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requesting pull of bug fixes and performance improvements that should be merged into amaya-library #61

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requesting pull of bug fixes and performance improvements that should be merged into amaya-library #61

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alecjohnson
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merge2amaya includes code for vectorization and rudimentary sorting that will be further developed, but this is turned off.

@alecjohnson
MIC requires that mpi.h be included before stdio.h (issue CmPA#12)
c694d90
@alecjohnson
Issue CmPA#29: add errors.h for diagnostics: eprintf() and invalid_va…
c4eaee2 
…lue_error()
@alecjohnson
issue CmPA#30: MPIdata should be a singleton
37414e3
@alecjohnson
debug.h was broken under commit bd0fa30. This uses MPIdata singleton …
984f599 
…to fix it.
@alecjohnson
issue#31: consistently use stdout rather than stderr
da737d9
@alecjohnson
issue CmPA#32: implemented USING_PARALLEL_HDF5 so that users are not …
aeccc32 
…forced to compile with parallel hdf5
@alecjohnson
Restored implementation of TimeTasks (issue CmPA#17). Some communicat…
6c90362 
…ion time for accumulating moments was being reckoned as calculation time.
@alecjohnson
issue CmPA#27: rhocs last dimension is allocated incorrectly in EMfie…
b8a1a58 
…lds.cpp
@alecjohnson
issue CmPA#35: making MPI_Barrier() a no-op
c201c8c
@alecjohnson
issue CmPA#36: use int rather than long long in critical particle loops
7e4d4d1
@alecjohnson
fixed typo in TimeTask output introduced in commit 6c90362
23f510c
@alecjohnson
Local omp.h was conflicting with system omp.h
3687a02
@alecjohnson
issue CmPA#33: making grid accessors inline again
bb6ec5f
@alecjohnson
issues CmPA#23 and issue CmPA#33: using one preallocated Moments inst…
2bcd750 
…ance per thread
@alecjohnson
issue CmPA#23 and CmPA#33: accumulating Moments using multiple instan…
4cbe820 
…ces for OpenMP

  Using a grid-sized instance of Moments for every OpenMP thread
  will consume too much memory if a very large number of OpenMP
  threads are used and so is something of a stop-gap.  But the
  current serial code would be unacceptably slow in that case,
  so this shouldn't really break anything.  EMfields should be
  redesigned to contain a set of Moments instances to be passed
  from the particle solver to the field solver.
@alecjohnson
issue CmPA#33: eliminating iostream header from asserts.h
499c8bf
@alecjohnson
issue CmPA#39: removed asgArr3 and asgArr4
cdc05b3
@alecjohnson
issue#31: use stdout rather than stderr in debug.h
e8982ee
@alecjohnson
issue CmPA#40: replacing node_coordinate and center_coordinate arrays
ed7accf
@alecjohnson
issue#41: interpP2G reimplemented as sumMoments in EMfields class
1c2ff24
@alecjohnson
remove code commented in previous commit (iss CmPA#41)
8187fbd
@alecjohnson
removed unused code obsoleted under iss#41
c3b88b1
@alecjohnson
issue CmPA#42: Support -fno-exceptions: replacing throw with eprintf
8556e6c
@alecjohnson
issue CmPA#43: implemented new array classes
31ebd95
@alecjohnson
fixed compiler errors introduced in previous commit (g++)
9b4962a
@alecjohnson
implemented use of doubleArr3 for Moments class
5221388
@alecjohnson
iss CmPA#43: implemented array classes; fixes iss CmPA#44 (memory leak)
c532855
@alecjohnson
eliminated unnecessary reference for arrays
f2fe840
@alecjohnson
committing settings for large number of particles (for MIC)
967631a
@alecjohnson
using arr4_double(nxn,nyn,nzn,10) instance to sum moments
dc4a2dc
@alecjohnson
added TimeTasks: TRANSPOSE_PCLS_TO_SOA and TRANSPOSE_PCLS_TO_AOS
4d5156e
@alecjohnson
restricted TimeTasks to master thread of rank 0 process
ba67737
@alecjohnson
created sumMoments_AoS(). code blowing up at 10 cycles.
1a5b131
@alecjohnson
Fixed compile errors on Xeon Phi
9164960
@alecjohnson
Implemented support for 'ipic run' and 'ipic show' commands
6b150e8
@alecjohnson
ipic run: calculate number of threads based on number of processes
9f04251
@alecjohnson
regularized Parameters options for mover_PC
ed23f3e
@alecjohnson
fixed AoS bugs and turned off sorting and vectorization in Parameters…
e5a84d3 
….cpp
@alecjohnson
Merge branch 'premerge' into merge2head
7086947 
Conflicts:
	CMakeLists.txt
	fields/EMfields3D.cpp
	scripts/ipic.py
@alecjohnson
fixed bug in "ipic cmake" command
48b1031
@alecjohnson
fixed ipic cmake
af34642
@alecjohnson
implemented mover_PC_AoS_vec
6c7cd96
@alecjohnson
created utility/Basic.cpp for methods that need not be inline
fe2a01a
@alecjohnson
inserted #include "errors.h" forgotten in commit fe2a01a
d3ae3cf
@alecjohnson
created former_MPI_Barrier macro
fb3473f
@alecjohnson
moved MPI_Allreduce calls from .h to .cpp
091349a
@alecjohnson
commented out unused declarations in MPIdata.h
b6639f2
@alecjohnson
changed "ipic run" to call mpirun rather than mpiexec
645af80
@alecjohnson
added number of threads to utility/MPIdata.cpp output
4bd2416
@alecjohnson
issue#62: changed getVelocityDistribution to make one MPI_Allreduce c…
f500fad 
…all (untested)
@alecjohnson
issue#35: replaced MPI_Barrier with former_MPI_Barrier; MPI_Barrier i…
699f6c0 
…s no longer no-op
@alecjohnson
issue CmPA#63: made invalid_value_error thread safe
88ee39e
@alecjohnson
warning messages should issue warning and proceed, not exit
8a17293
@alecjohnson
implemented MPIdata::exit(code) to exit after calling MPI_Finalize()
0996301
@alecjohnson
issue CmPA#64: MPI should be initialized immediately
507e0a6
@alecjohnson
issue CmPA#66: moving includes out of Collective.h
333cae3
@alecjohnson
iss CmPA#65, iss CmPA#67: defined options for second-order accuracy
965aeaf
@alecjohnson
fixed compile errors on icpc probably introduced two commits ago
776da31
@alecjohnson
"ipic exec" now calls mpiexec, just as "ipic run" calls mpirun
e5fa332
@alecjohnson
removed unnecessary header includes in Grid3DCU.h (iss CmPA#66)
8c8d657
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@alecjohnson