Tool for debugging binary IO. More...

#include <IODebugTrack.hpp>

Collaboration diagram for moab::IODebugTrack:

Classes
struct	DRange

Public Member Functions
	IODebugTrack (bool enable, const std::string &table_name, std::ostream &output_stream, unsigned long table_size=0)
	Constuctor requires stream to which to log errors. More...

	IODebugTrack (bool enable, const std::string &table_name, unsigned long table_size=0)
	Constuctor requires stream to which to log errors. More...

	~IODebugTrack ()
	Destructor prints errors about unaccessed ranges. More...

void	record_io (unsigned long begin, unsigned long count)
	Notify of IO request. More...

void	all_reduce ()
	Push all data to root process. More...

Private Member Functions
void	record_io (DRange data)

Private Attributes
bool	enableOutput

std::string	tableName

std::list< DRange >	dataSet

std::ostream &	ostr

unsigned long	maxSize

int	mpiRank

bool	haveMPI

Detailed Description

Tool for debugging binary IO.

Track which ranges of a table of data have been read/written, watching for overlapping IO requests and ranges of unaccessed data.

Notes: This class assumes MPI_COMM_WORLD is the communicator for parallel.

Definition at line 20 of file IODebugTrack.hpp.

Constructor & Destructor Documentation

◆ IODebugTrack() [1/2]

moab::IODebugTrack::IODebugTrack	(	bool	enable,
		const std::string &	table_name,
		std::ostream &	output_stream,
		unsigned long	table_size = `0`
	)

Constuctor requires stream to which to log errors.

Parameters

table_name	Used to tag output
output_stream	Stream to which to print error messages
table_size	Max table size. No limit if unspecified

Definition at line 16 of file IODebugTrack.cpp.

   20     : enableOutput( enabled ), tableName( name ), ostr( output_stream ), maxSize( table_size ), haveMPI( false )
   21 {
   22 #ifdef MOAB_HAVE_MPI
   23     MPI_Comm_rank( MPI_COMM_WORLD, &mpiRank );
   24 #else
   25     mpiRank = 0;
   26 #endif
   27 }

References mpiRank.

◆ IODebugTrack() [2/2]

moab::IODebugTrack::IODebugTrack	(	bool	enable,
		const std::string &	table_name,
		unsigned long	table_size = `0`
	)

Constuctor requires stream to which to log errors.

Parameters

table_name	Used to tag output
table_size	Max table size. No limit if unspecified

Definition at line 29 of file IODebugTrack.cpp.

   30     : enableOutput( enabled ), tableName( name ), ostr( std::cerr ), maxSize( table_size )
   31 {
   32     mpiRank = 0;
   33     haveMPI = false;
   34 #ifdef MOAB_HAVE_MPI
   35     int have_init = 0;
   36     MPI_Initialized( &have_init );
   37     if( have_init )
   38     {
   39         haveMPI = true;
   40         MPI_Comm_rank( MPI_COMM_WORLD, &mpiRank );
   41     }
   42 #endif
   43 }

References haveMPI, and mpiRank.

◆ ~IODebugTrack()

moab::IODebugTrack::~IODebugTrack ( )

Destructor prints errors about unaccessed ranges.

Definition at line 45 of file IODebugTrack.cpp.

   46 {
   47     if( !enableOutput || mpiRank )  // only root prints gap summary
   48         return;
   49  
   50     if( dataSet.empty() )
   51     {
   52         ostr << PFX << tableName << " : No Data Written!!!!" << std::endl;
   53         return;
   54     }
   55  
   56     std::list< DRange >::const_iterator i;
   57     if( !maxSize )
   58     {
   59         for( i = dataSet.begin(); i != dataSet.end(); ++i )
   60             if( i->end >= maxSize ) maxSize = i->end + 1;
   61     }
   62     Range processed;
   63     Range::iterator h = processed.begin();
   64     bool wrote_zero   = false;
   65     for( i = dataSet.begin(); i != dataSet.end(); ++i )
   66     {
   67         // ranges cannot contain zero
   68         assert( i->begin <= i->end );
   69         if( i->begin )
   70             h = processed.insert( h, i->begin, i->end );
   71         else
   72         {
   73             wrote_zero = true;
   74             if( i->end ) h = processed.insert( h, i->begin + 1, i->end );
   75         }
   76     }
   77  
   78     // ranges cannot contain zero
   79     Range unprocessed;
   80     if( maxSize > 1 ) unprocessed.insert( 1, maxSize - 1 );
   81     unprocessed = subtract( unprocessed, processed );
   82     if( unprocessed.empty() ) return;
   83  
   84     Range::const_pair_iterator j;
   85     for( j = unprocessed.const_pair_begin(); j != unprocessed.const_pair_end(); ++j )
   86     {
   87         unsigned long b = j->first;
   88         unsigned long e = j->second;
   89         if( b == 1 && !wrote_zero ) b = 0;
   90  
   91         ostr << PFX << tableName << " : range not read/written: [" << b << "," << e << "]" << std::endl;
   92         ostr.flush();
   93     }
   94 }

References moab::Range::begin(), moab::Range::const_pair_begin(), moab::Range::const_pair_end(), dataSet, moab::Range::empty(), enableOutput, moab::Range::insert(), maxSize, mpiRank, ostr, PFX, moab::subtract(), and tableName.

Member Function Documentation

◆ all_reduce()

void moab::IODebugTrack::all_reduce ( )

Push all data to root process.

Does nothing if MPI support is not enabled

Definition at line 142 of file IODebugTrack.cpp.

  143 {
  144 #ifdef MOAB_HAVE_MPI
  145     if( !enableOutput || !haveMPI ) return;
  146  
  147     int commsize;
  148     MPI_Comm_size( MPI_COMM_WORLD, &commsize );
  149     int count = 3 * dataSet.size();
  150     std::vector< int > displs( commsize ), counts( commsize );
  151     MPI_Gather( &count, 1, MPI_INT, &counts[0], 1, MPI_INT, 0, MPI_COMM_WORLD );
  152     displs[0] = 0;
  153     for( int i = 1; i < commsize; ++i )
  154         displs[i] = displs[i - 1] + counts[i - 1];
  155     int total = ( displs.back() + counts.back() ) / 3;
  156     count /= 3;
  157  
  158     std::vector< DRange > send( dataSet.size() ), recv( total );
  159     std::copy( dataSet.begin(), dataSet.end(), send.begin() );
  160     MPI_Gatherv( (void*)&send[0], 3 * send.size(), MPI_UNSIGNED_LONG, (void*)&recv[0], &counts[0], &displs[0],
  161                  MPI_UNSIGNED_LONG, 0, MPI_COMM_WORLD );
  162  
  163     if( 0 == mpiRank )
  164     {
  165         for( int i = count; i < total; ++i )
  166             record_io( recv[i] );
  167     }
  168     else
  169     {
  170         dataSet.clear();
  171     }
  172 #endif
  173 }

References dataSet, enableOutput, haveMPI, mpiRank, and record_io().

Referenced by moab::ReadHDF5::read_node_adj_elems(), moab::WriteHDF5::write_adjacencies(), moab::WriteHDF5::write_elems(), moab::WriteHDF5::write_nodes(), moab::WriteHDF5::write_sets(), moab::WriteHDF5::write_sparse_ids(), moab::WriteHDF5::write_sparse_tag(), moab::WriteHDF5::write_tag_values(), moab::WriteHDF5::write_var_len_data(), and moab::WriteHDF5::write_var_len_indices().

◆ record_io() [1/2]

void moab::IODebugTrack::record_io ( DRange data )

private

Definition at line 105 of file IODebugTrack.cpp.

  106 {
  107     if( !enableOutput ) return;
  108  
  109     // only root should get non-local data
  110     assert( !mpiRank || ins.rank == (unsigned)mpiRank );
  111     assert( ins.begin <= ins.end );
  112  
  113     // test for out-of-bounds write
  114     if( maxSize && ins.end >= maxSize )
  115         ostr << ": Out of bounds write on rank " << mpiRank << ": [" << ins.begin << "," << ins.end
  116              << "] >= " << maxSize << std::endl;
  117  
  118     // test for overlap with all existing ranges
  119     std::list< DRange >::iterator i;
  120     for( i = dataSet.begin(); i != dataSet.end(); ++i )
  121     {
  122         if( i->end >= ins.begin && i->begin <= ins.end )
  123         {  // if overlap
  124             ostr << PFX << tableName;
  125             if( i->rank == ins.rank )
  126             {
  127                 if( mpiRank == (int)ins.rank ) ostr << ": Local overwrite on rank " << mpiRank;
  128  
  129                 // otherwise should have been logged on remote proc, do nothing here
  130             }
  131             else
  132                 ostr << ": Conflicting write for ranks " << i->rank << " and " << ins.rank;
  133  
  134             ostr << ": [" << i->begin << "," << i->end << "] and [" << ins.begin << "," << ins.end << "]" << std::endl;
  135             ostr.flush();
  136         }
  137     }
  138  
  139     dataSet.push_back( ins );
  140 }

References moab::IODebugTrack::DRange::begin, dataSet, enableOutput, moab::IODebugTrack::DRange::end, maxSize, mpiRank, ostr, PFX, moab::IODebugTrack::DRange::rank, and tableName.

Referenced by all_reduce(), moab::ReadHDF5::read_node_adj_elems(), record_io(), moab::WriteHDF5::write_adjacencies(), moab::WriteHDF5::write_elems(), moab::WriteHDF5::write_nodes(), moab::WriteHDF5::write_set_data(), moab::WriteHDF5::write_sets(), moab::WriteHDF5::write_sparse_ids(), moab::WriteHDF5::write_tag_values(), moab::WriteHDF5::write_var_len_data(), and moab::WriteHDF5::write_var_len_indices().

◆ record_io() [2/2]

void moab::IODebugTrack::record_io	(	unsigned long	begin,
		unsigned long	count
	)

Notify of IO request.

Parameters

begin	First table row being read/written
count	Num consecutive table rows being read/written

Definition at line 96 of file IODebugTrack.cpp.

   97 {
   98     if( enableOutput && count )
   99     {
  100         DRange ins = { begin, begin + count - 1, static_cast< long unsigned >( mpiRank ) };
  101         record_io( ins );
  102     }
  103 }

References enableOutput, mpiRank, and record_io().

Member Data Documentation

◆ dataSet

std::list< DRange > moab::IODebugTrack::dataSet

private

Definition at line 32 of file IODebugTrack.hpp.

Referenced by all_reduce(), record_io(), and ~IODebugTrack().

◆ enableOutput

bool moab::IODebugTrack::enableOutput

private

Definition at line 30 of file IODebugTrack.hpp.

Referenced by all_reduce(), record_io(), and ~IODebugTrack().

◆ haveMPI

bool moab::IODebugTrack::haveMPI

private

Definition at line 36 of file IODebugTrack.hpp.

Referenced by all_reduce(), and IODebugTrack().

◆ maxSize

unsigned long moab::IODebugTrack::maxSize

private

Definition at line 34 of file IODebugTrack.hpp.

Referenced by record_io(), and ~IODebugTrack().

◆ mpiRank

int moab::IODebugTrack::mpiRank

private

Definition at line 35 of file IODebugTrack.hpp.

Referenced by all_reduce(), IODebugTrack(), record_io(), and ~IODebugTrack().

◆ ostr

std::ostream& moab::IODebugTrack::ostr

private

Definition at line 33 of file IODebugTrack.hpp.

Referenced by record_io(), and ~IODebugTrack().

◆ tableName

std::string moab::IODebugTrack::tableName

private

Definition at line 31 of file IODebugTrack.hpp.

Referenced by record_io(), and ~IODebugTrack().

The documentation for this class was generated from the following files:

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ IODebugTrack() [1/2]

◆ IODebugTrack() [2/2]

◆ ~IODebugTrack()

Member Function Documentation

◆ all_reduce()

◆ record_io() [1/2]

◆ record_io() [2/2]

Member Data Documentation

◆ dataSet

◆ enableOutput

◆ haveMPI

◆ maxSize

◆ mpiRank

◆ ostr

◆ tableName