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Nbc rebase#602

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mdavezac wants to merge 104 commits intomainhemelb-codes/hemelb:mainfrom nbc_rebasehemelb-codes/hemelb:nbc_rebaseCopy head branch name to clipboard

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Commits

Commits on Oct 24, 2015

• Add basic wrapping of asynchronous MPI calls

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  bc112a6

• Add a helper function MapAllToAll that takes a std::map keyed on rank and only sends to ranks with associated values.

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  314fee8

• Factor the NeighbouringDataManager to use the MapAllToAll and fix a bug in that

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  483cd77

• Remove AllToAll from the net class hierarchy (as it's unused)

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  cb881bb

• Remove a load of random extra parentheses in the code

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  0240e8c

• Reimplement the StabilityTester with a non-blocking collective

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  f0ef956

• Move the stability tester implementation into an .hpp file

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  d057876

• MAke the StabilityTester use the wrapped MPI async interface

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  6446e55

• Remove the unphysical Mazzeo collisions used in his BCs

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  a3b63db

• Remove some unneeded specialisations of PhasedBroadcast from the vis::Control class

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  9b963a9

• remove the DensityTracker class from IncompressibilityChecker

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  b07157c

• Create a CollectiveAction base class and make the IncompressibiltyChecker use it

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  9ea2cbd

• Make the IncompressibiltyCHecker unittests pass.

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  17f369f

• Actually register the IncompressibilityChecker to do it's communication

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  f7cb9cc

• Make the StabilityTester a CollectiveAction

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  b558efa

• Make the EntropyTester a CollectiveAction instead of a PhasedBroadcast

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  679dbc8

• Make the steering data distribution object (SteeringComponent) a CollectiveAction

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  9c0a7b8

• Remove the PhasedBroadcastRegular class template as it's unused.

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  cac78c8

• Organise the timers used by the CollectiveActions in the monitoring.

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  305cc19

• Avoid the use of C++11 extensions to the standard library vectors (cbegin and cend member functions)

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  0f09679

• Record Archer configuration options in fabric

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  63d7f8e

• Ensure that the MPI_Wait calls of the CollectiveActions are timed by the mpiWait timer

  

  Rupert Nash

  authored and

  Mayeul d'Avezac

  committed
  075df29

Commits on Oct 29, 2015

• Fix the debugger start up on OSX Yosemite

  

  Rupert Nash

  committed
  384bedb

Commits on Nov 16, 2015

• Merge branch 'master' into nbc_rebase

  

  Rupert Nash

  committed
  0772dec

Commits on Dec 3, 2015

• Make the collective actions test rather than wait

  

  Rupert Nash

  committed
  030a951

• First pass at removing visualisation - unit tests pass

  

  Rupert Nash

  committed
  544cd0f

• Remove the DoRayTracing template parameter from the LB

  

  Rupert Nash

  committed
  876cab3

• tidy doc strings

  

  Rupert Nash

  committed
  e2fbbd4

• remove vis section from xml

  

  Rupert Nash

  committed
  4e9d6d4

Commits on Dec 4, 2015

• Remove images from Fabric et al

  

  Rupert Nash

  committed
  cc8655b

• Remove visim and python image reader

  

  Rupert Nash

  committed
  6a934cc

• remove dangling .project file

  

  Rupert Nash

  committed
  16409a6

• Remove the min and max density and pressure members from iolets etc

  

  Rupert Nash

  committed
  e9bd7b0

• Remove phased broadcast

  

  Rupert Nash

  committed
  ee9820a

• remove some missed references to streaklines

  

  Rupert Nash

  committed
  b6cbeef

• Remove redundant all-to-all from mixins

  

  Rupert Nash

  committed
  dbc08ee

Commits on Apr 4, 2016

• merge master into nbc_rebase branch

  

  Rupert Nash

  committed
  948e4d9

Commits on Apr 5, 2016

• Add CMake to check MPI standard version

  

  Rupert Nash

  committed
  3e0d62a

• fix capitalisation - stupid case insensitive OS

  

  Rupert Nash

  committed
  4f4ad37

Commits on Apr 11, 2016

• merge master in again

  

  Rupert Nash

  committed
  11c6d6e

• minor MPI cmake edits

  

  Rupert Nash

  committed
  0549aec

Commits on Apr 13, 2016

• tidy up ARCHER section of machines.yml #649

  

  Rupert Nash

  committed
  da47fbd

• sort out the cmake and c++11

  

  Rupert Nash

  committed
  8d7a04d

• have the cmake use the source dir to look for the git repo

  

  Rupert Nash

  committed
  7b85ddb

• Dependencies cmake: tweak boost install and update ctemplate to 2.3 from github

  

  Rupert Nash

  committed
  6383203

• cmake: ensure boost install copies correctly

  

  Rupert Nash

  committed
  58a79f7

• cmake: remove quoting of boost INSTALL_COMMAND

  

  Rupert Nash

  committed
  67bb525

• cmake: revert move of CMAKE_MODULE_PATH addition that wasn't meant to be committed

  

  Rupert Nash

  committed
  8c9e590

Commits on Sep 26, 2016

• merge master into nbc

  

  Rupert Nash

  committed
  9f5a2a9

Commits on Oct 4, 2016

• implement MPI GatherV

  

  Rupert Nash

  committed
  8470814

Commits on Oct 14, 2016

• deal with NBC synchronisation issues

  

  Rupert Nash

  committed
  7e28e85

• revise debug resume script for new OS X

  

  Rupert Nash

  committed
  a8cdd69

• fix mis-renamed variable

  

  Rupert Nash

  committed
  9074b54

• Replace HEMELB_STATIC_ASSERT with c++11 static_assert

  

  Rupert Nash

  committed
  579ba09

• replace boost::shared_ptr with std::shared_ptr

  

  Rupert Nash

  committed
  2347e75

Commits on Oct 17, 2016

• replace net-based gathers with communicator gathers

  

  Rupert Nash

  committed
  7e7a6ae

• remove gathering from the net object

  

  Rupert Nash

  committed
  8acfa4a

Commits on Oct 18, 2016

• move debug over to new style comms

  

  Rupert Nash

  committed
  b6a7b3f

• move extraction to new style comms

  

  Rupert Nash

  committed
  28ae19d

• move log to new style comms

  

  Rupert Nash

  committed
  9250bda

• move reporting to new style comms

  

  Rupert Nash

  committed
  12f8ded

• move util to new style comms

  

  Rupert Nash

  committed
  1bf5515

Commits on Oct 19, 2016

• move colloids to new style comms

  

  Rupert Nash

  committed
  8338e77

• most of the actual new comms stuff

  

  Rupert Nash

  committed
  03b1bef

• move comms to using std::shared_ptr

  

  Rupert Nash

  committed
  950cf89

• minor fixes and move geometry to new comms

  

  Rupert Nash

  committed
  ff9a920

• tweaks the colloids

  

  Rupert Nash

  committed
  709affb

• move net to the new comms - involves temp friend access for p2p mixins

  

  Rupert Nash

  committed
  a5b599c

Commits on Oct 20, 2016

• move remaining non-test stuff over

  

  Rupert Nash

  committed
  d3cc2a8

• sort out lists of requests

  

  Rupert Nash

  committed
  536e215

• sort the build cmake

  

  Rupert Nash

  committed
  860d705

• fix debugger

  

  Rupert Nash

  committed
  fc6d5a5

• update the multiscale sim master and add AllGatherV to comms

  

  Rupert Nash

  committed
  34e3484

• fix allocation bug in net

  

  Rupert Nash

  committed
  6d9648d

Commits on Oct 21, 2016

• make comm::RequestList accept shared pointers

  

  Rupert Nash

  committed
  93ba9ff

Commits on Oct 23, 2016

• update the unit tests

  

  Rupert Nash

  committed
  357ae7b

• move colloids and some geometry away from the net

  

  Rupert Nash

  committed
  ef5d20b

Commits on Oct 24, 2016

• move more away from net

  

  Rupert Nash

  committed
  d4fda7b

Commits on Oct 27, 2016

• remove the net from most of the rest

  

  Rupert Nash

  committed
  03f78a4

• remove the steering!

  

  Rupert Nash

  committed
  91e460c

• remove the net object of horror

  

  Rupert Nash

  committed
  830a7fa

• remove ProcComms and StoredRequest as redundant

  

  Rupert Nash

  committed
  3d515bf

Commits on Oct 28, 2016

• get most unittests passing

  

  Rupert Nash

  committed
  3613104

• fix final unittests

  

  Rupert Nash

  committed
  e732501

Commits on Oct 31, 2016

• minor tweaks to the communicator for sanity check and speed of Rank()/Size()

  

  Rupert Nash

  committed
  12a5e96

Commits on Nov 1, 2016

• start on replacing the net::phased stuff with new timestep ns

  

  Rupert Nash

  committed
  e2265eb

Commits on Feb 7, 2017

• remove most traces of net; new stuff only part-functioning

  

  Rupert Nash

  committed
  1e00030

Commits on Feb 21, 2017

• fix ordering bug in step manager

  

  Rupert Nash

  committed
  9935c88

• add missing include

  

  Rupert Nash

  committed
  8e38972

• missing include

  

  Rupert Nash

  committed
  4216145

• move linux debugger to new comms

  

  Rupert Nash

  committed
  618f01f

• tidy the debugger instantiation

  

  Rupert Nash

  committed
  2775de6

• missing include

  

  Rupert Nash

  committed
  b6a1f8b

• missing include

  

  Rupert Nash

  committed
  2801a6d

Commits on Feb 22, 2017

• Merge pull request #672 from UCL-CCS/nbc_no_net

  Show description for b5402fc
  rupertnash

  authored
  b5402fc

Commits on Feb 23, 2017

• remove empty StabiltiyTester.cc

  

  Rupert Nash

  committed
  ffbc38f

Commits on Feb 28, 2017

• ARCHER/fabric tweaks

  

  Rupert Nash

  committed
  072e2ac

Commits on Mar 14, 2017

• further tidy the cmake/fabric and ensure correct MPI is found on ARCHER

  

  Rupert Nash

  committed
  938fd04

Commits on Apr 28, 2017

• MPI versions functions know about MPI and CXX flags

  

  Mayeul d'Avezac

  authored and

  rupertnash

  committed
  ca9fe04

• revise mpi CMake in light of Mayeul's comments

  

  Rupert Nash

  committed
  6bff83c

• Py3: move from file() to open()

  

  Rupert Nash

  committed
  27a3c6f

• Py3: replace a few __builtins__.xrange calls

  

  Rupert Nash

  committed
  927db5d

Commits on May 1, 2017

• Py3: deal with str/bytes/unicode issues between versions for xdr encoded ASCII strings

  

  Rupert Nash

  committed
  cea72ef

• remove final traces of net namespace

  

  Rupert Nash

  committed
  080bf3f