Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
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#include "moab/Core.hpp"
#include "moab/Range.hpp"
#include "moab/CN.hpp"
#include <iostream>
#include <iomanip>
#include <sstream>
#include <string>
#include <cstdio>
#include <cstdlib>
#include <sys/times.h>
#include <sys/resource.h>
#include <unistd.h>
Go to the source code of this file.
Classes | |
struct | MemStats |
Enumerations | |
enum | Units { HUMAN, BYTES, KILOBYTES, MEGABYTES, GIGABYTES } |
Functions | |
static void | usage (const char *argv0, bool help=false) |
static void | print_memory_stats (moab::Interface &mb, bool per_type=true, bool per_tag=true, bool totals=true, bool sysstats=true) |
static void | do_test_mode () |
int | main (int argc, char *argv[]) |
static bool | is_zero (const MemStats &stats) |
static void | get_mem_stats (moab::Interface &mb, MemStats &data, moab::EntityType type=moab::MBMAXTYPE) |
static std::string | memstr (unsigned long long val) |
static std::string | tag_type_string (moab::Interface &mb, moab::Tag tag) |
static std::string | tag_storage_string (moab::Interface &mb, moab::Tag tag) |
static std::string | center (const char *str, size_t width) |
static unsigned long long | rdiv (unsigned long long num, unsigned long long den) |
Variables | |
Units | UNITS = HUMAN |
enum Units |
std::string center | ( | const char * | str, |
size_t | width | ||
) | [static] |
Definition at line 495 of file mbmem.cpp.
Referenced by moab::GeomUtil::box_hex_overlap(), moab::GeomUtil::box_tet_overlap(), moab::BVHTree::Bucket::bucket_index(), moab::Bvh_tree< _Entity_handles, _Box, _Moab, _Parametrizer >::bucket_index(), FBiGeom_getEntBoundBox(), moab::GeomTopoTool::get_bounding_coords(), get_gnomonic_plane(), moab::FBEngine::getEntBoundBox(), moab::IntxUtils::global_gnomonic_projection(), moab::TempestOnlineMap::LinearRemapGLLtoGLL2_MOAB(), moab::TempestOnlineMap::LinearRemapSE4_Tempest_MOAB(), localize_quad_coordinates(), main(), moab::Bvh_tree< _Entity_handles, _Box, _Moab, _Parametrizer >::median_order(), obbvis_create(), moab::HiReconstruction::obtain_nring_ngbvs(), print_memory_stats(), and moab::OrientedBoxTreeTool::sphere_intersect_triangles().
{ std::string text( str ); if( text.size() >= width ) return text; width -= text.size(); if( 1u == width ) { text += " "; return text; } std::ostringstream s; s << std::setw( width / 2 ) << ' ' << text << std::setw( width / 2 + width % 2 ) << ' '; return s.str(); }
void do_test_mode | ( | ) | [static] |
Definition at line 512 of file mbmem.cpp.
References moab::Range::begin(), moab::Range::clear(), moab::Interface::create_element(), moab::Interface::create_vertex(), moab::Range::end(), ErrorCode, moab::Interface::get_adjacencies(), moab::Interface::get_coords(), moab::Interface::get_entities_by_type(), mb, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TYPE_BIT, MB_TYPE_DOUBLE, MB_TYPE_INTEGER, MBQUAD, MBTRI, MBVERTEX, print_memory_stats(), moab::Range::size(), moab::Interface::tag_get_handle(), and moab::Interface::tag_set_data().
Referenced by main().
{ const char prefix[] = "****************"; moab::Core mbcore; moab::Interface& mb = mbcore; moab::ErrorCode rval; moab::Range handles; moab::EntityHandle h; moab::Range::iterator jt, it; const unsigned N = 1000; // creating some vertices double coords[3] = { 1, 2, 3 }; for( unsigned i = 0; i < N; ++i ) mb.create_vertex( coords, h ); std::cout << std::endl << prefix << "Created " << N << " vertices" << std::endl; print_memory_stats( mb, true, false, true, true ); for( unsigned i = 0; i < N; ++i ) mb.create_vertex( coords, h ); std::cout << std::endl << prefix << "Created another " << N << " vertices" << std::endl; print_memory_stats( mb, true, false, true, true ); for( int i = 0; i < 100; ++i ) { for( unsigned j = 0; j < N; ++j ) mb.create_vertex( coords, h ); } std::cout << std::endl << prefix << "Created another " << 100 * N << " vertices" << std::endl; print_memory_stats( mb, true, false, true, true ); // create some elements handles.clear(); mb.get_entities_by_type( 0, moab::MBVERTEX, handles ); it = handles.begin(); for( unsigned i = 0; i < N - 2; ++i, ++it ) { jt = it; moab::EntityHandle conn[3]; conn[0] = *jt; ++jt; conn[1] = *jt; ++jt; conn[2] = *jt; ++jt; mb.create_element( moab::MBTRI, conn, 3, h ); } std::cout << std::endl << prefix << "Created " << N - 2 << " triangles" << std::endl; print_memory_stats( mb, true, false, true, true ); it = handles.begin(); for( unsigned i = 0; i < N - 3; ++i, ++it ) { jt = it; moab::EntityHandle conn[4]; conn[0] = *jt; ++jt; conn[1] = *jt; ++jt; conn[2] = *jt; ++jt; conn[3] = *jt; ++jt; mb.create_element( moab::MBQUAD, conn, 4, h ); } std::cout << std::endl << prefix << "Created " << N - 3 << " quads" << std::endl; print_memory_stats( mb, true, false, true, true ); for( int i = 0; i < 100; ++i ) { it = handles.begin(); for( unsigned j = 0; j < N - 3; ++j, ++it ) { jt = it; moab::EntityHandle conn[4]; conn[0] = *jt; ++jt; conn[1] = *jt; ++jt; conn[2] = *jt; ++jt; conn[3] = *jt; ++jt; mb.create_element( moab::MBQUAD, conn, 4, h ); } } std::cout << std::endl << prefix << "Created another " << 100 * ( N - 3 ) << " quads" << std::endl; print_memory_stats( mb, true, false, true, true ); // set global ID moab::Tag tag; rval = mb.tag_get_handle( "GLOBAL_ID", 1, moab::MB_TYPE_INTEGER, tag ); if( moab::MB_SUCCESS != rval ) { std::cerr << "Failed to get GLOBAL_ID tag handle" << std::endl; return; } handles.clear(); mb.get_entities_by_type( 0, moab::MBVERTEX, handles ); int id = 1; for( it = handles.begin(); it != handles.end(); ++it ) { mb.tag_set_data( tag, &*it, 1, &id ); ++id; } std::cout << std::endl << prefix << "Set global ID tag on " << handles.size() << " vertices" << std::endl; print_memory_stats( mb, true, true, true, true ); handles.clear(); mb.get_entities_by_type( 0, moab::MBQUAD, handles ); id = 1; for( it = handles.begin(); it != handles.end(); ++it ) { mb.tag_set_data( tag, &*it, 1, &id ); ++id; } std::cout << std::endl << prefix << "Set global ID tag on " << handles.size() << " quads" << std::endl; print_memory_stats( mb, true, true, true, true ); // create and set a sparse tag mb.tag_get_handle( "mem_test_tag", 3, moab::MB_TYPE_DOUBLE, tag, moab::MB_TAG_SPARSE | moab::MB_TAG_CREAT ); handles.clear(); mb.get_entities_by_type( 0, moab::MBVERTEX, handles ); for( it = handles.begin(); it != handles.end(); ++it ) { mb.get_coords( &*it, 1, coords ); mb.tag_set_data( tag, &*it, 1, coords ); } std::cout << std::endl << prefix << "Copied vertex coords to sparse tag for " << handles.size() << " vertices" << std::endl; print_memory_stats( mb, true, true, true, true ); // create and set bit tag mb.tag_get_handle( "mem_test_bit", 1, moab::MB_TYPE_BIT, tag, moab::MB_TAG_CREAT ); handles.clear(); mb.get_entities_by_type( 0, moab::MBTRI, handles ); for( it = handles.begin(); it != handles.end(); ++it ) { char byte = '\001'; mb.tag_set_data( tag, &*it, 1, &byte ); } std::cout << std::endl << prefix << "Set 1-bit tag for " << handles.size() << " triangles" << std::endl; print_memory_stats( mb, true, true, true, true ); // create vertex to element adjacency data handles.clear(); mb.get_entities_by_type( 0, moab::MBVERTEX, handles ); std::vector< moab::EntityHandle > adj_vec; mb.get_adjacencies( &*handles.begin(), 1, 2, false, adj_vec ); std::cout << std::endl << prefix << "Created vertex-to-element adjacencies" << std::endl; print_memory_stats( mb, true, false, true, true ); std::cout << std::endl; }
void get_mem_stats | ( | moab::Interface & | mb, |
MemStats & | data, | ||
moab::EntityType | type = moab::MBMAXTYPE |
||
) | [static] |
Definition at line 352 of file mbmem.cpp.
References MemStats::adjacency_amortized, MemStats::adjacency_storage, MemStats::entity_amortized, MemStats::entity_storage, moab::Interface::estimated_memory_use(), moab::Interface::get_entities_by_type(), MBMAXTYPE, MemStats::tag_amortized, MemStats::tag_storage, MemStats::total_amortized, and MemStats::total_storage.
Referenced by print_memory_stats().
{ if( type != moab::MBMAXTYPE ) { moab::Range range; mb.get_entities_by_type( 0, type, range ); mb.estimated_memory_use( range, &data.total_storage, &data.total_amortized, &data.entity_storage, &data.entity_amortized, &data.adjacency_storage, &data.adjacency_amortized, 0, 0, &data.tag_storage, &data.tag_amortized ); } else { mb.estimated_memory_use( 0, 0, &data.total_storage, &data.total_amortized, &data.entity_storage, &data.entity_amortized, &data.adjacency_storage, &data.adjacency_amortized, 0, 0, &data.tag_storage, &data.tag_amortized ); } }
Definition at line 347 of file mbmem.cpp.
References MemStats::total_amortized.
Referenced by print_memory_stats().
{ return stats.total_amortized == 0; }
int main | ( | int | argc, |
char * | argv[] | ||
) |
Definition at line 60 of file mbmem.cpp.
References BYTES, do_test_mode(), ErrorCode, moab::Interface::get_error_string(), moab::Interface::get_last_error(), GIGABYTES, HUMAN, KILOBYTES, moab::Interface::load_file(), mb, MB_SUCCESS, MEGABYTES, print_memory_stats(), UNITS, and usage.
{ moab::ErrorCode rval; bool no_more_flags = false; bool test_mode = false; std::vector< int > input_file_list; // load each file specified on command line for( int i = 1; i < argc; ++i ) { if( !no_more_flags && argv[i][0] == '-' ) { if( !strcmp( argv[i], "-H" ) ) UNITS = HUMAN; else if( !strcmp( argv[i], "-b" ) ) UNITS = BYTES; else if( !strcmp( argv[i], "-k" ) ) UNITS = KILOBYTES; else if( !strcmp( argv[i], "-m" ) ) UNITS = MEGABYTES; else if( !strcmp( argv[i], "-g" ) ) UNITS = GIGABYTES; else if( !strcmp( argv[i], "-T" ) ) test_mode = true; else if( !strcmp( argv[i], "-h" ) ) usage( argv[0], true ); else if( !strcmp( argv[i], "--" ) ) no_more_flags = true; else { std::cerr << argv[0] << ": Invalid flag: \"" << argv[i] << "\"." << std::endl << std::endl; usage( argv[0] ); } } else { input_file_list.push_back( i ); } } if( test_mode ) { do_test_mode(); if( input_file_list.empty() ) return 0; } moab::Core mbcore; moab::Interface& mb = mbcore; for( std::vector< int >::iterator it = input_file_list.begin(); it != input_file_list.end(); ++it ) { rval = mb.load_file( argv[*it] ); // if file load failed, print some info and exit if( moab::MB_SUCCESS != rval ) { std::string message; mb.get_last_error( message ); std::cerr << mb.get_error_string( rval ) << ": " << message << std::endl << argv[*it] << ": Failed to read file." << std::endl; return 1; } std::cout << "Loaded file: " << argv[*it] << std::endl; } // print summary of MOAB's memory use print_memory_stats( mb ); return 0; }
std::string memstr | ( | unsigned long long | val | ) | [static] |
Definition at line 376 of file mbmem.cpp.
References BYTES, GIGABYTES, HUMAN, KILOBYTES, mb, MEGABYTES, rdiv(), and UNITS.
Referenced by print_memory_stats().
{ const unsigned long long kb = 1024; const unsigned long long mb = kb * kb; const unsigned long long gb = kb * mb; const unsigned long long tb = kb * gb; std::ostringstream s; if( UNITS == HUMAN ) { if( val >= 10 * tb ) s << rdiv( val, tb ) << "TB"; else if( val >= 10 * gb ) s << rdiv( val, gb ) << "GB"; else if( val >= 10 * mb ) s << rdiv( val, mb ) << "MB"; else if( val >= 10 * kb ) s << rdiv( val, kb ) << "kB"; else if( val > 0 ) s << val << " B"; else s << "0 "; } else { unsigned long long den = 1; switch( UNITS ) { case BYTES: den = 1; break; case KILOBYTES: den = kb; break; case MEGABYTES: den = mb; break; case GIGABYTES: den = gb; break; case HUMAN: break; // handled above, list here to suppress warning } s << rdiv( val, den ); } return s.str(); }
void print_memory_stats | ( | moab::Interface & | mb, |
bool | per_type = true , |
||
bool | per_tag = true , |
||
bool | totals = true , |
||
bool | sysstats = true |
||
) | [static] |
Definition at line 162 of file mbmem.cpp.
References MemStats::adjacency_amortized, MemStats::adjacency_storage, center(), MemStats::entity_amortized, MemStats::entity_storage, moab::CN::EntityTypeName(), ErrorCode, moab::Interface::estimated_memory_use(), get_mem_stats(), is_zero(), MB_SUCCESS, MBMAXTYPE, MBVERTEX, memstr(), t, MemStats::tag_amortized, moab::Interface::tag_get_name(), moab::Interface::tag_get_tags(), MemStats::tag_storage, tag_storage_string(), tag_type_string(), MemStats::total_amortized, and MemStats::total_storage.
Referenced by do_test_mode(), and main().
{ moab::ErrorCode rval; const char ANON_TAG_NAME[] = "(anonymous)"; const int TYPE_WIDTH = 10; const int MEM_WIDTH = 7; const int MEM2_WIDTH = 2 * MEM_WIDTH + 1; const int MIN_TAG_NAME_WIDTH = strlen( ANON_TAG_NAME ); const int DTYPE_WIDTH = 12; const int STORAGE_WIDTH = 8; // per-entity-type table header MemStats stats; if( per_type ) { std::cout.fill( ' ' ); std::cout << std::left << std::setw( TYPE_WIDTH ) << "Type" << ' ' << center( "Total", MEM2_WIDTH ) << ' ' << center( "Entity", MEM2_WIDTH ) << ' ' << center( "Adjacency", MEM2_WIDTH ) << ' ' << center( "Tag", MEM2_WIDTH ) << ' ' << std::endl << std::setw( TYPE_WIDTH ) << " "; for( int i = 0; i < 4; ++i ) std::cout << ' ' << std::left << std::setw( MEM_WIDTH ) << "Used" << ' ' << std::left << std::setw( MEM_WIDTH ) << "Alloc"; std::cout << std::endl; std::cout.fill( '-' ); std::cout << std::setw( TYPE_WIDTH ) << '-'; for( int i = 0; i < 8; ++i ) std::cout << ' ' << std::setw( MEM_WIDTH ) << '-'; std::cout.fill( ' ' ); std::cout << std::endl; // per-entity-type memory use for( moab::EntityType t = moab::MBVERTEX; t != moab::MBMAXTYPE; ++t ) { get_mem_stats( mb, stats, t ); if( is_zero( stats ) ) continue; // skip types with no allocated memory std::cout << std::left << std::setw( TYPE_WIDTH ) << moab::CN::EntityTypeName( t ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.total_storage ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.total_amortized ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.entity_storage ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.entity_amortized ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.adjacency_storage ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.adjacency_amortized ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.tag_storage ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( stats.tag_amortized ) << std::endl; } } // end per_type if( per_tag ) { // get list of tags std::vector< moab::Tag > tags; std::vector< moab::Tag >::const_iterator ti; mb.tag_get_tags( tags ); // figure out required field with to fit longest tag name unsigned maxlen = MIN_TAG_NAME_WIDTH; for( ti = tags.begin(); ti != tags.end(); ++ti ) { std::string name; rval = mb.tag_get_name( *ti, name ); if( moab::MB_SUCCESS != rval ) continue; if( name.size() > maxlen ) maxlen = name.size(); } // print header for per-tag data if( !tags.empty() ) { std::cout.fill( ' ' ); std::cout << std::endl << std::left << std::setw( maxlen ) << "Tag Name" << ' ' << std::left << std::setw( DTYPE_WIDTH ) << "Type" << ' ' << std::left << std::setw( STORAGE_WIDTH ) << "Storage" << ' ' << std::left << std::setw( MEM_WIDTH ) << "Used" << ' ' << std::left << std::setw( MEM_WIDTH ) << "Alloc" << std::endl; std::cout.fill( '-' ); std::cout << std::setw( maxlen ) << '-' << ' ' << std::setw( DTYPE_WIDTH ) << '-' << ' ' << std::setw( STORAGE_WIDTH ) << '-' << ' ' << std::setw( MEM_WIDTH ) << '-' << ' ' << std::setw( MEM_WIDTH ) << '-' << std::endl; std::cout.fill( ' ' ); } // print per-tag memory use for( ti = tags.begin(); ti != tags.end(); ++ti ) { std::string name; rval = mb.tag_get_name( *ti, name ); if( moab::MB_SUCCESS != rval || name.empty() ) name = ANON_TAG_NAME; unsigned long long occupied, allocated; mb.estimated_memory_use( 0, 0, 0, 0, 0, 0, 0, 0, &*ti, 1, &occupied, &allocated ); std::cout << std::left << std::setw( maxlen ) << name << ' ' << std::right << std::setw( DTYPE_WIDTH ) << tag_type_string( mb, *ti ) << ' ' << std::right << std::setw( STORAGE_WIDTH ) << tag_storage_string( mb, *ti ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( occupied ) << ' ' << std::right << std::setw( MEM_WIDTH ) << memstr( allocated ) << std::endl; } } // end per_tag if( totals ) { // print summary of overall memory use get_mem_stats( mb, stats ); std::cout << std::endl << "TOTAL: (Used/Allocated)" << std::endl << "memory: " << memstr( stats.total_storage ) << "/" << memstr( stats.total_amortized ) << std::endl << "entity: " << memstr( stats.entity_storage ) << "/" << memstr( stats.entity_amortized ) << std::endl << "adjacency: " << memstr( stats.adjacency_storage ) << "/" << memstr( stats.adjacency_amortized ) << std::endl << "tag: " << memstr( stats.tag_storage ) << "/" << memstr( stats.tag_amortized ) << std::endl << std::endl; } // end totals if( sysstats ) { std::FILE* filp = std::fopen( "/proc/self/stat", "r" ); unsigned long long vsize; long rss; if( filp && 2 == std::fscanf( filp, "%*d " // pid "%*s " // comm "%*c " // state "%*d " // ppid "%*d " // pgrp "%*d " // session "%*d " // tty_nr "%*d " // tpgid "%*u " // flags "%*u " // minflt "%*u " // cminflt "%*u " // majflt "%*u " // cmajflt "%*u " // utime "%*u " // stime "%*d " // cutime "%*d " // cstime "%*d " // priority "%*d " // nice "%*d " // num_threads "%*d " // itrealvalue "%*u " // starttime "%llu " // vsize "%ld", // rss &vsize, &rss ) ) { #ifndef _WIN32 long long tmprss = rss * getpagesize(); #endif std::cout << std::endl << "SYSTEM:" << std::endl << "Virtual memory: " << memstr( vsize ) #ifndef _WIN32 << std::endl << "Resident set size: " << memstr( tmprss ) #endif << std::endl; } else { #ifndef _WIN32 struct rusage sysdata; if( getrusage( RUSAGE_SELF, &sysdata ) ) { std::cerr << "getrusage failed" << std::endl; } else { rss = sysdata.ru_maxrss; long long tmprss = rss * getpagesize(); std::cerr << std::endl << "SYSTEM:" << std::endl << "Resident set size: " << memstr( tmprss ) << std::endl; } #endif } if( filp ) fclose( filp ); } // end sysstats }
static unsigned long long rdiv | ( | unsigned long long | num, |
unsigned long long | den | ||
) | [static] |
std::string tag_storage_string | ( | moab::Interface & | mb, |
moab::Tag | tag | ||
) | [static] |
Definition at line 475 of file mbmem.cpp.
References ErrorCode, MB_SUCCESS, MB_TAG_BIT, MB_TAG_DENSE, MB_TAG_SPARSE, moab::Interface::tag_get_type(), and TagType.
Referenced by print_memory_stats().
{ moab::ErrorCode rval; moab::TagType type; rval = mb.tag_get_type( tag, type ); if( moab::MB_SUCCESS != rval ) return std::string(); switch( type ) { case moab::MB_TAG_DENSE: return "dense"; case moab::MB_TAG_SPARSE: return "sparse"; case moab::MB_TAG_BIT: return "bit"; default: return "(none)"; } }
std::string tag_type_string | ( | moab::Interface & | mb, |
moab::Tag | tag | ||
) | [static] |
Definition at line 425 of file mbmem.cpp.
References ErrorCode, MB_SUCCESS, MB_TYPE_BIT, MB_TYPE_DOUBLE, MB_TYPE_HANDLE, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, MB_VARIABLE_DATA_LENGTH, size, moab::Interface::tag_get_data_type(), and moab::Interface::tag_get_length().
Referenced by print_memory_stats().
{ moab::ErrorCode rval; std::ostringstream s; moab::DataType type; rval = mb.tag_get_data_type( tag, type ); if( moab::MB_SUCCESS != rval ) return std::string(); int typesize; std::string typestr; switch( type ) { case moab::MB_TYPE_INTEGER: typestr = "int"; typesize = sizeof( int ); break; case moab::MB_TYPE_DOUBLE: typestr = "double"; typesize = sizeof( double ); break; case moab::MB_TYPE_HANDLE: typestr = "handle"; typesize = sizeof( moab::EntityHandle ); break; case moab::MB_TYPE_BIT: typesize = 1; typestr = "bits"; break; case moab::MB_TYPE_OPAQUE: typesize = 1; typestr = "bytes"; break; default: typesize = 1; typestr = "???"; break; } int size; rval = mb.tag_get_length( tag, size ); if( moab::MB_VARIABLE_DATA_LENGTH == rval ) s << "VAR " << typestr; else if( moab::MB_SUCCESS == rval ) s << size / typesize << " " << typestr; // else do nothing return s.str(); }
static void usage | ( | const char * | argv0, |
bool | help = false |
||
) | [static] |
Definition at line 18 of file mbmem.cpp.
References help().
{ std::ostream& str = help ? std::cout : std::cerr; str << "Usage: " << argv0 << " [-H|-b|-k|-m] <filename> [<filename> ...]" << std::endl << " " << argv0 << " [-H|-b|-k|-m] -T" << std::endl; if( !help ) { str << " " << argv0 << " -h" << std::endl; std::exit( 1 ); } std::cerr << " -H : human readable units" << std::endl << " -b : bytes" << std::endl << " -k : kilobytes (1 kB == 1024 bytes)" << std::endl << " -m : megabytes (1 MB == 1024 kB)" << std::endl << " -g : gigabytes (1 GB == 1024 MB)" << std::endl << " -T : test mode" << std::endl << std::endl; std::exit( 0 ); }