Nbc rebase - #602

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mdavezac wants to merge 104 commits into

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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
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b6a7b3f
move extraction to new style comms
Rupert Nash
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28ae19d
move log to new style comms
Rupert Nash
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9250bda
move reporting to new style comms
Rupert Nash
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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
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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
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