[petsc-users] Newbie Question - Really slow - PetscMemCpy

[Parker, Andrew (UK Filton)]

Hi,
 
I'm new to these postings.  On very large cases, regardless of where I
stop the debugger it is always copying data.  I've put it into a
debugger because on smaller cases it runs fine, on larger it takes a
while (very long time) to get going.  The stack trace always gives
something like:
 
memcpy
PetscMemCpy
MatSetValues_SeqAIJ
MatSetValues
my own wrapper to add values to a location within the matrix.
 
I'm using Seq_BAIJ.  My bets are that I've got the sparsity wrong, or
the preallocation wrong, but I'm not sure why.  I know this could be
anything, but has anybody got any thoughts, remember stopping the
debugger at random, regardless of the frequency always gives the
above....
 
I set up the matrix like this
 
  MatCreate(PETSC_COMM_SELF,&_storage);
 
MatSetSizes(_storage,PETSC_DECIDE,PETSC_DECIDE,numVars*numLocs,numVars*n
umLocs);
  MatSetFromOptions(_storage);
  MatSeqBAIJSetPreallocation(_storage,numVars,PETSC_NULL,sparsityStart);
 
However, using this makes zero difference to the speed
 
   MatCreateSeqBAIJ(PETSC_COMM_SELF,
      numVars,
      numVars*numLocs,
      numVars*numLocs,
      0,  
       sparsityStart,
      &_storage);
 
It is so slow that it has not even completed one cycle of the solver....
 
Cheers again,
Andy

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