int main(int argc, char *argv[])
{
#if TRACKMEM
mcheck(CheckFailed);
#endif
CSumItApplication app;
app.Run();
gPrefs->WritePrefFile();
delete gPrefs;
CFontStyle::Cleanup();
#if TRACKMEM
FREE(gFuncs);
FREE(gFuncArrayByName);
FREE(gFuncDescriptions);
FREE(gFuncPasteStrings);
PrintUndisposed();
#endif
return 0;
}
/*
===============
main
===============
*/
int main( int argc, const char** argv )
{
// DG: needed for Sys_ReLaunch()
cmdargc = argc;
cmdargv = argv;
// DG end
#ifdef ID_MCHECK
// must have -lmcheck linkage
mcheck( abrt_func );
Sys_Printf( "memory consistency checking enabled\n" );
#endif
Posix_EarlyInit( );
if( argc > 1 )
{
common->Init( argc - 1, &argv[1], NULL );
}
else
{
common->Init( 0, NULL, NULL );
}
Posix_LateInit( );
while( 1 )
{
common->Frame();
}
}
int
mcheck_pedantic (void (*func) (enum mcheck_status))
{
int res = mcheck (func);
if (res == 0)
pedantic = 1;
return res;
}
list *list_create(int key, int score) {
list *l = (list *) malloc(sizeof(list));
mcheck(l);
l->key = key;
l->score = score;
l->tail = NULL;
return l;
}
/*
* You can ask malloc to check the consistency of dynamic memory by using the mcheck function.
* This function is a GNU extension, declared in mcheck.h.
* Calling mcheck tells malloc to perform occasional consistency checks. These will catch things such as
* writing past the end of a block that was allocated with malloc.
* It is too late to begin allocation checking once you have allocated anything with malloc.
* So mcheck does nothing in that case. The function returns -1 if you call it too late,
* and 0 otherwise (when it is successful).
* function prototype: mcheck (void (*abortfn) (enum mcheck_status status))
*/
void
FC_FUNC_(clib_mcheck,CLIB_MCHECK)
(int* ierr)
{
#ifdef HAVE_MCHECK_H
*ierr = mcheck (NULL);
#else
*ierr = 2;
#endif
}
static void
s_once_proc(void) {
char *a;
uintptr_t b;
#if 0
(void)mcheck(s_mcheck_proc);
#endif
a = (char *)malloc(10);
b = (uintptr_t)sbrk((intptr_t)0);
if (b <= (uintptr_t)&end || (uintptr_t)a >= b) {
s_is_running_under_valgrind = true;
}
free((void *)a);
}
int main()
{
mcheck(0);
nz_rc rc = run();
if(rc != NZ_SUCCESS)
{
fprintf(stderr, "Noise error %d: %s\n", rc, nz_error_rc_str(rc));
fprintf(stderr, "File: %s line %d\n", nz_error_file, nz_error_line);
if(nz_error_string) {
fprintf(stderr, "%s\n", nz_error_string);
nz_free_str(nz_error_string);
}
return 1;
}
return 0;
}
/*
===============
main
===============
*/
int main( int argc, const char **argv ) {
#ifdef ID_MCHECK
// must have -lmcheck linkage
mcheck( abrt_func );
Sys_Printf( "memory consistency checking enabled\n" );
#endif
Posix_EarlyInit( );
if( argc > 1 ) {
common->Init( argc - 1, &argv[1], NULL );
} else {
common->Init( 0, NULL, NULL );
}
Posix_LateInit( );
while( true ) {
common->Frame();
}
}
int
main (void)
{
int * table_int;
int i;
if (mcheck (fonction_d_erreur) != 0) {
perror ("mcheck");
exit (1);
}
fprintf (stdout, "Allocation de la table\n");
table_int = calloc (NB_INT, sizeof (int));
fprintf (stdout, "On déborde vers le haut\n");
for (i = 0; i <= NB_INT; i ++)
table_int [i] = 1;
fprintf (stdout, "Libération de la table\n");
free (table_int);
fprintf (stdout, "Allocation de la table\n");
table_int = calloc (NB_INT, sizeof (int));
fprintf (stdout, "On déborde vers le bas\n");
i = NB_INT;
while (i >= 0)
table_int [--i] = 1;
fprintf (stdout, "Libération de la table\n");
free (table_int);
fprintf (stdout, "Allocation de la table\n");
table_int = calloc (NB_INT, sizeof (int));
fprintf (stdout, "Ecriture normale\n");
for (i = 0; i < NB_INT; i ++)
table_int [i] = 0;
fprintf (stdout, "Libération de la table\n");
free (table_int);
fprintf (stdout, "Et re-libération de la table !\n");
free (table_int);
return (0);
}
/*
* INVOCATION
*
* $0 INPUT-FILENAME OUTPUT-FILENAME
*
* The input file must be in sg0 format; the output file is in sg1 format.
*/
int main(int argc, char **argv)
{
#ifndef NDEBUG
if (mcheck(NULL)) exit(1);
#endif
if (argc != 3) {
fprintf(stderr, "*** Invalid number of arguments\n");
exit(1);
}
const char *filename_in= argv[1];
const char *filename_out= argv[2];
struct sgraph0_reader_a r;
if (0 > sgraph0_open_read_a(filename_in, &r, COLS_ALL)) {
exit(1);
}
if (0 > sgraph0_advise_a(&r, MADV_SEQUENTIAL)) {
perror(filename_in);
goto error_close;
}
struct graph_a g;
graph_read_sgraph0_a(&g, &r);
sgraph0_close_a(&r);
graph_sort_a(&g);
if (0 > sgraph1_write_a(&g, filename_out)) {
exit(1);
}
exit(0);
error_close:
sgraph0_close_a(&r);
exit(1);
}
int main(int argc, char **argv) {
#ifdef MLR_USE_MCHECK
if (mcheck(NULL) != 0) {
printf("Could not set up mcheck\n");
exit(1);
}
printf("Set up mcheck\n");
#endif // MLR_USE_MCHECK
char *result = run_all_tests();
printf("\n");
if (result != 0) {
printf("Not all unit tests passed\n");
}
else {
printf("TEST_LREC: ALL UNIT TESTS PASSED\n");
}
printf("Tests passed: %d of %d\n", tests_run - tests_failed, tests_run);
printf("Assertions passed: %d of %d\n", assertions_run - assertions_failed, assertions_run);
return result != 0;
}
static void
turn_on_mcheck (void)
{
mcheck (NULL);
}
/**
* Test program looping and reading LLDP/CDP packets and exercising most of the packet
* send/receive mechanism and a good bit of nanoprobe and CMA basic infrastructure.
*
* It plays both sides of the game - the CMA and the nanoprobe.
*
* It leaves most of the work of starting up the nanoprobe code to nano_start_full()
*/
int
main(int argc, char **argv)
{
const guint8 loopback[] = CONST_IPV6_LOOPBACK;
//const guint8 mcastaddrstring[] = CONST_ASSIM_DEFAULT_V4_MCAST;
//NetAddr* mcastaddr;
const guint8 otheradstring[] = {127,0,0,1};
const guint8 otheradstring2[] = {10,10,10,4};
const guint8 anyadstring[] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
guint16 testport = TESTPORT;
SignFrame* signature = signframe_glib_new(G_CHECKSUM_SHA256, 0);
Listener* otherlistener;
ConfigContext* config = configcontext_new(0);
PacketDecoder* decoder = nano_packet_decoder();
AuthListener* listentonanoprobes;
ReliableUDP* rtransport;
#if 0
# ifdef HAVE_MCHECK_PEDANTIC
g_assert(mcheck_pedantic(NULL) == 0);
# else
# ifdef HAVE_MCHECK
g_assert(mcheck(NULL) == 0);
# endif
# endif
#endif
g_setenv("G_MESSAGES_DEBUG", "all", TRUE);
#if 0
proj_class_incr_debug(NULL);
proj_class_incr_debug(NULL);
proj_class_incr_debug(NULL);
proj_class_incr_debug(NULL);
#endif
g_log_set_fatal_mask(NULL, G_LOG_LEVEL_ERROR);
if (argc > 1) {
maxpkts = atol(argv[1]);
g_debug("Max packet count is "FMT_64BIT"d", maxpkts);
}
if (netio_is_dual_ipv4v6_stack()) {
g_message("Our OS supports dual ipv4/v6 sockets. Hurray!");
}else{
g_warning("Our OS DOES NOT support dual ipv4/v6 sockets - this may not work!!");
}
config->setframe(config, CONFIGNAME_OUTSIG, &signature->baseclass);
// Create a network transport object for normal UDP packets
rtransport = reliableudp_new(0, config, decoder, 0);
rtransport->_protocol->window_size = 8;
nettransport = &(rtransport->baseclass.baseclass);
g_return_val_if_fail(NULL != nettransport, 2);
// Set up the parameters the 'CMA' is going to send to our 'nanoprobe'
// in response to their request for configuration data.
nanoconfig = configcontext_new(0);
nanoconfig->setint(nanoconfig, CONFIGNAME_INTERVAL, 1);
nanoconfig->setint(nanoconfig, CONFIGNAME_TIMEOUT, 3);
nanoconfig->setint(nanoconfig, CONFIGNAME_CMAPORT, testport);
// Construct the NetAddr we'll talk to (i.e., ourselves) and listen from
destaddr = netaddr_ipv6_new(loopback, testport);
g_return_val_if_fail(NULL != destaddr, 3);
config->setaddr(config, CONFIGNAME_CMAINIT, destaddr);
nanoconfig->setaddr(nanoconfig, CONFIGNAME_CMAADDR, destaddr);
nanoconfig->setaddr(nanoconfig, CONFIGNAME_CMAFAIL, destaddr);
nanoconfig->setaddr(nanoconfig, CONFIGNAME_CMADISCOVER, destaddr);
// Construct another couple of NetAddrs to talk to and listen from
// for good measure...
otheraddr = netaddr_ipv4_new(otheradstring, testport);
g_return_val_if_fail(NULL != otheraddr, 4);
otheraddr2 = netaddr_ipv4_new(otheradstring2, testport);
g_return_val_if_fail(NULL != otheraddr2, 4);
// Construct another NetAddr to bind to (anything)
anyaddr = netaddr_ipv6_new(anyadstring, testport);
g_return_val_if_fail(NULL != destaddr, 5);
// Bind to ANY address (as noted above)
g_return_val_if_fail(nettransport->bindaddr(nettransport, anyaddr, FALSE),16);
//g_return_val_if_fail(nettransport->bindaddr(nettransport, destaddr),16);
g_message("NOT Joining multicast address.");
#if 0
// We can't do this because of encryption and we will likely screw up
// others on our network even if that weren't a problem...
mcastaddr = netaddr_ipv4_new(mcastaddrstring, testport);
g_return_val_if_fail(nettransport->mcastjoin(nettransport, mcastaddr, NULL), 17);
UNREF(mcastaddr);
g_message("multicast join succeeded.");
#endif
// Connect up our network transport into the g_main_loop paradigm
// so we get dispatched when packets arrive
netpkt = netgsource_new(nettransport, NULL, G_PRIORITY_HIGH, FALSE, NULL, 0, NULL);
// Set up so that we can observe all unclaimed packets
otherlistener = listener_new(config, 0);
otherlistener->got_frameset = gotnetpkt;
netpkt->addListener(netpkt, 0, otherlistener);
otherlistener->associate(otherlistener,netpkt);
// Unref the "other" listener - we hold other references to it
UNREF(otherlistener);
// Pretend to be the CMA...
// Listen for packets from our nanoprobes - scattered throughout space...
listentonanoprobes = authlistener_new(0, cmalist, config, TRUE, NULL);
listentonanoprobes->baseclass.associate(&listentonanoprobes->baseclass, netpkt);
nano_start_full("netconfig", 900, netpkt, config, test_cma_authentication);
g_timeout_add_seconds(1, timeout_agent, NULL);
mainloop = g_main_loop_new(g_main_context_default(), TRUE);
/********************************************************************
* Start up the main loop - run our test program...
* (the one pretending to be both the nanoprobe and the CMA)
********************************************************************/
g_main_loop_run(mainloop);
/********************************************************************
* We exited the main loop. Shut things down.
********************************************************************/
nano_shutdown(TRUE); // Tell it to shutdown and print stats
g_message("Count of 'other' pkts received:\t%d", wirepktcount);
UNREF(nettransport);
// Main loop is over - shut everything down, free everything...
g_main_loop_unref(mainloop); mainloop=NULL;
// Unlink misc dispatcher - this should NOT be necessary...
netpkt->addListener(netpkt, 0, NULL);
// Dissociate packet actions from the packet source.
listentonanoprobes->baseclass.dissociate(&listentonanoprobes->baseclass);
// Unref the AuthListener object
UNREF2(listentonanoprobes);
g_source_destroy(&netpkt->baseclass);
g_source_unref(&netpkt->baseclass);
//g_main_context_unref(g_main_context_default());
// Free signature frame
UNREF2(signature);
// Free misc addresses
UNREF(destaddr);
UNREF(otheraddr);
UNREF(otheraddr2);
UNREF(anyaddr);
// Free config object
UNREF(config);
UNREF(nanoconfig);
// At this point - nothing should show up - we should have freed everything
if (proj_class_live_object_count() > 0) {
g_warning("Too many objects (%d) alive at end of test.",
proj_class_live_object_count());
proj_class_dump_live_objects();
++errcount;
}else{
g_message("No objects left alive. Awesome!");
}
proj_class_finalize_sys(); // Shut down object system to make valgrind happy :-D
return(errcount <= 127 ? errcount : 127);
}
void SweepGenblock::BlockAndDecimate (SweepParams &sweepParams, SpinBlock& system, SpinBlock& newSystem, const bool &useSlater, const bool& dot_with_sys, int stateA, int stateB)
{
if (dmrginp.outputlevel() > 0)
mcheck("at the start of block and decimate");
p1out << "\t\t\t Performing Blocking"<<endl;
dmrginp.guessgenT -> start();
// figure out if we are going forward or backwards
bool forward = (system.get_sites() [0] == 0);
SpinBlock systemDot;
int systemDotStart, systemDotEnd;
int systemDotSize = sweepParams.get_sys_add() - 1;
if (forward)
{
systemDotStart = dmrginp.spinAdapted() ? *system.get_sites().rbegin () + 1 : (*system.get_sites().rbegin ())/2 + 1 ;
systemDotEnd = systemDotStart + systemDotSize;
}
else
{
systemDotStart = dmrginp.spinAdapted() ? system.get_sites()[0] - 1 : (system.get_sites()[0])/2 - 1 ;
systemDotEnd = systemDotStart - systemDotSize;
}
vector<int> spindotsites(2);
spindotsites[0] = systemDotStart;
spindotsites[1] = systemDotEnd;
dmrginp.sysdotmake->start();
systemDot = SpinBlock(systemDotStart, systemDotEnd, system.get_integralIndex(), stateA==stateB);
dmrginp.sysdotmake->stop();
const int nexact = forward ? sweepParams.get_forward_starting_size() : sweepParams.get_backward_starting_size();
dmrginp.guessgenT -> stop();
dmrginp.datatransfer -> start();
system.addAdditionalCompOps();
dmrginp.datatransfer -> stop();
dmrginp.initnewsystem->start();
InitBlocks::InitNewSystemBlock(system, systemDot, newSystem, stateA, stateB, sweepParams.get_sys_add(), dmrginp.direct(), system.get_integralIndex(), DISTRIBUTED_STORAGE, dot_with_sys, true);
dmrginp.initnewsystem->stop();
pout << "\t\t\t System Block"<<newSystem;
newSystem.printOperatorSummary();
std::vector<Matrix> leftrotateMatrix, rightrotateMatrix;
LoadRotationMatrix (newSystem.get_sites(), leftrotateMatrix, stateA);
LoadRotationMatrix (newSystem.get_sites(), rightrotateMatrix, stateB);
#ifndef SERIAL
mpi::communicator world;
broadcast(world, leftrotateMatrix, 0);
broadcast(world, rightrotateMatrix, 0);
#endif
p1out <<"\t\t\t Performing Renormalization "<<endl<<endl;
dmrginp.operrotT->start();
if (stateB == stateA)
newSystem.transform_operators(leftrotateMatrix);
else
newSystem.transform_operators(leftrotateMatrix, rightrotateMatrix);
dmrginp.operrotT->stop();
if (dmrginp.outputlevel() > 0)
//mcheck("after rotation and transformation of block");
p2out <<newSystem<<endl;
newSystem.printOperatorSummary();
//mcheck("After renorm transform");
p2out << *dmrginp.guessgenT<<" "<<*dmrginp.multiplierT<<" "<<*dmrginp.operrotT<< " "<<globaltimer.totalwalltime()<<" timer "<<endl;
p2out << *dmrginp.makeopsT<<" "<<*dmrginp.initnewsystem<<" "<<*dmrginp.sysdotmake<<" "<<*dmrginp.buildcsfops<<" makeops "<<endl;
p2out << *dmrginp.datatransfer<<" datatransfer "<<endl;
p2out <<"oneindexopmult twoindexopmult Hc couplingcoeff"<<endl;
p2out << *dmrginp.oneelecT<<" "<<*dmrginp.twoelecT<<" "<<*dmrginp.hmultiply<<" "<<*dmrginp.couplingcoeff<<" hmult"<<endl;
p2out << *dmrginp.buildsumblock<<" "<<*dmrginp.buildblockops<<" build block"<<endl;
p2out << *dmrginp.blockintegrals<<" "<<*dmrginp.blocksites<<" "<<*dmrginp.statetensorproduct<<" "<<*dmrginp.statecollectquanta<<" "<<*dmrginp.buildsumblock<<" "<<*dmrginp.builditeratorsT<<" "<<*dmrginp.diskio<<" build sum block"<<endl;
p2out << "addnoise S_0_opxop S_1_opxop S_2_opxop"<<endl;
p3out << *dmrginp.addnoise<<" "<<*dmrginp.s0time<<" "<<*dmrginp.s1time<<" "<<*dmrginp.s2time<<endl;
}
int main (int argc, char *argv[])
{
errcode_t retval = 0;
int exit_value = FSCK_OK;
ext2_filsys fs = 0;
io_manager io_ptr;
struct ext2_super_block *sb;
const char *lib_ver_date;
int my_ver, lib_ver;
e2fsck_t ctx;
struct problem_context pctx;
int flags, run_result;
clear_problem_context(&pctx);
#ifdef MTRACE
mtrace();
#endif
#ifdef MCHECK
mcheck(0);
#endif
#ifdef ENABLE_NLS
setlocale(LC_MESSAGES, "");
setlocale(LC_CTYPE, "");
bindtextdomain(NLS_CAT_NAME, LOCALEDIR);
textdomain(NLS_CAT_NAME);
#endif
my_ver = ext2fs_parse_version_string(my_ver_string);
lib_ver = ext2fs_get_library_version(0, &lib_ver_date);
if (my_ver > lib_ver) {
fprintf( stderr, _("Error: ext2fs library version "
"out of date!\n"));
show_version_only++;
}
retval = PRS(argc, argv, &ctx);
if (retval) {
com_err("e2fsck", retval,
_("while trying to initialize program"));
exit(FSCK_ERROR);
}
reserve_stdio_fds();
#ifdef RESOURCE_TRACK
init_resource_track(&ctx->global_rtrack);
#endif
if (!(ctx->options & E2F_OPT_PREEN) || show_version_only)
fprintf(stderr, "e2fsck %s (%s)\n", my_ver_string,
my_ver_date);
if (show_version_only) {
fprintf(stderr, _("\tUsing %s, %s\n"),
error_message(EXT2_ET_BASE), lib_ver_date);
exit(FSCK_OK);
}
check_mount(ctx);
if (!(ctx->options & E2F_OPT_PREEN) &&
!(ctx->options & E2F_OPT_NO) &&
!(ctx->options & E2F_OPT_YES)) {
if (!ctx->interactive)
fatal_error(ctx,
_("need terminal for interactive repairs"));
}
ctx->superblock = ctx->use_superblock;
restart:
#ifdef CONFIG_TESTIO_DEBUG
io_ptr = test_io_manager;
test_io_backing_manager = unix_io_manager;
#else
io_ptr = unix_io_manager;
#endif
flags = 0;
if ((ctx->options & E2F_OPT_READONLY) == 0)
flags |= EXT2_FLAG_RW;
if ((ctx->mount_flags & EXT2_MF_MOUNTED) == 0)
flags |= EXT2_FLAG_EXCLUSIVE;
if (ctx->superblock && ctx->blocksize) {
retval = ext2fs_open2(ctx->filesystem_name, ctx->io_options,
flags, ctx->superblock, ctx->blocksize,
io_ptr, &fs);
} else if (ctx->superblock) {
int blocksize;
for (blocksize = EXT2_MIN_BLOCK_SIZE;
blocksize <= EXT2_MAX_BLOCK_SIZE; blocksize *= 2) {
retval = ext2fs_open2(ctx->filesystem_name,
ctx->io_options, flags,
ctx->superblock, blocksize,
io_ptr, &fs);
if (!retval)
break;
}
} else
retval = ext2fs_open2(ctx->filesystem_name, ctx->io_options,
flags, 0, 0, io_ptr, &fs);
if (!ctx->superblock && !(ctx->options & E2F_OPT_PREEN) &&
!(ctx->flags & E2F_FLAG_SB_SPECIFIED) &&
((retval == EXT2_ET_BAD_MAGIC) ||
((retval == 0) && ext2fs_check_desc(fs)))) {
if (!fs || (fs->group_desc_count > 1)) {
printf(_("%s trying backup blocks...\n"),
retval ? _("Couldn't find ext2 superblock,") :
_("Group descriptors look bad..."));
get_backup_sb(ctx, fs, ctx->filesystem_name, io_ptr);
if (fs)
ext2fs_close(fs);
goto restart;
}
}
if (retval) {
com_err(ctx->program_name, retval, _("while trying to open %s"),
ctx->filesystem_name);
if (retval == EXT2_ET_REV_TOO_HIGH) {
printf(_("The filesystem revision is apparently "
"too high for this version of e2fsck.\n"
"(Or the filesystem superblock "
"is corrupt)\n\n"));
fix_problem(ctx, PR_0_SB_CORRUPT, &pctx);
} else if (retval == EXT2_ET_SHORT_READ)
printf(_("Could this be a zero-length partition?\n"));
else if ((retval == EPERM) || (retval == EACCES))
printf(_("You must have %s access to the "
"filesystem or be root\n"),
(ctx->options & E2F_OPT_READONLY) ?
"r/o" : "r/w");
else if (retval == ENXIO)
printf(_("Possibly non-existent or swap device?\n"));
else if (retval == EBUSY)
printf(_("Filesystem mounted or opened exclusively "
"by another program?\n"));
#ifdef EROFS
else if (retval == EROFS)
printf(_("Disk write-protected; use the -n option "
"to do a read-only\n"
"check of the device.\n"));
#endif
else
fix_problem(ctx, PR_0_SB_CORRUPT, &pctx);
fatal_error(ctx, 0);
}
ctx->fs = fs;
fs->priv_data = ctx;
fs->now = ctx->now;
sb = fs->super;
if (sb->s_rev_level > E2FSCK_CURRENT_REV) {
com_err(ctx->program_name, EXT2_ET_REV_TOO_HIGH,
_("while trying to open %s"),
ctx->filesystem_name);
get_newer:
fatal_error(ctx, _("Get a newer version of e2fsck!"));
}
/*
* Set the device name, which is used whenever we print error
* or informational messages to the user.
*/
if (ctx->device_name == 0 &&
(sb->s_volume_name[0] != 0)) {
ctx->device_name = string_copy(ctx, sb->s_volume_name,
sizeof(sb->s_volume_name));
}
if (ctx->device_name == 0)
ctx->device_name = ctx->filesystem_name;
/*
* Make sure the ext3 superblock fields are consistent.
*/
retval = e2fsck_check_ext3_journal(ctx);
if (retval) {
com_err(ctx->program_name, retval,
_("while checking ext3 journal for %s"),
ctx->device_name);
fatal_error(ctx, 0);
}
/*
* Check to see if we need to do ext3-style recovery. If so,
* do it, and then restart the fsck.
*/
if (sb->s_feature_incompat & EXT3_FEATURE_INCOMPAT_RECOVER) {
if (ctx->options & E2F_OPT_READONLY) {
printf(_("Warning: skipping journal recovery "
"because doing a read-only filesystem "
"check.\n"));
io_channel_flush(ctx->fs->io);
} else {
if (ctx->flags & E2F_FLAG_RESTARTED) {
/*
* Whoops, we attempted to run the
* journal twice. This should never
* happen, unless the hardware or
* device driver is being bogus.
*/
com_err(ctx->program_name, 0,
_("unable to set superblock flags on %s\n"), ctx->device_name);
fatal_error(ctx, 0);
}
retval = e2fsck_run_ext3_journal(ctx);
if (retval) {
com_err(ctx->program_name, retval,
_("while recovering ext3 journal of %s"),
ctx->device_name);
fatal_error(ctx, 0);
}
ext2fs_close(ctx->fs);
ctx->fs = 0;
ctx->flags |= E2F_FLAG_RESTARTED;
goto restart;
}
}
/*
* Check for compatibility with the feature sets. We need to
* be more stringent than ext2fs_open().
*/
if ((sb->s_feature_compat & ~EXT2_LIB_FEATURE_COMPAT_SUPP) ||
(sb->s_feature_incompat & ~EXT2_LIB_FEATURE_INCOMPAT_SUPP)) {
com_err(ctx->program_name, EXT2_ET_UNSUPP_FEATURE,
"(%s)", ctx->device_name);
goto get_newer;
}
if (sb->s_feature_ro_compat & ~EXT2_LIB_FEATURE_RO_COMPAT_SUPP) {
com_err(ctx->program_name, EXT2_ET_RO_UNSUPP_FEATURE,
"(%s)", ctx->device_name);
goto get_newer;
}
#ifdef ENABLE_COMPRESSION
if (sb->s_feature_incompat & EXT2_FEATURE_INCOMPAT_COMPRESSION)
com_err(ctx->program_name, 0,
_("Warning: compression support is experimental.\n"));
#endif
#ifndef ENABLE_HTREE
if (sb->s_feature_compat & EXT2_FEATURE_COMPAT_DIR_INDEX) {
com_err(ctx->program_name, 0,
_("E2fsck not compiled with HTREE support,\n\t"
"but filesystem %s has HTREE directories.\n"),
ctx->device_name);
goto get_newer;
}
#endif
/*
* If the user specified a specific superblock, presumably the
* master superblock has been trashed. So we mark the
* superblock as dirty, so it can be written out.
*/
if (ctx->superblock &&
!(ctx->options & E2F_OPT_READONLY))
ext2fs_mark_super_dirty(fs);
/*
* We only update the master superblock because (a) paranoia;
* we don't want to corrupt the backup superblocks, and (b) we
* don't need to update the mount count and last checked
* fields in the backup superblock (the kernel doesn't
* update the backup superblocks anyway).
*/
fs->flags |= EXT2_FLAG_MASTER_SB_ONLY;
ehandler_init(fs->io);
if (ctx->superblock)
set_latch_flags(PR_LATCH_RELOC, PRL_LATCHED, 0);
ext2fs_mark_valid(fs);
check_super_block(ctx);
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
fatal_error(ctx, 0);
check_if_skip(ctx);
if (bad_blocks_file)
read_bad_blocks_file(ctx, bad_blocks_file, replace_bad_blocks);
else if (cflag)
read_bad_blocks_file(ctx, 0, !keep_bad_blocks); /* Test disk */
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
fatal_error(ctx, 0);
#ifdef ENABLE_SWAPFS
if (normalize_swapfs) {
if ((fs->flags & EXT2_FLAG_SWAP_BYTES) ==
ext2fs_native_flag()) {
fprintf(stderr, _("%s: Filesystem byte order "
"already normalized.\n"), ctx->device_name);
fatal_error(ctx, 0);
}
}
if (swapfs) {
swap_filesys(ctx);
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
fatal_error(ctx, 0);
}
#endif
/*
* Mark the system as valid, 'til proven otherwise
*/
ext2fs_mark_valid(fs);
retval = ext2fs_read_bb_inode(fs, &fs->badblocks);
if (retval) {
com_err(ctx->program_name, retval,
_("while reading bad blocks inode"));
preenhalt(ctx);
printf(_("This doesn't bode well,"
" but we'll try to go on...\n"));
}
run_result = e2fsck_run(ctx);
e2fsck_clear_progbar(ctx);
if (run_result == E2F_FLAG_RESTART) {
printf(_("Restarting e2fsck from the beginning...\n"));
retval = e2fsck_reset_context(ctx);
if (retval) {
com_err(ctx->program_name, retval,
_("while resetting context"));
fatal_error(ctx, 0);
}
ext2fs_close(fs);
goto restart;
}
if (run_result & E2F_FLAG_CANCEL) {
printf(_("%s: e2fsck canceled.\n"), ctx->device_name ?
ctx->device_name : ctx->filesystem_name);
exit_value |= FSCK_CANCELED;
}
if (run_result & E2F_FLAG_ABORT)
fatal_error(ctx, _("aborted"));
#ifdef MTRACE
mtrace_print("Cleanup");
#endif
if (ext2fs_test_changed(fs)) {
exit_value |= FSCK_NONDESTRUCT;
if (!(ctx->options & E2F_OPT_PREEN))
printf(_("\n%s: ***** FILE SYSTEM WAS MODIFIED *****\n"),
ctx->device_name);
if (ctx->mount_flags & EXT2_MF_ISROOT) {
printf(_("%s: ***** REBOOT LINUX *****\n"),
ctx->device_name);
exit_value |= FSCK_REBOOT;
}
}
if (!ext2fs_test_valid(fs) ||
((exit_value & FSCK_CANCELED) &&
(sb->s_state & EXT2_ERROR_FS))) {
printf(_("\n%s: ********** WARNING: Filesystem still has "
"errors **********\n\n"), ctx->device_name);
exit_value |= FSCK_UNCORRECTED;
exit_value &= ~FSCK_NONDESTRUCT;
}
if (exit_value & FSCK_CANCELED) {
int allow_cancellation;
profile_get_boolean(ctx->profile, "options",
"allow_cancellation", 0, 0,
&allow_cancellation);
exit_value &= ~FSCK_NONDESTRUCT;
if (allow_cancellation && ext2fs_test_valid(fs) &&
(sb->s_state & EXT2_VALID_FS) &&
!(sb->s_state & EXT2_ERROR_FS))
exit_value = 0;
} else {
show_stats(ctx);
if (!(ctx->options & E2F_OPT_READONLY)) {
if (ext2fs_test_valid(fs)) {
if (!(sb->s_state & EXT2_VALID_FS))
exit_value |= FSCK_NONDESTRUCT;
sb->s_state = EXT2_VALID_FS;
} else
sb->s_state &= ~EXT2_VALID_FS;
sb->s_mnt_count = 0;
sb->s_lastcheck = ctx->now;
ext2fs_mark_super_dirty(fs);
}
}
e2fsck_write_bitmaps(ctx);
ext2fs_close(fs);
ctx->fs = NULL;
free(ctx->filesystem_name);
free(ctx->journal_name);
#ifdef RESOURCE_TRACK
if (ctx->options & E2F_OPT_TIME)
print_resource_track(NULL, &ctx->global_rtrack);
#endif
e2fsck_free_context(ctx);
return exit_value;
}
/*
* Go through the whole list, stopping if you find a match. Process all
* the continuations of that match before returning.
*
* We support multi-level continuations:
*
* At any time when processing a successful top-level match, there is a
* current continuation level; it represents the level of the last
* successfully matched continuation.
*
* Continuations above that level are skipped as, if we see one, it
* means that the continuation that controls them - i.e, the
* lower-level continuation preceding them - failed to match.
*
* Continuations below that level are processed as, if we see one,
* it means we've finished processing or skipping higher-level
* continuations under the control of a successful or unsuccessful
* lower-level continuation, and are now seeing the next lower-level
* continuation and should process it. The current continuation
* level reverts to the level of the one we're seeing.
*
* Continuations at the current level are processed as, if we see
* one, there's no lower-level continuation that may have failed.
*
* If a continuation matches, we bump the current continuation level
* so that higher-level continuations are processed.
*/
char *
magic_match(u_char *s, int len)
{
int i, cont_level = 0;
union VALUETYPE p;
static int32_t *tmpoff = NULL;
static size_t tmplen = 0;
int32_t oldoff = 0;
Match[0] = '\0';
if (tmpoff == NULL)
if ((tmpoff = (int32_t *) malloc(tmplen = 20)) == NULL)
err(1, "malloc");
for (i = 0; i < Magiccnt; i++) {
/* if main entry matches, print it... */
if (!mget(&p, s, &Magic[i], len) || !mcheck(&p, &Magic[i])) {
/*
* main entry didn't match,
* flush its continuations
*/
while (i < Magiccnt && Magic[i + 1].cont_level != 0)
i++;
continue;
}
tmpoff[cont_level] = mprint(&p, &Magic[i]);
/* and any continuations that match */
if (++cont_level >= tmplen) {
tmplen += 20;
if (!(tmpoff = (int32_t *) realloc(tmpoff, tmplen)))
err(1, "magic_match: malloc");
}
while (Magic[i + 1].cont_level != 0 && ++i < Magiccnt) {
if (cont_level >= Magic[i].cont_level) {
if (cont_level > Magic[i].cont_level) {
/*
* We're at the end of the level
* "cont_level" continuations.
*/
cont_level = Magic[i].cont_level;
}
if (Magic[i].flag & ADD) {
oldoff = Magic[i].offset;
Magic[i].offset +=
tmpoff[cont_level - 1];
}
if (mget(&p, s, &Magic[i], len) &&
mcheck(&p, &Magic[i])) {
/* This continuation matched. */
tmpoff[cont_level] =
mprint(&p, &Magic[i]);
/*
* If we see any continuations
* at a higher level, process them.
*/
if (++cont_level >= tmplen) {
tmplen += 20;
if (!(tmpoff = (int32_t *)
realloc(tmpoff, tmplen)))
err(1, "magic_check: "
"malloc");
}
}
if (Magic[i].flag & ADD) {
Magic[i].offset = oldoff;
}
}
}
return (strlen(Match) ? Match : NULL); /* all through */
}
return (NULL); /* no match at all */
}
void SpinAdapted::InitBlocks::InitNewEnvironmentBlock(SpinBlock &environment, SpinBlock& environmentDot, SpinBlock &newEnvironment,
const SpinBlock &system, SpinBlock &systemDot, int leftState, int rightState,
const int &sys_add, const int &env_add, const bool &forward, const bool &direct,
const bool &onedot, const bool &nexact, const bool &useSlater, int integralIndex,
bool haveNormops, bool haveCompops, const bool& dot_with_sys, int constraint, const std::vector<SpinQuantum>& braquanta, const std::vector<SpinQuantum>& ketquanta) {
// now initialise environment Dot
int systemDotStart, systemDotEnd, environmentDotStart, environmentDotEnd, environmentStart, environmentEnd;
int systemDotSize = sys_add - 1;
int environmentDotSize = env_add - 1;
if (forward) {
systemDotStart = dmrginp.spinAdapted() ? *system.get_sites().rbegin () + 1 : (*system.get_sites().rbegin ())/2 + 1 ;
systemDotEnd = systemDotStart + systemDotSize;
environmentDotStart = systemDotEnd + 1;
environmentDotEnd = environmentDotStart + environmentDotSize;
environmentStart = environmentDotEnd + 1;
environmentEnd = dmrginp.spinAdapted() ? dmrginp.last_site() - 1 : dmrginp.last_site()/2 - 1;
} else {
systemDotStart = dmrginp.spinAdapted() ? system.get_sites()[0] - 1 : (system.get_sites()[0])/2 - 1 ;
systemDotEnd = systemDotStart - systemDotSize;
environmentDotStart = systemDotEnd - 1;
environmentDotEnd = environmentDotStart - environmentDotSize;
environmentStart = environmentDotEnd - 1;
environmentEnd = 0;
}
std::vector<int> environmentSites;
environmentSites.resize(abs(environmentEnd - environmentStart) + 1);
for (int i = 0; i < abs(environmentEnd - environmentStart) + 1; ++i) *(environmentSites.begin () + i) = min(environmentStart,environmentEnd) + i;
// now initialise environment
if (useSlater) { // for FCI
StateInfo system_stateinfo = system.get_stateInfo();
StateInfo sysdot_stateinfo = systemDot.get_stateInfo();
StateInfo tmp;
TensorProduct (system_stateinfo, sysdot_stateinfo, tmp, NO_PARTICLE_SPIN_NUMBER_CONSTRAINT);
// tmp has the system+dot quantum numbers
tmp.CollectQuanta ();
// exact environment
if (dmrginp.do_fci() || environmentSites.size() == nexact) {
if ((!dot_with_sys && onedot) || !onedot) { // environment has dot
environment.set_integralIndex() = integralIndex;
environment.default_op_components(!forward, leftState==rightState);
environment.setstoragetype(DISTRIBUTED_STORAGE);
environment.BuildTensorProductBlock(environmentSites); // exact block
SpinBlock::store (true, environmentSites, environment, leftState, rightState);
}
else { // environment has no dot, so newEnv = Env
newEnvironment.set_integralIndex() = integralIndex;
newEnvironment.default_op_components(!forward, leftState==rightState);
newEnvironment.setstoragetype(DISTRIBUTED_STORAGE);
newEnvironment.BuildTensorProductBlock(environmentSites);
SpinBlock::store (true, environmentSites, newEnvironment, leftState, rightState);
}
} else if (dmrginp.warmup() == LOCAL2 || dmrginp.warmup() == LOCAL3 || dmrginp.warmup() == LOCAL4) {
int nactiveSites, ncoreSites;
if (dmrginp.warmup() == LOCAL2) {
nactiveSites = 1;
} else if (dmrginp.warmup() == LOCAL3) {
nactiveSites = 2;
} else if (dmrginp.warmup() == LOCAL4) {
nactiveSites = 3;
}
if (dot_with_sys && onedot) {
nactiveSites += 1;
}
if (nactiveSites > environmentSites.size()) {
nactiveSites = environmentSites.size();
}
ncoreSites = environmentSites.size() - nactiveSites;
// figure out what sites are in the active and core sites
int environmentActiveEnd = forward ? environmentStart + nactiveSites - 1 : environmentStart - nactiveSites + 1;
int environmentCoreStart = forward ? environmentActiveEnd + 1 : environmentActiveEnd - 1;
std::vector<int> activeSites(nactiveSites), coreSites(ncoreSites);
for (int i = 0; i < nactiveSites; ++i) {
activeSites[i] = min(environmentStart,environmentActiveEnd) + i;
}
for (int i = 0; i < ncoreSites; ++i) {
coreSites[i] = min(environmentCoreStart,environmentEnd) + i;
}
SpinBlock environmentActive, environmentCore;
environmentActive.nonactive_orb() = system.nonactive_orb();
environmentCore.nonactive_orb() = system.nonactive_orb();
if (coreSites.size() > 0) {
environmentActive.set_integralIndex() = integralIndex;
environmentCore.set_integralIndex() = integralIndex;
environmentActive.default_op_components(!forward, leftState==rightState);
environmentActive.setstoragetype(DISTRIBUTED_STORAGE);
environmentCore.default_op_components(!forward, leftState==rightState);
environmentCore.setstoragetype(DISTRIBUTED_STORAGE);
environmentActive.BuildTensorProductBlock(activeSites);
environmentCore.BuildSingleSlaterBlock(coreSites);
dmrginp.datatransfer -> start();
environmentCore.addAdditionalCompOps();
environmentActive.addAdditionalCompOps();
dmrginp.datatransfer -> stop();
if ((!dot_with_sys && onedot) || !onedot) {
environment.set_integralIndex() = integralIndex;
environment.default_op_components(!forward, leftState == rightState);
environment.setstoragetype(DISTRIBUTED_STORAGE);
environment.BuildSumBlock(constraint, environmentCore, environmentActive,braquanta,ketquanta);
} else {
newEnvironment.set_integralIndex() = integralIndex;
newEnvironment.default_op_components(direct, environmentCore, environmentActive, haveNormops, haveCompops, leftState == rightState);
newEnvironment.setstoragetype(DISTRIBUTED_STORAGE);
newEnvironment.BuildSumBlock(constraint, environmentCore, environmentActive,braquanta,ketquanta);
if (dmrginp.outputlevel() > 0) {
pout << "\t\t\t NewEnvironment block " << endl << newEnvironment << endl;
newEnvironment.printOperatorSummary();
}
}
} else { // no core
if ((!dot_with_sys && onedot) || !onedot) {
environment.set_integralIndex() = integralIndex;
environment.default_op_components(!forward, leftState==rightState);
environment.setstoragetype(DISTRIBUTED_STORAGE);
environment.BuildTensorProductBlock(environmentSites); // exact block
} else {
newEnvironment.set_integralIndex() = integralIndex;
newEnvironment.default_op_components(!forward, leftState==rightState);
newEnvironment.setstoragetype(DISTRIBUTED_STORAGE);
newEnvironment.BuildTensorProductBlock(environmentSites);
}
}
} else { //used for warmup guess environemnt
std::vector<SpinQuantum> quantumNumbers;
std::vector<int> distribution;
std::map<SpinQuantum, int> quantaDist;
std::map<SpinQuantum, int>::iterator quantaIterator;
bool environmentComplementary = !forward;
StateInfo tmp2;
// tmp is the quantum numbers of newSystem (sys + sysdot)
if (onedot) tmp.quanta_distribution (quantumNumbers, distribution, true);
else {
StateInfo environmentdot_stateinfo = environmentDot.get_stateInfo();
TensorProduct (tmp, environmentdot_stateinfo, tmp2, constraint);
tmp2.CollectQuanta ();
tmp2.quanta_distribution (quantumNumbers, distribution, true);
}
for (int i = 0; i < distribution.size (); ++i) {
quantaIterator = quantaDist.find(quantumNumbers[i]);
if (quantaIterator != quantaDist.end()) distribution[i] += quantaIterator->second;
distribution [i] /= 4; distribution [i] += 1;
if (distribution [i] > dmrginp.nquanta()) distribution [i] = dmrginp.nquanta();
if(quantaIterator != quantaDist.end()) {
quantaIterator->second = distribution[i];
} else {
quantaDist[quantumNumbers[i]] = distribution[i];
}
}
if (dmrginp.outputlevel() > 0) pout << "\t\t\t Quantum numbers and states used for warm up :: " << endl << "\t\t\t ";
quantumNumbers.clear(); quantumNumbers.reserve(distribution.size());
distribution.clear();distribution.reserve(quantumNumbers.size());
std::map<SpinQuantum, int>::iterator qit = quantaDist.begin();
for (; qit != quantaDist.end(); qit++) {
quantumNumbers.push_back( qit->first); distribution.push_back(qit->second);
if (dmrginp.outputlevel() > 0) {
pout << quantumNumbers.back() << " = " << distribution.back() << ", ";
if (! (quantumNumbers.size() - 6) % 6) pout << endl << "\t\t\t ";
}
}
pout << endl;
if(dot_with_sys && onedot) {
newEnvironment.set_integralIndex() = integralIndex;
newEnvironment.BuildSlaterBlock (environmentSites, quantumNumbers, distribution, false, false);
} else {
environment.set_integralIndex() = integralIndex;
environment.BuildSlaterBlock (environmentSites, quantumNumbers, distribution, false, haveNormops);
}
}
} else {
if (dmrginp.outputlevel() > 0) pout << "\t\t\t Restoring block of size " << environmentSites.size () << " from previous iteration" << endl;
if(dot_with_sys && onedot) {
newEnvironment.set_integralIndex() = integralIndex;
SpinBlock::restore (!forward, environmentSites, newEnvironment, leftState, rightState);
} else {
environment.set_integralIndex() = integralIndex;
SpinBlock::restore (!forward, environmentSites, environment, leftState, rightState);
}
if (dmrginp.outputlevel() > 0)
mcheck("");
}
// now initialise newEnvironment
if (!dot_with_sys || !onedot) {
dmrginp.datatransfer -> start();
environment.addAdditionalCompOps();
dmrginp.datatransfer -> stop();
newEnvironment.set_integralIndex() = integralIndex;
newEnvironment.default_op_components(direct, environment, environmentDot, haveNormops, haveCompops, leftState==rightState);
newEnvironment.setstoragetype(DISTRIBUTED_STORAGE);
newEnvironment.BuildSumBlock (constraint, environment, environmentDot,braquanta,ketquanta);
if (dmrginp.outputlevel() > -1) {
pout << "\t\t\t Environment block " << endl << environment << endl;
environment.printOperatorSummary();
pout << "\t\t\t NewEnvironment block " << endl << newEnvironment << endl;
newEnvironment.printOperatorSummary();
}
} else if (dmrginp.outputlevel() > 0) {
pout << "\t\t\t Environment block " << endl << newEnvironment << endl;
newEnvironment.printOperatorSummary();
}
}
int
main(int argc, char *argv[])
{
int count;
seq_t seq1, seq2;
hash_env_t he;
collec_t res, rev_res;
#if defined(DEBUG) && (DEBUG > 1)
mcheck(NULL);
mtrace();
#endif
argv0 = argv[0];
if (setlocale(LC_ALL, "POSIX") == NULL)
fprintf(stderr, "%s: Warning: could not set locale to POSIX\n", argv[0]);
signal(SIGSEGV, bug_handler);
#ifndef __MINGW32__
signal(SIGBUS, bug_handler);
#endif
/* Default options. */
options.C = DEFAULT_C;
options.cutoff = DIST_CUTOFF;
options.gapPct = DEFAULT_GAPPCT;
options.intron_window = 6;
options.K = DEFAULT_K;
options.splice_type_list = "GTAG,GCAG,GTAC,ATAC";
options.nbSplice = 4;
options.scoreSplice_window = 10;
options.mismatchScore = MISMATCH;
options.reverse = 2;
options.matchScore = MATCH;
options.W = DEFAULT_W;
options.X = DEFAULT_X;
options.filterPct = DEFAULT_FILTER;
options.minScore_cutoff = MATCH_CUTOFF;
while (1) {
int c = getopt(argc, argv, "A:C:c:E:f:g:I:K:L:M:o:q:R:r:W:X:");
if (c == -1)
break;
switch (c) {
case 'A':
options.ali_flag = atoi(optarg);
if (options.ali_flag < 0 || options.ali_flag > 4)
fatal("A must be one of 0, 1, 2, 3, or 4.\n");
break;
case 'C': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option C must be non-negative.\n");
options.C = val;
break;
}
case 'c': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option c must be non-negative.\n");
options.minScore_cutoff = val;
break;
}
case 'E':
options.cutoff = atoi(optarg);
if (options.cutoff < 3 || options.cutoff > 10)
fatal("Cutoff (E) must be within [3,10].\n");
break;
case 'f':
options.filterPct = atoi(optarg);
if (options.filterPct > 100)
fatal("Filter in percent (f) must be within [0,100].\n");
break;
case 'g':
options.gapPct = atoi(optarg);
break;
case 'I':
options.intron_window = atoi(optarg);
break;
case 'K': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option K must be non-negative.\n");
options.K = val;
break;
}
case 'L': {
size_t i;
size_t len = strlen(optarg);
options.splice_type_list = optarg;
options.nbSplice = 1;
if (len % 5 != 4)
fatal("Splice types list has illegal length (%zu)\n", len);
for (i = 0; i < len; i++)
if (i % 5 == 4) {
if (options.splice_type_list[i] != ',')
fatal("Comma expected instead of %c at position %zu"
"in splice types list.\n",
options.splice_type_list[i], i);
options.nbSplice += 1;
} else {
if (options.splice_type_list[i] != 'A'
&& options.splice_type_list[i] != 'C'
&& options.splice_type_list[i] != 'G'
&& options.splice_type_list[i] != 'T')
fatal("Expected 'A', 'C', 'G' or 'T' instead of '%c' at"
"position %zu in splice types list.\n",
options.splice_type_list[i], i);
}
break;
}
case 'M': {
int val = atoi(optarg);
if (val < 0)
fatal("Value for option M must be non-negative.\n");
options.scoreSplice_window = val;
break;
}
case 'o':
options.dnaOffset = atoi(optarg);
break;
case 'q':
options.mismatchScore = atoi(optarg);
break;
case 'R':
options.reverse = atoi(optarg);
if (options.reverse < 0 || options.reverse > 2)
fatal("R must be one of 0, 1, or 2.\n");
break;
case 'r':
options.matchScore = atoi(optarg);
break;
case 'W':
options.W = atoi(optarg);
if (options.W < 1 || options.W > 15)
fatal("W must be within [1,15].\n");
break;
case 'X':
options.X = atoi(optarg);
if (options.X < 1)
fatal("X must be positive.\n");
break;
case '?':
break;
default:
fprintf(stderr, "?? getopt returned character code 0%o ??\n", c);
}
}
if (optind + 2 != argc) {
fprintf(stderr, Usage, argv[0], options.ali_flag, options.C,
options.minScore_cutoff, options.cutoff,
options.filterPct, options.gapPct, options.intron_window,
options.K, options.splice_type_list, options.scoreSplice_window,
options.dnaOffset, options.mismatchScore, options.reverse,
options.matchScore, options.W, options.X);
return 1;
}
/* read seq1 */
init_seq(argv[optind], &seq1);
if (get_next_seq(&seq1, options.dnaOffset, 1) != 0)
fatal("Cannot read sequence from %s.\n", argv[optind]);
strncpy(dna_seq_head, seq1.header, 256);
/* read seq2 */
init_seq(argv[optind + 1], &seq2);
if (get_next_seq(&seq2, 0, 0) != 0)
fatal("Cannot read sequence from %s.\n", argv[optind + 1]);
init_encoding();
init_hash_env(&he, options.W, seq1.seq, seq1.len);
init_col(&res, 1);
init_col(&rev_res, 1);
bld_table(&he);
init_splice_junctions();
count = 0;
while (!count || get_next_seq(&seq2, 0, 0) == 0) {
unsigned int curRes;
strncpy(rna_seq_head, seq2.header, 256);
++count;
switch (options.reverse) {
case 0:
SIM4(&he, &seq2, &res);
break;
case 2:
SIM4(&he, &seq2, &res);
case 1:
seq_revcomp_inplace(&seq2);
SIM4(&he, &seq2, &rev_res);
break;
default:
fatal ("Unrecognized request for EST orientation.\n");
}
/* Keep only the best matches, according to filterPct. */
if (options.filterPct > 0) {
unsigned int max_nmatches = 0;
for (curRes = 0; curRes < rev_res.nb; curRes++) {
result_p_t r = rev_res.e.result[curRes];
if (r->st.nmatches > max_nmatches)
max_nmatches = r->st.nmatches;
}
for (curRes = 0; curRes < res.nb; curRes++) {
result_p_t r = res.e.result[curRes];
if (r->st.nmatches > max_nmatches)
max_nmatches = r->st.nmatches;
}
max_nmatches = (max_nmatches * options.filterPct) / 100;
for (curRes = 0; curRes < rev_res.nb; curRes++) {
result_p_t r = rev_res.e.result[curRes];
if (r->st.nmatches < max_nmatches)
r->st.nmatches = 0;
}
for (curRes = 0; curRes < res.nb; curRes++) {
result_p_t r = res.e.result[curRes];
if (r->st.nmatches < max_nmatches)
r->st.nmatches = 0;
}
}
/* Now, print results. */
for (curRes = 0; curRes < rev_res.nb; curRes++)
print_res(rev_res.e.result[curRes], 1, &seq1, &seq2);
rev_res.nb = 0;
if (options.reverse && options.ali_flag)
/* reverse-complement back seq2 for alignment */
seq_revcomp_inplace(&seq2);
for (curRes = 0; curRes < res.nb; curRes++)
print_res(res.e.result[curRes], 0, &seq1, &seq2);
res.nb = 0;
}
#ifdef DEBUG
fprintf(stderr, "DEBUG mode: freeing all memory...\n");
fflush(stdout);
fflush(stderr);
free_hash_env(&he);
free_seq(&seq1);
free_seq(&seq2);
free(options.splice);
free(res.e.elt);
free(rev_res.e.elt);
#endif
return 0;
}
void
main (int argc, char *argv[])
{
char c, *p, *name = argv[0];
extern char *optarg; /* getopt stuff */
extern int optind; /* getopt stuff */
int errors = 0;
int daemon = 0;
char *port = "ricd";
char *rib_file = NULL;
int kernel_read_flag = 1;
int kernel_install_flag4 = 1;
int kernel_install_flag6 = 1;
int rib_install_flag = 1;
char *usage = "Usage: %s [-f config_file] [-p uii_port ] [-v] [-n]\n";
char *config_file = NULL;
trace_t *default_trace;
if ((p = strrchr (name, '/')) != NULL) {
name = p + 1;
}
if (strcasecmp (name, "ricd") == 0 ||
strcasecmp (name, "ricd.purify") == 0) {
config_file = "/etc/ricd.conf"; /* unix convension */
daemon = 1;
}
#ifdef MCHECK
mcheck (0);
#endif
default_trace = New_Trace2 ("RICd");
set_trace (default_trace, TRACE_PREPEND_STRING, "RICD", 0);
set_trace (default_trace, TRACE_MAX_ERRORS, DEFAULT_MAX_ERRORS, 0);
/* set_trace (default_trace, TRACE_FLAGS, TR_ALL, 0); */
while ((c = getopt (argc, argv, "46rhnkvf:p:l:i:")) != -1)
switch (c) {
case 'v': /* verbose */
set_trace (default_trace, TRACE_FLAGS, TR_ALL,
TRACE_LOGFILE, "stdout",
0);
daemon = 0;
break;
case 'f': /* config file */
config_file = optarg;
break;
case '4':
kernel_install_flag4 = 0;
break;
case '6':
kernel_install_flag6 = 0;
break;
case 'n': /* no kernel installation */
kernel_install_flag4 = 0;
kernel_install_flag6 = 0;
daemon = 0;
break;
case 'k': /* no kernel read */
kernel_read_flag = 0;
break;
case 'r': /* no rib installation */
rib_install_flag = 0;
break;
case 'p': /* uii port number */
port = optarg;
break;
case 'l': /* load rib on disk (mainly for testing) */
case 'i': /* load rib on disk (mainly for testing) */
rib_file = optarg;
break;
case 'h':
default:
errors++;
break;
}
if (errors) {
fprintf (stderr, usage, name);
printf ("\nMRT %s compiled on %s\n\n",
RICD_VERSION, __DATE__);
exit (1);
}
#ifdef notdef
if (getuid ()) {
fprintf (stderr, "must be root\n");
exit (1);
}
#endif
/* init_trace (name, daemon); */
init_trace (name, 1); /* always syslog */
/* no thread creates here */
init_mrt (default_trace);
init_uii (default_trace);
init_uii_port (port);
init_mrt_reboot (argc, argv);
trace (TR_INFO, MRT->trace, "%s compiled on %s started\n",
MRT->version, MRT->date);
if (daemon) {
/*
* Now going into daemon mode
*/
MRT->daemon_mode = 1;
daemonize ();
}
/* read information on all interfaces from the kernel */
init_interfaces (default_trace);
init_mrtd_config (default_trace);
ricd_init (default_trace, AF_INET);
#ifdef HAVE_IPV6
ricd_init (default_trace, AF_INET6);
#endif /* HAVE_IPV6 */
set_uii (UII, UII_PROMPT, UII_UNPREV, "Password: "******"RICD> ", 0);
kernel_init (); /* open routing socket */
/*
* read configuration here
*/
ricd_init_config ();
/* default_trace may be modified by debug statement in config file */
if (config_from_file (default_trace, config_file) < 0) {
config_create_default ();
}
/* CONFIGURATION DEPENDENT INITIALIZATION PART */
ricd_start (AF_INET);
#ifdef HAVE_IPV6
ricd_start (AF_INET6);
#endif /* HAVE_IPV6 */
listen_uii2 (NULL);
if (daemon) {
int status = 0;
if (write (channel[1], &status, sizeof (int)) < 0)
perror ("write");
}
/* timers never fire until going into loop */
/* select never fire until going into loop */
mrt_main_loop ();
exit (0);
}
void SweepGenblock::BlockAndDecimate (SweepParams &sweepParams, SpinBlock& system, SpinBlock& newSystem, const bool &useSlater, const bool& dot_with_sys, int state)
{
if (dmrginp.outputlevel() > 0)
mcheck("at the start of block and decimate");
// figure out if we are going forward or backwards
pout << "\t\t\t Performing Blocking"<<endl;
dmrginp.guessgenT -> start();
bool forward = (system.get_sites() [0] == 0);
SpinBlock systemDot;
int systemDotStart, systemDotEnd;
int systemDotSize = sweepParams.get_sys_add() - 1;
if (forward)
{
systemDotStart = *system.get_sites().rbegin () + 1;
systemDotEnd = systemDotStart + systemDotSize;
}
else
{
systemDotStart = system.get_sites() [0] - 1;
systemDotEnd = systemDotStart - systemDotSize;
}
vector<int> spindotsites(2);
spindotsites[0] = systemDotStart;
spindotsites[1] = systemDotEnd;
systemDot = SpinBlock(systemDotStart, systemDotEnd);
const int nexact = forward ? sweepParams.get_forward_starting_size() : sweepParams.get_backward_starting_size();
system.addAdditionalCompOps();
InitBlocks::InitNewSystemBlock(system, systemDot, newSystem, sweepParams.get_sys_add(), dmrginp.direct(), DISTRIBUTED_STORAGE, dot_with_sys, true);
pout << "\t\t\t System Block"<<newSystem;
if (dmrginp.outputlevel() > 0)
newSystem.printOperatorSummary();
std::vector<Matrix> rotateMatrix;
if (!dmrginp.get_fullrestart()) {
//this should be done when we actually have wavefunctions stored, otherwise not!!
SpinBlock environment, environmentDot, newEnvironment;
int environmentDotStart, environmentDotEnd, environmentStart, environmentEnd;
InitBlocks::InitNewEnvironmentBlock(environment, systemDot, newEnvironment, system, systemDot,
sweepParams.get_sys_add(), sweepParams.get_env_add(), forward, dmrginp.direct(),
sweepParams.get_onedot(), nexact, useSlater, true, true, true);
SpinBlock big;
InitBlocks::InitBigBlock(newSystem, newEnvironment, big);
DiagonalMatrix e;
std::vector<Wavefunction> solution(1);
GuessWave::guess_wavefunctions(solution[0], e, big, sweepParams.get_guesstype(), true, state, true, 0.0);
solution[0].SaveWavefunctionInfo (big.get_stateInfo(), big.get_leftBlock()->get_sites(), state);
DensityMatrix tracedMatrix;
tracedMatrix.allocate(newSystem.get_stateInfo());
tracedMatrix.makedensitymatrix(solution, big, std::vector<double>(1, 1.0), 0.0, 0.0, false);
rotateMatrix.clear();
if (!mpigetrank())
double error = newSystem.makeRotateMatrix(tracedMatrix, rotateMatrix, sweepParams.get_keep_states(), sweepParams.get_keep_qstates());
}
else
LoadRotationMatrix (newSystem.get_sites(), rotateMatrix, state);
#ifndef SERIAL
mpi::communicator world;
broadcast(world, rotateMatrix, 0);
#endif
if (!dmrginp.get_fullrestart())
SaveRotationMatrix (newSystem.get_sites(), rotateMatrix, state);
pout <<"\t\t\t Performing Renormalization "<<endl<<endl;
newSystem.transform_operators(rotateMatrix);
if (dmrginp.outputlevel() > 0)
mcheck("after rotation and transformation of block");
if (dmrginp.outputlevel() > 0)
pout <<newSystem<<endl;
if (dmrginp.outputlevel() > 0)
newSystem.printOperatorSummary();
//mcheck("After renorm transform");
}
static void
DEFUN_VOID (turn_on_mcheck)
{
mcheck (NULL);
}
void SweepGenblock::BlockAndDecimate (SweepParams &sweepParams, SpinBlock& system, SpinBlock& newSystem, const bool &useSlater, const bool& dot_with_sys, int stateA, int stateB)
{
if (dmrginp.outputlevel() > 0)
mcheck("at the start of block and decimate");
pout << "\t\t\t Performing Blocking"<<endl;
dmrginp.guessgenT -> start();
// figure out if we are going forward or backwards
bool forward = (system.get_sites() [0] == 0);
SpinBlock systemDot;
int systemDotStart, systemDotEnd;
int systemDotSize = sweepParams.get_sys_add() - 1;
if (forward)
{
systemDotStart = dmrginp.spinAdapted() ? *system.get_sites().rbegin () + 1 : (*system.get_sites().rbegin ())/2 + 1 ;
systemDotEnd = systemDotStart + systemDotSize;
}
else
{
systemDotStart = dmrginp.spinAdapted() ? system.get_sites()[0] - 1 : (system.get_sites()[0])/2 - 1 ;
systemDotEnd = systemDotStart - systemDotSize;
}
vector<int> spindotsites(2);
spindotsites[0] = systemDotStart;
spindotsites[1] = systemDotEnd;
systemDot = SpinBlock(systemDotStart, systemDotEnd, stateA==stateB);
const int nexact = forward ? sweepParams.get_forward_starting_size() : sweepParams.get_backward_starting_size();
system.addAdditionalCompOps();
InitBlocks::InitNewSystemBlock(system, systemDot, newSystem, stateA, stateB, sweepParams.get_sys_add(), dmrginp.direct(), DISTRIBUTED_STORAGE, dot_with_sys, true);
pout << "\t\t\t System Block"<<newSystem;
if (dmrginp.outputlevel() > 0)
newSystem.printOperatorSummary();
std::vector<Matrix> leftrotateMatrix, rightrotateMatrix;
LoadRotationMatrix (newSystem.get_sites(), leftrotateMatrix, stateA);
LoadRotationMatrix (newSystem.get_sites(), rightrotateMatrix, stateB);
#ifndef SERIAL
mpi::communicator world;
broadcast(world, leftrotateMatrix, 0);
broadcast(world, rightrotateMatrix, 0);
#endif
pout <<"\t\t\t Performing Renormalization "<<endl<<endl;
if (stateB == stateA)
newSystem.transform_operators(leftrotateMatrix);
else
newSystem.transform_operators(leftrotateMatrix, rightrotateMatrix);
if (dmrginp.outputlevel() > 0)
//mcheck("after rotation and transformation of block");
if (dmrginp.outputlevel() > 0)
pout <<newSystem<<endl;
if (dmrginp.outputlevel() > 0)
newSystem.printOperatorSummary();
//mcheck("After renorm transform");
}
void SpinAdapted::InitBlocks::InitNewOverlapEnvironmentBlock(SpinBlock &environment, SpinBlock& environmentDot, SpinBlock &newEnvironment,
const SpinBlock &system, SpinBlock &systemDot, int leftState, int rightState,
const int &sys_add, const int &env_add, const bool &forward, int integralIndex,
const bool &onedot, const bool& dot_with_sys, int constraint)
{
// now initialise environment Dot
int systemDotStart, systemDotEnd, environmentDotStart, environmentDotEnd, environmentStart, environmentEnd;
int systemDotSize = sys_add - 1;
int environmentDotSize = env_add - 1;
if (forward)
{
systemDotStart = dmrginp.spinAdapted() ? *system.get_sites().rbegin () + 1 : (*system.get_sites().rbegin ())/2 + 1 ;
systemDotEnd = systemDotStart + systemDotSize;
environmentDotStart = systemDotEnd + 1;
environmentDotEnd = environmentDotStart + environmentDotSize;
environmentStart = environmentDotEnd + 1;
environmentEnd = dmrginp.spinAdapted() ? dmrginp.last_site() - 1 : dmrginp.last_site()/2 - 1;
}
else
{
systemDotStart = dmrginp.spinAdapted() ? system.get_sites()[0] - 1 : (system.get_sites()[0])/2 - 1 ;
systemDotEnd = systemDotStart - systemDotSize;
environmentDotStart = systemDotEnd - 1;
environmentDotEnd = environmentDotStart - environmentDotSize;
environmentStart = environmentDotEnd - 1;
environmentEnd = 0;
}
std::vector<int> environmentSites;
environmentSites.resize(abs(environmentEnd - environmentStart) + 1);
for (int i = 0; i < abs(environmentEnd - environmentStart) + 1; ++i) *(environmentSites.begin () + i) = min(environmentStart,environmentEnd) + i;
p2out << "\t\t\t Restoring block of size " << environmentSites.size () << " from previous iteration" << endl;
if(dot_with_sys && onedot) {
newEnvironment.set_integralIndex() = integralIndex;
SpinBlock::restore (!forward, environmentSites, newEnvironment, leftState, rightState);
}
else {
environment.set_integralIndex() = integralIndex;
SpinBlock::restore (!forward, environmentSites, environment, leftState, rightState);
}
if (dmrginp.outputlevel() > 0)
mcheck("");
// now initialise newEnvironment
if (!dot_with_sys || !onedot)
{
newEnvironment.set_integralIndex() = integralIndex;
newEnvironment.initialise_op_array(OVERLAP, false);
//newEnvironment.set_op_array(OVERLAP) = boost::shared_ptr<Op_component<Overlap> >(new Op_component<Overlap>(false));
newEnvironment.setstoragetype(DISTRIBUTED_STORAGE);
newEnvironment.BuildSumBlock (constraint, environment, environmentDot);
p2out << "\t\t\t Environment block " << endl << environment << endl;
environment.printOperatorSummary();
p2out << "\t\t\t NewEnvironment block " << endl << newEnvironment << endl;
newEnvironment.printOperatorSummary();
}
else {
p2out << "\t\t\t Environment block " << endl << newEnvironment << endl;
newEnvironment.printOperatorSummary();
}
}
int main (int argc, char *argv[])
{
errcode_t retval = 0, retval2 = 0, orig_retval = 0;
int exit_value = FSCK_OK;
ext2_filsys fs = 0;
io_manager io_ptr;
struct ext2_super_block *sb;
const char *lib_ver_date;
int my_ver, lib_ver;
e2fsck_t ctx;
blk_t orig_superblock;
struct problem_context pctx;
int flags, run_result;
int journal_size;
int sysval, sys_page_size = 4096;
__u32 features[3];
char *cp;
klog_init();
E2F_DBG_INFO("e2fsck start...");
#ifdef E2FSCK_PIPE_DEBUG_
memset(pipe_msg_temp, 0, MSG_LEN);
memcpy(pipe_msg_temp, argv[2], strlen(argv[2]));
pipe_open();
pipe_write(C_IN_START);
#endif
clear_problem_context(&pctx);
#ifdef MTRACE
mtrace();
#endif
#ifdef MCHECK
mcheck(0);
#endif
#ifdef ENABLE_NLS
setlocale(LC_MESSAGES, "");
setlocale(LC_CTYPE, "");
bindtextdomain(NLS_CAT_NAME, LOCALEDIR);
textdomain(NLS_CAT_NAME);
#endif
my_ver = ext2fs_parse_version_string(my_ver_string);
lib_ver = ext2fs_get_library_version(0, &lib_ver_date);
if (my_ver > lib_ver) {
fprintf( stderr, _("Error: ext2fs library version "
"out of date!\n"));
show_version_only++;
}
retval = PRS(argc, argv, &ctx);
if (retval) {
com_err("e2fsck", retval,
_("while trying to initialize program"));
exit(FSCK_ERROR);
}
reserve_stdio_fds();
init_resource_track(&ctx->global_rtrack, NULL);
if (!(ctx->options & E2F_OPT_PREEN) || show_version_only)
fprintf(stderr, "e2fsck %s (%s)\n", my_ver_string,
my_ver_date);
if (show_version_only) {
fprintf(stderr, _("\tUsing %s, %s\n"),
error_message(EXT2_ET_BASE), lib_ver_date);
exit(FSCK_OK);
}
check_mount(ctx);
if (!(ctx->options & E2F_OPT_PREEN) &&
!(ctx->options & E2F_OPT_NO) &&
!(ctx->options & E2F_OPT_YES)) {
if (!ctx->interactive)
fatal_error(ctx,
_("need terminal for interactive repairs"));
}
ctx->superblock = ctx->use_superblock;
restart:
#ifdef CONFIG_TESTIO_DEBUG
if (getenv("TEST_IO_FLAGS") || getenv("TEST_IO_BLOCK")) {
io_ptr = test_io_manager;
test_io_backing_manager = unix_io_manager;
} else
#endif
io_ptr = unix_io_manager;
flags = EXT2_FLAG_NOFREE_ON_ERROR;
if ((ctx->options & E2F_OPT_READONLY) == 0)
flags |= EXT2_FLAG_RW;
if ((ctx->mount_flags & EXT2_MF_MOUNTED) == 0)
flags |= EXT2_FLAG_EXCLUSIVE;
retval = try_open_fs(ctx, flags, io_ptr, &fs);
if (!ctx->superblock && !(ctx->options & E2F_OPT_PREEN) &&
!(ctx->flags & E2F_FLAG_SB_SPECIFIED) &&
((retval == EXT2_ET_BAD_MAGIC) ||
(retval == EXT2_ET_CORRUPT_SUPERBLOCK) ||
((retval == 0) && (retval2 = ext2fs_check_desc(fs))))) {
if (retval2 == ENOMEM) {
retval = retval2;
goto failure;
}
if (fs->flags & EXT2_FLAG_NOFREE_ON_ERROR) {
ext2fs_free(fs);
fs = NULL;
}
if (!fs || (fs->group_desc_count > 1)) {
printf(_("%s: %s trying backup blocks...\n"),
ctx->program_name,
retval ? _("Superblock invalid,") :
_("Group descriptors look bad..."));
orig_superblock = ctx->superblock;
get_backup_sb(ctx, fs, ctx->filesystem_name, io_ptr);
if (fs)
ext2fs_close(fs);
orig_retval = retval;
retval = try_open_fs(ctx, flags, io_ptr, &fs);
if ((orig_retval == 0) && retval != 0) {
if (fs)
ext2fs_close(fs);
com_err(ctx->program_name, retval,
"when using the backup blocks");
printf(_("%s: going back to original "
"superblock\n"), ctx->program_name);
ctx->superblock = orig_superblock;
retval = try_open_fs(ctx, flags, io_ptr, &fs);
}
}
}
if (((retval == EXT2_ET_UNSUPP_FEATURE) ||
(retval == EXT2_ET_RO_UNSUPP_FEATURE)) &&
fs && fs->super) {
sb = fs->super;
features[0] = (sb->s_feature_compat &
~EXT2_LIB_FEATURE_COMPAT_SUPP);
features[1] = (sb->s_feature_incompat &
~EXT2_LIB_FEATURE_INCOMPAT_SUPP);
features[2] = (sb->s_feature_ro_compat &
~EXT2_LIB_FEATURE_RO_COMPAT_SUPP);
if (features[0] || features[1] || features[2])
goto print_unsupp_features;
}
failure:
if (retval) {
if (orig_retval)
retval = orig_retval;
com_err(ctx->program_name, retval, _("while trying to open %s"),
ctx->filesystem_name);
if (retval == EXT2_ET_REV_TOO_HIGH) {
printf(_("The filesystem revision is apparently "
"too high for this version of e2fsck.\n"
"(Or the filesystem superblock "
"is corrupt)\n\n"));
fix_problem(ctx, PR_0_SB_CORRUPT, &pctx);
} else if (retval == EXT2_ET_SHORT_READ)
printf(_("Could this be a zero-length partition?\n"));
else if ((retval == EPERM) || (retval == EACCES))
printf(_("You must have %s access to the "
"filesystem or be root\n"),
(ctx->options & E2F_OPT_READONLY) ?
"r/o" : "r/w");
else if (retval == ENXIO)
printf(_("Possibly non-existent or swap device?\n"));
else if (retval == EBUSY)
printf(_("Filesystem mounted or opened exclusively "
"by another program?\n"));
else if (retval == ENOENT)
printf(_("Possibly non-existent device?\n"));
#ifdef EROFS
else if (retval == EROFS)
printf(_("Disk write-protected; use the -n option "
"to do a read-only\n"
"check of the device.\n"));
#endif
else
fix_problem(ctx, PR_0_SB_CORRUPT, &pctx);
fatal_error(ctx, 0);
}
/*
* We only update the master superblock because (a) paranoia;
* we don't want to corrupt the backup superblocks, and (b) we
* don't need to update the mount count and last checked
* fields in the backup superblock (the kernel doesn't update
* the backup superblocks anyway). With newer versions of the
* library this flag is set by ext2fs_open2(), but we set this
* here just to be sure. (No, we don't support e2fsck running
* with some other libext2fs than the one that it was shipped
* with, but just in case....)
*/
fs->flags |= EXT2_FLAG_MASTER_SB_ONLY;
if (!(ctx->flags & E2F_FLAG_GOT_DEVSIZE)) {
__u32 blocksize = EXT2_BLOCK_SIZE(fs->super);
int need_restart = 0;
pctx.errcode = ext2fs_get_device_size2(ctx->filesystem_name,
blocksize,
&ctx->num_blocks);
/*
* The floppy driver refuses to allow anyone else to
* open the device if has been opened with O_EXCL;
* this is unlike other block device drivers in Linux.
* To handle this, we close the filesystem and then
* reopen the filesystem after we get the device size.
*/
if (pctx.errcode == EBUSY) {
ext2fs_close(fs);
need_restart++;
pctx.errcode =
ext2fs_get_device_size2(ctx->filesystem_name,
blocksize,
&ctx->num_blocks);
}
if (pctx.errcode == EXT2_ET_UNIMPLEMENTED)
ctx->num_blocks = 0;
else if (pctx.errcode) {
fix_problem(ctx, PR_0_GETSIZE_ERROR, &pctx);
ctx->flags |= E2F_FLAG_ABORT;
fatal_error(ctx, 0);
}
ctx->flags |= E2F_FLAG_GOT_DEVSIZE;
if (need_restart)
goto restart;
}
ctx->fs = fs;
fs->priv_data = ctx;
fs->now = ctx->now;
sb = fs->super;
if (sb->s_rev_level > E2FSCK_CURRENT_REV) {
com_err(ctx->program_name, EXT2_ET_REV_TOO_HIGH,
_("while trying to open %s"),
ctx->filesystem_name);
get_newer:
fatal_error(ctx, _("Get a newer version of e2fsck!"));
}
/*
* Set the device name, which is used whenever we print error
* or informational messages to the user.
*/
if (ctx->device_name == 0 &&
(sb->s_volume_name[0] != 0)) {
ctx->device_name = string_copy(ctx, sb->s_volume_name,
sizeof(sb->s_volume_name));
}
if (ctx->device_name == 0)
ctx->device_name = string_copy(ctx, ctx->filesystem_name, 0);
for (cp = ctx->device_name; *cp; cp++)
if (isspace(*cp) || *cp == ':')
*cp = '_';
ehandler_init(fs->io);
if ((ctx->mount_flags & EXT2_MF_MOUNTED) &&
!(sb->s_feature_incompat & EXT3_FEATURE_INCOMPAT_RECOVER))
goto skip_journal;
/*
* Make sure the ext3 superblock fields are consistent.
*/
retval = e2fsck_check_ext3_journal(ctx);
if (retval) {
com_err(ctx->program_name, retval,
_("while checking ext3 journal for %s"),
ctx->device_name);
fatal_error(ctx, 0);
}
/*
* Check to see if we need to do ext3-style recovery. If so,
* do it, and then restart the fsck.
*/
if (sb->s_feature_incompat & EXT3_FEATURE_INCOMPAT_RECOVER) {
if (ctx->options & E2F_OPT_READONLY) {
printf(_("Warning: skipping journal recovery "
"because doing a read-only filesystem "
"check.\n"));
io_channel_flush(ctx->fs->io);
} else {
if (ctx->flags & E2F_FLAG_RESTARTED) {
/*
* Whoops, we attempted to run the
* journal twice. This should never
* happen, unless the hardware or
* device driver is being bogus.
*/
com_err(ctx->program_name, 0,
_("unable to set superblock flags on %s\n"), ctx->device_name);
fatal_error(ctx, 0);
}
retval = e2fsck_run_ext3_journal(ctx);
if (retval) {
com_err(ctx->program_name, retval,
_("while recovering ext3 journal of %s"),
ctx->device_name);
fatal_error(ctx, 0);
}
ext2fs_close(ctx->fs);
ctx->fs = 0;
ctx->flags |= E2F_FLAG_RESTARTED;
goto restart;
}
}
skip_journal:
/*
* Check for compatibility with the feature sets. We need to
* be more stringent than ext2fs_open().
*/
features[0] = sb->s_feature_compat & ~EXT2_LIB_FEATURE_COMPAT_SUPP;
features[1] = sb->s_feature_incompat & ~EXT2_LIB_FEATURE_INCOMPAT_SUPP;
features[2] = (sb->s_feature_ro_compat &
~EXT2_LIB_FEATURE_RO_COMPAT_SUPP);
print_unsupp_features:
if (features[0] || features[1] || features[2]) {
int i, j;
__u32 *mask = features, m;
fprintf(stderr, _("%s has unsupported feature(s):"),
ctx->filesystem_name);
for (i=0; i <3; i++,mask++) {
for (j=0,m=1; j < 32; j++, m<<=1) {
if (*mask & m)
fprintf(stderr, " %s",
e2p_feature2string(i, m));
}
}
putc('\n', stderr);
goto get_newer;
}
#ifdef ENABLE_COMPRESSION
if (sb->s_feature_incompat & EXT2_FEATURE_INCOMPAT_COMPRESSION)
com_err(ctx->program_name, 0,
_("Warning: compression support is experimental.\n"));
#endif
#ifndef ENABLE_HTREE
if (sb->s_feature_compat & EXT2_FEATURE_COMPAT_DIR_INDEX) {
com_err(ctx->program_name, 0,
_("E2fsck not compiled with HTREE support,\n\t"
"but filesystem %s has HTREE directories.\n"),
ctx->device_name);
goto get_newer;
}
#endif
/*
* If the user specified a specific superblock, presumably the
* master superblock has been trashed. So we mark the
* superblock as dirty, so it can be written out.
*/
if (ctx->superblock &&
!(ctx->options & E2F_OPT_READONLY))
ext2fs_mark_super_dirty(fs);
/*
* Calculate the number of filesystem blocks per pagesize. If
* fs->blocksize > page_size, set the number of blocks per
* pagesize to 1 to avoid division by zero errors.
*/
#ifdef _SC_PAGESIZE
sysval = sysconf(_SC_PAGESIZE);
if (sysval > 0)
sys_page_size = sysval;
#endif /* _SC_PAGESIZE */
ctx->blocks_per_page = sys_page_size / fs->blocksize;
if (ctx->blocks_per_page == 0)
ctx->blocks_per_page = 1;
if (ctx->superblock)
set_latch_flags(PR_LATCH_RELOC, PRL_LATCHED, 0);
ext2fs_mark_valid(fs);
check_super_block(ctx);
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
fatal_error(ctx, 0);
check_if_skip(ctx);
check_resize_inode(ctx);
if (bad_blocks_file)
read_bad_blocks_file(ctx, bad_blocks_file, replace_bad_blocks);
else if (cflag)
read_bad_blocks_file(ctx, 0, !keep_bad_blocks); /* Test disk */
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
fatal_error(ctx, 0);
/*
* Mark the system as valid, 'til proven otherwise
*/
ext2fs_mark_valid(fs);
retval = ext2fs_read_bb_inode(fs, &fs->badblocks);
if (retval) {
com_err(ctx->program_name, retval,
_("while reading bad blocks inode"));
preenhalt(ctx);
printf(_("This doesn't bode well,"
" but we'll try to go on...\n"));
}
/*
* Save the journal size in megabytes.
* Try and use the journal size from the backup else let e2fsck
* find the default journal size.
*/
if (sb->s_jnl_backup_type == EXT3_JNL_BACKUP_BLOCKS)
journal_size = sb->s_jnl_blocks[16] >> 20;
else
void main(int argc,String *argv) {
mcheck();
randomise();
a=ArgParser(argc,argv);
nnname=a.argafter("-nn","nn name","current.net");
tsname=a.argafter("-ts","trainset name","current.pat");
eacq=a.intafter("-eqcq","Edge Angle Cancelling histogram quantisation",16);
eacrad=a.intafter("-eacrad","Default radius for eac",6);
glq=a.intafter("-glq","greylevel quantisation",32);
glhistrad=a.intafter("-glvr","Default radius for gl variance",3);
windres=a.intafter("-wskip","pixel skip for window segmentation",5);
botres=a.intafter("-br","bottom res for neighbour segmenter (botres*2^n=topres)",2);
topres=a.intafter("-tr","top res",32);
notext=a.floatafter("-nt","not text if < than",-4.5);
istext=a.floatafter("-it","is text if > than",-2.0);
show=a.argexists("-show","show results of measures");
usenumpostrainexs=a.intafter("-nptes","number of positive training examples to output",50);
usenumnegtrainexs=a.intafter("-nntes","number of positive training examples to output",50);
scale=a.floatafter("-s","scale",0.5);
morphrad=a.intafter("-mr","radius for morphology",3);
twooutnodes=true; // a.argexists("-to","two output nodes");
minarea=a.intafter("-ms","minimum size of kept region",200);
// ghistscale=a.floatafter("-ghs","scale for hist stability",0.5);
a.opts.add("task = trainset | newnn | trainnn | scan | test");
String task=a.arg("task");
if (Seq(task,"trainset")) {
a.opts.add("trainset task = new | image | finish");
String task2=a.arg("trainset task");
if (Seq(task2,"new")) {
tsname=a.argor(tsname);
a.done();
makenewtrainingset();
} else if (Seq(task2,"image")) {
iname=a.arg("image file");
a.done();
trainimage();
} else if(Seq(task2,"finish")) {
a.done();
finishtrainingset();
} else {
a.done();
error("Please choose a task for the training set");
}
} else if (Seq(task,"newnn")) {
a.opts.add("nn type = hopfield | banana");
String type=a.arg("nn type");
a.done();
makenewnn(type);
} else if (Seq(task,"trainnn")) {
a.done();
trainnetwork();
} else if (Seq(task,"scan")) {
iname=a.arg("image file");
a.done();
scanimage();
} else if (Seq(task,"test")) {
iname=a.arg("image file");
a.done();
testimage();
} else {
a.done();
error("Please choose a task.");
}
printf("jnn : Finished.\n");
