ADaPS_fetch(plist.data, "sigma_v_%s", species_name);
else
sigma_v_array = NULL;
// ... and write this species' particles
for(i_rank = 0; i_rank < SID.n_proc; i_rank++) {
if(SID.My_rank == i_rank) {
if(j_species == 0 && i_rank == 0)
fp_out = fopen(filename_out, "w");
else
fp_out = fopen(filename_out, "a");
for(i_particle = 0; i_particle < n_particles; i_particle++) {
fprintf(fp_out,
"%2d %11.4le %11.4le %11.4le",
i_species,
(double)x_array[i_particle] * h_Hubble / M_PER_MPC,
(double)y_array[i_particle] * h_Hubble / M_PER_MPC,
(double)z_array[i_particle] * h_Hubble / M_PER_MPC);
if(r_smooth_array != NULL)
fprintf(fp_out, " %10.4le", (double)r_smooth_array[i_particle] * h_Hubble / M_PER_MPC);
if(rho_array != NULL)
fprintf(fp_out, " %10.4le", (double)rho_array[i_particle] / (M_SOL * pow(h_Hubble / M_PER_MPC, 3.)));
if(sigma_v_array != NULL)
fprintf(fp_out, " %10.4le", (double)sigma_v_array[i_particle] * 1e-3);
fprintf(fp_out, "\n");
}
fclose(fp_out);
}
SID_Barrier(SID_COMM_WORLD);
}
j_species++;
SID_log("Done.", SID_LOG_CLOSE);
}
}
// Clean-up
free_plist(&plist);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
static char *
extract_pkgname(int fd)
{
package_t plist;
plist_t *p;
struct archive *a;
struct archive_entry *entry;
char *buf;
ssize_t len;
int r;
a = archive_read_new();
archive_read_support_compression_all(a);
archive_read_support_format_all(a);
if (archive_read_open_fd(a, fd, 1024)) {
warnx("Cannot open binary package: %s",
archive_error_string(a));
archive_read_finish(a);
return NULL;
}
r = archive_read_next_header(a, &entry);
if (r != ARCHIVE_OK) {
warnx("Cannot extract package name: %s",
r == ARCHIVE_EOF ? "EOF" : archive_error_string(a));
archive_read_finish(a);
return NULL;
}
if (strcmp(archive_entry_pathname(entry), "+CONTENTS") != 0) {
warnx("Invalid binary package, doesn't start with +CONTENTS");
archive_read_finish(a);
return NULL;
}
if (archive_entry_size(entry) > SSIZE_MAX - 1) {
warnx("+CONTENTS too large to process");
archive_read_finish(a);
return NULL;
}
len = archive_entry_size(entry);
buf = xmalloc(len + 1);
if (archive_read_data(a, buf, len) != len) {
warnx("Short read when extracing +CONTENTS");
free(buf);
archive_read_finish(a);
return NULL;
}
buf[len] = '\0';
archive_read_finish(a);
parse_plist(&plist, buf);
free(buf);
p = find_plist(&plist, PLIST_NAME);
if (p != NULL) {
buf = xstrdup(p->name);
} else {
warnx("Invalid PLIST: missing @name");
buf = NULL;
}
free_plist(&plist);
if (lseek(fd, 0, SEEK_SET) != 0) {
warn("Cannot seek in archive");
free(buf);
return NULL;
}
return buf;
}
/*
* Assumes CWD is in /var/db/pkg/<pkg>!
*/
static void
check1pkg(const char *pkgdir, int *filecnt, int *pkgcnt)
{
FILE *f;
plist_t *p;
package_t Plist;
char *PkgName, *dirp = NULL, *md5file;
char file[MaxPathSize];
char *content;
content = pkgdb_pkg_file(pkgdir, CONTENTS_FNAME);
f = fopen(content, "r");
if (f == NULL)
err(EXIT_FAILURE, "can't open %s", content);
free(content);
read_plist(&Plist, f);
p = find_plist(&Plist, PLIST_NAME);
if (p == NULL)
errx(EXIT_FAILURE, "Package %s has no @name, aborting.",
pkgdir);
PkgName = p->name;
for (p = Plist.head; p; p = p->next) {
switch (p->type) {
case PLIST_FILE:
if (dirp == NULL) {
warnx("dirp not initialized, please send-pr!");
abort();
}
(void) snprintf(file, sizeof(file), "%s/%s", dirp, p->name);
if (isfile(file) || islinktodir(file)) {
if (p->next && p->next->type == PLIST_COMMENT) {
if (strncmp(p->next->name, CHECKSUM_HEADER, ChecksumHeaderLen) == 0) {
if ((md5file = MD5File(file, NULL)) != NULL) {
/* Mismatch? */
if (strcmp(md5file, p->next->name + ChecksumHeaderLen) != 0)
printf("%s fails MD5 checksum\n", file);
free(md5file);
}
} else if (strncmp(p->next->name, SYMLINK_HEADER, SymlinkHeaderLen) == 0) {
char buf[MaxPathSize + SymlinkHeaderLen];
int cc;
(void) strlcpy(buf, SYMLINK_HEADER, sizeof(buf));
if ((cc = readlink(file, &buf[SymlinkHeaderLen],
sizeof(buf) - SymlinkHeaderLen - 1)) < 0) {
warnx("can't readlink `%s'", file);
} else {
buf[SymlinkHeaderLen + cc] = 0x0;
if (strcmp(buf, p->next->name) != 0) {
printf("symlink (%s) is not same as recorded value, %s: %s\n",
file, buf, p->next->name);
}
}
}
}
(*filecnt)++;
} else if (isbrokenlink(file)) {
warnx("%s: Symlink `%s' exists and is in %s but target does not exist!", PkgName, file, CONTENTS_FNAME);
} else {
warnx("%s: File `%s' is in %s but not on filesystem!", PkgName, file, CONTENTS_FNAME);
}
break;
case PLIST_CWD:
if (strcmp(p->name, ".") != 0)
dirp = p->name;
else
dirp = pkgdb_pkg_dir(pkgdir);
break;
case PLIST_IGNORE:
p = p->next;
break;
case PLIST_SHOW_ALL:
case PLIST_SRC:
case PLIST_CMD:
case PLIST_CHMOD:
case PLIST_CHOWN:
case PLIST_CHGRP:
case PLIST_COMMENT:
case PLIST_NAME:
case PLIST_UNEXEC:
case PLIST_DISPLAY:
case PLIST_PKGDEP:
case PLIST_DIR_RM:
case PLIST_OPTION:
case PLIST_PKGCFL:
case PLIST_BLDDEP:
case PLIST_PKGDIR:
break;
}
}
free_plist(&Plist);
fclose(f);
(*pkgcnt)++;
}
/*
* add1pkg(<pkg>)
* adds the files listed in the +CONTENTS of <pkg> into the
* pkgdb.byfile.db database file in the current package dbdir. It
* returns the number of files added to the database file.
*/
static int
add_pkg(const char *pkgdir, void *vp)
{
FILE *f;
plist_t *p;
package_t Plist;
char *contents;
char *PkgName, *dirp;
char file[MaxPathSize];
struct pkgdb_count *count;
if (!pkgdb_open(ReadWrite))
err(EXIT_FAILURE, "cannot open pkgdb");
count = vp;
++count->packages;
contents = pkgdb_pkg_file(pkgdir, CONTENTS_FNAME);
if ((f = fopen(contents, "r")) == NULL)
errx(EXIT_FAILURE, "%s: can't open `%s'", pkgdir, CONTENTS_FNAME);
free(contents);
read_plist(&Plist, f);
if ((p = find_plist(&Plist, PLIST_NAME)) == NULL) {
errx(EXIT_FAILURE, "Package `%s' has no @name, aborting.", pkgdir);
}
PkgName = p->name;
dirp = NULL;
for (p = Plist.head; p; p = p->next) {
switch(p->type) {
case PLIST_FILE:
if (dirp == NULL) {
errx(EXIT_FAILURE, "@cwd not yet found, please send-pr!");
}
(void) snprintf(file, sizeof(file), "%s/%s", dirp, p->name);
if (!(isfile(file) || islinktodir(file))) {
if (isbrokenlink(file)) {
warnx("%s: Symlink `%s' exists and is in %s but target does not exist!",
PkgName, file, CONTENTS_FNAME);
} else {
warnx("%s: File `%s' is in %s but not on filesystem!",
PkgName, file, CONTENTS_FNAME);
}
} else {
pkgdb_store(file, PkgName);
++count->files;
}
break;
case PLIST_PKGDIR:
add_pkgdir(PkgName, dirp, p->name);
++count->directories;
break;
case PLIST_CWD:
if (strcmp(p->name, ".") != 0)
dirp = p->name;
else
dirp = pkgdb_pkg_dir(pkgdir);
break;
case PLIST_IGNORE:
p = p->next;
break;
case PLIST_SHOW_ALL:
case PLIST_SRC:
case PLIST_CMD:
case PLIST_CHMOD:
case PLIST_CHOWN:
case PLIST_CHGRP:
case PLIST_COMMENT:
case PLIST_NAME:
case PLIST_UNEXEC:
case PLIST_DISPLAY:
case PLIST_PKGDEP:
case PLIST_DIR_RM:
case PLIST_OPTION:
case PLIST_PKGCFL:
case PLIST_BLDDEP:
break;
}
}
free_plist(&Plist);
fclose(f);
pkgdb_close();
return 0;
}
int main(int argc, char *argv[]) {
plist_info plist;
char filename_root[256];
char filename_log[256];
char filename_number[256];
char filename_in_halos[256];
char filename_out_groups[256];
char filename_out_groups_A[256];
char filename_out_groups_B[256];
char filename_out_groups_C[256];
char filename_out_subgroups[256];
char filename_out_subgroups_A[256];
char filename_out_subgroups_B[256];
char filename_out_hierarchy[256];
char filename_out_hierarchy_A[256];
char filename_out_hierarchy_B[256];
char filename_out_particles[256];
char i_match_txt[5];
int n_groups_AHF;
int n_groups;
int n_subgroups;
int n_subgroups_matched;
int n_subgroups_group;
size_t n_particles;
size_t n_particles_in_groups;
size_t n_particles_in_subgroups;
size_t n_particles_AHF_not_used;
int n_particles_temp;
int * n_p_1 = NULL;
int flag_continue;
int flag_long_ids;
int i_match;
int match_id_next;
int * match_id = NULL;
int * match_id_initial = NULL;
FILE * fp = NULL;
FILE * fp_in_halos = NULL;
FILE * fp_out = NULL;
int n_match;
int * id_2 = NULL;
size_t * particle_ids_AHF = NULL;
size_t * particle_ids_AHF_index = NULL;
size_t id_largest;
int id_byte_size;
size_t * group_particles = NULL;
int group_id;
int subgroup_id;
int i_group;
int j_group;
int k_group;
size_t n_particles_AHF;
int * subgroup_size = NULL;
int * hierarchy_level = NULL;
int * hierarchy_match = NULL;
int subgroup_size_max;
int * subgroup_size_list = NULL;
int * subgroup_index_list = NULL;
size_t * subgroup_size_list_index = NULL;
int * group_offsets = NULL;
size_t group_index;
int * group_size = NULL;
int * group_size_AHF = NULL;
int * group_offsets_AHF = NULL;
int max_subgroup_size;
int i_subgroup;
int j_subgroup;
int n_subgroups_group_max;
size_t * group_size_index = NULL;
size_t * match_id_index = NULL;
size_t subgroup_index;
int group_offset;
int subgroup_offset;
int group_count;
size_t * group_particles_index = NULL;
size_t * subgroup_particles = NULL;
int * particle_group = NULL;
size_t * particle_group_index = NULL;
size_t i_particle;
size_t j_particle;
size_t k_particle;
int i_file;
int i_file_start;
int i_file_stop;
size_t * match_index = NULL;
int flag_match_subgroups;
FILE * fp_log = NULL;
FILE * fp_in = NULL;
FILE * fp_out_particles = NULL;
FILE * fp_out_groups = NULL;
FILE * fp_out_groups_A = NULL;
FILE * fp_out_groups_B = NULL;
FILE * fp_out_groups_C = NULL;
FILE * fp_out_subgroups_A = NULL;
FILE * fp_out_subgroups_B = NULL;
FILE * fp_out_hierarchy_A = NULL;
FILE * fp_out_hierarchy_B = NULL;
FILE * fp_test = NULL;
int substructure_level;
int substructure_level_max;
halo_properties_info *properties = NULL;
void * particle_buffer = NULL;
int flag_found;
SID_Init(&argc, &argv, NULL);
strcpy(filename_root, argv[1]);
i_file_start = atoi(argv[2]);
i_file_stop = atoi(argv[3]);
SID_log("Converting files #%d->#%d from AHF to subfind format...", SID_LOG_OPEN | SID_LOG_TIMER, i_file_start, i_file_stop);
sprintf(filename_log, "%s_%dto%d.convert_AHF_log", filename_root, i_file_start, i_file_stop);
// Loop over all files
for(i_file = i_file_start; i_file <= i_file_stop; i_file++) {
SID_log("Processing file #%d...", SID_LOG_OPEN | SID_LOG_TIMER, i_file);
// Read catalogs
if(i_file < 10)
sprintf(filename_number, "00%1d", i_file);
else if(i_file < 100)
sprintf(filename_number, "0%2d", i_file);
else
sprintf(filename_number, "%3d", i_file);
// Read AHF group file
init_plist(&plist, NULL, GADGET_LENGTH, GADGET_MASS, GADGET_VELOCITY);
read_groups_AHF(filename_root, i_file, READ_GROUPS_ALL, &plist, filename_number);
n_groups_AHF = ((int *)ADaPS_fetch(plist.data, "n_groups_%s", filename_number))[0];
n_groups = 0;
n_subgroups = 0;
n_subgroups_matched = 0;
n_subgroups_group = 0;
n_particles = 0;
n_particles_in_groups = 0;
n_particles_in_subgroups = 0;
n_particles_AHF_not_used = 0;
n_subgroups_group_max = 0;
if(n_groups_AHF > 0) {
n_particles_AHF = (size_t)((size_t *)ADaPS_fetch(plist.data, "n_particles_%s", filename_number))[0];
group_size_AHF = (int *)ADaPS_fetch(plist.data, "n_particles_group_%s", filename_number);
group_offsets_AHF = (int *)ADaPS_fetch(plist.data, "particle_offset_group_%s", filename_number);
particle_ids_AHF = (size_t *)ADaPS_fetch(plist.data, "particle_ids_%s", filename_number);
// Find largest id so we know what size to write the ids with
for(i_particle = 0, id_largest = 0; i_particle < n_particles_AHF; i_particle++)
id_largest = GBP_MAX(id_largest, particle_ids_AHF[i_particle]);
if(id_largest > INT_MAX) {
flag_long_ids = GBP_TRUE;
id_byte_size = sizeof(size_t);
} else {
flag_long_ids = GBP_FALSE;
id_byte_size = sizeof(int);
}
// Match AHF groups against themselves to find substructure
match_halos(&plist, NULL, i_file, NULL, 0, &plist, NULL, i_file, NULL, 0, "substructure", MATCH_SUBSTRUCTURE, MATCH_SCORE_RANK_INDEX);
match_id_initial = (int *)ADaPS_fetch(plist.data, "match_substructure");
hierarchy_match = match_id_initial; // Fore readability
// Assign sub-...-sub-structures to parent (ie. top-level) halos
SID_log("Assigning substructures to groups...", SID_LOG_OPEN);
group_size = (int *)SID_malloc(sizeof(int) * n_groups_AHF);
subgroup_size = (int *)SID_malloc(sizeof(int) * n_groups_AHF);
hierarchy_level = (int *)SID_malloc(sizeof(int) * n_groups_AHF);
particle_group = (int *)SID_malloc(sizeof(int) * n_particles_AHF);
for(i_group = 0, i_particle = 0; i_group < n_groups_AHF; i_group++) {
group_size[i_group] = 0;
subgroup_size[i_group] = 0;
for(j_particle = 0; j_particle < group_size_AHF[i_group]; i_particle++, j_particle++)
particle_group[i_particle] = i_group;
}
match_id = (int *)SID_malloc(sizeof(int) * n_groups_AHF);
for(i_group = 0, substructure_level_max = 0; i_group < n_groups_AHF; i_group++) {
substructure_level = 0;
match_id_next = match_id_initial[i_group];
match_id[i_group] = match_id_next;
while(match_id_next >= 0) {
substructure_level++;
match_id[i_group] = match_id_next; // Tie subgroups to their top-level group
match_id_next = match_id_initial[match_id_next];
}
if(match_id[i_group] < 0)
match_id[i_group] = i_group; // Unmatched halos should be matched to themselves
hierarchy_level[i_group] = substructure_level;
substructure_level_max = GBP_MAX(substructure_level, substructure_level_max);
}
// needed? ADaPS_store(&(plist.data),(void *)(match_id),"match_substructure",ADaPS_DEFAULT);
SID_log("Done.", SID_LOG_CLOSE);
// Make sure the deepest substructures are given particle ownership
SID_log("Assigning particles to subgroups...", SID_LOG_OPEN);
merge_sort(
(void *)particle_ids_AHF, (size_t)n_particles_AHF, &particle_ids_AHF_index, SID_SIZE_T, SORT_COMPUTE_INDEX, SORT_COMPUTE_NOT_INPLACE);
for(i_particle = 0, n_particles_AHF_not_used = 0; i_particle < n_particles_AHF; i_particle += k_particle) {
// Count the number of times this particle id is used
j_particle = i_particle;
while(particle_ids_AHF[particle_ids_AHF_index[j_particle]] == particle_ids_AHF[particle_ids_AHF_index[i_particle]] &&
j_particle < (n_particles_AHF - 2))
j_particle++;
if(particle_ids_AHF[particle_ids_AHF_index[j_particle]] == particle_ids_AHF[particle_ids_AHF_index[i_particle]])
j_particle++;
k_particle = j_particle - i_particle;
// Find the deepest substructure using this particle id...
i_group = particle_group[particle_ids_AHF_index[i_particle]];
for(j_particle = 1; j_particle < k_particle; j_particle++) {
j_group = particle_group[particle_ids_AHF_index[i_particle + j_particle]];
if(group_size_AHF[j_group] < group_size_AHF[i_group])
i_group = j_group;
}
// ... and set particle's group to a dummy value if this particle instance is not from the deepest group
for(j_particle = 0, flag_found = GBP_FALSE; j_particle < k_particle; j_particle++) {
if(particle_group[particle_ids_AHF_index[i_particle + j_particle]] != i_group || flag_found) {
particle_group[particle_ids_AHF_index[i_particle + j_particle]] = -1;
n_particles_AHF_not_used++;
} else
flag_found = GBP_TRUE;
}
}
SID_free((void **)&particle_ids_AHF_index);
SID_log("Done.", SID_LOG_CLOSE);
// Generate subgroup_size array
for(i_group = 0; i_group < n_groups_AHF; i_group++)
subgroup_size[i_group] = 0;
for(i_particle = 0; i_particle < n_particles_AHF; i_particle++) {
i_group = particle_group[i_particle];
if(i_group >= 0)
subgroup_size[i_group]++;
}
// Get rid of groups that are too small
for(i_particle = 0; i_particle < n_particles_AHF; i_particle++) {
i_group = particle_group[i_particle];
if(i_group >= 0) {
if(subgroup_size[i_group] < 20) {
n_particles_AHF_not_used++;
particle_group[i_particle] = -1;
}
}
}
// Regenerate subgroup_size array
for(i_group = 0; i_group < n_groups_AHF; i_group++)
subgroup_size[i_group] = 0;
for(i_particle = 0; i_particle < n_particles_AHF; i_particle++) {
i_group = particle_group[i_particle];
if(i_group >= 0)
subgroup_size[i_group]++;
}
// Find the largest subgroup's size
for(i_group = 0, n_subgroups = 0, subgroup_size_max = 0; i_group < n_groups_AHF; i_group++)
subgroup_size_max = GBP_MAX(subgroup_size[i_group], subgroup_size_max);
// Generate group_size array
for(i_group = 0; i_group < n_groups_AHF; i_group++)
group_size[match_id[i_group]] += subgroup_size[i_group]; // update group size
// Sort groups in order of size
merge_sort((void *)group_size, (size_t)n_groups_AHF, &group_size_index, SID_INT, SORT_COMPUTE_INDEX, SORT_COMPUTE_NOT_INPLACE);
merge_sort((void *)match_id, (size_t)n_groups_AHF, &match_id_index, SID_INT, SORT_COMPUTE_INDEX, SORT_COMPUTE_NOT_INPLACE);
// Count groups, subgroups, etc.
SID_log("Counting groups & subgroups...", SID_LOG_OPEN);
for(i_group = 0, n_groups = 0, n_subgroups = 0; i_group < n_groups_AHF; i_group++) {
group_index = group_size_index[n_groups_AHF - i_group - 1];
// Find start of subgroup list for this group
j_group = find_index_int(match_id, group_index, n_groups_AHF, match_id_index);
while(group_index > match_id[match_id_index[j_group]] && j_group < (n_groups_AHF - 2))
j_group++;
if(group_index > match_id[match_id_index[j_group]])
j_group++;
// Count subgroups
n_subgroups_group = 0;
while(match_id[match_id_index[j_group]] == group_index && j_group < (n_groups_AHF - 2)) {
if(subgroup_size[match_id_index[j_group]] > 0)
n_subgroups_group++;
j_group++;
}
if(match_id[match_id_index[j_group]] == group_index) {
if(subgroup_size[match_id_index[j_group]] > 0)
n_subgroups_group++;
j_group++;
}
n_subgroups += n_subgroups_group;
// Largest number of subgroups
n_subgroups_group_max = GBP_MAX(n_subgroups_group_max, n_subgroups_group);
// Count groups
if(n_subgroups_group > 0)
n_groups++;
}
SID_log("Done.", SID_LOG_CLOSE);
}
// Find largest subgroup and count the number of particles in groups
for(i_group = 0, max_subgroup_size = 0, n_particles_in_groups = 0; i_group < n_groups_AHF; i_group++) {
max_subgroup_size = GBP_MAX(max_subgroup_size, subgroup_size[i_group]);
if(subgroup_size[i_group] > 0)
n_particles_in_groups += (size_t)subgroup_size[i_group];
}
// Write some statistics
SID_log("Substructure statistics:", SID_LOG_OPEN);
SID_log("Number of groups =%d", SID_LOG_COMMENT, n_groups);
SID_log("Number of subgroups =%d", SID_LOG_COMMENT, n_subgroups);
SID_log("Max number of subgroups per group=%d", SID_LOG_COMMENT, n_subgroups_group_max);
SID_log("Largest subgroup =%d particles", SID_LOG_COMMENT, subgroup_size_max);
SID_log("Depth of substructure heirarchy =%d levels", SID_LOG_COMMENT, substructure_level_max);
SID_log("Number of AHF particles used =%lld", SID_LOG_COMMENT, n_particles_in_groups);
SID_log("Number of AHF particles NOT used =%lld", SID_LOG_COMMENT, n_particles_AHF_not_used);
SID_log("", SID_LOG_CLOSE | SID_LOG_NOPRINT);
// Open files
SID_set_verbosity(SID_SET_VERBOSITY_RELATIVE, 0);
SID_log("Writing %d groups, %d subgroups and %lld particles to files...",
SID_LOG_OPEN | SID_LOG_TIMER,
n_groups,
n_subgroups,
n_particles_in_groups);
sprintf(filename_out_groups, "%s_%s.catalog_groups", filename_root, filename_number);
sprintf(filename_out_groups_A, "%s_%s.catalog_groups_A", filename_root, filename_number);
sprintf(filename_out_groups_B, "%s_%s.catalog_groups_B", filename_root, filename_number);
sprintf(filename_out_groups_C, "%s_%s.catalog_groups_C", filename_root, filename_number);
sprintf(filename_out_subgroups, "%s_%s.catalog_subgroups", filename_root, filename_number);
sprintf(filename_out_subgroups_A, "%s_%s.catalog_subgroups_A", filename_root, filename_number);
sprintf(filename_out_subgroups_B, "%s_%s.catalog_subgroups_B", filename_root, filename_number);
sprintf(filename_out_hierarchy, "%s_%s.catalog_hierarchy", filename_root, filename_number);
sprintf(filename_out_hierarchy_A, "%s_%s.catalog_hierarchy_A", filename_root, filename_number);
sprintf(filename_out_hierarchy_B, "%s_%s.catalog_hierarchy_B", filename_root, filename_number);
sprintf(filename_out_particles, "%s_%s.catalog_particles", filename_root, filename_number);
fp_out_groups_A = fopen(filename_out_groups_A, "w");
fp_out_groups_B = fopen(filename_out_groups_B, "w");
fp_out_groups_C = fopen(filename_out_groups_C, "w");
fp_out_subgroups_A = fopen(filename_out_subgroups_A, "w");
fp_out_subgroups_B = fopen(filename_out_subgroups_B, "w");
fp_out_hierarchy_A = fopen(filename_out_hierarchy_A, "w");
fp_out_hierarchy_B = fopen(filename_out_hierarchy_B, "w");
fp_out_particles = fopen(filename_out_particles, "w");
// Write headers
fwrite(&n_groups, sizeof(int), 1, fp_out_groups_A);
fwrite(&n_subgroups, sizeof(int), 1, fp_out_subgroups_A);
fwrite(&n_subgroups, sizeof(int), 1, fp_out_hierarchy_A);
fwrite(&id_byte_size, sizeof(int), 1, fp_out_particles);
switch(flag_long_ids) {
case GBP_TRUE:
fwrite(&n_particles_in_groups, sizeof(size_t), 1, fp_out_particles);
break;
default:
n_particles_temp = (int)n_particles_in_groups;
fwrite(&n_particles_temp, sizeof(int), 1, fp_out_particles);
break;
}
// Write files; group and subgroup files in parts (to be concatinated together later)
subgroup_size_list = (int *)SID_malloc(sizeof(int) * n_subgroups_group_max);
subgroup_index_list = (int *)SID_malloc(sizeof(int) * n_subgroups_group_max);
particle_buffer = (void *)SID_malloc(id_byte_size * subgroup_size_max);
subgroup_offset = 0;
group_offset = 0;
for(i_group = n_groups_AHF - 1; i_group >= n_groups_AHF - n_groups; i_group--) {
group_index = group_size_index[i_group];
// Find start of subgroup list for this group
i_subgroup = find_index_int(match_id, group_index, n_groups_AHF, match_id_index);
while(group_index > match_id[match_id_index[i_subgroup]] && i_subgroup < (n_groups_AHF - 2))
i_subgroup++;
if(group_index > match_id[match_id_index[i_subgroup]])
i_subgroup++;
// Create a list of subgroups for this group and sort it by size
n_subgroups_group = 0;
subgroup_index = match_id_index[i_subgroup];
while(match_id[subgroup_index] == group_index && i_subgroup < (n_groups_AHF - 2)) {
if(subgroup_size[subgroup_index] > 0) {
subgroup_size_list[n_subgroups_group] = subgroup_size[subgroup_index];
subgroup_index_list[n_subgroups_group] = (int)subgroup_index;
n_subgroups_group++;
}
i_subgroup++;
subgroup_index = match_id_index[i_subgroup];
}
if(match_id[subgroup_index] == group_index) {
if(subgroup_size[subgroup_index] > 0) {
subgroup_size_list[n_subgroups_group] = subgroup_size[subgroup_index];
subgroup_index_list[n_subgroups_group] = (int)subgroup_index;
n_subgroups_group++;
}
i_subgroup++;
subgroup_index = match_id_index[i_subgroup];
}
merge_sort((void *)subgroup_size_list,
(size_t)n_subgroups_group,
&subgroup_size_list_index,
SID_INT,
SORT_COMPUTE_INDEX,
SORT_COMPUTE_NOT_INPLACE);
// Perform writes for subgroups and particle lists
for(i_subgroup = 0, i_particle = 0; i_subgroup < n_subgroups_group; i_subgroup++) {
j_subgroup = subgroup_index_list[subgroup_size_list_index[n_subgroups_group - i_subgroup - 1]];
// ... subgroups ...
fwrite(&(subgroup_size[j_subgroup]), sizeof(int), 1, fp_out_subgroups_A);
fwrite(&(subgroup_offset), sizeof(int), 1, fp_out_subgroups_B);
fwrite(&(hierarchy_match[j_subgroup]), sizeof(int), 1, fp_out_hierarchy_A);
fwrite(&(hierarchy_level[j_subgroup]), sizeof(int), 1, fp_out_hierarchy_B);
subgroup_offset += subgroup_size[j_subgroup];
// ... and particles
for(j_particle = group_offsets_AHF[j_subgroup], k_particle = 0, i_particle = 0; k_particle < group_size_AHF[j_subgroup];
j_particle++, k_particle++) {
if(particle_group[j_particle] == j_subgroup) {
switch(flag_long_ids) {
case GBP_TRUE:
((size_t *)particle_buffer)[i_particle++] = (size_t)(particle_ids_AHF[j_particle]);
break;
default:
((int *)particle_buffer)[i_particle++] = (int)(particle_ids_AHF[j_particle]);
break;
}
}
}
if(i_particle == subgroup_size[j_subgroup])
fwrite(particle_buffer, id_byte_size, i_particle, fp_out_particles);
else
SID_exit_error("Subgroup size mismatch!", SID_ERROR_LOGIC);
}
SID_free((void **)&subgroup_size_list_index);
// Perform writes for groups
fwrite(&(group_size[group_index]), sizeof(int), 1, fp_out_groups_A);
fwrite(&group_offset, sizeof(int), 1, fp_out_groups_B);
fwrite(&n_subgroups_group, sizeof(int), 1, fp_out_groups_C);
group_offset += group_size[group_index];
}
SID_free((void **)&subgroup_size_list);
SID_free((void **)&subgroup_index_list);
SID_free((void **)&particle_buffer);
fclose(fp_out_groups_A);
fclose(fp_out_groups_B);
fclose(fp_out_groups_C);
fclose(fp_out_subgroups_A);
fclose(fp_out_subgroups_B);
fclose(fp_out_hierarchy_A);
fclose(fp_out_hierarchy_B);
fclose(fp_out_particles);
// Concatinate group and subgroup temp files into final files
SID_cat_files(filename_out_groups, SID_CAT_CLEAN, 3, filename_out_groups_A, filename_out_groups_B, filename_out_groups_C);
SID_cat_files(filename_out_subgroups, SID_CAT_CLEAN, 2, filename_out_subgroups_A, filename_out_subgroups_B);
SID_cat_files(filename_out_hierarchy, SID_CAT_CLEAN, 2, filename_out_hierarchy_A, filename_out_hierarchy_B);
// Clean-up
SID_free((void **)&subgroup_size);
SID_free((void **)&hierarchy_level);
SID_free((void **)&group_size);
SID_free((void **)&group_size_index);
SID_free((void **)&match_id_index);
free_plist(&plist);
SID_set_verbosity(SID_SET_VERBOSITY_DEFAULT);
SID_log("Done.", SID_LOG_CLOSE);
// Write log file
SID_log("Writing to log file...", SID_LOG_OPEN);
// Write a header for the log file
if(i_file == i_file_start) {
fp_log = fopen(filename_log, "w");
fprintf(fp_log, "# (1): filenumber\n");
fprintf(fp_log, "# (2): n_groups_AHF\n");
fprintf(fp_log, "# (3): n_particles_AHF\n");
fprintf(fp_log, "# (4): n_groups\n");
fprintf(fp_log, "# (5): n_subgroups\n");
fprintf(fp_log, "# (6): max number of subgroups per group\n");
fprintf(fp_log, "# (7): largest subgroup\n");
fprintf(fp_log, "# (8): depth of substructure heirarchy\n");
fprintf(fp_log, "# (9): number of AHF particles used\n");
fprintf(fp_log, "# (10): number of AHF particles NOT used\n");
} else
fp_log = fopen(filename_log, "a");
fprintf(fp_log,
"%4d %9d %12zd %9d %9d %9d %9d %9d %12zd %12zd\n",
i_file,
n_groups_AHF,
n_particles_AHF,
n_groups,
n_subgroups,
n_subgroups_group_max,
subgroup_size_max,
substructure_level_max,
n_particles_in_groups,
n_particles_AHF_not_used);
fclose(fp_log);
SID_log("Done.", SID_LOG_CLOSE);
SID_log("Done.", SID_LOG_CLOSE);
}
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
static
void discrim_bind_delete(Term t, Discrim root, void *object)
{
Discrim end, d2, d3, parent;
Plist tp1, tp2;
Plist dp1, path;
/* First find the correct leaf. path is used to help with */
/* freeing nodes, because nodes don't have parent pointers. */
path = NULL;
end = discrim_bind_end(t, root, &path);
if (end == NULL) {
fatal_error("discrim_bind_delete, cannot find end.");
}
/* Free the pointer in the leaf-list */
tp1 = end->u.data;
tp2 = NULL;
while(tp1 && tp1->v != object) {
tp2 = tp1;
tp1 = tp1->next;
}
if (tp1 == NULL) {
fatal_error("discrim_bind_delete, cannot find term.");
}
if (tp2 == NULL)
end->u.data = tp1->next;
else
tp2->next = tp1->next;
free_plist(tp1);
if (end->u.data == NULL) {
/* free tree nodes from bottom up, using path to get parents */
end->u.kids = NULL; /* probably not necessary */
dp1 = path;
while (end->u.kids == NULL && end != root) {
parent = (Discrim) dp1->v;
dp1 = dp1->next;
d2 = parent->u.kids;
d3 = NULL;
while (d2 != end) {
d3 = d2;
d2 = d2->next;
}
if (d3 == NULL)
parent->u.kids = d2->next;
else
d3->next = d2->next;
free_discrim(d2);
end = parent;
}
}
/* free path list */
while (path) {
dp1 = path;
path = path->next;
free_plist(dp1);
}
} /* discrim_bind_delete */
int main(int argc, char *argv[]) {
SID_Init(&argc, &argv, NULL);
// Fetch user inputs
char filename_halos_root[256];
char filename_catalog_root[256];
char filename_PHKs_root[256];
double box_size;
double dx;
int i_file_lo_in;
int i_file_hi_in;
int i_file_skip;
strcpy(filename_halos_root, argv[1]);
strcpy(filename_catalog_root, argv[2]);
strcpy(filename_PHKs_root, argv[3]);
box_size = atof(argv[4]);
dx = atof(argv[5]);
i_file_lo_in = atoi(argv[6]);
i_file_hi_in = atoi(argv[7]);
i_file_skip = atoi(argv[8]);
int i_file_lo;
int i_file_hi;
if(i_file_lo_in < i_file_hi_in) {
i_file_lo = i_file_lo_in;
i_file_hi = i_file_hi_in;
} else {
i_file_lo = i_file_hi_in;
i_file_hi = i_file_lo_in;
}
SID_log("Generating group PH keys for files #%d->#%d...", SID_LOG_OPEN | SID_LOG_TIMER, i_file_lo, i_file_hi);
for(int i_file = i_file_lo; i_file <= i_file_hi; i_file += i_file_skip) {
SID_log("Processing file #%03d...", SID_LOG_OPEN | SID_LOG_TIMER, i_file);
SID_set_verbosity(SID_SET_VERBOSITY_RELATIVE, 0);
// Read group info from the halo catalogs
plist_info plist;
int * PHK_group = NULL;
size_t * PHK_group_index = NULL;
char * filename_number = (char *)SID_malloc(sizeof(char) * 10);
init_plist(&plist, NULL, GADGET_LENGTH, GADGET_MASS, GADGET_VELOCITY);
sprintf(filename_number, "%03d", i_file);
ADaPS_store(&(plist.data), (void *)filename_number, "read_catalog", ADaPS_DEFAULT);
read_groups(filename_halos_root, i_file, READ_GROUPS_ALL | READ_GROUPS_MBP_IDS_ONLY, &plist, filename_number);
int n_groups_all = ((int *)ADaPS_fetch(plist.data, "n_groups_all_%s", filename_number))[0];
int n_groups = ((int *)ADaPS_fetch(plist.data, "n_groups_%s", filename_number))[0];
// If there's any groups to analyze ...
int * n_particles_groups = NULL;
size_t n_particles_cumulative = 0;
int n_bits = 0; // Default value if there are no groups
if(n_groups > 0) {
// Fetch the halo sizes
n_particles_groups = (int *)ADaPS_fetch(plist.data, "n_particles_group_%s", filename_number);
// Read MBP data from halo catalogs
SID_log("Reading most-bound-particle positions...", SID_LOG_OPEN);
halo_properties_info group_properties;
fp_catalog_info fp_group_properties;
double * x_array = (double *)SID_malloc(sizeof(double) * n_groups);
double * y_array = (double *)SID_malloc(sizeof(double) * n_groups);
double * z_array = (double *)SID_malloc(sizeof(double) * n_groups);
fopen_catalog(filename_catalog_root, i_file, READ_CATALOG_GROUPS | READ_CATALOG_PROPERTIES, &fp_group_properties);
if(fp_group_properties.n_halos_total != n_groups)
SID_exit_error("Halo counts in group files and catalogs don't match (ie. %d!=%d)", SID_ERROR_LOGIC,
fp_group_properties.n_halos_total, n_groups);
for(int i_group = 0; i_group < n_groups; i_group++) {
fread_catalog_file(&fp_group_properties, NULL, NULL, &group_properties, NULL, i_group);
x_array[i_group] = group_properties.position_MBP[0];
y_array[i_group] = group_properties.position_MBP[1];
z_array[i_group] = group_properties.position_MBP[2];
// Enforce periodic BCs
if(x_array[i_group] < 0.)
x_array[i_group] += box_size;
if(x_array[i_group] >= box_size)
x_array[i_group] -= box_size;
if(y_array[i_group] < 0.)
y_array[i_group] += box_size;
if(y_array[i_group] >= box_size)
y_array[i_group] -= box_size;
if(z_array[i_group] < 0.)
z_array[i_group] += box_size;
if(z_array[i_group] >= box_size)
z_array[i_group] -= box_size;
}
fclose_catalog(&fp_group_properties);
SID_log("Done.", SID_LOG_CLOSE);
// Determine the number of bits to use for the PHKs
for(n_bits = N_BITS_MIN; (box_size / pow(2., (double)(n_bits + 1))) > dx && n_bits <= 20;)
n_bits++;
// Compute PHKs
SID_log("Computing PHKs (using %d bits per dimension)...", SID_LOG_OPEN, n_bits);
PHK_group = (int *)SID_malloc(sizeof(int) * n_groups);
for(int i_group = 0; i_group < n_groups; i_group++) {
// Compute the key for this group
PHK_group[i_group] = compute_PHK_from_Cartesian(
n_bits, 3, (double)x_array[i_group] / box_size, (double)y_array[i_group] / box_size, (double)z_array[i_group] / box_size);
}
SID_free(SID_FARG x_array);
SID_free(SID_FARG y_array);
SID_free(SID_FARG z_array);
SID_log("Done.", SID_LOG_CLOSE);
// Sort PHKs
SID_log("Sorting PHKs...", SID_LOG_OPEN);
merge_sort((void *)PHK_group, n_groups, &PHK_group_index, SID_INT, SORT_COMPUTE_INDEX, GBP_FALSE);
SID_log("Done.", SID_LOG_CLOSE);
// Count the number of particles
for(int i_group = 0; i_group < n_groups; i_group++)
n_particles_cumulative += n_particles_groups[PHK_group_index[i_group]];
}
// Write results
SID_log("Writing results for %d groups...", SID_LOG_OPEN, n_groups);
char filename_output_properties[256];
sprintf(filename_output_properties, "%s_%s.catalog_PHKs", filename_PHKs_root, filename_number);
FILE *fp_PHKs = fopen(filename_output_properties, "w");
fwrite(&n_groups, sizeof(int), 1, fp_PHKs);
fwrite(&n_bits, sizeof(int), 1, fp_PHKs);
fwrite(&n_particles_cumulative, sizeof(size_t), 1, fp_PHKs);
n_particles_cumulative = 0;
for(int i_group = 0; i_group < n_groups; i_group++) {
int index_temp = (int)PHK_group_index[i_group];
n_particles_cumulative += n_particles_groups[index_temp];
fwrite(&(PHK_group[index_temp]), sizeof(int), 1, fp_PHKs);
fwrite(&index_temp, sizeof(int), 1, fp_PHKs);
fwrite(&n_particles_cumulative, sizeof(size_t), 1, fp_PHKs);
}
fclose(fp_PHKs);
SID_log("Done.", SID_LOG_CLOSE);
// Clean-up
free_plist(&plist);
if(n_groups > 0) {
SID_free(SID_FARG PHK_group);
SID_free(SID_FARG PHK_group_index);
}
SID_set_verbosity(SID_SET_VERBOSITY_DEFAULT);
SID_log("Done.", SID_LOG_CLOSE);
}
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}