fixed up formatting of references in manualpages to consistent style

References:
+ 1. - ref1
. 2. - ref2
- 3. - ref3

previously the formatting was varied and ugly

removed checking of alignment of DMNetwork structures since on some systems they are not aligned

Reported-by: Hong Zhang

user.sbase was broadcast using an MPI_DOUBLE when it should have been MPIU_REAL
Also initialized datastructures with zeros to prevent valgrind warnings about communicating uninitialized data
between

user.sbase was broadcast using an MPI_DOUBLE when it should have been MPIU_REAL
Also initialized datastructures with zeros to prevent valgrind warnings about communicating uninitialized data
between processes.

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bugfix from Shri: MPIU_INT -> MPI_INT in DMNetworkDistribute(); add parallel tests of pf.c and pipes1.c

Code declared entire struct and copied it all
DMNetworkComponent component = network->component[componentkey];
in order to access the size record
Since DMNetworkComponent is now declared with P

Code declared entire struct and copied it all
DMNetworkComponent component = network->component[componentkey];
in order to access the size record
Since DMNetworkComponent is now declared with PETSC_ATTRIBUTEALIGNED and compilers do not
align automatic variables instead simplify the code by just using the pointer

Time: .1 hour
Reported-by: Nightly tests

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dmnetwork: fix valgrind messages with quad build

==17427== Conditional jump or move depends on uninitialised value(s)
==17427== at 0x85FB313: __extenddftf2 (in /usr/lib64/libgcc_s-5.3.1-20151207.

dmnetwork: fix valgrind messages with quad build

==17427== Conditional jump or move depends on uninitialised value(s)
==17427== at 0x85FB313: __extenddftf2 (in /usr/lib64/libgcc_s-5.3.1-20151207.so.1)
==17427== by 0x5AA823F: DMPlexBuildCoordinates_Private (plexcreate.c:1521)
==17427== by 0x5AA8935: DMPlexCreateFromCellList (plexcreate.c:1596)
==17427== by 0x59A7290: DMNetworkLayoutSetUp (network.c:116)
==17427== by 0x40761B: main (pf.c:471)

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Begin renaming the PetscOptions objects for the future where PetscOptions will not be a singleton

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>
Suggested-by: Patrick Lacasse <placasse@giref.ulaval.ca>

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bugfix as reported by the nightly tests

add example pipes1.c

add DMNetworkMonitor developed by Sean Shahkarami of UIUC in the summer of 2015