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updating MPI sim layer for blocking receives, updating dragonfly model for the message remainders, checking for negative byte size in dumpi traces

Adding lp suspend for wait operations in MPI Sim layer, adding commit_f in dumpi workload debug utility

Bug fix in dfly routing

Change-Id: I53f278953f2e287bf122cf20694a7db3bd1fd336

See merge request !7

Change-Id: I53f278953f2e287bf122cf20694a7db3bd1fd336

Slimfly LP-IO Update

Fixed issue #152 .
Updated Slim Fly workload README accordingly

See merge request !6

Commit function

The ROSS API has changed to add a commit function (see [d3bdc07](https://github.com/carothersc/ROSS/commit/d3bdc077a0c4d1481dc06c4b4d4f1eb8e4e6fbf6)).

This merge request updates the various CODES models to the latest ROSS API. All  test pass. It also updates the documentation to CODES v 0.5.2 and ROSS v d3bdc07. 

See merge request !5

Adding updated allocation generator script (uses random number seeds for multiple allocation files), torus cleanups

distcheck still doesn't succeed - there are a bunch of test files that don't
get cleaned up. moving on, but will make a ticket for it.