[Nek5000-users] Restart problem

Mon Jan 16 03:46:12 CST 2012

Hi

I tested new restart both with and without projection and it works. What
is the problem with passive scalars? I use them, but they are not
crucial at this point. However, I thought to use them as storage for
eigenvalues for my arnoldi implementation.
Best regards

Adam

On Thu, 2012-01-05 at 03:13 -0600, nek5000-users at lists.mcs.anl.gov
wrote:
> Do you have any passive scalars?
> 
> There are some issues w.r.t passive scalar i/o that we're working
> to resolve.
> 
> Paul
> 
> 
> On Thu, 5 Jan 2012, nek5000-users at lists.mcs.anl.gov wrote:
> 
> > On Thu, 2011-12-22 at 22:22 -0600, nek5000-users at lists.mcs.anl.gov
> > wrote:
> >
> > Hi
> >
> > Thank you Paul. I've made short test with jet in crossflow and it seem
> > to work, but I've got sometimes following warning
> >
> > WARNING: restart file has a NSPCAL > LDIMT
> > read only part of the fld-data!
> > WARNING: NPSCAL read from restart file differs from
> > currently used NPSCAL!
> >
> > What's strange this warning doesn't show up at every restart. I'm going
> > to make some longer tests now.
> > Regards
> > Adam
> >
> >
> >
> >>> Hi
> >>>
> >>> I simulate jet in crossflow problem with nek5000 and I've got serius
> >>> problems with restarting the simulation. It causes strong spurious
> >>> velocity oscillation and I cannot get rid of them. I've implemented
> >>> restarting procedure described in prepost.f, but it doesn't help much.
> >>> Playing with file format (parameters p66, p67) and projection (p94, p95)
> >>> I can only decrease oscillations amplitude, but they are still there.
> >>> Surprisingly saving output files in double precision (p63=8) makes
> >>> everything worse. Has anybody got similar problems?
> >>> Best regards
> >>>
> >>> Adam
> >>
> >> Hi,
> >>
> >> I think that the full restart capability should now work with
> >> the current version of the source.
> >>
> >> There is a 2D example in the repo, with a README that I also
> >> provide below.
> >>
> >> Basically, you will now save 4 files each time you wish to
> >> checkpoint.  The files come in two sets, A and B, and the A
> >> set is then overwritten by the 3rd checkpoint, etc. so that
> >> you have at most 8 checkpoint files on hand at any one time.
> >> The files are 64 bit and thus cannot be used by VisIt --- thus,
> >> they are truly designated as checkpoint/restart files and not
> >> analysis files.   More information in the README below.
> >>
> >> Please let me know if you have comments or questions.
> >>
> >> Best regards,
> >>
> >> Paul
> >>
> >> -------------------------------------------------------------------------
> >>> From the examples/cyl_restart directory:
> >>
> >> SET UP:
> >> =======
> >>
> >> This directory contains an example of full restart capabilities for
> >> Nek5000.
> >>
> >> The model flow is a von Karman street in the wake of a 2D cylinder.
> >> The quantity of interest is taken to be the lift, which is monitored
> >> via "grep agy logfile" in the run_test script.   A matlab file, doit.m,
> >> can be used to analyze the output files containing the lift history
> >> of the four cases.  The cases are:
> >>
> >> ca   -   initial run (no projection)
> >> cb   -   restart run for ca case
> >>
> >> pa   -   initial run (with projection)
> >> pb   -   restart run for pa case
> >>
> >> BACKGROUND:
> >> ===========
> >>
> >> Timestepping in Nek5000 is based on BDFk/EXTk (k=3, typ.), which uses kth-order
> >> backward-difference formulae (BDFk) to evaluate velocity time derivatives and
> >> kth-order extrapolation (EXTk) for explicit evaluation of the nonlinear and
> >> pressure boundary terms.  Under normal conditions, the velocity and pressure
> >> for preceding timesteps are required to advance the the solution at each step.
> >>
> >> At startup, the timestepper is typically bootstrapped using a lower-order
> >> BDF/EXT formula that, given the artificiality of most initial conditions,
> >> is typically adequate.    The velocity field often has enough inertia and
> >> sufficient signature such that the same bootstrap procedure also works when
> >> restarting from an existing solution (i.e., a .fnnnnn or .fldnn file, stored
> >> in 32-bit precision).
> >>
> >> For some cases, it is important to have reproducibility of the time history
> >> to the working precision (14 digits, typ.) of the code.  The full restart
> >> feature is designed to provide this capability.   The main features of
> >> full restart are:
> >>
> >> .Preserve alternating sets of snapshots (4 per set) in 64-bit precision.
> >>   (Alternating sets are saved in case the job fails in the middle of
> >>    saving a set.)
> >>
> >> .Use the most recent set to restart the computation by overwriting
> >>   the solution for the first steps, 0 through 3, with the preserved
> >>   snapshots.
> >>
> >>
> >> Full restart is triggered through the .usr file.    In the given example
> >> cases, "ca" and "cb" the restart-save is illustrated in ca.usr and the
> >> actual restart, plus the save, is illustrated in cb.usr.   For these cases,
> >> the restart is encapsulated in the user-provided routine "my_full_restart"
> >> shown below, along with the calling format in userchk:
> >>
> >>
> >> c-----------------------------------------------------------------------
> >>        subroutine userchk
> >>        include 'SIZE'
> >>        include 'TOTAL'
> >>
> >>        logical if_drag_out,if_torq_out
> >>
> >>        call my_full_restart
> >>
> >>        scale = 1.
> >>        if_drag_out = .true.
> >>        if_torq_out = .false.
> >>        call torque_calc(scale,x0,if_drag_out,if_torq_out)
> >>
> >>        return
> >>        end
> >> c-----------------------------------------------------------------------
> >>        subroutine my_full_restart
> >>
> >>        character*80 s80(4)
> >>
> >>        call blank(s80,4*80)
> >>        s80(1) ='rs8ca0.f00005'
> >>        s80(2) ='rs8ca0.f00006'
> >>        s80(3) ='rs8ca0.f00007'
> >>        s80(4) ='rs8ca0.f00008'
> >>
> >>        call full_restart(s80,4)  ! Will overload 5-8 onto steps 0-3
> >>
> >>
> >>        iosave = iostep           ! Trigger save based on iostep
> >>        call full_restart_save(iosave)
> >>
> >>        return
> >>        end
> >> c-----------------------------------------------------------------------
> >>
> >>
> >> Note that in the example above, the set enumerated 5--8 is used to restart
> >> the computation.   This set is generated by first running the "ca" case.
> >>
> >> Note that the frequency of the restart output is coincident with the
> >> standard output frequency of field files (snapshots).  This might be too
> >> frequent if one is, say, making a movie where snapshots are typically
> >> dumped every 10 steps.   It would make more sense in this case to set
> >> iosave=1000, say.
> >>
> >> Note also that if one is initiating a computation from something other
> >> than the full restart mode then the full_restart() call should be commented
> >> out.
> >>
> >>
> >> COMMENTS:
> >> =========
> >>
> >> Full reproducibility of the solution is predicated on having sufficient
> >> history information to replicate the state of "a" when running "b".
> >> While such replication is possible, it does preclude acceleration of the
> >> iterative solvers by projection onto prior solution spaces [1,2], since
> >> these projections typically retain relatively long sequences of information
> >> (e.g., spanning tens of steps) to maximally extract all the regularity in the
> >> solution history.   Consequently, _full_ reproducibility is not retained with
> >> projection turned on.  In this case, the solution is reproduced only to the
> >> tolerance of the iterative solvers, which is in any case the maximum level
> >> of accuracy attainable in the solution.   To illustrate the difference,
> >> we provide a test case pairing, "pa" and "pb", which is essentially the
> >> same as the ca/cb pair save that projection is turned on for pa/pb.
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >
> >
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users