Examples » Inciter: Integrating the scalar advection-diffusion equation

This example runs Inciter to integrate the advection-diffusion equation (see e.g., PDE/Transport/CGTransport.h) configured to solve the shear-diffusion (inciter::TransportProblemShearDiff) problem.

Control file

# vim: filetype=sh:
# This is a comment
# Keywords are case-sensitive

title "Dispersion from a point source in simple shear flow"

inciter

  #nstep 11     # Max number of time steps
  t0   0.1     # Start time
  term 0.3     # Max time
  cfl 0.5
  ttyi 10      # TTY output interval

  transport
    physics advdiff
    problem shear_diff
    ncomp 1
    depvar c
    diffusivity 3.0 2.0 1.0 end
    u0 10.0 end
    lambda 0.5 1.0 end
  end

  plotvar
    interval 50
  end

end

Example run on 80 CPUs

./charmrun +p80 Main/inciter -v -c shear.q -i shear_centered_190k.exo

Output

Running on 80 processors:  Main/inciter -v -c shear.q -i shear_centered_190k.exo
charmrun>  /usr/bin/setarch x86_64 -R  mpirun -np 80  Main/inciter -v -c shear.q -i shear_centered_190k.exo
App launch reported: 5 (out of 5) daemons - 64 (out of 80) procs
Charm++> Running on MPI version: 3.1
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 80
Converse/Charm++ Commit ID:
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 5 unique compute nodes (16-way SMP).
Charm++> cpu topology info is gathered in 0.027 seconds.

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.;;+        ;;;# ;;;'      ;:   ;;;'   ;#;;;`    ;#  ;;@      `;;+   .;#;;;.
;;;#        :;;' ;;;'      ;:   ;;;'   ;# ;;;    ;# ;;;@       ;;;   ;# ;;;+
;;;#        .;;; ;;;'      ;:   ;;;'   ;# ,;;;   ;# ;;;#       ;;;:  ;@  ;;;
;;;#        .;;' ;;;'      ;:   ;;;'   ;#  ;;;;  ;# ;;;'       ;;;+ ;',  ;;;@
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    :;;;;;;.     .___              .__  __
   .;@+@';;;;;;' |   | ____   ____ |__|/  |_  ___________
    `     '#''@` |   |/    \_/ ___\|  \   __\/ __ \_  __ \
                 |   |   |  \  \___|  ||  | \  ___/|  | \/
                 |___|___|  /\___  >__||__|  \___  >__|
                          \/     \/              \/

                                 < ENVIRONMENT >
                                 ------ o ------

 * Build environment:
 --------------------
     Hostname                       : pi012.localdomain
     Executable                     : inciter
     Version                        : 0.1 (C16015)
     Revision SHA1                  : Quinoa_v0.1-914-g40abfa9
     CMake build type               : RELEASE
     Asserts                        : off (turn on: CMAKE_BUILD_TYPE=DEBUG)
     Exception trace                : off (turn on: CMAKE_BUILD_TYPE=DEBUG)
     MPI C++ wrapper                : /usr/projects/hpcsoft/toss2/pinto/openmpi/2.0.2-gcc-6.1.0/bin/mpicxx
     Underlying C++ compiler        : /usr/projects/hpcsoft/toss2/common/gcc/6.1.0/bin/g++
     Build date                     : Sun Jun  4 13:54:29 MDT 2017

 * Run-time environment:
 -----------------------
     Date, time                     : Mon Jun  5 08:42:26 2017
     Work directory                 : /net/scratch2/jbakosi/code/quinoa/build/gnup
     Executable (rel. to work dir)  : Main/inciter
     Command line arguments         : '-v -c shear.q -i shear_centered_190k.exo'
     Output                         : verbose (quiet: omit -v)
     Control file                   : shear.q
     Parsed control file            : success


                                   < FACTORY >
                                   ---- o ----

 * Unknowns data layout (CMake: FIELD_DATA_LAYOUT):
 --------------------------------------------------
     unknown-major

 * Registered partial differential equations:
 --------------------------------------------
     Unique equation types          : 2
     With all policy combinations   : 12

     Legend: equation name : supported policies

     Policy codes:
      * h: physics configuration:
        A - Advection
        D - Advection + diffusion
        L - Laplace
        N - Navier-Stokes
        E - Euler
      * r: problem:
        U - User-defined
        S - Shear-diffusion
        D - Dirichlet & Neumann
        V - Vortical flow
        V - Nonlinear energy growth
        V - Rayleigh-Taylor
        Z - Zalesak's slotted cylinder

     Compressible flow              : h:EN, r:UV
     Transport                      : h:AD, r:SZ


                                   < PROBLEM >
                                   ---- o ----

 * Title: Dispersion from a point source in simple shear flow
 ------------------------------------------------------------

 * Partial differential equations integrated (1):
 ------------------------------------------------
   < Transport >
     problem                        : Shear-diffusion
     start offset in unknowns array : 0
     number of components           : 1
     coeff diffusivity [1]          : { 3 2 1 }
     coeff u0 [1]                   : { 10 }
     coeff lambda [1]               : { 0.5 1 }

 * Discretization parameters:
 ----------------------------
     Number of time steps           : 18446744073709551615
     Start time                     : 0.1
     Terminate time                 : 0.3
     CFL coefficient                : 0.5
     Mass diffusion coeff           : 1

 * Output filenames:
 -------------------
     Field                          : out.<chareid>
     Diagnostics                    : diag

 * Output intervals:
 -------------------
     TTY                            : 10
     Field                          : 50
     Diagnostics                    : 1

Quinoa> Reading side sets ... done
Quinoa> Creating linear system mergers
Quinoa> Creating particle writers
Quinoa> Creating partitioners and reading mesh graph ... done

 * Input mesh graph statistics:
 ------------------------------
     Number of tetrahedra           : 190249
     Number of nodes                : 35879

 * Load distribution:
 --------------------
     Virtualization [0.0...1.0]     : 0
     Load (number of tetrahedra)    : 190249
     Number of processing elements  : 80
     Number of work units           : 80 (79*2378+2387)

 * Initial mesh partitioning:
 ----------------------------
     Mesh partitioning algorithm    : recursive coordinate bisection

Quinoa> Mesh read time: 0.033075 sec
Quinoa> Partitioning and distributing mesh ... ZOLTAN Load balancing method = 3 (RCB)
Build configuration:

  ZOLTAN_ID_TYPE: unsigned int (4 bytes)
  ZOLTAN_GNO_TYPE: ssize_t, (8 bytes)
  MPI_Datatype for ZOLTAN_ID_TYPE: MPI_UNSIGNED
  MPI_Datatype for ZOLTAN_GNO_TYPE: MPI_LONG

ZOLTAN Parameter IMBALANCE_TOL[0] = 1.100000
ZOLTAN Parameter AUTO_MIGRATE = FALSE
ZOLTAN Parameter MIGRATE_ONLY_PROC_CHANGES = 1
ZOLTAN Parameter OBJ_WEIGHT_DIM = 0
ZOLTAN Parameter EDGE_WEIGHT_DIM = 0
ZOLTAN Parameter DEBUG_LEVEL = 1
ZOLTAN Parameter DEBUG_PROCESSOR = 0
ZOLTAN Parameter DETERMINISTIC = TRUE
ZOLTAN Parameter TIMER = 1 (wall)
ZOLTAN Parameter NUM_GID_ENTRIES = 2
ZOLTAN Parameter NUM_LID_ENTRIES = 2
ZOLTAN Parameter RETURN_LISTS = PARTITION ASSIGNMENTS
ZOLTAN Parameter NUM_GLOBAL_PARTS = 80
ZOLTAN Parameter NUM_LOCAL_PARTS = -1
ZOLTAN Parameter REMAP = 1
ZOLTAN Parameter SEED = 123456789 (123456789)
ZOLTAN Parameter LB_APPROACH = repartition
ZOLTAN Parameter RCB_OVERALLOC = 1.200000
ZOLTAN Parameter RCB_REUSE = 0
ZOLTAN Parameter CHECK_GEOM = 1
ZOLTAN Parameter RCB_OUTPUT_LEVEL = 0
ZOLTAN Parameter KEEP_CUTS = 0
ZOLTAN Parameter RCB_LOCK_DIRECTIONS = 0
ZOLTAN Parameter RCB_SET_DIRECTIONS = 0
ZOLTAN Parameter RCB_RECTILINEAR_BLOCKS = 0
ZOLTAN Parameter OBJ_WEIGHTS_COMPARABLE = 0
ZOLTAN Parameter RCB_MULTICRITERIA_NORM = 1
ZOLTAN Parameter RCB_MAX_ASPECT_RATIO = 10.000000
ZOLTAN Parameter AVERAGE_CUTS = 0
ZOLTAN Parameter RANDOM_PIVOTS = 0
ZOLTAN Parameter RCB_RECOMPUTE_BOX = 0
ZOLTAN Parameter REDUCE_DIMENSIONS = 0
ZOLTAN Parameter DEGENERATE_RATIO = 0.000000
ZOLTAN Parameter FINAL_OUTPUT = 0
ZOLTAN Parameter KEEP_CUTS = 0
ZOLTAN Parameter REDUCE_DIMENSIONS = 0
ZOLTAN Parameter DEGENERATE_RATIO = 10.000000
done
Quinoa> Reordering mesh ... done
Quinoa> Creating workers
Quinoa> Linear system communication cost: avg = 0.301399, std = 0.172255
Quinoa> Reading mesh node coordinates, computing nodal volumes
Quinoa> Mesh statistics: min/max/avg(edgelength) = 0.114060 / 0.458321 / 0.277343
Quinoa> Mesh statistics: min/max/avg(V^{1/3}) = 0.019927 / 0.179225 / 0.123264
Quinoa> Computing row IDs, querying BCs, outputting mesh done
Quinoa> Setting and outputting ICs, computing initial dt, computing LHS ... done
Quinoa> Starting time stepping ...

 * Time integration: Unstructured-mesh PDE solver testbed
 --------------------------------------------------------
     Legend: it - iteration count
              t - time
             dt - time step size
            ETE - estimated time elapsed (h:m:s)
            ETA - estimated time for accomplishment (h:m:s)
            out - output-saved flags (F: field, D: diagnostics)

      it             t            dt        ETE        ETA   out
 ---------------------------------------------------------------
      10  1.003309e-01  3.309130e-05  000:00:00  000:03:17  D
      20  1.006618e-01  3.309130e-05  000:00:00  000:03:16  D
      30  1.009927e-01  3.309130e-05  000:00:00  000:03:14  D
      40  1.013237e-01  3.309130e-05  000:00:01  000:03:13  D
      50  1.016546e-01  3.309130e-05  000:00:01  000:03:12  FD
      60  1.019855e-01  3.309130e-05  000:00:01  000:03:12  D
      70  1.023164e-01  3.309130e-05  000:00:02  000:03:11  D
      80  1.026473e-01  3.309130e-05  000:00:02  000:03:11  D
      90  1.029782e-01  3.309130e-05  000:00:02  000:03:10  D
     100  1.033091e-01  3.309130e-05  000:00:03  000:03:10  FD
     110  1.036400e-01  3.309130e-05  000:00:03  000:03:10  D
     120  1.039710e-01  3.309130e-05  000:00:03  000:03:09  D
     130  1.043019e-01  3.309130e-05  000:00:04  000:03:09  D
     140  1.046328e-01  3.309130e-05  000:00:04  000:03:09  D
     150  1.049637e-01  3.309130e-05  000:00:04  000:03:09  FD
     160  1.052946e-01  3.309130e-05  000:00:05  000:03:09  D
     170  1.056255e-01  3.309130e-05  000:00:05  000:03:08  D
     180  1.059564e-01  3.309130e-05  000:00:05  000:03:08  D
     190  1.062873e-01  3.309130e-05  000:00:06  000:03:07  D
     200  1.066183e-01  3.309130e-05  000:00:06  000:03:07  FD
     210  1.069492e-01  3.309130e-05  000:00:06  000:03:07  D
     220  1.072801e-01  3.309130e-05  000:00:07  000:03:06  D
     230  1.076110e-01  3.309130e-05  000:00:07  000:03:06  D
     240  1.079419e-01  3.309130e-05  000:00:07  000:03:06  D
     250  1.082728e-01  3.309130e-05  000:00:08  000:03:05  FD
     260  1.086037e-01  3.309130e-05  000:00:08  000:03:05  D
     270  1.089347e-01  3.309130e-05  000:00:08  000:03:05  D
     280  1.092656e-01  3.309130e-05  000:00:08  000:03:04  D
     290  1.095965e-01  3.309130e-05  000:00:09  000:03:04  D
     300  1.099274e-01  3.309130e-05  000:00:09  000:03:04  FD
     310  1.102583e-01  3.309130e-05  000:00:09  000:03:03  D
     320  1.105892e-01  3.309130e-05  000:00:10  000:03:03  D
     330  1.109201e-01  3.309130e-05  000:00:10  000:03:03  D
     340  1.112510e-01  3.309130e-05  000:00:10  000:03:02  D
     350  1.115820e-01  3.309130e-05  000:00:11  000:03:02  FD
     360  1.119129e-01  3.309130e-05  000:00:11  000:03:02  D
     370  1.122438e-01  3.309130e-05  000:00:11  000:03:02  D
     380  1.125747e-01  3.309130e-05  000:00:12  000:03:01  D
     390  1.129056e-01  3.309130e-05  000:00:12  000:03:01  D
     400  1.132365e-01  3.309130e-05  000:00:12  000:03:01  FD
     410  1.135674e-01  3.309130e-05  000:00:13  000:03:00  D
     420  1.138983e-01  3.309130e-05  000:00:13  000:03:00  D
     430  1.142293e-01  3.309130e-05  000:00:13  000:03:00  D
     440  1.145602e-01  3.309130e-05  000:00:14  000:02:59  D
     450  1.148911e-01  3.309130e-05  000:00:14  000:02:59  FD
     460  1.152220e-01  3.309130e-05  000:00:14  000:02:59  D
     470  1.155529e-01  3.309130e-05  000:00:15  000:02:59  D
     480  1.158838e-01  3.309130e-05  000:00:15  000:02:58  D
     490  1.162147e-01  3.309130e-05  000:00:15  000:02:58  D
     500  1.165457e-01  3.309130e-05  000:00:16  000:02:58  FD
     510  1.168766e-01  3.309130e-05  000:00:16  000:02:57  D
     520  1.172075e-01  3.309130e-05  000:00:16  000:02:57  D
     530  1.175384e-01  3.309130e-05  000:00:17  000:02:57  D
     540  1.178693e-01  3.309130e-05  000:00:17  000:02:56  D
     550  1.182002e-01  3.309130e-05  000:00:17  000:02:56  FD
     560  1.185311e-01  3.309130e-05  000:00:18  000:02:56  D
     570  1.188620e-01  3.309130e-05  000:00:18  000:02:56  D
     580  1.191930e-01  3.309130e-05  000:00:18  000:02:55  D
     590  1.195239e-01  3.309130e-05  000:00:18  000:02:55  D
     600  1.198548e-01  3.309130e-05  000:00:19  000:02:55  FD
     610  1.201857e-01  3.309130e-05  000:00:19  000:02:54  D
     620  1.205166e-01  3.309130e-05  000:00:19  000:02:54  D
     630  1.208475e-01  3.309130e-05  000:00:20  000:02:54  D
     640  1.211784e-01  3.309130e-05  000:00:20  000:02:54  D
     650  1.215093e-01  3.309130e-05  000:00:20  000:02:53  FD
     660  1.218403e-01  3.309130e-05  000:00:21  000:02:53  D
     670  1.221712e-01  3.309130e-05  000:00:21  000:02:53  D
     680  1.225021e-01  3.309130e-05  000:00:21  000:02:52  D
     690  1.228330e-01  3.309130e-05  000:00:22  000:02:52  D
     700  1.231639e-01  3.309130e-05  000:00:22  000:02:52  FD
     710  1.234948e-01  3.309130e-05  000:00:22  000:02:51  D
     720  1.238257e-01  3.309130e-05  000:00:23  000:02:51  D
     730  1.241567e-01  3.309130e-05  000:00:23  000:02:51  D
     740  1.244876e-01  3.309130e-05  000:00:23  000:02:51  D
     750  1.248185e-01  3.309130e-05  000:00:24  000:02:50  FD
     760  1.251494e-01  3.309130e-05  000:00:24  000:02:50  D
     770  1.254803e-01  3.309130e-05  000:00:24  000:02:50  D
     780  1.258112e-01  3.309130e-05  000:00:25  000:02:49  D
     790  1.261421e-01  3.309130e-05  000:00:25  000:02:49  D
     800  1.264730e-01  3.309130e-05  000:00:25  000:02:49  FD
     810  1.268040e-01  3.309130e-05  000:00:26  000:02:49  D
     820  1.271349e-01  3.309130e-05  000:00:26  000:02:48  D
     830  1.274658e-01  3.309130e-05  000:00:26  000:02:48  D
     840  1.277967e-01  3.309130e-05  000:00:27  000:02:48  D
     850  1.281276e-01  3.309130e-05  000:00:27  000:02:47  FD
     860  1.284585e-01  3.309130e-05  000:00:27  000:02:47  D
     870  1.287894e-01  3.309130e-05  000:00:28  000:02:47  D
     880  1.291203e-01  3.309130e-05  000:00:28  000:02:47  D
     890  1.294513e-01  3.309130e-05  000:00:28  000:02:46  D
     900  1.297822e-01  3.309130e-05  000:00:29  000:02:46  FD
     910  1.301131e-01  3.309130e-05  000:00:29  000:02:46  D
     920  1.304440e-01  3.309130e-05  000:00:29  000:02:45  D
     930  1.307749e-01  3.309130e-05  000:00:30  000:02:45  D
     940  1.311058e-01  3.309130e-05  000:00:30  000:02:45  D
     950  1.314367e-01  3.309130e-05  000:00:30  000:02:45  FD
     960  1.317676e-01  3.309130e-05  000:00:31  000:02:44  D
     970  1.320986e-01  3.309130e-05  000:00:31  000:02:44  D
     980  1.324295e-01  3.309130e-05  000:00:31  000:02:44  D
     990  1.327604e-01  3.309130e-05  000:00:32  000:02:43  D
    1000  1.330913e-01  3.309130e-05  000:00:32  000:02:43  FD
    1010  1.334222e-01  3.309130e-05  000:00:32  000:02:43  D
    1020  1.337531e-01  3.309130e-05  000:00:33  000:02:43  D
    1030  1.340840e-01  3.309130e-05  000:00:33  000:02:42  D
    1040  1.344150e-01  3.309130e-05  000:00:33  000:02:42  D
    1050  1.347459e-01  3.309130e-05  000:00:34  000:02:42  FD
    1060  1.350768e-01  3.309130e-05  000:00:34  000:02:41  D
    1070  1.354077e-01  3.309130e-05  000:00:34  000:02:41  D
    1080  1.357386e-01  3.309130e-05  000:00:35  000:02:41  D
    1090  1.360695e-01  3.309130e-05  000:00:35  000:02:40  D
    1100  1.364004e-01  3.309130e-05  000:00:35  000:02:40  FD
    1110  1.367313e-01  3.309130e-05  000:00:36  000:02:40  D
    1120  1.370623e-01  3.309130e-05  000:00:36  000:02:39  D
    1130  1.373932e-01  3.309130e-05  000:00:36  000:02:39  D
    1140  1.377241e-01  3.309130e-05  000:00:37  000:02:39  D
    1150  1.380550e-01  3.309130e-05  000:00:37  000:02:39  FD
    1160  1.383859e-01  3.309130e-05  000:00:37  000:02:38  D
    1170  1.387168e-01  3.309130e-05  000:00:38  000:02:38  D
    1180  1.390477e-01  3.309130e-05  000:00:38  000:02:38  D
    1190  1.393786e-01  3.309130e-05  000:00:38  000:02:37  D
    1200  1.397096e-01  3.309130e-05  000:00:39  000:02:37  FD
    1210  1.400405e-01  3.309130e-05  000:00:39  000:02:37  D
    1220  1.403714e-01  3.309130e-05  000:00:39  000:02:36  D
    1230  1.407023e-01  3.309130e-05  000:00:40  000:02:36  D
    1240  1.410332e-01  3.309130e-05  000:00:40  000:02:36  D
    1250  1.413641e-01  3.309130e-05  000:00:40  000:02:35  FD
    1260  1.416950e-01  3.309130e-05  000:00:40  000:02:35  D
    1270  1.420260e-01  3.309130e-05  000:00:41  000:02:35  D
    1280  1.423569e-01  3.309130e-05  000:00:41  000:02:35  D
    1290  1.426878e-01  3.309130e-05  000:00:41  000:02:34  D
    1300  1.430187e-01  3.309130e-05  000:00:42  000:02:34  FD
    1310  1.433496e-01  3.309130e-05  000:00:42  000:02:34  D
    1320  1.436805e-01  3.309130e-05  000:00:42  000:02:33  D
    1330  1.440114e-01  3.309130e-05  000:00:43  000:02:33  D
    1340  1.443423e-01  3.309130e-05  000:00:43  000:02:33  D
    1350  1.446733e-01  3.309130e-05  000:00:43  000:02:32  FD
    1360  1.450042e-01  3.309130e-05  000:00:44  000:02:32  D
    1370  1.453351e-01  3.309130e-05  000:00:44  000:02:32  D
    1380  1.456660e-01  3.309130e-05  000:00:44  000:02:31  D
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    1930  1.638662e-01  3.309130e-05  000:01:03  000:02:15  D
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    1950  1.645280e-01  3.309130e-05  000:01:04  000:02:15  FD
    1960  1.648590e-01  3.309130e-05  000:01:04  000:02:15  D
    1970  1.651899e-01  3.309130e-05  000:01:05  000:02:14  D
    1980  1.655208e-01  3.309130e-05  000:01:05  000:02:14  D
    1990  1.658517e-01  3.309130e-05  000:01:05  000:02:14  D
    2000  1.661826e-01  3.309130e-05  000:01:06  000:02:14  FD
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    5930  2.962314e-01  3.309130e-05  000:03:33  000:00:04  D
    5940  2.965623e-01  3.309130e-05  000:03:33  000:00:03  D
    5950  2.968932e-01  3.309130e-05  000:03:34  000:00:03  FD
    5960  2.972242e-01  3.309130e-05  000:03:34  000:00:03  D
    5970  2.975551e-01  3.309130e-05  000:03:34  000:00:02  D
    5980  2.978860e-01  3.309130e-05  000:03:35  000:00:02  D
    5990  2.982169e-01  3.309130e-05  000:03:35  000:00:01  D
    6000  2.985478e-01  3.309130e-05  000:03:36  000:00:01  FD
    6010  2.988787e-01  3.309130e-05  000:03:36  000:00:01  D
    6020  2.992096e-01  3.309130e-05  000:03:36  000:00:00  D
    6030  2.995406e-01  3.309130e-05  000:03:37  000:00:00  D
    6040  2.998715e-01  3.309130e-05  000:03:37  000:00:00  D

     Normal finish, maximum time reached: 0.300000

 * Timers (h:m:s):
 -----------------
     Migrate global-scope data                                                   : 0:0:0
     Total runtime                                                               : 0:3:38

[Partition 0][Node 0] End of program

Example visualization

Example visualization of the 3D field data result with ParaView.

paraview out.0