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RE: Running a nonh=1 with instat=stat with OpenMPI on Linux

HE
Hisham Elsafti, modified 3 Years ago.

Running a nonh=1 with instat=stat with OpenMPI on Linux

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
Dear all,

I am trying to start a 1D simulation (ny=0) for a wave flume with regular (resolved) waves. I have compiled Xbeach on Ubuntu using OpenMPI and it seems to work for 'jons' with no problem (as far as I know, finishes normally and output is dumped to files as expected). When I run a nonh=1 simulation with instat=stat, though, the simulation halt after a small time. Here is the output until it hangs:


  **********************************************************
                     Welcome to XBeach

               version 1.22.
               dateMo 4. Jul 01:20:20 CEST 2016
     URL:
  **********************************************************

  Simulation started: YYYYMMDD    hh:mm:ss     time zone (UTC)
                      20160823  09:23:12     +0200

    running in:/home/hisham/substituteseastate/xbeachOutput
  General Input Module
   MPI version, running on           3 processes
  Reading input parameters:
  --------------------------------
  Physical processes:
   XBeach reading fromparams.txt
                    cyclic =0 (no record found, default value used)
                     swave =1 (no record found, default value used)
                single_dir =0 (no record found, default value used)
                     lwave =1 (no record found, default value used)
                      flow =1 (no record found, default value used)
                  sedtrans =1 (no record found, default value used)
                morphology =1 (no record found, default value used)
               avalanching =1 (no record found, default value used)
                      nonh =1
                    gwflow =0 (no record found, default value used)
                     ships =0 (no record found, default value used)
                vegetation =0 (no record found, default value used)
                  setbathy =0 (no record found, default value used)
                 viscosity =1 (no record found, default value used)
                 advection =1 (no record found, default value used)
                      wind =1 (no record found, default value used)
  --------------------------------
  Grid parameters:
                  gridform =xbeach (no record found, default value used)
                      xori =.0000
                      yori =.0000
                      alfa =.0000
                        nx =209
                        ny =0
                    posdwn =.0000
                   depfile =bed.dep
                     vardx =1
                        dx =-1.0000 (no record found, default value used)
                        dy =-1.0000 (no record found, default value used)
                     xfile =x.grd
                     yfile =y.grd
                  thetamin =135.0000
                  thetamax =45.0000
                 thetanaut =1
                    dtheta =90.0000 Warning: value > recommended value of20.0000
  --------------------------------
  Model time parameters:
                       CFL =.7000 (no record found, default value used)
                     dtset =.0000 (no record found, default value used)
                     tstop =100.0000
                  maxdtfac =500.0000 (no record found, default value used)
  --------------------------------
  Physical constants:
                       rho =1025.0000 (no record found, default value used)
                         g =9.8100 (no record found, default value used)
                depthscale =1.0000 (no record found, default value used)
  --------------------------------
  Initial conditions:
                zsinitfile = None specified
  --------------------------------
  Wave boundary condition parameters:
                    instat =stat
                     taper =100.0000 (no record found, default value used)
                      nmax =.8000 (no record found, default value used)
              nonhspectrum =1 (no record found, default value used)
                      Hrms =1.0000 (no record found, default value used)
                      Tm01 =10.0000 (no record found, default value used)
                      Trep =10.0000 (no record found, default value used)
                      dir0 =270.0000 (no record found, default value used)
                         m =10 (no record found, default value used)
               lateralwave =neumann (no record found, default value used)
  --------------------------------
  Flow boundary condition parameters:
                     front =abs_2d (no record found, default value used)
                      left =neumann (no record found, default value used)
                     right =neumann (no record found, default value used)
                      back =abs_2d (no record found, default value used)
                       ARC =1 (no record found, default value used)
                     order =2.0000 (no record found, default value used)
                   carspan =0 (no record found, default value used)
                  freewave =0 (no record found, default value used)
                      epsi =-1.0000 (no record found, default value used)
                  tidetype =velocity (no record found, default value used)
  --------------------------------
  Tide boundary conditions:
                   tideloc =0
                       zs0 =.0000 (no record found, default value used)
  --------------------------------
  Discharge boundary conditions:
            disch_loc_file = None specified
     disch_timeseries_file = None specified
                ndischarge =0 (no record found, default value used)
               ntdischarge =0 (no record found, default value used)
                      beta =.1000 (no record found, default value used)
  --------------------------------
  Wave breaking parameters:
                     break =baldock (no record found, default value used)
                     gamma =.7800 (no record found, default value used)
                     alpha =1.0000 (no record found, default value used)
                         n =10.0000 (no record found, default value used)
                    gammax =2.0000 (no record found, default value used)
                     delta =.0000 (no record found, default value used)
                        fw =.0000 (no record found, default value used)
                    fwfile = None specified
                  fwcutoff =1000.0000 (no record found, default value used)
              breakerdelay =1 (no record found, default value used)
  --------------------------------
  Roller parameters:
                    roller =1 (no record found, default value used)
                       rfb =0 (no record found, default value used)
  --------------------------------
  Wave-current interaction parameters:
                       wci =0 (no record found, default value used)
                      hwci =.1000 (no record found, default value used)
                   hwcimax =100.0000 (no record found, default value used)
                      cats =4.0000 (no record found, default value used)
  --------------------------------
  Flow parameters:
               bedfriction =chezy (no record found, default value used)
               bedfriccoef =55.0000 (no record found, default value used)
                       nuh =.1000 (no record found, default value used)
                    nuhfac =1.0000 (no record found, default value used)
                      smag =1 (no record found, default value used)
  --------------------------------
  Coriolis force parameters:
                    wearth =.0417 (no record found, default value used)
                       lat =.0000 (no record found, default value used)
  --------------------------------
  Wind parameters:
                      rhoa =1.2500 (no record found, default value used)
                        Cd =.0020 (no record found, default value used)
                  windfile = None specified
                     windv =.0000 (no record found, default value used)
                    windth =270.0000 (no record found, default value used)
  --------------------------------
  Non-hydrostatic correction parameters:
                    solver =tridiag (no record found, default value used)
                     kdmin =.0000 (no record found, default value used)
                      Topt =10.0000 (no record found, default value used)
                 nhbreaker =2 (no record found, default value used)
                     dispc =-1.0000 (no record found, default value used)
              breakvisclen =1.0000 (no record found, default value used)
                maxbrsteep =.6000 (no record found, default value used)
                secbrsteep =.3000 (no record found, default value used)
  --------------------------------
  Sediment transport parameters:
                      form =vanthiel_vanrijn (no record found, default value used)
                  waveform =vanthiel (no record found, default value used)
                       sws =1 (no record found, default value used)
                       lws =1 (no record found, default value used)
                     BRfac =1.0000 (no record found, default value used)
                     facsl =1.6000 (no record found, default value used)
                        z0 =.0060 (no record found, default value used)
                      smax =-1.0000 (no record found, default value used)
                     tsfac =.1000 (no record found, default value used)
                     facua =.1000 (no record found, default value used)
                     facSk =.1000 (no record found, default value used)
                     facAs =.1000 (no record found, default value used)
                   turbadv =none (no record found, default value used)
                      turb =bore_averaged (no record found, default value used)
                     Tbfac =1.0000 (no record found, default value used)
                     Tsmin =.5000 (no record found, default value used)
                       lwt =0 (no record found, default value used)
                     betad =1.0000 (no record found, default value used)
                       sus =1 (no record found, default value used)
                       bed =1 (no record found, default value used)
                      bulk =0 (no record found, default value used)
                     facDc =1.0000 (no record found, default value used)
                fallvelred =0 (no record found, default value used)
                 dilatancy =0 (no record found, default value used)
               reposeangle =30.0000 (no record found, default value used)
               bdslpeffmag =roelvink_total (no record found, default value used)
               bdslpeffini =none (no record found, default value used)
               bdslpeffdir =none (no record found, default value used)
  --------------------------------
  Bed composition parameters:
                       ngd =1 (no record found, default value used)
                        nd =3 (no record found, default value used)
                       por =.4000 (no record found, default value used)
   D50 =.0002 (no record found, default value used)
   D90 =.0003 (no record found, default value used)
                      rhos =2650.0000 (no record found, default value used)
                       dzg =.1000 (no record found, default value used)
                      dzg1 =.1000 (no record found, default value used)
                      dzg2 =.1000 (no record found, default value used)
                      dzg3 =.1000 (no record found, default value used)
   sedcal =1.0000 (no record found, default value used)
   ucrcal =1.0000 (no record found, default value used)
  --------------------------------
  Morphology parameters:
                    morfac =1.0000 (no record found, default value used)
                 morfacopt =1 (no record found, default value used)
                  morstart =250.0000
                   morstop =100.0000 (no record found, default value used)
                    wetslp =.3000 (no record found, default value used)
                    dryslp =1.0000 (no record found, default value used)
                   hswitch =.1000 (no record found, default value used)
                     dzmax =.0500 (no record found, default value used)
                    struct =0 (no record found, default value used)
  --------------------------------
  Output variables:
                   timings =1 (no record found, default value used)
                    tunits = None specified
                    tstart =.0000
                      tint =1.0000 (no record found, default value used)
                  tsglobal = None specified
                     tintg =50.0000
                  tspoints = None specified
                     tintp =1.0000 (no record found, default value used)
                    tsmean = None specified
                     tintm =100.0000 (no record found, default value used)
                nglobalvar =-1 (no record found, default value used)
                   npoints =0 (no record found, default value used)
                  nrugauge =0 (no record found, default value used)
                 npointvar =0 (no record found, default value used)
                 nrugdepth =1 (no record found, default value used)
   rugdepth =.0000 (no record found, default value used)
                  nmeanvar =0 (no record found, default value used)
              outputformat =fortran (no record found, default value used)
  --------------------------------
  Output projection:
                projection = None specified
                    rotate =1 (no record found, default value used)
  --------------------------------
  Wave numerics parameters:
                    scheme =upwind_2 (no record found, default value used)
                    wavint =60.0000 (no record found, default value used)
                  maxerror =.0001 (no record found, default value used)
                   maxiter =500 (no record found, default value used)
                    snells =1 (no record found, default value used)
  --------------------------------
  Flow numerics parameters:
                       eps =.0050 (no record found, default value used)
                    eps_sd =.5000 (no record found, default value used)
                      umin =.0000 (no record found, default value used)
                      hmin =.2000 (no record found, default value used)
                  secorder =0 (no record found, default value used)
  --------------------------------
  Sediment transport numerics parameters:
                  thetanum =1.0000 (no record found, default value used)
                sourcesink =0 (no record found, default value used)
                      cmax =.1000 (no record found, default value used)
  --------------------------------
  Bed update numerics parameters:
                   frac_dz =.7000 (no record found, default value used)
                    nd_var =2 (no record found, default value used)
                     split =1.0100 (no record found, default value used)
                     merge =.0100 (no record found, default value used)
  --------------------------------
  MPI parameters:
               mpiboundary =auto (no record found, default value used)
  --------------------------------
  Finished reading input parameters
  --------------------------------
  Warning: Automatically turning on 2nd order correction in flow for
           non-hydrostatic module [secorder=1]
  Warning: Automatically changing to wbcversion 3 for
           non-hydrostatic spectral boundary condition [nonhspectrum=1]
  Warning: 2D absorbing boundary condition [front=abs_2d] reduces to a
           1D absorbing boundary condition [front=abs_1d] in
           1D mode [ny=0]
  Warning: 2D absorbing boundary condition [back=abs_2d] reduces to a
           1D absorbing boundary condition [back=abs_1d] in
           1D mode [ny=0]
   Unknown, unused or multiple statements of parameterDTBC inparams.txt
   Unknown, unused or multiple statements of parameterBCFILE inparams.txt
   Unknown, unused or multiple statements of parameterZS0FILE inparams.txt
   Unknown, unused or multiple statements of parameterRT inparams.txt
  ------------------------------------
  Building Grid and Bathymetry
  ------------------------------------
   processor grid:           3  X           1
  Initializing .....
  --------------------------------
  MPI implementation:
  Distribution of matrix on processors
   proc   is   lm   js   ln
      0    1   73    1    1
      1   70   73    1    1
      2  139   72    1    1
   proc   left right top bot
             0 T T T F
             1 T T F F
             2 T T F T
  --------------------------------
  --------------------------------
  computational domains on processors
     proc   icgs   icge   jcgs   jcge   icls   icle   jcls   jcle
        0      1     71      1      1      1     71      1      1
        1     72    140      1      1      3     71      1      1
        2    141    210      1      1      3     72      1      1
  --------------------------------
  Fortran outputformat
  Setting up boundary conditions
  Boundary conditions complete, starting computation
  Wave propagation row   2, iteration   1
  Wave propagation row   3, iteration   1
  Wave propagation row   4, iteration   1
  Wave propagation row   5, iteration   1
  Wave propagation row   6, iteration   1
  Wave propagation row   7, iteration   1
  Wave propagation row   8, iteration   1
  Wave propagation row   9, iteration   1
  Wave propagation row  10, iteration   1
  Wave propagation row  11, iteration   1
  Wave propagation row  12, iteration   1
  Wave propagation row  13, iteration   1
  Wave propagation row  14, iteration   1
  Wave propagation row  15, iteration   1
  Wave propagation row  16, iteration   1
  Wave propagation row  17, iteration   1
  Wave propagation row  18, iteration   1
  Wave propagation row  19, iteration   1
  Wave propagation row  20, iteration   1
  Wave propagation row  21, iteration   1
  Wave propagation row  22, iteration   1
  Wave propagation row  23, iteration   1
  Wave propagation row  24, iteration   1
  Wave propagation row  25, iteration   1
  Wave propagation row  26, iteration   1
  Wave propagation row  27, iteration   1
  Wave propagation row  28, iteration   1
  Wave propagation row  29, iteration   1
  Wave propagation row  30, iteration   1
  Wave propagation row  31, iteration   1
  Wave propagation row  32, iteration   1
  Wave propagation row  33, iteration   1
  Wave propagation row  34, iteration   1
  Wave propagation row  35, iteration   1
  Wave propagation row  36, iteration   1
  Wave propagation row  37, iteration   1
  Wave propagation row  38, iteration   1
  Wave propagation row  39, iteration   1
  Wave propagation row  40, iteration   1
  Wave propagation row  41, iteration   1
  Wave propagation row  42, iteration   1
  Wave propagation row  43, iteration   1
  Wave propagation row  44, iteration   1
  Wave propagation row  45, iteration   1
  Wave propagation row  46, iteration   1
  Wave propagation row  47, iteration   1
  Wave propagation row  48, iteration   1
  Wave propagation row  49, iteration   1
  Wave propagation row  50, iteration   1
  Wave propagation row  51, iteration   1
  Wave propagation row  52, iteration   1
  Wave propagation row  53, iteration   1
  Wave propagation row  54, iteration   1
  Wave propagation row  55, iteration   1
  Wave propagation row  56, iteration   1
  Wave propagation row  57, iteration   1
  Wave propagation row  58, iteration   1
  Wave propagation row  59, iteration   1
  Wave propagation row  60, iteration   1
  Wave propagation row  61, iteration   1
  Wave propagation row  62, iteration   1
  Wave propagation row  63, iteration   1
  Wave propagation row  64, iteration   1
  Wave propagation row  65, iteration   1
  Wave propagation row  66, iteration   1
  Wave propagation row  67, iteration   1
  Wave propagation row  68, iteration   1
  Wave propagation row  69, iteration   1
  Wave propagation row  70, iteration   1
  Wave propagation row  71, iteration   1


So what am I doing wrong?

I found that according to this pdf page 52 (https://oss.deltares.nl/documents/48999/49476/non-hydrostatic_report_draft.pdf), nonh does not work with mpi. I did not get any error though, thought it might be an outdated document.

Additionally, I tried compiling Xbeach without mpi (did not give the --with-mpi option for ./configure), but make exits complaining of no reference to some mpi related functions in Xbeach. So if indeed I need Xbeach without mpi, how can I go about it???

Best regards,
Hisham
Arnold van Rooijen, modified 3 Years ago.

RE: Running a nonh=1 with instat=stat with OpenMPI on Linux

Swell Posts: 239 Join Date: 11/7/11 Recent Posts
Hi Hisham,

The report you are referring too is a bit outdated, it's better to refer to the new (Kingsday) manual. MPI should work with nonhydrostatic, so that should not be the issue.

One parameter that caught my eye is swave, which is set at 1 in your simulations. That means that XBeach will use the wave action balance which should not be used in case of non-hydrostatic simulations. I'm not sure if this will solve the issue but it would be good to try with swave = 0. For the rest I don't see any unusual input in your XBlog file. But if you want I can have a better look if you upload the model input files (e.g params.txt, bcfile, grid, bathy etc.).

Cheers,
Arnold
HE
Hisham Elsafti, modified 3 Years ago.

RE: Running a nonh=1 with instat=stat with OpenMPI on Linux

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
Hi Arnold,

Thanks a lot for your reply. I could just now run xbeach with nonh=1 for instat=jons, and had the same response (as posted above) for nonh=0 and instat=stat. So it seems that instat=stat is the problem here. Adding swave=0 makes the simulation go complete but the water surface for the last time step is just zeros (H.dat).

So let me go back for a second. What I want to do is: simulate regular waves in a 1D wave flume. What is the best configuration for that??

Best regards,
Hisham
Arnold van Rooijen, modified 3 Years ago.

RE: Running a nonh=1 with instat=stat with OpenMPI on Linux

Swell Posts: 239 Join Date: 11/7/11 Recent Posts
Hi Hisham,

When you are running in non-hydrostatic mode you are not using the short wave energy balance (swave = 0) so your wave height output (H) will also be zero. As the sea-swell waves will be fully resolved, your results will be in the water surface elevation (zs). Based on that output you can compute the wave height (either by using a full zs timeseries or using the variance).

So, yes this should be the right set up for a flume set-up.

Hope this helps.

Cheers,
Arnold

PS: instat = ts_nonh is another option to do this, but then you will have to create a timeseries at the boundary. If you use instat = stat, xbeach will do it for you
HE
Hisham Elsafti, modified 3 Years ago.

RE: Running a nonh=1 with instat=stat with OpenMPI on Linux

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
Hi again,

I have found the problem. I use now the instat=ts_nonh or 8. with swave=0. Now I have other problems. But I I guess a new question maybe better than changing the subject here.

Thanks again.

Best regards,
Hisham