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September 11, 2008, 10:35 
Hi there!
I'm working withi

#1 
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Carsten Thorenz
Join Date: Mar 2009
Location: Germany
Posts: 34
Rep Power: 14 
Hi there!
I'm working within the Federal Waterway Research Institute in Germany and am currently evaluating the possibilities to use OpenFOAM for our tasks. Currently we're using an Universitycode (NaSt3D) and a commercial code (Comet, CDAdapco). After successfully compiling OpenFOAM and all of its dependencies on our cluster (HP, ~550 cores, it was a $§%& to do it) I started a series of scaling tests. During these tests I observed, that the serial version of lesInterFoam is more stable than the parallel version. In the appended protocol you can see, that the serial version keeps the timestep length (based on CFLnumber) approximately constant, while the parallel version suddenly diverges and thus heavily decreases the timestep length. I tried to tighten the solver tolerances a little (switched from relative to absolute tolerances) and observed that the parallel solver has more difficulties (=needs more iterations) to reach the same residuals. Can anybody help me out? Thanks, Carsten ********************************************* Protocol of serial run: ********************************************* thorenz@manager:/cwork/home/thorenz/OpenFOAM/thorenz1.5/run/test/lesInter> lesInterFoam /**\  =========    \ / F ield  OpenFOAM: The Open Source CFD Toolbox   \ / O peration  Version: 1.5   \ / A nd  Web: http://www.OpenFOAM.org   \/ M anipulation   \**/ Exec : lesInterFoam Date : Sep 11 2008 Time : 15:16:43 Host : manager PID : 3366 Case : /cwork/home/thorenz/OpenFOAM/thorenz1.5/run/test/lesInter nProcs : 1 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Reading environmentalProperties Reading field pd Reading field gamma Reading field U Reading/calculating face flux field phi Reading transportProperties Selecting incompressible transport model Newtonian Selecting incompressible transport model Newtonian Calculating field g.h Selecting LES turbulence model oneEqEddy oneEqEddyCoeffs { ck 0.07; ce 1.05; } time step continuity errors : sum local = 1.90779e06, global = 5.47287e11, cumulative = 5.47287e11 GAMG: Solving for pcorr, Initial residual = 1, Final residual = 0.00933394, No Iterations 2 GAMG: Solving for pcorr, Initial residual = 0.0512361, Final residual = 0.000329517, No Iterations 3 GAMG: Solving for pcorr, Initial residual = 0.0104888, Final residual = 8.43108e05, No Iterations 3 time step continuity errors : sum local = 3.49924e10, global = 5.72863e20, cumulative = 5.47287e11 Courant Number mean: 0.00198285 max: 0.0870045 Starting time loop Courant Number mean: 0.00911609 max: 0.4 deltaT = 0.00459746 Time = 0.00459746 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 1, Final residual = 7.93338e08, No Iterations 3 GAMG: Solving for pd, Initial residual = 1, Final residual = 0.00320971, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.0167016, Final residual = 9.48718e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00380673, Final residual = 2.70428e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00432735, Final residual = 3.22664e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000806934, Final residual = 4.26216e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000406143, Final residual = 3.9094e06, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.000464116, Final residual = 2.95828e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000104657, Final residual = 8.68852e07, No Iterations 3 GAMG: Solving for pd, Initial residual = 2.20723e05, Final residual = 1.40261e07, No Iterations 4 time step continuity errors : sum local = 7.32954e12, global = 3.03771e19, cumulative = 5.47287e11 ExecutionTime = 246.65 s ClockTime = 247 s Courant Number mean: 0.00911652 max: 0.349656 deltaT = 0.0051234 Time = 0.00972087 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 0.0908774, Final residual = 2.74663e07, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.091115, Final residual = 0.000455897, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.0105126, Final residual = 5.57734e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.0020783, Final residual = 1.13856e05, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.00458803, Final residual = 2.51287e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000711904, Final residual = 7.00776e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00020928, Final residual = 1.67668e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000257756, Final residual = 2.29231e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 5.52424e05, Final residual = 3.29901e07, No Iterations 4 GAMG: Solving for pd, Initial residual = 2.64538e05, Final residual = 2.04274e07, No Iterations 2 time step continuity errors : sum local = 7.20551e12, global = 3.81516e19, cumulative = 5.47287e11 ExecutionTime = 425.79 s ClockTime = 426 s Courant Number mean: 0.0101599 max: 0.38734 deltaT = 0.00529085 Time = 0.0150117 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 0.0281467, Final residual = 1.8522e07, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.110235, Final residual = 0.000596557, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.0224509, Final residual = 0.000128465, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00580166, Final residual = 4.29631e05, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.00530598, Final residual = 2.74172e05, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.00113712, Final residual = 6.09731e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000345295, Final residual = 2.0767e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000285847, Final residual = 2.27749e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 6.69878e05, Final residual = 5.03613e07, No Iterations 4 GAMG: Solving for pd, Initial residual = 2.31656e05, Final residual = 1.10384e07, No Iterations 4 time step continuity errors : sum local = 4.11883e12, global = 3.21917e19, cumulative = 5.47287e11 ExecutionTime = 614.52 s ClockTime = 615 s Courant Number mean: 0.0104904 max: 0.374926 deltaT = 0.00564469 Time = 0.0206564 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 0 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 0.0149358, Final residual = 1.07743e07, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.111377, Final residual = 0.000546566, No Iterations 5 GAMG: Solving for pd, Initial residual = 0.0443143, Final residual = 0.000378587, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.00348986, Final residual = 2.93438e05, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.00580005, Final residual = 3.25267e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00090779, Final residual = 5.57326e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000202187, Final residual = 8.91621e07, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000261984, Final residual = 1.46064e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 8.81133e05, Final residual = 6.75653e07, No Iterations 3 GAMG: Solving for pd, Initial residual = 2.19288e05, Final residual = 1.23339e07, No Iterations 4 time step continuity errors : sum local = 5.2089e12, global = 2.91032e20, cumulative = 5.47287e11 ExecutionTime = 806.01 s ClockTime = 807 s End ********************************************* Protocol of (small) parallel run: ********************************************* thorenz@manager:/cwork/home/thorenz/OpenFOAM/thorenz1.5/run/test/lesInter> ShowOutput caesar 8303.manager JOBNAME: lesInter Running on cn113 in directory /cwork/home/thorenz/OpenFOAM/thorenz1.5/run/test/lesInter /**\  =========    \ / F ield  OpenFOAM: The Open Source CFD Toolbox   \ / O peration  Version: 1.5   \ / A nd  Web: http://www.OpenFOAM.org   \/ M anipulation   \**/ Exec : /home/thorenz/OpenFOAM/OpenFOAM1.5/applications/bin/linux64GccDPOpt/lesInterFoa m parallel Date : Sep 11 2008 Time : 15:58:06 Host : cn113 PID : 14560 Case : /cwork/home/thorenz/OpenFOAM/thorenz1.5/run/test/lesInter nProcs : 4 Slaves : 3 ( cn113.14561 cn113.14562 cn113.14563 ) Pstream initialized with: floatTransfer : 1 nProcsSimpleSum : 0 commsType : nonBlocking // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Reading environmentalProperties Reading field pd Reading field gamma Reading field U Reading/calculating face flux field phi Reading transportProperties Selecting incompressible transport model Newtonian Selecting incompressible transport model Newtonian Calculating field g.h Selecting LES turbulence model oneEqEddy oneEqEddyCoeffs { ck 0.07; ce 1.05; } time step continuity errors : sum local = 1.95216e06, global = 2.19068e08, cumulative = 2.19068e08 GAMG: Solving for pcorr, Initial residual = 1, Final residual = 0.00789225, No Iterations 4 GAMG: Solving for pcorr, Initial residual = 0.124184, Final residual = 0.000873301, No Iterations 3 GAMG: Solving for pcorr, Initial residual = 0.00939945, Final residual = 5.94039e05, No Iterations 5 time step continuity errors : sum local = 2.82378e10, global = 9.42772e16, cumulative = 2.19068e08 Courant Number mean: 0.00197842 max: 0.0866421 Starting time loop Courant Number mean: 0.00913374 max: 0.4 deltaT = 0.00461669 Time = 0.00461669 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 1.37317e09 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 2.09824e08 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 1, Final residual = 8.32085e08, No Iterations 3 GAMG: Solving for pd, Initial residual = 1, Final residual = 0.00905161, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.030631, Final residual = 0.000249962, No Iterations 5 GAMG: Solving for pd, Initial residual = 0.0279553, Final residual = 0.000215157, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.0061856, Final residual = 3.29705e05, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.0010291, Final residual = 5.35965e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000249627, Final residual = 2.24523e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000487803, Final residual = 3.99529e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000113732, Final residual = 8.44721e07, No Iterations 4 GAMG: Solving for pd, Initial residual = 2.91779e05, Final residual = 2.47841e07, No Iterations 5 time step continuity errors : sum local = 1.42955e11, global = 2.7288e13, cumulative = 2.19071e08 ExecutionTime = 107.67 s ClockTime = 111 s Courant Number mean: 0.00913342 max: 0.350108 deltaT = 0.00514415 Time = 0.00976084 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 8.75307e09 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 2.95853e09 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 0.090851, Final residual = 2.60962e07, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.103055, Final residual = 0.000658385, No Iterations 7 GAMG: Solving for pd, Initial residual = 0.0534587, Final residual = 0.000471622, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.00457859, Final residual = 3.11229e05, No Iterations 6 GAMG: Solving for pd, Initial residual = 0.00674019, Final residual = 4.25671e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000957393, Final residual = 6.8116e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000305495, Final residual = 2.13162e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000338653, Final residual = 2.22752e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 9.83227e05, Final residual = 8.53568e07, No Iterations 4 GAMG: Solving for pd, Initial residual = 1.96595e05, Final residual = 1.80463e07, No Iterations 6 time step continuity errors : sum local = 7.49885e12, global = 6.0042e13, cumulative = 2.19077e08 ExecutionTime = 195.31 s ClockTime = 199 s Courant Number mean: 0.0101748 max: 0.387677 deltaT = 0.00530766 Time = 0.0150685 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 1.13155e08 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 3.14748e09 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 0.0280745, Final residual = 2.50708e07, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.135927, Final residual = 0.0008367, No Iterations 6 GAMG: Solving for pd, Initial residual = 0.12072, Final residual = 0.000949937, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.0067283, Final residual = 6.02786e05, No Iterations 6 GAMG: Solving for pd, Initial residual = 0.0110492, Final residual = 9.74167e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00167134, Final residual = 1.60604e05, No Iterations 5 GAMG: Solving for pd, Initial residual = 0.000762118, Final residual = 5.91042e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.000432036, Final residual = 3.90235e06, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.0001005, Final residual = 9.58262e07, No Iterations 5 GAMG: Solving for pd, Initial residual = 3.66069e05, Final residual = 3.42478e07, No Iterations 13 time step continuity errors : sum local = 1.73401e11, global = 1.14339e12, cumulative = 2.19088e08 ExecutionTime = 291.55 s ClockTime = 296 s Courant Number mean: 0.010502 max: 2.84169 deltaT = 0.000747113 Time = 0.0158156 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 4.97554e09 Max(gamma) = 1 MULES: Solving for gamma MULES: Solving for gamma Liquid phase volume fraction = 0.634909 Min(gamma) = 2.17027e08 Max(gamma) = 1 DILUPBiCG: Solving for k, Initial residual = 0.00198818, Final residual = 3.3322e07, No Iterations 1 GAMG: Solving for pd, Initial residual = 0.279262, Final residual = 0.00205902, No Iterations 5 GAMG: Solving for pd, Initial residual = 0.25002, Final residual = 0.00172857, No Iterations 2 GAMG: Solving for pd, Initial residual = 0.017356, Final residual = 0.000112756, No Iterations 6 GAMG: Solving for pd, Initial residual = 0.0192683, Final residual = 0.00017176, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00822677, Final residual = 6.5594e05, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.00343701, Final residual = 2.67641e05, No Iterations 4 GAMG: Solving for pd, Initial residual = 0.00187906, Final residual = 1.08599e05, No Iterations 5 GAMG: Solving for pd, Initial residual = 0.00078521, Final residual = 7.42016e06, No Iterations 3 GAMG: Solving for pd, Initial residual = 0.000177669, Final residual = 1.20193e06, No Iterations 9 time step continuity errors : sum local = 2.14555e12, global = 1.17363e13, cumulative = 2.19089e08 ExecutionTime = 378.51 s ClockTime = 383 s Courant Number mean: 0.00147797 max: 0.109817 deltaT = 0.000896536 Time = 0.0167122 [snipped] 

September 11, 2008, 11:15 
Solver convergence behaviour i

#2 
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Join Date: Mar 2009
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Solver convergence behaviour is indeed affected by running in parallel because the effectiveness of the preconditioning and smoothing operations is reduced in the cells adjacent to the processor boundaries which usually causes a modest increase in the number of iterations. But it doesn't look like this is the root of your problems, take a look at the solution and find out where in the domain the Courant number has jumped.
H 

September 11, 2008, 11:24 
P.S. your pdFinal tolerance ap

#3 
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P.S. your pdFinal tolerance appears to vary, are you running with a relative tolerance on pdFinal? It should be relTol = 0. Also for efficiency you may benefit from running with fewer correctors and use the GAMG preconditioned CG solver for pdFinal; take a look at the lesInterFoam tutorial.
H 

September 11, 2008, 11:32 
Hi Henry,
thanks for your e

#4 
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Carsten Thorenz
Join Date: Mar 2009
Location: Germany
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Rep Power: 14 
Hi Henry,
thanks for your explanation about the effectiveness of preconditioning in parallel (didn't know that). Relative tolerance: Yes. But the main problem is not influenced by this. When I switched to constant tolerances, the general behaviour stays the same. (i.e. more iterations in parallel than in serial runs, sudden jumps of the velocity). I will try to find out were it occurs. Many thanks, Carsten 

September 11, 2008, 12:08 
You seem to be currently runni

#5 
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Mattijs Janssens
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You seem to be currently running with floatTransfer (i.e. all doubles get converted to floats just before transfer). This will loose precision which might affect the solver.


September 12, 2008, 02:48 
@Mattijs:
Thanks for your c

#6 
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Carsten Thorenz
Join Date: Mar 2009
Location: Germany
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@Mattijs:
Thanks for your comment. That might result in severe truncation errors. I will try it. @Henry: Switching the PDsolver to AMGpreconditioned PCG increased reliability significantly. Thanks a lot. Now I can start some scaling tests on our machine. Allow me one more question (though in the wrong forum): Did I understand it correctly, that the pressure p is replaced by pd+rho*g*h? As I understand it, this removes the hydrostatic pressure from the solution and thus results in "less work" for the solver. But this will only be successful, if the waterlevel is located at z=0, otherwise it will be (strongly) contraproductiv? Wouldn't it be more useful to remove the pressure field of the last timestep from the solution and thus express p_new=p_old+pd (with pd=p_newp_old) and relax updating of p_old? Bye, Carsten 

September 12, 2008, 03:58 
Yes pd is solved for rather th

#7 
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Yes pd is solved for rather than p but this is not an approximation, it is a reformulation, note the corresponding change to the buoyancy term. This reformulation allows the buoyancy term to be handled in the pd equation in a much better way in the collocated grid arrangement we use.
H 

September 12, 2008, 05:51 
I agree that it is just a refo

#8 
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Carsten Thorenz
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I agree that it is just a reformulation. But I'm not sure if is useful _in_general_. I.e. in my oppinion it only has a positive effect, if the watertable nearly horizontal?
Just a comment, not an offense Carsten 

September 12, 2008, 06:10 
@Mattijs:
I tried to set fl

#9 
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Carsten Thorenz
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Location: Germany
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@Mattijs:
I tried to set floatTransfer to 0 in my controlDict, but it is not recognized. Where should I set it? Is it hardcoded? Thanks, Carsten 

September 12, 2008, 06:14 
It is a necessary reformulatio

#10 
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It is a necessary reformulation for numerical reasons and does not introduce any error or restriction.
H 

September 12, 2008, 09:58 
floatTransfer: I found that it

#11 
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Carsten Thorenz
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floatTransfer: I found that it must be changed in the _global_ controlDict.
Finally, I think the behaviour is a bug. Well, let's say an overoptimization floatTransfer should default to 0. It is not reasonable, to decrease the accuracy during mpitransmission for doubleprecision compilations. Why should I use doubleprecision at all if I loose the precision again? About performance: On our machine, the code runs faster with floatTransfer set to 0. The stability is much better (forget all of the above about solver settings) and it needs less iterations to converge. The overhead for the mpitransmissions is negligible. So, please change the floatTransfer default value to 0 (again). Bye, Carsten 

September 12, 2008, 11:16 
floatTransfer is not a bug but

#12 
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floatTransfer is not a bug but a carefully formulated method to get the most accuracy from least comms overhead and has proved very effective when running on cluster machines with Gbit networking for with the overhead of the MPI transmissions is significant. However it is not always appropriate as you have found and I agree that it should not be the default and I will change it in our git repository.
Thanks for sending details of your experience with floatTransfer. H 

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