[Users] McLachlan help
Ian Hinder
ian.hinder at aei.mpg.de
Tue Aug 11 07:52:44 CDT 2015
On 28 Jul 2015, at 16:56, Erik Schnetter <schnetter at cct.lsu.edu> wrote:
> Yosef, James
>
> I'd like to at least try to see whether the McLachlan performance you're seeing is in the right ballpark. Can you post the parameter file you're using?
You can get an idea of where time is spent by using
Carpet::output_timer_tree_every = 256
or similar. I also recommend
Carpet::sync_barriers = yes
to account for load imbalance, otherwise you might attribute time to a routine when it's really just waiting for other processors to catch up.
McLachlan is very careful to make sure that results are "correct" in a strict mesh refinement sense, and therefore does quite a lot of work in bins such as CCTK_POSTRESTRICT. In many situations, you may be able to deduce that these are unnecessary (or you may think you do not care), but they are necessary in some corner cases, and hence are enabled by default. I suggest comparing the timer trees from the two runs, and seeing which routines are different.
>
> -erik
>
> On Tue, Jul 28, 2015 at 9:19 AM, Yosef Zlochower <yosef at astro.rit.edu> wrote:
> Hi Erik,
>
> Our standard choice is to use 8th order centered
> differencing with 5th-order dissipation. For this
> test, Jim used 8th-order with upwinding and
> thus used 5 ghost zones (rather than 4).
> We use the full complement of 4*ghost buffer
> zones. Near the boundary we reduce the order of the
> stencil from 8 to 6 to 4 to 2 and on the boundary
> we apply Sommerfeld boundary conditions (implemented as
> modifications to RHS).
>
> For the gauge, we evolve
> d0 alpha = -2 alpha K
> and
> dt beta = 3/4 Gamma^i
> (we don't introduce the auxiliary B field).
>
> We precalculate the mixed derivatives and
> only calculate first derivatives and non-mixed second
> derivatives in the main loop. We apply
> dissipation to all variables, but apply it
> one variable at a time (i.e., we go through
> a full 3d loop nvars times).
>
>
> The conformal factor is W = sqrt(chi).
>
> We use the admbase variables alpha and beta
> and fill in kij and gij after each ministep
> of the RK4 integrator. We similarly enforce
> the algebraic constraints at each ministep.
> We calculate the constraints using the BSSN
> variables, but use a 4th order stencil and implement
> mixed derivatives using one dimensional derivatives
> along the diagonal (this is less accurate, but
> faster).
>
>
> The FD order is a compile time option and
> we can test the code with and without upwinding,
> with FD orders of 2nd through 8, and we can
> use the standard or "quick" mixed derivatives
> for the constraint. We can similarly use
> 3, 5, 7, 9 order dissipation.
>
> We use openmp parallelization along the "z" direction
> of our loops
>
>
>
>
> On 07/27/2015 10:21 PM, Erik Schnetter wrote:
> Jim
>
> By default, McLachlan is configured to be generic, i.e. many choices can
> be made at run time. For example, there are 4 additional gauge variables
> evolved (A and B^i). If you are willing to restrict your run-time
> choices, for example by fixing derivative order, disabling multi-block
> systems, choosing a particular gauge, choice of conformal factor, etc.,
> then this will lead to a more efficient code. You can easily do so for
> McLachlan by generating a new version in Kranc. If you look in the
> beginning of McLachlan_BSSN.m in the section "Choose code to generate",
> then you'll see the parameters you can choose. We have made a particular
> set of choices for a configuration "BSSN_bench", but these are
> apparently different from LazEv. For example, we use 4th order finite
> differencing, and evolve B^i in time as well.
>
> Can you specify all the details of your formulation? I notice that you
> didn't respond to my request to point me to the source code, and there
> are quite a few details that you also didn't describe yet (and are also
> not described in your paper), such as your choice of conformal factor,
> whether/how your code is integrated with ADMBase, whether the
> constraints are calculated from the BSSN or the ADM variables, how
> advection derivatives are handled, etc. For a true comparison, this all
> needs to be known. Unless we both know exactly what both the codes do,
> we'll never know where the physics differences are.
>
> -erik
>
>
> On Mon, Jul 27, 2015 at 5:39 PM, James Healy <jchsma at rit.edu
> <mailto:jchsma at rit.edu>> wrote:
>
> Hi Erik,
>
> We evolve alpha and beta for the gauge variables as given in
> equations 7a and 7b of http://arxiv.org/pdf/1506.06153.pdf. The
> number I reported for LazEv was using 5th order dissipation applied
> to all 21 evolved variables (alp, beta^i, At_{ij}, gt_{ij},
> Gammat^{i}, trK, and xi).
>
> LazEv is calculating the Hamiltonian and Momentum constraints as
> well as the constraints on Gammat^i using 4th order stencils.
>
> I also forgot to mention that I did these tests on 16 nodes, and the
> memory usage was relatively low ( ~2 GB/MPI process ).
>
> I will give the internal dissipation for McLachlan a try.
>
> Thanks,
> Jim
>
>
> On 07/27/2015 05:56 PM, Erik Schnetter wrote:
> Jim
>
> Thanks for posting the details.
>
> Can you give us more details about the LazEv scheme? In particular
> there may be differences in the gauge. What (gauge) variables do
> you evolve? What gauge conditions do you use? And what kind of
> dissipation do you apply? Can you point us to the source code?
>
> For the new McLachlan, you would probably use the built-in
> dissipation instead of thorn Dissipation, which should lead to a
> small speed-up.
>
> -erik
>
> On Mon, Jul 27, 2015 at 4:43 PM, James Healy <jchsma at rit.edu
> <mailto:jchsma at rit.edu>> wrote:
>
> Hello,
>
> I have been running some tests on Stampede comparing the run
> speed of McLachlan to RIT's evolution thorn LazEv. I started
> with the qc0-mclachlan.par parameter file included with the
> Einstein Toolkit, added a few refinement levels, increased the
> resolution and changed McLachlan to be 8th order (and
> increased the number of ghost zones to 5). I also increased
> the initial separation so the finest grids aren't already
> overlapping. To compare with LazEv, I removed the McLachlan
> and Dissipation thorns and replaced them with LazEv.
> Everything else in the parameter file is exactly the same. I
> tried using both the McLachlan master and rewrite branches.
>
> The grid setup is 10 levels of refinement, dx=4M on the
> coarsest with outer boundary at 400M, M/128 on the finest with
> r=0.6M, CFL is 0.25. Both use 8th order spatial differencing
> with ghost_size=5 and 5th order dissipation.
>
> Below is a summary of the results as reported at iteration 256
> from Carpet::physical_time_per_hour:
>
> McLachlan - rewrite branch: 3.0596110 M/hr
> McLachlan - master branch: 3.8033607 M/hr
> LazEv - 4.1941544 M/hr
>
> I am using the stampede-impi.cfg configuration file in
> simfactory. "module list" returns:
>
> 1) TACC-paths 3) cluster-paths 5) xalt/0.4.6 7) TACC
> 2) Linux 4) intel/13.0.2.146 <http://13.0.2.146> 6)
> cluster 8) impi/4.1.0.030 <http://4.1.0.030>
>
>
> Attached is my parameter file. I pasted the McLachlan
> parameters below. Are there any optimizations that I can use
> for McLachlan? Are the parameters I am using for it what would
> be used for production runs?
>
> ML_BSSN::harmonicN = 1 # 1+log
> ML_BSSN::harmonicF = 2.0 # 1+log
> ML_BSSN::ShiftGammaCoeff = 0.75
> ML_BSSN::BetaDriver = 1.0
> ML_BSSN::LapseAdvectionCoeff = 1.0
> ML_BSSN::ShiftAdvectionCoeff = 1.0
>
> ML_BSSN::MinimumLapse = 1.0e-8
>
> ML_BSSN::my_initial_boundary_condition = "extrapolate-gammas"
> ML_BSSN::my_rhs_boundary_condition = "NewRad"
> Boundary::radpower = 2
>
> ML_BSSN::ML_log_confac_bound = "none"
> ML_BSSN::ML_metric_bound = "none"
> ML_BSSN::ML_Gamma_bound = "none"
> ML_BSSN::ML_trace_curv_bound = "none"
> ML_BSSN::ML_curv_bound = "none"
> ML_BSSN::ML_lapse_bound = "none"
> ML_BSSN::ML_dtlapse_bound = "none"
> ML_BSSN::ML_shift_bound = "none"
> ML_BSSN::ML_dtshift_bound = "none"
>
> ML_BSSN::fdOrder = 8
>
> ActiveThorns = "Dissipation"
>
> Dissipation::order = 5
> Dissipation::vars = "
> ML_BSSN::ML_metric
> ML_BSSN::ML_trace_curv
> ML_BSSN::ML_curv
> ML_BSSN::ML_Gamma
> ML_BSSN::ML_lapse
> ML_BSSN::ML_shift
> ML_BSSN::ML_dtlapse
> ML_BSSN::ML_dtshift
> "
>
> ActiveThorns = "ML_ADMConstraints"
>
>
> Thanks,
> Jim Healy
>
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>
> --
> Erik Schnetter <schnetter at cct.lsu.edu <mailto:schnetter at cct.lsu.edu>>
> http://www.perimeterinstitute.ca/personal/eschnetter/
>
>
>
>
> --
> Erik Schnetter <schnetter at cct.lsu.edu <mailto:schnetter at cct.lsu.edu>>
> http://www.perimeterinstitute.ca/personal/eschnetter/
>
>
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>
>
> --
> Dr. Yosef Zlochower
> Center for Computational Relativity and Gravitation
> Associate Professor
> School of Mathematical Sciences
> Rochester Institute of Technology
> 85 Lomb Memorial Drive
> Rochester, NY 14623
>
> Office:74-2067
> Phone: +1 585-475-6103
>
> yosef at astro.rit.edu
>
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>
> --
> Erik Schnetter <schnetter at cct.lsu.edu>
> http://www.perimeterinstitute.ca/personal/eschnetter/
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--
Ian Hinder
http://members.aei.mpg.de/ianhin
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