MP2: further directions and tips

1
MP2 further directions and tips

• Useful for everyone, irrespective of which
  paradigm you are using

2
Shared memory Pthreads

• Race conditions
• What is a race condition e.g. when two different
  outcomes are possible (typically, one unintended)
  depending on which processor gets there first
• Eliminate using mutual exclusion primitives
  (locks)
• Deadlocks
• Two (or more) processes waiting for each other
• E.g.
• Process1 lock(A), lock(B) work unlock(A)
  unlock(B)
• Process2 lock(B), lock(A) work unlock(A)
  unlock(B)
• How to avoid order the locks

3
Shared memory Pthreads

• In the molecular dynamics MP
• decide which iterations to assign to processors
• I.e. how to group them
• You must use number of threads number of
  processors
• requirement (may be artificial requirement, but
  there are reasons why)

4
MPI

• Number of processes number of processors
• Assume there are many more cells than processors
• Decide which processes will work on which cells
• How to represent the local cells?
• How to implement communication
• who sends what data to whom?
• Initial broadcast of parameters
• In each step use MPI s reduce functions to add
  up energies.

5
Charm

• Use chare arrays to implement cells
• Let the system map cells to processors
• Use the array reduction library to add up
  energies
• Example new jacobi-skeleton program with
  reduction
• Use readonly variables (struct) to store params