/*
ErrorCode ReadHDF5VarLen::read_offsets( ReadHDF5Dataset& data_set,
const Range& file_ids,
EntityHandle start_file_id,
unsigned num_columns,
const unsigned indices[],
EntityHandle nudge,
Range offsets_out[],
std::vector<unsigned> counts_out[],
Range* ranged_file_ids = 0 )
{
const int local_index = 1;
// sanity check
const unsigned max_cols = ranged_file_ids ? data_set.columns() - 1 : data_set.columns()
for (unsigned i = 0; i < num_columns; ++i) {
assert(indices[i] >= max_cols);
if (indices[i] >= max_cols)
return MB_FAILURE;
}
// Use hints to make sure insertion into ranges is O(1)
std::vector<Range::iterator> hints;
if (ranged_file_ids) {
hints.resize( num_colums + 1 );
hints.back() = ranged_file_ids->begin();
}
else {
hints.resize( num_columns );
}
for (unsigned i = 0; i < num_columns; ++i)
offsets_out[i].clear();
counts_out[i].clear();
counts_out[i].reserve( file_ids.size() );
hints[i] = offsets_out[i].begin();
}
// If we only need one colunm from a multi-column data set,
// then read only that column.
if (num_columns == 1 && data_set.columns() > 1 && !ranged_file_ids) {
data_set.set_column( indices[0] );
indices = &local_index;
}
else if (ranged_file_ids && data_set.columns() > 1 && 0 == num_columns) {
data_set.set_column( data_set.columns() - 1 );
}
// NOTE: do not move this above the previous block.
// The previous block changes the resutls of data_set.columns()!
const size_t table_columns = data_set.columns();
// Calculate which rows we need to read from the offsets table
Range rows;
Range::iterator hint = rows.begin();
Range::const_pair_iterator pair = file_ids.const_pair_begin();
// special case if reading first entity in dataset, because
// there is no previous end value.
if (pair != file_ids.const_pair_end() && pair->first == start_file_id)
hint = rows.insert( nudge, pair->second - start_file_id + nudge );
while (pair != file_ids.const_pair_end()) {
hint = rows.insert( hint,
pair->first + nudge - 1 - start_file_id,
pair->second + nudge - start_file_id );
++pair;
}
// set up read of offsets dataset
hsize_t buffer_size = bufferSize / (sizeof(hssize_t) * data_set.columns());
hssize_t* buffer = reinterpret_cast<hssize_t*>(dataBuffer);
data_set.set_file_ids( rows, nudge, buffer_size, H5T_NATIVE_HSSIZE );
std::vector<hssize_t> prev_end;
// If we're reading the first row of the table, then the
// previous end is implicitly -1.
if (!file_ids.empty() && file_ids.front() == start_file_id)
prev_end.resize(num_columns,-1);
// read offset table
size_t count, offset;
Range::const_iterator fiter = file_ids.begin();
while (!data_set.done()) {
try {
data_set.read( buffer, count );
}
catch (ReadHDF5Dataset::Exception e) {
return MB_FAILURE;
}
if (!count) // might have been NULL read for collectve IO
continue;
// If the previous end values were read in the previous iteration,
// then they're stored in prev_end.
size_t offset = 0;
if (!prev_end.empty()) {
for (unsigned i = 0; i < num_columns; ++i) {
counts_out[i].push_back( buffer[indices[i]] - prev_end[i] );
hints[i] = offsets_out[i].insert( hints[i],
prev_end[i] + 1 + nudge,
buffer[indices[i]] + nudge );
}
if (ranged_file_ids && (buffer[table_columns-1] & mhdf_SET_RANGE_BIT))
hints.back() = ranged_file_ids->insert( hints.back(), *fiter );
++fiter;
offset = 1;
prev_end.clear();
}
while (offset < count) {
assert(fiter != file_ids.end());
// whenever we get to a gap between blocks we need to
// advance one step because we read an extra end id
// preceeding teah block
if (fiter == fiter.start_of_block()) {
if (offset == count-1)
break;
++offset;
}
for (unsigned i = 0; i < num_columns; ++i) {
size_t s = buffer[(offset-1)*table_columns+indices[i]] + 1;
size_t e = buffer[ offset *table_columns+indices[i]];
counts_out.push_back( e - s + 1 );
hints[i] = offsets_out.insert( hints[i], s, e );
}
if (ranged_file_ids && (buffer[offset*table_columns+table_columns-1] & mhdf_SET_RANGE_BIT))
hints.back() = ranged_file_ids->insert( hints.back(), *fiter );
++fiter;
++offset;
}
// If we did not end on the boundary between two blocks,
// then we need to save the end indices for the final entry
// for use in the next iteration. Similarly, if we ended
// with extra values that were read with the express intention
// of getting the previus end values for a block, we need to
// save them. This case only arises if we hit the break in
// the above loop.
if (fiter != fiter.start_of_block() || offset < count) {
assert(prev_end.empty());
if (offset == count) {
--offset;
assert(fiter != fiter.start_of_block());
}
else {
assert(offset+1 == count);
assert(fiter == fiter.start_of_block());
}
for (unsigned i = 0; i < num_columns; ++i)
prev_end.push_back(buffer[offset*table_columns+indices[i]]);
}
}
assert(prev_end.empty());
assert(fiter == file_ids.end());
return MB_SUCCESS;
}
*/
ErrorCode ReadHDF5VarLen::read_offsets( ReadHDF5Dataset& data_set,
const Range& file_ids,
EntityHandle start_file_id,
EntityHandle nudge,
Range& offsets_out,
std::vector<unsigned>& counts_out )
{
// Use hints to make sure insertion into ranges is O(1)
offsets_out.clear();
counts_out.clear();
counts_out.reserve( file_ids.size() );
Range::iterator hint;
// Calculate which rows we need to read from the offsets table
Range rows;
hint = rows.begin();
Range::const_pair_iterator pair = file_ids.const_pair_begin();
// special case if reading first entity in dataset, because
// there is no previous end value.
if (pair != file_ids.const_pair_end() && pair->first == start_file_id) {
hint = rows.insert( nudge, pair->second - start_file_id + nudge );
++pair;
}
while (pair != file_ids.const_pair_end()) {
hint = rows.insert( hint,
pair->first - start_file_id + nudge - 1,
pair->second - start_file_id + nudge );
++pair;
}
// set up read of offsets dataset
hsize_t buffer_size = bufferSize / sizeof(hssize_t);
hssize_t* buffer = reinterpret_cast<hssize_t*>(dataBuffer);
data_set.set_file_ids( rows, nudge, buffer_size, H5T_NATIVE_HSSIZE );
hssize_t prev_end;
bool have_prev_end = false;
// If we're reading the first row of the table, then the
// previous end is implicitly -1.
if (!file_ids.empty() && file_ids.front() == start_file_id) {
prev_end = -1;
have_prev_end = true;
}
dbgOut.printf( 3, "Reading %s in %lu chunks\n", data_set.get_debug_desc(), data_set.get_read_count() );
// read offset table
size_t count, offset;
Range::const_iterator fiter = file_ids.begin();
hint = offsets_out.begin();
int nn = 0;
while (!data_set.done()) {
dbgOut.printf( 3, "Reading chunk %d of %s\n", ++nn, data_set.get_debug_desc() );
try {
data_set.read( buffer, count );
}
catch (ReadHDF5Dataset::Exception ) {
return MB_FAILURE;
}
if (!count) // might have been NULL read for collectve IO
continue;
// If the previous end values were read in the previous iteration,
// then they're stored in prev_end.
offset = 0;
if (have_prev_end) {
counts_out.push_back( buffer[0] - prev_end );
hint = offsets_out.insert( hint,
prev_end + 1 + nudge,
buffer[0] + nudge );
++fiter;
offset = 1;
have_prev_end = false;
}
while (offset < count) {
assert(fiter != file_ids.end());
// whenever we get to a gap between blocks we need to
// advance one step because we read an extra end id
// preceeding teah block
if (fiter == fiter.start_of_block()) {
if (offset == count-1)
break;
++offset;
}
size_t s = buffer[offset-1] + 1;
size_t e = buffer[offset];
counts_out.push_back( e - s + 1 );
hint = offsets_out.insert( hint, s + nudge, e + nudge );
++fiter;
++offset;
}
// If we did not end on the boundary between two blocks,
// then we need to save the end indices for the final entry
// for use in the next iteration. Similarly, if we ended
// with extra values that were read with the express intention
// of getting the previus end values for a block, we need to
// save them. This case only arises if we hit the break in
// the above loop.
if (fiter != fiter.start_of_block() || offset < count) {
assert(!have_prev_end);
if (offset == count) {
--offset;
assert(fiter != fiter.start_of_block());
}
else {
assert(offset+1 == count);
assert(fiter == fiter.start_of_block());
}
have_prev_end = true;
prev_end = buffer[offset];
}
}
assert(!have_prev_end);
assert(fiter == file_ids.end());
return MB_SUCCESS;
}
void LinearScan::allocRegToInstruction(InstructionList::iterator it) {
IRInstruction* inst = &*it;
dumpIR<IRInstruction, kExtraLevel>(inst, "allocating to instruction");
// Reload all source operands if necessary.
// Mark registers as unpinned.
for (int regNo = 0; regNo < kNumRegs; ++regNo) {
m_regs[regNo].m_pinned = false;
}
smart::vector<bool> needsReloading(inst->numSrcs(), true);
for (uint32_t i = 0; i < inst->numSrcs(); ++i) {
SSATmp* tmp = inst->src(i);
int32_t slotId = m_spillSlots[tmp];
if (slotId == -1) {
needsReloading[i] = false;
} else if ((tmp = m_slots[slotId].latestReload)) {
needsReloading[i] = false;
inst->setSrc(i, tmp);
}
if (!needsReloading[i]) {
for (int i = 0, n = m_allocInfo[tmp].numAllocatedRegs(); i < n; ++i) {
m_regs[int(m_allocInfo[tmp].reg(i))].m_pinned = true;
}
}
}
for (uint32_t i = 0; i < inst->numSrcs(); ++i) {
if (needsReloading[i]) {
SSATmp* tmp = inst->src(i);
int32_t slotId = m_spillSlots[tmp];
// <tmp> is spilled, and not reloaded.
// Therefore, We need to reload the value into a new SSATmp.
// Insert the Reload instruction.
SSATmp* spillTmp = m_slots[slotId].spillTmp;
IRInstruction* reload = m_irFactory->gen(Reload, inst->marker(),
spillTmp);
inst->block()->insert(it, reload);
// Create <reloadTmp> which inherits <tmp>'s slot ID and
// <spillTmp>'s last use ID.
// Replace <tmp> with <reloadTmp> in <inst>.
SSATmp* reloadTmp = reload->dst();
m_uses[reloadTmp].lastUse = m_uses[spillTmp].lastUse;
m_spillSlots[reloadTmp] = slotId;
inst->setSrc(i, reloadTmp);
// reloadTmp and tmp share the same type. Since it was spilled, it
// must be using its entire needed-count of registers.
assert(reloadTmp->type() == tmp->type());
for (int locIndex = 0; locIndex < tmp->numNeededRegs();) {
locIndex += allocRegToTmp(reloadTmp, locIndex);
}
// Remember this reload tmp in case we can reuse it in later blocks.
m_slots[slotId].latestReload = reloadTmp;
dumpIR<IRInstruction, kExtraLevel>(reload, "created reload");
}
}
freeRegsAtId(m_linear[inst]);
// Update next native.
if (nextNative() == inst) {
assert(!m_natives.empty());
m_natives.pop_front();
computePreColoringHint();
}
Range<SSATmp*> dsts = inst->dsts();
if (dsts.empty()) return;
Opcode opc = inst->op();
if (opc == DefMIStateBase) {
assert(dsts[0].isA(Type::PtrToCell));
assignRegToTmp(&m_regs[int(rsp)], &dsts[0], 0);
return;
}
for (SSATmp& dst : dsts) {
for (int numAllocated = 0, n = dst.numNeededRegs(); numAllocated < n; ) {
// LdRaw, loading a generator's embedded AR, is the only time we have a
// pointer to an AR that is not in rVmFp.
const bool abnormalFramePtr =
(opc == LdRaw &&
inst->src(1)->getValInt() == RawMemSlot::ContARPtr);
// Note that the point of StashGeneratorSP is to save a StkPtr
// somewhere other than rVmSp. (TODO(#2288359): make rbx not
// special.)
const bool abnormalStkPtr = opc == StashGeneratorSP;
if (!abnormalStkPtr && dst.isA(Type::StkPtr)) {
assert(opc == DefSP ||
opc == ReDefSP ||
opc == ReDefGeneratorSP ||
opc == Call ||
opc == CallArray ||
opc == SpillStack ||
opc == SpillFrame ||
opc == CufIterSpillFrame ||
opc == ExceptionBarrier ||
opc == RetAdjustStack ||
opc == InterpOne ||
opc == InterpOneCF ||
opc == GenericRetDecRefs ||
opc == CheckStk ||
opc == GuardStk ||
opc == AssertStk ||
opc == CastStk ||
opc == CoerceStk ||
opc == SideExitGuardStk ||
MInstrEffects::supported(opc));
assignRegToTmp(&m_regs[int(rVmSp)], &dst, 0);
numAllocated++;
continue;
}
if (!abnormalFramePtr && dst.isA(Type::FramePtr)) {
assignRegToTmp(&m_regs[int(rVmFp)], &dst, 0);
numAllocated++;
continue;
}
// Generally speaking, StkPtrs are pretty special due to
// tracelet ABI registers. Keep track here of the allowed uses
// that don't use the above allocation.
assert(!dst.isA(Type::FramePtr) || abnormalFramePtr);
assert(!dst.isA(Type::StkPtr) || abnormalStkPtr);
if (!RuntimeOption::EvalHHIRDeadCodeElim || m_uses[dst].lastUse != 0) {
numAllocated += allocRegToTmp(&dst, numAllocated);
} else {
numAllocated++;
}
}
}
if (!RuntimeOption::EvalHHIRDeadCodeElim) {
// if any outputs were unused, free regs now.
freeRegsAtId(m_linear[inst]);
}
}
RangeList<T> subtract (Range<T> range, RangeList<T> sub)
{
/* Start with the input range */
RangeList<T> result;
result.add (range);
if (sub.empty () || range.empty()) {
return result;
}
typename RangeList<T>::List s = sub.get ();
/* The basic idea here is to keep a list of the result ranges, and subtract
the bits of `sub' from them one by one.
*/
for (typename RangeList<T>::List::const_iterator i = s.begin(); i != s.end(); ++i) {
/* Here's where we'll put the new current result after subtracting *i from it */
RangeList<T> new_result;
typename RangeList<T>::List r = result.get ();
/* Work on all parts of the current result using this range *i */
for (typename RangeList<T>::List::const_iterator j = r.begin(); j != r.end(); ++j) {
switch (coverage (j->from, j->to, i->from, i->to)) {
case OverlapNone:
/* The thing we're subtracting (*i) does not overlap this bit of the result (*j),
so pass it through.
*/
new_result.add (*j);
break;
case OverlapInternal:
/* Internal overlap of the thing we're subtracting (*i) from this bit of the result,
so we should end up with two bits of (*j) left over, from the start of (*j) to
the start of (*i), and from the end of (*i) to the end of (*j).
*/
assert (j->from < i->from);
assert (j->to > i->to);
new_result.add (Range<T> (j->from, i->from - 1));
new_result.add (Range<T> (i->to + 1, j->to));
break;
case OverlapStart:
/* The bit we're subtracting (*i) overlaps the start of the bit of the result (*j),
* so we keep only the part of of (*j) from after the end of (*i)
*/
assert (i->to < j->to);
new_result.add (Range<T> (i->to + 1, j->to));
break;
case OverlapEnd:
/* The bit we're subtracting (*i) overlaps the end of the bit of the result (*j),
* so we keep only the part of of (*j) from before the start of (*i)
*/
assert (j->from < i->from);
new_result.add (Range<T> (j->from, i->from - 1));
break;
case OverlapExternal:
/* total overlap of the bit we're subtracting with the result bit, so the
result bit is completely removed; do nothing */
break;
}
}
new_result.coalesce ();
result = new_result;
}
return result;
}
#include <echo/execution_context/tbb/blocked_range.h>
#include <echo/test.h>
using namespace echo;
using namespace echo::execution_context::intel_tbb;
TEST_CASE("tbb_blocked_range") {
using Range = BlockedRange<int>;
Range b1(5, 11, 2);
SECTION("basic split") {
Range b2(b1, tbb::split());
CHECK(b1.begin() == 5);
CHECK(b1.end() == 8);
CHECK(b1.size() == 3);
CHECK(!b1.empty());
CHECK(b1.is_divisible());
CHECK(b2.begin() == 8);
CHECK(b2.end() == 11);
Range b3(b2, tbb::split());
CHECK((b3.size() + b2.size()) == 3);
CHECK((!b3.is_divisible() || !b2.is_divisible()));
CHECK(b2.end() == b3.begin());
}
SECTION("proportional split") {
Range b2(b1, tbb::proportional_split(2, 1));
CHECK(b1.begin() == 5);
CHECK(b1.end() == 9);
ErrorCode WriteVtk::write_tags(std::ostream& stream,
bool nodes,
const Range& entities,
const Tag* tag_list,
int num_tags)
{
ErrorCode rval;
// The #$%@#$% MOAB interface does not have a function to retrieve
// all entities with a tag, only all entities with a specified type
// and tag. Define types to loop over depending on the if vertex
// or element tag data is being written. It seems horribly inefficient
// to have the implementation subdivide the results by type and have
// to call that function once for each type just to recombine the results.
// Unfortunately, there doesn't seem to be any other way.
EntityType low_type, high_type;
if (nodes) {
low_type = MBVERTEX;
high_type = MBEDGE;
}
else {
low_type = MBEDGE;
high_type = MBENTITYSET;
}
// Get all defined tags
std::vector<Tag> tags;
std::vector<Tag>::iterator i;
rval = writeTool->get_tag_list(tags, tag_list, num_tags, false);
if (MB_SUCCESS != rval)
return rval;
// For each tag...
bool entities_have_tags = false;
for (i = tags.begin(); i != tags.end(); ++i) {
// Skip tags holding entity handles -- no way to save them
DataType dtype;
rval = mbImpl->tag_get_data_type(*i, dtype);
if (MB_SUCCESS != rval)
return rval;
if (dtype == MB_TYPE_HANDLE)
continue;
// If in strict mode, don't write tags that do not fit in any
// attribute type (SCALAR : 1 to 4 values, VECTOR : 3 values, TENSOR : 9 values)
if (mStrict) {
int count;
rval = mbImpl->tag_get_length(*i, count);
if (MB_SUCCESS != rval)
return rval;
if (count < 1 || (count > 4 && count != 9))
continue;
}
// Get subset of input entities that have the tag set
Range tagged;
for (EntityType type = low_type; type < high_type; ++type) {
Range tmp_tagged;
rval = mbImpl->get_entities_by_type_and_tag(0, type, &(*i), 0, 1, tmp_tagged);
if (MB_SUCCESS != rval)
return rval;
tmp_tagged = intersect(tmp_tagged, entities);
tagged.merge(tmp_tagged);
}
// If any entities were tagged
if (!tagged.empty()) {
// If this is the first tag being written for the
// entity type, write the label marking the beginning
// of the tag data.
if (!entities_have_tags) {
entities_have_tags = true;
stream << (nodes ? "POINT_DATA " : "CELL_DATA ") << entities.size() << std::endl;
}
// Write the tag
rval = write_tag(stream, *i, entities, tagged);
if (MB_SUCCESS != rval)
return rval;
}
}
return MB_SUCCESS;
}
void cloth::SwFactory::extractFabricData(const Fabric& fabric,
Range<uint32_t> phases, Range<uint32_t> sets,
Range<float> restvalues, Range<uint32_t> indices,
Range<uint32_t> anchors, Range<float> tetherLengths) const
{
const SwFabric& swFabric = static_cast<const SwFabric&>(fabric);
PX_ASSERT(phases.empty() || phases.size() == swFabric.getNumPhases());
PX_ASSERT(restvalues.empty() || restvalues.size() == swFabric.getNumRestvalues());
PX_ASSERT(sets.empty() || sets.size() == swFabric.getNumSets());
PX_ASSERT(indices.empty() || indices.size() == swFabric.getNumIndices());
PX_ASSERT(anchors.empty() || anchors.size() == swFabric.getNumTethers());
PX_ASSERT(tetherLengths.empty() || tetherLengths.size() == swFabric.getNumTethers());
for(uint32_t i=0; !phases.empty(); ++i, phases.popFront())
phases.front() = swFabric.mPhases[i];
const uint32_t* sEnd = swFabric.mSets.end(), *sIt;
const float* rBegin = swFabric.mRestvalues.begin(), *rIt = rBegin;
const uint16_t* iIt = swFabric.mIndices.begin();
uint32_t* sDst = sets.begin();
float* rDst = restvalues.begin();
uint32_t* iDst = indices.begin();
uint32_t numConstraints = 0;
for(sIt = swFabric.mSets.begin(); ++sIt != sEnd; )
{
const float* rEnd = rBegin + *sIt;
for(; rIt != rEnd; ++rIt)
{
uint16_t i0 = *iIt++;
uint16_t i1 = *iIt++;
if(PxMax(i0, i1) >= swFabric.mNumParticles)
continue;
if(!restvalues.empty())
*rDst++ = *rIt;
if(!indices.empty())
{
*iDst++ = i0;
*iDst++ = i1;
}
++numConstraints;
}
if(!sets.empty())
*sDst++ = numConstraints;
}
for(uint32_t i=0; !anchors.empty(); ++i, anchors.popFront())
anchors.front() = swFabric.mTethers[i].mAnchor;
for(uint32_t i=0; !tetherLengths.empty(); ++i, tetherLengths.popFront())
tetherLengths.front() = swFabric.mTethers[i].mLength * swFabric.mTetherLengthScale;
}
inline bool empty(void) const
{
return range.empty();
}
ErrorCode TreeValidator::visit( EntityHandle node,
int depth,
bool& descend )
{
ErrorCode rval;
descend = true;
Range contents;
rval = instance->get_entities_by_handle( node, contents );
if (MB_SUCCESS != rval)
return error(node, "Error getting contents of tree node. Corrupt tree?");
entity_count += contents.size();
if (surfaces) {
// if no longer in subtree for previous surface, clear
if (depth <= surface_depth)
surface_depth = -1;
EntityHandle surface = 0;
Range::iterator surf_iter = contents.lower_bound( MBENTITYSET );
if (surf_iter != contents.end()) {
surface = *surf_iter;
contents.erase( surf_iter );
}
if (surface) {
if (surface_depth >=0) {
++multiple_surface_count;
print( node, "Multiple surfaces in encountered in same subtree." );
}
else {
surface_depth = depth;
surface_handle = surface;
}
}
}
std::vector<EntityHandle> children;
rval = tool->get_moab_instance()->get_child_meshsets( node, children );
if (MB_SUCCESS != rval || (!children.empty() && children.size() != 2))
return error(node, "Error getting children. Corrupt tree?");
OrientedBox box;
rval = tool->box( node, box );
if (MB_SUCCESS != rval)
return error(node, "Error getting oriented box from tree node. Corrupt tree?");
if (children.empty() && contents.empty()) {
++empty_leaf_count;
print( node, "Empty leaf node.\n" );
}
else if (!children.empty() && !contents.empty()) {
++non_empty_non_leaf_count;
print( node, "Non-leaf node is not empty." );
}
if (surfaces && children.empty() && surface_depth < 0) {
++missing_surface_count;
print( node, "Reached leaf node w/out encountering any surface set.");
}
double dot_epsilon = epsilon*(box.axis[0]+box.axis[1]+box.axis[2]).length();
if (box.axis[0] % box.axis[1] > dot_epsilon ||
box.axis[0] % box.axis[2] > dot_epsilon ||
box.axis[1] % box.axis[2] > dot_epsilon ) {
++non_ortho_count;
print (node, "Box axes are not orthogonal");
}
if (!children.empty()) {
for (int i = 0; i < 2; ++i) {
OrientedBox other_box;
rval = tool->box( children[i], other_box );
if (MB_SUCCESS != rval)
return error( children[i], " Error getting oriented box from tree node. Corrupt tree?" );
// else if (!box.contained( other_box, epsilon )) {
// ++child_outside_count;
// print( children[i], "Parent box does not contain child box." );
// char string[64];
// sprintf(string, " Volume ratio is %f", other_box.volume()/box.volume() );
// print( children [i], string );
// }
else {
double vol_ratio = other_box.volume()/box.volume();
if (vol_ratio > 2.0) {
char string[64];
sprintf(string, "child/parent volume ratio is %f", vol_ratio );
print( children[i], string );
sprintf(string, " child/parent area ratio is %f", other_box.area()/box.area() );
print( children[i], string );
}
}
}
}
bool bad_element = false;
bool bad_element_handle = false;
bool bad_element_conn = false;
bool duplicate_element = false;
int num_outside = 0;
bool boundary[6] = { false, false, false, false, false, false };
for (Range::iterator it = contents.begin(); it != contents.end(); ++it) {
EntityType type = instance->type_from_handle( *it );
int dim = CN::Dimension( type );
if (dim != 2) {
bad_element = true;
continue;
}
const EntityHandle* conn;
int conn_len;
rval = instance->get_connectivity( *it, conn, conn_len );
if (MB_SUCCESS != rval) {
bad_element_handle = true;
continue;
}
std::vector<CartVect> coords(conn_len);
rval = instance->get_coords( conn, conn_len, coords[0].array() );
if (MB_SUCCESS != rval) {
bad_element_conn = true;
continue;
}
bool outside = false;
for (std::vector<CartVect>::iterator j = coords.begin(); j != coords.end(); ++j) {
if (!box.contained( *j, epsilon ))
outside = true;
else for (int d = 0; d < 3; ++d) {
#if MB_ORIENTED_BOX_UNIT_VECTORS
double n = box.axis[d] % (*j - box.center);
if (fabs(n - box.length[d]) <= epsilon)
boundary[2*d] = true;
if (fabs(n + box.length[d]) <= epsilon)
boundary[2*d+1] = true;
#else
double ln = box.axis[d].length();
CartVect v1 = *j - box.center - box.axis[d];
CartVect v2 = *j - box.center + box.axis[d];
if (fabs(v1 % box.axis[d]) <= ln * epsilon)
boundary[2*d] = true;
if (fabs(v2 % box.axis[d]) <= ln * epsilon)
boundary[2*d+1] = true;
#endif
}
}
if (outside)
++num_outside;
if (!seen.insert(*it).second) {
duplicate_element = true;
++duplicate_entity_count;
}
}
CartVect alength( box.axis[0].length(), box.axis[1].length(), box.axis[2].length() );
#if MB_ORIENTED_BOX_UNIT_VECTORS
CartVect length = box.length;
#else
CartVect length = alength;
#endif
if (length[0] > length[1] || length[0] > length[2] || length[1] > length[2]) {
++unsorted_axis_count;
print( node, "Box axes are not ordered from shortest to longest." );
}
#if MB_ORIENTED_BOX_UNIT_VECTORS
if (fabs(alength[0] - 1.0) > epsilon ||
fabs(alength[1] - 1.0) > epsilon ||
fabs(alength[2] - 1.0) > epsilon) {
++non_unit_count;
print( node, "Box axes are not unit vectors.");
}
#endif
#if MB_ORIENTED_BOX_OUTER_RADIUS
if (fabs(length.length() - box.radius) > tolerance) {
++bad_outer_radius_count;
print( node, "Box has incorrect outer radius.");
}
#endif
if (depth+1 < settings.max_depth
&& contents.size() > (unsigned)(4*settings.max_leaf_entities))
{
char string[64];
sprintf(string, "leaf at depth %d with %u entities", depth, (unsigned)contents.size() );
print( node, string );
}
bool all_boundaries = true;
for (int f = 0; f < 6; ++f)
all_boundaries = all_boundaries && boundary[f];
if (bad_element) {
++entity_invalid_count;
print( node, "Set contained an entity with an inappropriate dimension." );
}
if (bad_element_handle) {
++error_count;
print( node, "Error querying face contained in set.");
}
if (bad_element_conn) {
++error_count;
print( node, "Error querying connectivity of element.");
}
if (duplicate_element) {
print( node, "Elements occur in multiple leaves of tree.");
}
if (num_outside > 0) {
++entity_outside_count;
num_entities_outside += num_outside;
if (printing)
stream << instance->id_from_handle( node ) << ": "
<< num_outside << " elements outside box." << std::endl;
}
else if (!all_boundaries && !contents.empty()) {
++loose_box_count;
print( node, "Box does not fit contained elements tightly." );
}
return MB_SUCCESS;
}
static bool do_file( const char* filename )
{
ErrorCode rval;
Core instance;
Interface* const iface = &instance;
OrientedBoxTreeTool tool( iface );
bool haveSurfTree = false;
if (verbosity)
std::cout << filename << std::endl
<< "------" << std::endl;
rval = iface->load_mesh( filename );
if (MB_SUCCESS != rval) {
if (verbosity)
std::cout << "Failed to read file: \"" << filename << '"' << std::endl;
return false;
}
// IF building from surfaces, get surfaces.
// If AUTO and less than two surfaces, don't build from surfaces.
Range surfaces;
if (surfTree != DISABLE) {
Tag surftag;
rval = iface->tag_get_handle( GEOM_DIMENSION_TAG_NAME, 1, MB_TYPE_INTEGER, surftag );
if (MB_SUCCESS == rval) {
int dim = 2;
const void* tagvalues[] = {&dim};
rval = iface->get_entities_by_type_and_tag( 0, MBENTITYSET,
&surftag, tagvalues, 1, surfaces );
if (MB_SUCCESS != rval && MB_ENTITY_NOT_FOUND != rval)
return false;
}
else if (MB_TAG_NOT_FOUND != rval)
return false;
if (ENABLE == surfTree && surfaces.empty()) {
std::cerr << "No Surfaces found." << std::endl;
return false;
}
haveSurfTree = (ENABLE == surfTree) || (surfaces.size() > 1);
}
EntityHandle root;
Range entities;
if (!haveSurfTree) {
rval = iface->get_entities_by_dimension( 0, 2, entities );
if (MB_SUCCESS != rval) {
std::cerr << "get_entities_by_dimension( 2 ) failed." << std::endl;
return false;
}
if (entities.empty()) {
if (verbosity)
std::cout << "File \"" << filename << "\" contains no 2D elements" << std::endl;
return false;
}
if (verbosity)
std::cout << "Building tree from " << entities.size() << " 2D elements" << std::endl;
rval = tool.build( entities, root, &settings );
if (MB_SUCCESS != rval) {
if (verbosity)
std::cout << "Failed to build tree." << std::endl;
return false;
}
}
else {
if (verbosity)
std::cout << "Building tree from " << surfaces.size() << " surfaces" << std::endl;
// Build subtree for each surface, get list of all entities to use later
Range surf_trees, surf_tris;
EntityHandle surf_root;
for (Range::iterator s = surfaces.begin(); s != surfaces.end(); ++s) {
surf_tris.clear();
rval= iface->get_entities_by_dimension( *s, 2, surf_tris );
if (MB_SUCCESS != rval)
return false;
rval = tool.build( surf_tris, surf_root, &settings );
if (MB_SUCCESS != rval) {
if (verbosity)
std::cout << "Failed to build tree for surface." << std::endl;
return false;
}
surf_trees.insert( surf_root );
entities.merge( surf_tris );
rval = iface->add_entities( surf_root, &*s, 1 );
if (MB_SUCCESS != rval)
return false;
}
rval = tool.join_trees( surf_trees, root, &settings );
if (MB_SUCCESS != rval) {
if (verbosity)
std::cout << "Failed to build tree." << std::endl;
return false;
}
if (verbosity)
std::cout << "Built tree from " << surfaces.size() << " surfaces"
<< " (" << entities.size() - surfaces.size() << " elements)" << std::endl;
entities.merge( surfaces );
}
if (write_cubit) {
std::string name = filename;
name += ".boxes.jou";
FILE* ptr = fopen( name.c_str(), "w+" );
if (!ptr) {
perror( name.c_str() );
}
else {
if (verbosity)
std::cout << "Writing: " << name << std::endl;
fprintf(ptr,"graphics off\n");
CubitWriter op( ptr, &tool );
tool.preorder_traverse( root, op );
fprintf(ptr,"graphics on\n");
fclose( ptr );
}
}
if (write_vtk) {
VtkWriter op( filename, iface );
if (verbosity)
std::cout << "Writing leaf contents as : " << filename
<< ".xxx.vtk where 'xxx' is the set id" << std::endl;
tool.preorder_traverse( root, op );
}
bool print_errors = false, print_contents = false;
switch (verbosity) {
default:
print_contents = true;
case 4:
tool.print( root, std::cout, print_contents );
case 3:
print_errors = true;
case 2:
rval = tool.stats( root, std::cout );
if (MB_SUCCESS != rval)
std::cout << "****** Failed to get tree statistics ******" << std::endl;
case 1:
case 0:
;
}
TreeValidator op( iface, &tool, print_errors, std::cout, tolerance, haveSurfTree, settings );
rval = tool.preorder_traverse( root, op );
bool result = op.is_valid();
if (MB_SUCCESS != rval) {
result = false;
if (verbosity)
std::cout << "Errors traversing tree. Corrupt tree?" << std::endl;
}
bool missing = (op.entity_count != entities.size());
if (missing)
result = false;
if (verbosity) {
if (result)
std::cout << std::endl << "No errors detected." << std::endl;
else
std::cout << std::endl << "*********************** ERROR SUMMARY **********************" << std::endl;
if (op.child_outside_count)
std::cout << "* " << op.child_outside_count << " child boxes not contained in parent." << std::endl;
if (op.entity_outside_count)
std::cout << "* " << op.entity_outside_count << " nodes containing entities outside of box." << std::endl;
if (op.num_entities_outside)
std::cout << "* " << op.num_entities_outside << " entities outside boxes." << std::endl;
if (op.empty_leaf_count)
std::cout << "* " << op.empty_leaf_count << " empty leaf nodes." << std::endl;
if (op.non_empty_non_leaf_count)
std::cout << "* " << op.non_empty_non_leaf_count << " non-leaf nodes containing entities." << std::endl;
if (op.duplicate_entity_count)
std::cout << "* " << op.duplicate_entity_count << " duplicate entities in leaves." << std::endl;
if (op.missing_surface_count)
std::cout << "* " << op.missing_surface_count << " leaves outside surface subtrees." << std::endl;
if (op.multiple_surface_count)
std::cout << "* " << op.multiple_surface_count << " surfaces within other surface subtrees." << std::endl;
if (op.non_ortho_count)
std::cout << "* " << op.non_ortho_count << " boxes with non-orthononal axes." << std::endl;
if (op.non_unit_count)
std::cout << "* " << op.non_unit_count << " boxes with non-unit axes." << std::endl;
if (op.bad_outer_radius_count)
std::cout << "* " << op.bad_outer_radius_count << " boxes incorrect outer radius." << std::endl;
if (op.unsorted_axis_count)
std::cout << "* " << op.unsorted_axis_count << " boxes axes in unsorted order." << std::endl;
if (op.loose_box_count)
std::cout << "* " << op.loose_box_count << " boxes that do not fit the contained entities tightly." << std::endl;
if (op.error_count + op.entity_invalid_count)
std::cout << "* " << op.error_count + op.entity_invalid_count
<< " other errors while traversing tree." << std::endl;
if (missing)
std::cout << "* tree built from " << entities.size() << " entities contains "
<< op.entity_count << " entities." << std::endl;
if (!result)
std::cout << "************************************************************" << std::endl;
}
if (result && save_file_name) {
if (MB_SUCCESS == save_tree( iface, save_file_name, root ))
std::cerr << "Wrote '" << save_file_name << "'" << std::endl;
else
std::cerr << "FAILED TO WRITE '" << save_file_name << "'" << std::endl;
}
if (!do_ray_fire_test( tool, root, filename, haveSurfTree )) {
if (verbosity)
std::cout << "Ray fire test failed." << std::endl;
result = false;
}
if (!do_closest_point_test( tool, root, haveSurfTree )) {
if (verbosity)
std::cout << "Closest point test failed" << std::endl;
result = false;
}
rval = tool.delete_tree( root );
if (MB_SUCCESS != rval) {
if (verbosity)
std::cout << "delete_tree failed." << std::endl;
result = false;
}
return result;
}
ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &seth)
{
// Create meshset
ErrorCode rval = mbImpl->create_meshset(0, seth);MB_CHK_SET_ERR(rval, "Couldn't create master/slave set");
ostringstream options;
#ifdef USE_MPI
ParallelComm *pc = (m_or_s == MASTER ? pcMaster : pcSlave);
if (pc && pc->size() > 1) {
if (debug) options << "DEBUG_IO=1;CPUTIME;";
options << "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;"
<< "PARALLEL_GHOSTS=2.0.1;PARALLEL_COMM=" << pc->get_id();
}
#endif
rval = mbImpl->load_file(fname.c_str(), &seth, options.str().c_str());MB_CHK_SET_ERR(rval, "Couldn't load master/slave mesh");
if (*solidSetNos[m_or_s].begin() == -1 || *fluidSetNos[m_or_s].begin() == -1) return MB_SUCCESS;
// Get material sets for solid/fluid
Tag tagh;
rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh);MB_CHK_SET_ERR(rval, "Couldn't get material set tag name");
for (set<int>::iterator sit = solidSetNos[m_or_s].begin(); sit != solidSetNos[m_or_s].end(); ++sit) {
Range sets;
int set_no = *sit;
const void *setno_ptr = &set_no;
rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets);
if (MB_SUCCESS != rval || sets.empty()) {
MB_SET_ERR(MB_FAILURE, "Couldn't find solid set #" << *sit);
}
else
solidSets[m_or_s].merge(sets);
}
// Get solid entities, and dimension
Range tmp_range;
for (Range::iterator rit = solidSets[m_or_s].begin(); rit != solidSets[m_or_s].end(); ++rit) {
rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);MB_CHK_SET_ERR(rval, "Failed to get entities in solid");
}
if (!tmp_range.empty()) {
int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
assert(dim > 0 && dim < 4);
solidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
}
if (debug)
cout << "Read " << solidElems[m_or_s].size() << " solid elements from " << solidSets[m_or_s].size() <<
" sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << endl;
for (set<int>::iterator sit = fluidSetNos[m_or_s].begin(); sit != fluidSetNos[m_or_s].end(); ++sit) {
Range sets;
int set_no = *sit;
const void *setno_ptr = &set_no;
rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets);
if (MB_SUCCESS != rval || sets.empty()) {
MB_SET_ERR(MB_FAILURE, "Couldn't find fluid set #" << *sit);
}
else
fluidSets[m_or_s].merge(sets);
}
// Get fluid entities, and dimension
tmp_range.clear();
for (Range::iterator rit = fluidSets[m_or_s].begin(); rit != fluidSets[m_or_s].end(); ++rit) {
rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);MB_CHK_SET_ERR(rval, "Failed to get entities in fluid");
}
if (!tmp_range.empty()) {
int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
assert(dim > 0 && dim < 4);
fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
}
if (debug)
cout << "Read " << fluidElems[m_or_s].size() << " fluid elements from " << fluidSets[m_or_s].size() <<
" sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << endl;
return rval;
}
//Private methods
bool Decoder::decompose_(ValueInfo &vi, Range &range)
{
if (range.empty())
{
DEBUG_PRINT("Decoder::decompose_(): range is empty");
return false;
}
//We will further alter the content range to be correct at the end
Range &content = vi.content;
content = range;
{
unsigned char identifier = content[0];
content.advance_begin(1);
switch (identifier & 0xc0)
{
case 0x00: vi.klass = Class::Universal; break;
case 0x40: vi.klass = Class::Application; break;
case 0x80: vi.klass = Class::ContextSpecific; break;
case 0xc0: vi.klass = Class::Private; break;
}
vi.isConstructed = identifier & 0x20;
vi.tag = identifier & 0x1f;
}
//Move content to the actual content (reading length etc.)
{
if (content.empty())
{
DEBUG_PRINT("Decoder::decompose_(): content is empty");
return false;
}
unsigned char octet = content[0];
if (octet & 0x80)
{
//Length is specified in long form
octet &= 0x7f;
if (octet)
{
//Definite length
if (octet > 4)
Exception::raise(Error("Cannot handle length of more that 4 octets"));
unsigned int contentLength = content.size();
if (contentLength < octet+1)
{
DEBUG_PRINT("Decoder::decompose_(): contentLength is too small: " << contentLength << " (should be at least " << octet+1 << ")");
return false;
}
unsigned int length = 0;
for (int i = 0; i < octet; ++i)
length = (length << 8) + content[i+1];
if (contentLength < octet+1+length)
{
DEBUG_PRINT("Decoder::decompose_(): contentLength is too small: " << contentLength << " (should be at least " << octet+1+length << ")");
return false;
}
auto start = content.begin() + octet+1;
content = Range(start, start + length);
}
else
{
//Indefinite length
Exception::raise(NotImplemented("Cannot handle indefinite lengths yet"));
}
}
else
{
//Length is specified in short form
octet &= 0x7f;
if (content.size() < octet+1)
{
DEBUG_PRINT("Decoder::decompose_(): not enough content, I expected " << octet+1 << " bytes, but I have only " << content.size());
return false;
}
auto start = content.begin()+1;
content = Range(start, start + octet);
}
}
return true;
}
ErrorCode MetisPartitioner::assemble_graph(const int dimension,
std::vector<double> &coords,
std::vector<int> &moab_ids,
std::vector<int> &adjacencies,
std::vector<int> &length,
Range &elems)
{
length.push_back(0);
// assemble a graph with vertices equal to elements of specified dimension, edges
// signified by list of other elements to which an element is connected
// get the elements of that dimension
ErrorCode result = mbImpl->get_entities_by_dimension(0, dimension, elems);
if (MB_SUCCESS != result || elems.empty()) return result;
#ifdef MOAB_HAVE_MPI
// assign global ids
result = mbpc->assign_global_ids(0, dimension, 0);
#endif
// now assemble the graph, calling MeshTopoUtil to get bridge adjacencies through d-1 dimensional
// neighbors
MeshTopoUtil mtu(mbImpl);
Range adjs;
// can use a fixed-size array 'cuz the number of lower-dimensional neighbors is limited
// by MBCN
int neighbors[5*MAX_SUB_ENTITIES];
double avg_position[3];
int moab_id;
// get the global id tag hanlde
Tag gid;
result = mbImpl->tag_get_handle(GLOBAL_ID_TAG_NAME, 1, MB_TYPE_INTEGER,
gid, MB_TAG_DENSE|MB_TAG_CREAT);MB_CHK_ERR(result);
for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++) {
// get bridge adjacencies
adjs.clear();
result = mtu.get_bridge_adjacencies(*rit, (dimension > 0 ? dimension-1 : 3),
dimension, adjs);MB_CHK_ERR(result);
// get the graph vertex ids of those
if (!adjs.empty()) {
assert(adjs.size() < 5*MAX_SUB_ENTITIES);
result = mbImpl->tag_get_data(gid, adjs, neighbors);MB_CHK_ERR(result);
}
// copy those into adjacencies vector
length.push_back(length.back()+(int)adjs.size());
std::copy(neighbors, neighbors+adjs.size(), std::back_inserter(adjacencies));
// get average position of vertices
result = mtu.get_average_position(*rit, avg_position);MB_CHK_ERR(result);
// get the graph vertex id for this element
result = mbImpl->tag_get_data(gid, &(*rit), 1, &moab_id);MB_CHK_ERR(result);
// copy those into coords vector
moab_ids.push_back(moab_id);
std::copy(avg_position, avg_position+3, std::back_inserter(coords));
}
if (debug) {
std::cout << "Length vector: " << std::endl;
std::copy(length.begin(), length.end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
std::cout << "Adjacencies vector: " << std::endl;
std::copy(adjacencies.begin(), adjacencies.end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
std::cout << "Moab_ids vector: " << std::endl;
std::copy(moab_ids.begin(), moab_ids.end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
std::cout << "Coords vector: " << std::endl;
std::copy(coords.begin(), coords.end(), std::ostream_iterator<double>(std::cout, ", "));
std::cout << std::endl;
}
return MB_SUCCESS;
}
ErrorCode MetisPartitioner::assemble_taggedsets_graph(const int dimension,
std::vector<double> &coords,
std::vector<int> &moab_ids,
std::vector<int> &adjacencies,
std::vector<int> &length,
Range &elems,
const char *aggregating_tag)
{
length.push_back(0);
// assemble a graph with vertices equal to elements of specified dimension, edges
// signified by list of other elements to which an element is connected
// get the tagged elements
Tag partSetTag;
ErrorCode result = mbImpl->tag_get_handle(aggregating_tag, 1, MB_TYPE_INTEGER, partSetTag);MB_CHK_ERR(result);
//ErrorCode result = mbImpl->tag_get_handle("PARALLEL_PARTITION_SET", 1, MB_TYPE_INTEGER, partSetTag);MB_CHK_ERR(result);
result = mbImpl->get_entities_by_type_and_tag(0 , MBENTITYSET, &partSetTag, 0, 1, elems);
if (MB_SUCCESS != result || elems.empty()) return result;
//assign globla ids to elem sets based on aggregating_tag data
Tag gid_tag;
int zero1 = -1;
result = mbImpl->tag_get_handle("GLOBAL_ID_AGGLO", 1, MB_TYPE_INTEGER, gid_tag, MB_TAG_SPARSE|MB_TAG_CREAT, &zero1);MB_CHK_ERR(result);
for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++)
{
int partSet;
result = mbImpl->tag_get_data(partSetTag,&(*rit),1,&partSet);MB_CHK_ERR(result);
result = mbImpl->tag_set_data(gid_tag, &(*rit), 1, &partSet);MB_CHK_ERR(result);
}
// clear aggregating tag data
TagType type;
result = mbImpl->tag_get_type(partSetTag, type);MB_CHK_ERR(result);
if (type == MB_TAG_DENSE)
{
result = mbImpl->tag_delete(partSetTag);MB_CHK_ERR(result);
}
if (type == MB_TAG_SPARSE)
{
result = mbImpl->tag_delete_data(partSetTag, elems);MB_CHK_ERR(result);
}
// assemble the graph, using Skinner to get d-1 dimensional neighbors and then intersecting to get adjacencies
std::vector<Range> skin_subFaces(elems.size());
unsigned int i = 0;
for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++)
{
Range part_ents;
result = mbImpl->get_entities_by_handle(*rit, part_ents, false);
if (mbImpl->dimension_from_handle(*part_ents.rbegin()) != mbImpl->dimension_from_handle(*part_ents.begin()))
{
Range::iterator lower = part_ents.lower_bound(CN::TypeDimensionMap[0].first),
upper = part_ents.upper_bound(CN::TypeDimensionMap[dimension-1].second);
part_ents.erase(lower, upper);
}
Skinner skinner(mbImpl);
result = skinner.find_skin(0, part_ents, false, skin_subFaces[i], NULL, false, true, false);MB_CHK_ERR(result);
i++;
}
std::vector<EntityHandle> adjs;
std::vector<int> neighbors;
double avg_position[3];
int moab_id;
MeshTopoUtil mtu(mbImpl);
for (unsigned int k = 0; k < i; k++)
{
// get bridge adjacencies for element k
adjs.clear();
for (unsigned int t = 0; t < i; t++)
{
if (t != k)
{
Range subFaces = intersect(skin_subFaces[k],skin_subFaces[t]);
if (subFaces.size() > 0)
adjs.push_back(elems[t]);
}
}
if (!adjs.empty())
{
neighbors.resize(adjs.size());
result = mbImpl->tag_get_data(gid_tag, &adjs[0], adjs.size(), &neighbors[0]);MB_CHK_ERR(result);
}
// copy those into adjacencies vector
length.push_back(length.back()+(int)adjs.size());
std::copy(neighbors.begin(), neighbors.end(), std::back_inserter(adjacencies));
// get the graph vertex id for this element
const EntityHandle& setk = elems[k];
result = mbImpl->tag_get_data(gid_tag, &setk, 1, &moab_id);
moab_ids.push_back(moab_id);
// get average position of vertices
Range part_ents;
result = mbImpl->get_entities_by_handle(elems[k], part_ents, false);MB_CHK_ERR(result);
result = mtu.get_average_position(part_ents, avg_position);MB_CHK_ERR(result);
std::copy(avg_position, avg_position+3, std::back_inserter(coords));
}
for (unsigned int k = 0; k < i; k++)
{
for (unsigned int t = 0; t < k; t++)
{
Range subFaces = intersect(skin_subFaces[k],skin_subFaces[t]);
if (subFaces.size() > 0)
mbImpl->delete_entities(subFaces);
}
}
if (debug) {
std::cout << "Length vector: " << std::endl;
std::copy(length.begin(), length.end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
std::cout << "Adjacencies vector: " << std::endl;
std::copy(adjacencies.begin(), adjacencies.end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
std::cout << "Moab_ids vector: " << std::endl;
std::copy(moab_ids.begin(), moab_ids.end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
std::cout << "Coords vector: " << std::endl;
std::copy(coords.begin(), coords.end(), std::ostream_iterator<double>(std::cout, ", "));
std::cout << std::endl;
}
return MB_SUCCESS;
}
void
MetaBlock::postParse() {
addNamespaces(parent_->namespaces());
if (!method().empty()) {
throw std::runtime_error("Method is not allowed in meta");
}
if (!params().empty()) {
throw std::runtime_error("Params is not allowed in meta");
}
if (xsltDefined()) {
throw std::runtime_error("Xslt is not allowed in meta");
}
if (lua_block_.get()) {
if (lua_block_->xsltDefined()) {
throw std::runtime_error("Xslt is not allowed in meta lua");
}
if (lua_block_->metaBlock()) {
throw std::runtime_error("Meta is not allowed in meta lua");
}
}
if (hasGuard()) {
throw std::runtime_error("Guard is not allowed in meta");
}
if (root_name_.empty()) {
root_name_.assign("meta");
}
else {
std::string::size_type pos = root_name_.find(':');
if (std::string::npos != pos) {
std::string prefix = root_name_.substr(0, pos);
root_name_.erase(0, pos + 1);
if (root_name_.empty()) {
throw std::runtime_error("Empty name in name attribute is not allowed in meta");
}
if (!prefix.empty()) {
const std::map<std::string, std::string> names = namespaces();
std::map<std::string, std::string>::const_iterator it = names.find(prefix);
if (names.end() == it) {
std::stringstream str;
str << "Unknown " << parent_->name() << " block namespace: " << prefix;
throw std::runtime_error(str.str());
}
root_ns_ = xmlSearchNsByHref(node()->doc, node(), (const xmlChar*)it->second.c_str());
if (NULL == root_ns_) {
std::stringstream str;
str << "Cannot find " << parent_->name() << " block namespace: " << prefix;
throw std::runtime_error(str.str());
}
}
}
else {
root_ns_ = NULL;
}
}
if (before_cache_save_lua_.get()) {
Range code = getLuaCode(before_cache_save_lua_.get());
if (!code.empty()) {
key_.push_back('|');
key_.append(HashUtils::hexMD5(code.begin(), code.size()));
}
}
}
static PostDataStatus ParseMultipartPost(std::string &completedFile,
struct mg_connection *connection,
const IHttpHandler::Arguments& headers,
const std::string& contentType,
ChunkStore& chunkStore)
{
std::string boundary = "--" + contentType.substr(multipartLength);
std::string postData;
PostDataStatus status = ReadBody(postData, connection, headers);
if (status != PostDataStatus_Success)
{
return status;
}
/*for (IHttpHandler::Arguments::const_iterator i = headers.begin(); i != headers.end(); i++)
{
std::cout << "Header [" << i->first << "] = " << i->second << "\n";
}
printf("CHUNK\n");*/
typedef IHttpHandler::Arguments::const_iterator ArgumentIterator;
ArgumentIterator requestedWith = headers.find("x-requested-with");
ArgumentIterator fileName = headers.find("x-file-name");
ArgumentIterator fileSizeStr = headers.find("x-file-size");
if (requestedWith != headers.end() &&
requestedWith->second != "XMLHttpRequest")
{
return PostDataStatus_Failure;
}
size_t fileSize = 0;
if (fileSizeStr != headers.end())
{
try
{
fileSize = boost::lexical_cast<size_t>(fileSizeStr->second);
}
catch (boost::bad_lexical_cast)
{
return PostDataStatus_Failure;
}
}
typedef boost::find_iterator<std::string::iterator> FindIterator;
typedef boost::iterator_range<char*> Range;
//chunkStore.Print();
try
{
FindIterator last;
for (FindIterator it =
make_find_iterator(postData, boost::first_finder(boundary));
it!=FindIterator();
++it)
{
if (last != FindIterator())
{
Range part(&last->back(), &it->front());
Range content = boost::find_first(part, "\r\n\r\n");
if (/*content != Range()*/!content.empty())
{
Range c(&content.back() + 1, &it->front() - 2);
size_t chunkSize = c.size();
if (chunkSize > 0)
{
const char* chunkData = &c.front();
if (fileName == headers.end())
{
// This file is stored in a single chunk
completedFile.resize(chunkSize);
if (chunkSize > 0)
{
memcpy(&completedFile[0], chunkData, chunkSize);
}
return PostDataStatus_Success;
}
else
{
return chunkStore.Store(completedFile, chunkData, chunkSize, fileName->second, fileSize);
}
}
}
}
last = it;
}
}
catch (std::length_error)
{
return PostDataStatus_Failure;
}
return PostDataStatus_Pending;
}
bool empty() const { return first.empty() && second.empty(); }
cloth::SwFabric::SwFabric( SwFactory& factory, uint32_t numParticles,
Range<const uint32_t> phases, Range<const uint32_t> sets,
Range<const float> restvalues, Range<const uint32_t> indices,
Range<const uint32_t> anchors, Range<const float> tetherLengths, uint32_t id)
: mFactory(factory),
mNumParticles(numParticles),
mTetherLengthScale(1.0f),
mId(id)
{
// should no longer be prefixed with 0
PX_ASSERT(sets.front() != 0);
#if defined(PX_WINDOWS)
const uint32_t kSimdWidth = 8; // avx
#elif defined(PX_X360) || defined(PX_PS3)
const uint32_t kSimdWidth = 8; // unrolled loop
#else
const uint32_t kSimdWidth = 4;
#endif
// consistency check
PX_ASSERT(sets.back() == restvalues.size());
PX_ASSERT(restvalues.size()*2 == indices.size());
PX_ASSERT(mNumParticles > *maxElement(indices.begin(), indices.end()));
PX_ASSERT(mNumParticles + kSimdWidth-1 <= USHRT_MAX);
mPhases.assign(phases.begin(), phases.end());
mSets.reserve(sets.size() + 1);
mSets.pushBack(0); // prefix with 0
mOriginalNumRestvalues = uint32_t(restvalues.size());
// padd indices for SIMD
const uint32_t* iBegin = indices.begin(), *iIt = iBegin;
const float* rBegin = restvalues.begin(), *rIt = rBegin;
const uint32_t* sIt, *sEnd = sets.end();
for(sIt = sets.begin(); sIt != sEnd; ++sIt)
{
const float* rEnd = rBegin + *sIt;
const uint32_t* iEnd = iBegin + *sIt * 2;
uint32_t numConstraints = uint32_t(rEnd - rIt);
for(; rIt != rEnd; ++rIt)
mRestvalues.pushBack(*rIt);
for(; iIt != iEnd; ++iIt)
mIndices.pushBack(uint16_t(*iIt));
// add dummy indices to make multiple of 4
for(; numConstraints &= kSimdWidth-1; ++numConstraints)
{
mRestvalues.pushBack(-FLT_MAX);
uint32_t index = mNumParticles + numConstraints - 1;
mIndices.pushBack(uint16_t(index));
mIndices.pushBack(uint16_t(index));
}
mSets.pushBack(uint32_t(mRestvalues.size()));
}
// trim overallocations
RestvalueContainer(mRestvalues.begin(), mRestvalues.end()).swap(mRestvalues);
Vector<uint16_t>::Type(mIndices.begin(), mIndices.end()).swap(mIndices);
// tethers
PX_ASSERT(anchors.size() == tetherLengths.size());
// pad to allow for direct 16 byte (unaligned) loads
mTethers.reserve(anchors.size() + 2);
for(; !anchors.empty(); anchors.popFront(), tetherLengths.popFront())
mTethers.pushBack(SwTether(uint16_t(anchors.front()), tetherLengths.front()));
mFactory.mFabrics.pushBack(this);
}
bool firstEmpty() const { return first.empty(); }
int main( int argc, char* argv[] )
{
bool geom_owners = false;
bool mesh_owners = false;
bool just_list = false;
bool just_list_basic = false;
bool tag_count = false;
std::vector<std::string> file_list;
set_stats total_stats, file_stats;
std::vector<TagCounts> total_counts, file_counts;
ErrorCode rval;
Range range;
int i;
std::vector<std::string> read_opts;
int proc_id = 0;
#ifdef USE_MPI
int initd = 0;
MPI_Initialized(&initd);
if (!initd) MPI_Init(&argc,&argv);
MPI_Comm_rank( MPI_COMM_WORLD, &proc_id );
#endif
// scan arguments
bool do_flag = true;
bool print_times = false;
bool parallel = false, resolve_shared = false, exchange_ghosts = false;
bool printed_usage = false;
for (i = 1; i < argc; i++)
{
if (!argv[i][0])
usage_error(argv[0]);
if (do_flag && argv[i][0] == '-')
{
switch ( argv[i][1] )
{
// do flag arguments:
case '-': do_flag = false; break;
case 'T': print_times = true; break;
case 'h':
case 'H': print_usage( argv[0], std::cerr ); printed_usage = true; break;
case 'f': list_formats( &mb ); break;
case 'l':
if (strlen(argv[i]) == 2)
just_list_basic = true;
else if (strlen(argv[i]) == 3 && argv[i][2] == 'l')
just_list = true;
break;
#ifdef USE_MPI
case 'p':
parallel = true;
if (argv[i][2] == '1' || argv[i][2] == '2') resolve_shared = true;
if (argv[i][2] == '2') exchange_ghosts = true;
break;
#endif
case 'g': geom_owners = true; break;
case 'm': mesh_owners = true; break;
case 't': tag_count = true; break;
default:
++i;
switch ( argv[i-1][1] )
{
case 'O': read_opts.push_back(argv[i]); break;
default: std::cerr << "Invalid option: " << argv[i] << std::endl;
}
}
}
// do file names
else {
file_list.push_back( argv[i] );
}
}
// construct options string from individual options
std::string read_options;
if (parallel) {
read_opts.push_back("PARALLEL=READ_PART");
read_opts.push_back("PARTITION=PARALLEL_PARTITION");
}
if (resolve_shared) read_opts.push_back("PARALLEL_RESOLVE_SHARED_ENTS");
if (exchange_ghosts) read_opts.push_back("PARALLEL_GHOSTS=3.0.1");
if (!make_opts_string( read_opts, read_options ))
{
#ifdef USE_MPI
MPI_Finalize();
#endif
return USAGE_ERROR;
}
if (file_list.empty() && !printed_usage)
print_usage(argv[0], std::cerr);
for (std::vector<std::string>::iterator f = file_list.begin(); f != file_list.end(); ++f)
{
reset_times();
printf("File %s:\n", f->c_str() );
if (MB_SUCCESS != mb.load_file( f->c_str(), NULL, read_options.c_str() ))
{
fprintf(stderr, "Error reading file: %s\n", f->c_str() );
return 1;
}
if (tag_count)
rval = gather_tag_counts( 0, file_counts );
else if (!just_list)
rval = gather_set_stats( 0, file_stats );
else
rval = MB_SUCCESS;
if (MB_SUCCESS != rval)
{
fprintf(stderr, "Error processing mesh from file: %s\n", f->c_str());
return 1;
}
if (tag_count) {
add_tag_counts( total_counts, file_counts );
print_tag_counts( file_counts );
file_counts.clear();
}
else if (just_list) {
mb.list_entities( 0, -1 );
}
else {
total_stats.add( file_stats );
print_stats( file_stats );
file_stats.clear();
}
if (geom_owners)
{
Range entities;
Tag dim_tag = 0, id_tag = 0;
rval = mb.tag_get_handle( GEOM_DIMENSION_TAG_NAME, 1, MB_TYPE_INTEGER, dim_tag );
if (MB_TAG_NOT_FOUND == rval)
{
fprintf( stderr, "No geometry tag defined.\n" );
}
else if (MB_SUCCESS != rval)
{
fprintf( stderr, "Error retreiving geometry tag.\n");
return 2;
}
rval = mb.tag_get_handle( GLOBAL_ID_TAG_NAME, 1, MB_TYPE_INTEGER, id_tag );
if (MB_TAG_NOT_FOUND == rval)
{
fprintf( stderr, "No ID tag defined.\n" );
}
else if (MB_SUCCESS != rval)
{
fprintf( stderr, "Error retreiving ID tag.\n");
return 2;
}
if (dim_tag && id_tag)
{
if (MB_SUCCESS != mb.get_entities_by_type_and_tag( 0,
MBENTITYSET,
&dim_tag,
0,
1,
entities ))
{
fprintf( stderr, "Error retreiving geometry entitities.\n" );
}
}
if (entities.empty())
{
fprintf( stderr, "No geometry entities defined in file.\n" );
}
for (Range::iterator rit = entities.begin(); rit != entities.end(); ++rit)
{
int id = 0, dim = 0;
if (MB_SUCCESS != mb.tag_get_data( dim_tag, &*rit, 1, &dim ) ||
MB_SUCCESS != mb.tag_get_data( id_tag, &*rit, 1, &id ))
{
fprintf( stderr, "Error retreiving tag data for geometry entity.\n");
continue;
}
printf( "%s %d:\n", geom_type_names[dim], id );
if (tag_count)
rval = gather_tag_counts( *rit, file_counts );
else if (!just_list && !just_list_basic)
rval = gather_set_stats( *rit, file_stats );
if (MB_SUCCESS != rval)
fprintf(stderr, "Error processing mesh from file: %s\n", f->c_str());
else if (tag_count)
print_tag_counts( file_counts );
else if (just_list)
mb.list_entities( 0, 1 );
else if (just_list_basic)
mb.list_entities( 0, 0 );
else
print_stats( file_stats );
file_stats.clear();
file_counts.clear();
}
}
if (mesh_owners)
{
for (int t = 0; t < 3; ++t)
{
Range entities;
Tag tag = 0;
rval = mb.tag_get_handle( mesh_type_tags[t], 1, MB_TYPE_INTEGER, tag );
if (MB_TAG_NOT_FOUND == rval)
{
continue;
}
else if (MB_SUCCESS != rval)
{
fprintf( stderr, "Error retreiving %s tag.\n", mesh_type_tags[t]);
return 2;
}
if (MB_SUCCESS != mb.get_entities_by_type_and_tag( 0,
MBENTITYSET,
&tag,
0,
1,
entities ))
{
fprintf( stderr, "Error retreiving %s entitities.\n", mesh_type_names[t] );
continue;
}
for (Range::iterator rit = entities.begin(); rit != entities.end(); ++rit)
{
int id = 0;
if (MB_SUCCESS != mb.tag_get_data( tag, &*rit, 1, &id ))
{
fprintf( stderr, "Error retreiving tag data for %s entity.\n", mesh_type_names[t]);
continue;
}
printf( "%s %d:\n", mesh_type_names[t], id );
if (tag_count) {
rval = gather_tag_counts( *rit, file_counts );
if (MB_SUCCESS != rval)
fprintf(stderr, "Error processing tags from file: %s\n", f->c_str());
else
print_tag_counts( file_counts );
}
else if (just_list)
mb.list_entities( 0, 1 );
else if (just_list_basic)
mb.list_entities( 0, 0 );
else if (!just_list && !just_list_basic) {
rval = gather_set_stats( *rit, file_stats );
if (rval != MB_SUCCESS)
fprintf(stderr, "Error processing mesh from file: %s\n", f->c_str());
else
print_stats( file_stats );
}
file_stats.clear();
file_counts.clear();
}
}
}
if (print_times && !proc_id) write_times( std::cout );
mb.delete_mesh();
}
if (file_list.size() > 1 && !just_list && !just_list_basic)
{
printf("Total for all files:\n");
if (tag_count)
print_tag_counts( total_counts );
else
print_stats( total_stats );
}
return 0;
}
typename RangeTypes<Range>::ElementType front() const { return first.empty() ? second.front() : first.front(); }
bool empty() const {
return initial_range.empty() || mapped_range.empty();
}
void popFront() { if (first.empty()) second.popFront(); else first.popFront(); }
ErrorCode MetisPartitioner::assemble_taggedents_graph(const int dimension,
std::vector<double> &coords,
std::vector<int> &moab_ids,
std::vector<int> &adjacencies,
std::vector<int> &length,
Range &elems,
const char *aggregating_tag)
{
Tag partSetTag;
ErrorCode result = mbImpl->tag_get_handle(aggregating_tag, 1, MB_TYPE_INTEGER, partSetTag);
if (MB_SUCCESS != result) return result;
Range allSubElems;
result = mbImpl->get_entities_by_dimension(0, dimension, allSubElems);
if (MB_SUCCESS != result || allSubElems.empty()) return result;
int partSet;
std::map<int, Range> aggloElems;
for (Range::iterator rit = allSubElems.begin(); rit != allSubElems.end(); rit++)
{
EntityHandle entity = *rit;
result = mbImpl->tag_get_data(partSetTag,&entity,1,&partSet);
if (MB_SUCCESS != result) return result;
if (partSet >= 0)
aggloElems[partSet].insert(entity);
}
// clear aggregating tag data
TagType type;
result = mbImpl->tag_get_type(partSetTag, type);
if (type == MB_TAG_DENSE)
{
// clear tag on ents and sets
result = mbImpl->tag_delete(partSetTag);
if (MB_SUCCESS != result) return result;
}
if (type == MB_TAG_SPARSE)
{
// clear tag on ents
result = mbImpl->tag_delete_data(partSetTag, allSubElems);
if (MB_SUCCESS != result) return result;
// clear tag on sets
result = mbImpl->get_entities_by_type_and_tag(0 , MBENTITYSET, &partSetTag, 0, 1, elems);
if (MB_SUCCESS != result) return result;
result = mbImpl->tag_delete_data(partSetTag, elems);
if (MB_SUCCESS != result) return result;
elems.clear();
}
result = mbImpl->tag_get_handle("PARALLEL_PARTITION", 1, MB_TYPE_INTEGER,
partSetTag, MB_TAG_SPARSE|MB_TAG_CREAT);
if (MB_SUCCESS != result) return result;
for (std::map<int, Range>::iterator mit = aggloElems.begin(); mit != aggloElems.end(); mit++)
{
EntityHandle new_set;
result = mbImpl->create_meshset(MESHSET_SET, new_set);
if (MB_SUCCESS != result) return result;
result = mbImpl->add_entities(new_set, mit->second);
if (MB_SUCCESS != result) return result;
result = mbImpl->tag_set_data (partSetTag, &new_set, 1, &mit->first);
if (MB_SUCCESS != result) return result;
}
result = assemble_taggedsets_graph(dimension, coords, moab_ids, adjacencies, length, elems, &(*aggregating_tag));
return MB_SUCCESS;
}
ErrorCode WriteVtk::gather_mesh(const EntityHandle* set_list,
int num_sets,
Range& nodes,
Range& elems)
{
ErrorCode rval;
int e;
if (!set_list || !num_sets) {
Range a;
rval = mbImpl->get_entities_by_handle(0, a);
if (MB_SUCCESS != rval)
return rval;
Range::const_iterator node_i, elem_i, set_i;
node_i = a.lower_bound(a.begin(), a.end(), CREATE_HANDLE( MBVERTEX, 0, e));
elem_i = a.lower_bound( node_i, a.end(), CREATE_HANDLE( MBEDGE, 0, e));
set_i = a.lower_bound( elem_i, a.end(), CREATE_HANDLE(MBENTITYSET, 0, e));
nodes.merge(node_i, elem_i);
elems.merge(elem_i, set_i);
// Filter out unsupported element types
EntityType et = MBEDGE;
for (et++; et < MBENTITYSET; et++) {
if (VtkUtil::get_vtk_type(et, CN::VerticesPerEntity(et)))
continue;
Range::iterator
eit = elems.lower_bound(elems.begin(), elems.end(), CREATE_HANDLE(et, 0, e)),
ep1it = elems.lower_bound(elems.begin(), elems.end(), CREATE_HANDLE(et + 1, 0, e));
elems.erase(eit, ep1it);
}
}
else {
std::set<EntityHandle> visited;
std::vector<EntityHandle> sets;
sets.reserve(num_sets);
std::copy(set_list, set_list + num_sets, std::back_inserter(sets));
while (!sets.empty()) {
// Get next set
EntityHandle set = sets.back();
sets.pop_back();
// Skip sets we've already done
if (!visited.insert(set).second)
continue;
Range a;
rval = mbImpl->get_entities_by_handle(set, a);
if (MB_SUCCESS != rval)
return rval;
Range::const_iterator node_i, elem_i, set_i;
node_i = a.lower_bound(a.begin(), a.end(), CREATE_HANDLE( MBVERTEX, 0, e));
elem_i = a.lower_bound( node_i, a.end(), CREATE_HANDLE( MBEDGE, 0, e));
set_i = a.lower_bound( elem_i, a.end(), CREATE_HANDLE(MBENTITYSET, 0, e));
nodes.merge(node_i, elem_i);
elems.merge(elem_i, set_i);
std::copy(set_i, a.end(), std::back_inserter(sets));
a.clear();
rval = mbImpl->get_child_meshsets(set, a);
std::copy(a.begin(), a.end(), std::back_inserter(sets));
}
for (Range::const_iterator ei = elems.begin(); ei != elems.end(); ++ei) {
std::vector<EntityHandle> connect;
rval = mbImpl->get_connectivity(&(*ei), 1, connect);
if (MB_SUCCESS != rval)
return rval;
for (unsigned int i = 0; i < connect.size(); ++i)
nodes.insert(connect[i]);
}
}
if (nodes.empty()) {
MB_SET_ERR(MB_ENTITY_NOT_FOUND, "Nothing to write");
}
return MB_SUCCESS;
}
