Examples » Inciter: Integrating the scalar advection equation for a non-smooth problem

This example runs Inciter to integrate the advection equation (see e.g., PDE/Transport/CGTransport.h) configured to solve the Zalesak's slotted cylinder (inciter::TransportProblemSlotCyl) problem, which contains both smooth and non-smooth regions.

Control file

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

title "Zalesak's slotted cylinder"

inciter

  #nstep 10  # Max number of time steps
  #term 6.28318530718  # Max time = 2*pi
  term 1.57079632679  # Max time = pi/2
  #term 0.78539816339  # Max time = pi/4
  #term 0.39270  # Max time = pi/8
  cfl  0.5
  ttyi 10      # TTY output interval
  ctau 1.0  # FCT mass diffusivity

  transport
    physics advection
    problem slot_cyl
    ncomp 1
  end

  plotvar
    interval 100
  end

end

Example run on 80 CPUs

./charmrun +p80 Main/inciter -v -c slot_cyl.q -i unitcube_01_6M.exo

Output

Running on 80 processors:  Main/inciter -v -c slot_cyl.q -i unitcube_01_6M.exo
charmrun>  /usr/bin/setarch x86_64 -R  mpirun -np 80  Main/inciter -v -c slot_cyl.q -i unitcube_01_6M.exo
App launch reported: 5 (out of 5) daemons - 16 (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 0.029 seconds.

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

                                 < 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 09:44:41 2017
     Work directory                 : /net/scratch2/jbakosi/code/quinoa/build/gnup
     Executable (rel. to work dir)  : Main/inciter
     Command line arguments         : '-v -c slot_cyl.q -i unitcube_01_6M.exo'
     Output                         : verbose (quiet: omit -v)
     Control file                   : slot_cyl.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: Zalesak's slotted cylinder
 -----------------------------------

 * Partial differential equations integrated (1):
 ------------------------------------------------
   < Transport >
     problem                        : Zalesak's slotted cylinder
     start offset in unknowns array : 0
     number of components           : 1

 * Discretization parameters:
 ----------------------------
     Number of time steps           : 18446744073709551615
     Start time                     : 0
     Terminate time                 : 1.5708
     CFL coefficient                : 0.5
     Mass diffusion coeff           : 1

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

 * Output intervals:
 -------------------
     TTY                            : 10
     Field                          : 100
     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           : 6000000
     Number of nodes                : 1030301

 * Load distribution:
 --------------------
     Virtualization [0.0...1.0]     : 0
     Load (number of tetrahedra)    : 6000000
     Number of processing elements  : 80
     Number of work units           : 80 (79*75000+75000)

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

Quinoa> Mesh read time: 0.232970 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 = 0.112230, std = 0.070685
Quinoa> Reading mesh node coordinates, computing nodal volumes
Quinoa> Mesh statistics: min/max/avg(edgelength) = 0.010000 / 0.017321 / 0.012753
Quinoa> Mesh statistics: min/max/avg(V^{1/3}) = 0.005503 / 0.005503 / 0.005503
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  3.891359e-02  3.891359e-03  000:00:04  000:02:42  D
      20  7.782717e-02  3.891359e-03  000:00:08  000:02:38  D
      30  1.167408e-01  3.891359e-03  000:00:12  000:02:35  D
      40  1.556543e-01  3.891359e-03  000:00:16  000:02:32  D
      50  1.945679e-01  3.891359e-03  000:00:20  000:02:28  D
      60  2.334815e-01  3.891359e-03  000:00:25  000:02:24  D
      70  2.723951e-01  3.891359e-03  000:00:29  000:02:20  D
      80  3.113087e-01  3.891359e-03  000:00:33  000:02:16  D
      90  3.502223e-01  3.891359e-03  000:00:38  000:02:12  D
     100  3.891359e-01  3.891359e-03  000:00:59  000:03:01  FD
     110  4.280494e-01  3.891359e-03  000:01:04  000:02:51  D
     120  4.669630e-01  3.891359e-03  000:01:08  000:02:41  D
     130  5.058766e-01  3.891359e-03  000:01:12  000:02:33  D
     140  5.447902e-01  3.891359e-03  000:01:17  000:02:25  D
     150  5.837038e-01  3.891359e-03  000:01:21  000:02:17  D
     160  6.226174e-01  3.891359e-03  000:01:25  000:02:10  D
     170  6.615310e-01  3.891359e-03  000:01:30  000:02:04  D
     180  7.004445e-01  3.891359e-03  000:01:34  000:01:57  D
     190  7.393581e-01  3.891359e-03  000:01:39  000:01:51  D
     200  7.782717e-01  3.891359e-03  000:01:54  000:01:56  FD
     210  8.171853e-01  3.891359e-03  000:01:58  000:01:49  D
     220  8.560989e-01  3.891359e-03  000:02:03  000:01:42  D
     230  8.950125e-01  3.891359e-03  000:02:07  000:01:36  D
     240  9.339261e-01  3.891359e-03  000:02:12  000:01:30  D
     250  9.728396e-01  3.891359e-03  000:02:16  000:01:24  D
     260  1.011753e+00  3.891359e-03  000:02:21  000:01:18  D
     270  1.050667e+00  3.891359e-03  000:02:26  000:01:12  D
     280  1.089580e+00  3.891359e-03  000:02:30  000:01:06  D
     290  1.128494e+00  3.891359e-03  000:02:35  000:01:00  D
     300  1.167408e+00  3.891359e-03  000:02:41  000:00:55  FD
     310  1.206321e+00  3.891359e-03  000:02:46  000:00:50  D
     320  1.245235e+00  3.891359e-03  000:02:50  000:00:44  D
     330  1.284148e+00  3.891359e-03  000:02:54  000:00:39  D
     340  1.323062e+00  3.891359e-03  000:02:59  000:00:33  D
     350  1.361976e+00  3.891359e-03  000:03:03  000:00:28  D
     360  1.400889e+00  3.891359e-03  000:03:08  000:00:22  D
     370  1.439803e+00  3.891359e-03  000:03:12  000:00:17  D
     380  1.478716e+00  3.891359e-03  000:03:17  000:00:12  D
     390  1.517630e+00  3.891359e-03  000:03:21  000:00:07  D
     400  1.556543e+00  3.891359e-03  000:03:39  000:00:02  FD

     Normal finish, maximum time reached: 1.570796

 * Timers (h:m:s):
 -----------------
     Migrate global-scope data                                                   : 0:0:0
     Total runtime                                                               : 0:4:23

[Partition 0][Node 0] End of program

Example visualization

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

paraview out.0