Elmer-elmag example throws error

Matrixrifle · Post by **Matrixrifle** » 21 Feb 2024, 07:35

Hi,
I have been trying to run elmer-elmag examples on wsl(windows-subsytem-linux) and i have been getting weird errors while running the elmer-elmag example CircuitBuilder/2D/massive/transient https://github.com/ElmerCSC/elmer-elmag ... /transient

>> apt list -a elmerfem-csc
Listing... Done
elmerfem-csc/jammy 9.0-0ppa0-202402201703~dd4157a2c~ubuntu22.04.1 amd64

>>cat /etc/os-release
PRETTY_NAME="Ubuntu 22.04.3 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.3 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy

Code: Select all

$ cd elmer-elmag/CircuitBuilder/2D/massive/transient
$ ElmerSolver massive_coil.sif

ELMER SOLVER (v 9.0) STARTED AT: 2024/02/21 04:24:36
ParCommInit:  Initialize #PEs:            1
MAIN:
MAIN: =============================================================
MAIN: ElmerSolver finite element software, Welcome!
MAIN: This program is free software licensed under (L)GPL
MAIN: Copyright 1st April 1995 - , CSC - IT Center for Science Ltd.
MAIN: Webpage http://www.csc.fi/elmer, Email elmeradm@csc.fi
MAIN: Version: 9.0 (Rev: unknown, Compiled: 2024-02-20)
MAIN:  Running one task without MPI parallelization.
MAIN:  Running with just one thread per task.
MAIN:  HYPRE library linked in.
MAIN:  MUMPS library linked in.
MAIN:  Lua interpreter linked in.
MAIN: =============================================================
OpenIncludeFile: Trying to include file: "transient_circuit.definition"
MAIN:
MAIN:
MAIN: -------------------------------------
MAIN: Reading Model: massive_coil.sif
LoadInputFile: Scanning input file: massive_coil.sif
LoadInputFile: Scanning only size info
LoadInputFile: First time visiting
LoadInputFile: Reading base load of sif file
OpenIncludeFile: Trying to include file: "transient_circuit.definition"
LoadInputFile: Loading input file: massive_coil.sif
LoadInputFile: Reading base load of sif file
OpenIncludeFile: Trying to include file: "transient_circuit.definition"
CheckKeyword:  Unlisted keyword: [v1_source] in section: [body force 1]
LoadInputFile: Number of BCs: 1
LoadInputFile: Number of Body Forces: 1
LoadInputFile: Number of Initial Conditions: 0
LoadInputFile: Number of Materials: 2
LoadInputFile: Number of Equations: 1
LoadInputFile: Number of Solvers: 6
LoadInputFile: Number of Bodies: 3
ListTagKeywords: Setting weight for keywords!
ListTagKeywords: No parameters width suffix: normalize by area
ListTagKeywords: Setting weight for keywords!
ListTagKeywords: No parameters width suffix: normalize by volume
Loading user function library: [CircuitsAndDynamics]...[CircuitsAndDynamics_Init0]
Loading user function library: [MagnetoDynamics2D]...[MagnetoDynamics2D_Init0]
Loading user function library: [MagnetoDynamics]...[MagnetoDynamicsCalcFields_Init0]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_Init0]
Loading user function library: [CircuitsAndDynamics]...[CircuitsOutput_Init0]
Loading user function library: [SaveData]...[SaveScalars_Init0]
ElmerAsciiMesh: Base mesh name: ./round_coil
PermuteNodeNumbering: Performing node mapping
ReadTargetNames: Reading names info from file: ./round_coil/mesh.names
MapBodiesAndBCs: Minimum initial body index: 77
MapBodiesAndBCs: Maximum initial body index: 79
MapBodiesAndBCs: Minimum initial boundary index: 80
MapBodiesAndBCs: Maximum initial boundary index: 80
LoadMesh: Elapsed REAL time:     0.0147 (s)
MeshStabParams: Computing stabilization parameters
MeshStabParams: Elapsed REAL time:     0.0013 (s)
WARNING:: ListFind:
WARNING:: ListFind:  Requested property: [Equation], not found
WARNING:: ListFind:
MAIN: -------------------------------------
Loading user function library: [CircuitsAndDynamics]...[CircuitsAndDynamics_Init]
Loading user function library: [CircuitsAndDynamics]...[CircuitsAndDynamics_bulk]
Loading user function library: [CircuitsAndDynamics]...[CircuitsAndDynamics]
Loading user function library: [MagnetoDynamics2D]...[MagnetoDynamics2D_Init]
Loading user function library: [MagnetoDynamics2D]...[MagnetoDynamics2D_bulk]
Loading user function library: [MagnetoDynamics2D]...[MagnetoDynamics2D]
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: mgdyn2d
OptimizeBandwidth: Initial bandwidth for mgdyn2d: 7406
OptimizeBandwidth: Optimized bandwidth for mgdyn2d: 173
OptimizeBandwidth: ---------------------------------------------------------
Loading user function library: [MagnetoDynamics]...[MagnetoDynamicsCalcFields_Init]
Loading user function library: [MagnetoDynamics]...[MagnetoDynamicsCalcFields_bulk]
Loading user function library: [MagnetoDynamics]...[MagnetoDynamicsCalcFields]
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: calcfields
OptimizeBandwidth: Initial bandwidth for calcfields: 7406
OptimizeBandwidth: Optimized bandwidth for calcfields: 173
OptimizeBandwidth: ---------------------------------------------------------
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_Init]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_bulk]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver]
Loading user function library: [CircuitsAndDynamics]...[CircuitsOutput_Init]
Loading user function library: [CircuitsAndDynamics]...[CircuitsOutput_bulk]
Loading user function library: [CircuitsAndDynamics]...[CircuitsOutput]
Loading user function library: [SaveData]...[SaveScalars_Init]
Loading user function library: [SaveData]...[SaveScalars]
MAIN: Number of timesteps to be saved: 100
MAIN:
MAIN: -------------------------------------
MAIN: Time: 1/100:   2.000E-06
MAIN: -------------------------------------
MAIN:
CircuitsAndDynamics: Initializing electric circuits for transient simulation
AddComponentsToBodyList: "Body 1" associated to "Component 1"
AddComponentsToBodyList: "Body 2" associated to "Component 2"
CircuitsAndDynamics: Circuit equations associated with solver index: 2
MagnetoDynamics2D: ------------------------------------------------
MagnetoDynamics2D: Solving equation for magnetic vector potential
MagnetoDynamics2D: ------------------------------------------------
MagnetoDynamics2D: Performing legacy version of bulk element assembly
   gcr:     1  0.2685E-02  0.1000E+01
   gcr:     2  0.2685E-02  0.1298E-05
   gcr:     3  0.1743E-02  0.2043E-02
   gcr:     4  0.9928E-03  0.1432E-02
   gcr:     5  0.8587E-03  0.4984E-03
   gcr:     6  0.7746E-03  0.3705E-03
   gcr:     7  0.7275E-03  0.2662E-03
   gcr:     8  0.6848E-03  0.2454E-03
   gcr:     9  0.6328E-03  0.2619E-03
   gcr:    10  0.5888E-03  0.2318E-03
   gcr:    11  0.5384E-03  0.2384E-03
   gcr:    12  0.4938E-03  0.2145E-03
   gcr:    13  0.4415E-03  0.2212E-03
   gcr:    14  0.4053E-03  0.1750E-03
   gcr:    15  0.3718E-03  0.1613E-03
   gcr:    16  0.3258E-03  0.1791E-03
   gcr:    17  0.2925E-03  0.1435E-03
   gcr:    18  0.2658E-03  0.1222E-03
   gcr:    19  0.2506E-03  0.8855E-04
   gcr:    20  0.2379E-03  0.7881E-04
   gcr:    21  0.2267E-03  0.7206E-04
   gcr:    22  0.2156E-03  0.7004E-04
   gcr:    23  0.2009E-03  0.7844E-04
   gcr:    24  0.1848E-03  0.7866E-04
   gcr:    25  0.1688E-03  0.7516E-04
   gcr:    26  0.1531E-03  0.7115E-04
   gcr:    27  0.1421E-03  0.5699E-04
   gcr:    28  0.1324E-03  0.5161E-04
   gcr:    29  0.1263E-03  0.3971E-04
   gcr:    30  0.1215E-03  0.3457E-04
   gcr:    31  0.1158E-03  0.3658E-04
   gcr:    32  0.1103E-03  0.3534E-04
   gcr:    33  0.1043E-03  0.3598E-04
   gcr:    34  0.9947E-04  0.3135E-04
   gcr:    35  0.9426E-04  0.3177E-04
   gcr:    36  0.8827E-04  0.3308E-04
   gcr:    37  0.8417E-04  0.2657E-04
   gcr:    38  0.8123E-04  0.2205E-04
   gcr:    39  0.7872E-04  0.2006E-04
   gcr:    40  0.7659E-04  0.1819E-04
   gcr:    41  0.7378E-04  0.2054E-04
   gcr:    42  0.7066E-04  0.2123E-04
   gcr:    43  0.6774E-04  0.2012E-04
   gcr:    44  0.6560E-04  0.1686E-04
   gcr:    45  0.6390E-04  0.1484E-04
   gcr:    46  0.6099E-04  0.1907E-04
   gcr:    47  0.5768E-04  0.1981E-04
   gcr:    48  0.5558E-04  0.1544E-04
   gcr:    49  0.5435E-04  0.1159E-04
   gcr:    50  0.5294E-04  0.1234E-04
   gcr:    51  0.5061E-04  0.1552E-04
   gcr:    52  0.4824E-04  0.1530E-04
   gcr:    53  0.4619E-04  0.1392E-04
   gcr:    54  0.4459E-04  0.1204E-04
   gcr:    55  0.4295E-04  0.1200E-04
   gcr:    56  0.4152E-04  0.1099E-04
   gcr:    57  0.4042E-04  0.9476E-05
   gcr:    58  0.3925E-04  0.9661E-05
   gcr:    59  0.3803E-04  0.9689E-05
   gcr:    60  0.3691E-04  0.9197E-05
   gcr:    61  0.3615E-04  0.7430E-05
   gcr:    62  0.3543E-04  0.7162E-05
   gcr:    63  0.3411E-04  0.9583E-05
   gcr:    64  0.3271E-04  0.9676E-05
   gcr:    65  0.3162E-04  0.8373E-05
   gcr:    66  0.3084E-04  0.7008E-05
   gcr:    67  0.2982E-04  0.7859E-05
   gcr:    68  0.2848E-04  0.8819E-05
   gcr:    69  0.2711E-04  0.8735E-05
   gcr:    70  0.2569E-04  0.8648E-05
   gcr:    71  0.2441E-04  0.8020E-05
   gcr:    72  0.2323E-04  0.7500E-05
   gcr:    73  0.2226E-04  0.6633E-05
   gcr:    74  0.2136E-04  0.6283E-05
   gcr:    75  0.2041E-04  0.6303E-05
   gcr:    76  0.1956E-04  0.5807E-05
   gcr:    77  0.1875E-04  0.5594E-05
   gcr:    78  0.1794E-04  0.5449E-05
   gcr:    79  0.1715E-04  0.5260E-05
   gcr:    80  0.1630E-04  0.5332E-05
   gcr:    81  0.1544E-04  0.5227E-05
   gcr:    82  0.1459E-04  0.5037E-05
   gcr:    83  0.1376E-04  0.4868E-05
   gcr:    84  0.1294E-04  0.4657E-05
   gcr:    85  0.1230E-04  0.4018E-05
   gcr:    86  0.1177E-04  0.3583E-05
   gcr:    87  0.1129E-04  0.3342E-05
   gcr:    88  0.1080E-04  0.3271E-05
   gcr:    89  0.1022E-04  0.3491E-05
   gcr:    90  0.9646E-05  0.3387E-05
   gcr:    91  0.9044E-05  0.3354E-05
   gcr:    92  0.8408E-05  0.3329E-05
   gcr:    93  0.7818E-05  0.3096E-05
   gcr:    94  0.7256E-05  0.2910E-05
   gcr:    95  0.6731E-05  0.2711E-05
   gcr:    96  0.6286E-05  0.2406E-05
   gcr:    97  0.5809E-05  0.2401E-05
   gcr:    98  0.5372E-05  0.2211E-05
   gcr:    99  0.5015E-05  0.1926E-05
   gcr:   100  0.4646E-05  0.1888E-05
   gcr:   101  0.4611E-05  0.5689E-06
   gcr:   102  0.4602E-05 -0.2918E-06
   gcr:   103  0.4580E-05 -0.4521E-06
   gcr:   104  0.4323E-05  0.1511E-05
   gcr:   105  0.4081E-05  0.1425E-05
   gcr:   106  0.4073E-05  0.2582E-06
   gcr:   107  0.3835E-05  0.1373E-05
   gcr:   108  0.3538E-05  0.1480E-05
   gcr:   109  0.3230E-05  0.1444E-05
   gcr:   110  0.3069E-05  0.1007E-05
   gcr:   111  0.2980E-05  0.7324E-06
   gcr:   112  0.2732E-05  0.1192E-05
   gcr:   113  0.2585E-05  0.8827E-06
   gcr:   114  0.2397E-05  0.9697E-06
   gcr:   115  0.2236E-05  0.8614E-06
   gcr:   116  0.2125E-05  0.6981E-06
   gcr:   117  0.2009E-05  0.6920E-06
   gcr:   118  0.1920E-05  0.5889E-06
   gcr:   119  0.1830E-05  0.5809E-06
   gcr:   120  0.1791E-05  0.3763E-06
   gcr:   121  0.1776E-05  0.2311E-06
   gcr:   122  0.1756E-05  0.2673E-06
   gcr:   123  0.1739E-05  0.2458E-06
   gcr:   124  0.1727E-05  0.2036E-06
   gcr:   125  0.1717E-05  0.1843E-06
   gcr:   126  0.1700E-05  0.2411E-06
   gcr:   127  0.1685E-05  0.2226E-06
   gcr:   128  0.1684E-05  0.6461E-07
   gcr:   129  0.1683E-05 -0.7446E-07
   gcr:   130  0.1681E-05 -0.7165E-07
   gcr:   131  0.1659E-05  0.2712E-06
   gcr:   132  0.1612E-05  0.3929E-06
   gcr:   133  0.1575E-05  0.3429E-06
   gcr:   134  0.1518E-05  0.4203E-06
   gcr:   135  0.1451E-05  0.4447E-06
   gcr:   136  0.1377E-05  0.4585E-06
   gcr:   137  0.1285E-05  0.4945E-06
   gcr:   138  0.1187E-05  0.4917E-06
   gcr:   139  0.1063E-05  0.5280E-06
   gcr:   140  0.9825E-06  0.4065E-06
ComputeChange: NS (ITER=1) (NRM,RELC): ( 0.28812032E-02  2.0000000     ) :: mgdyn2d
MagnetoDynamicsCalcFields: ------------------------------
MagnetoDynamicsCalcFields: Computing postprocessed fields
MagnetoDynamicsCalcFields: Using potential variable: a
MagnetoDynamicsCalcFields: Solving for field: magnetic flux density[magnetic flux density:3]
ERROR:: SolveLinearSystem: Give "Linear System Solver", e.g. "linear" or "direct"
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1

The last two lines shows the error

ERROR:: SolveLinearSystem: Give "Linear System Solver", e.g. "linear" or "direct"
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

Let me know if I can run more tests to diagnose the problem.

kevinarden · Post by **kevinarden** » 21 Feb 2024, 13:18

Same result
NAME="Linux Mint"
VERSION="21.3 (Virginia)"
VERSION_CODENAME=virginia
UBUNTU_CODENAME=jammy

I noticed
MagnetoDynamicsCalcFields: Solving for field: magnetic flux density[magnetic flux density:3]
ERROR:: SolveLinearSystem: Give "Linear System Solver", e.g. "linear" or "direct"
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
something about calculating DOF 3 in a 2D problem

So Switched the field calculator to 2D instead of 3D and it ran
Procedure = "MagnetoDynamics2D" "bSolver"
The 3D one is supposed to be the right one.

Matrixrifle · Post by **Matrixrifle** » 21 Feb 2024, 13:23

Tried it with the latest windows version as well. Same error !!

Windows Elmer Version :
Version: 9.0 (Rev: Release, Compiled: 2024-02-20)

Matrixrifle · Post by **Matrixrifle** » 21 Feb 2024, 14:20

Hi Kevin
I tried the change you suggested still gave an error. Is it possible to upload the sif file please

raback · Post by **raback** » 21 Feb 2024, 15:30

Hi

It was previously possible not to define any linear solver settings. Then the code used defaults which happened to be "direct" solver with "banded" method. We thought that it was a very poor default so the user is now obliged to give one (for the CalcFields) solver.

Code: Select all

Linear System Solver = direct
Linear System Direct Method = umfpack

In this case I would however rather say

Code: Select all

Calculate Nodal Fields = False
Calculate Elemental Fields = True

Only the projection to nodes requires solution of linear system. Elemental fields are postprocessed one element at a time.

-Peter

kevinarden · Post by **kevinarden** » 21 Feb 2024, 15:46

Peter's fix works, that is the best approach.

Matrixrifle · Post by **Matrixrifle** » 21 Feb 2024, 17:11

Yes it works now. For future reference is it then a good idea to add the linear solver settings in the calcfields solver.

Should we add non linear solver settings as well in the calcfields solver if the system is non linear for example a problem with the 2 conductors but having a piece of iron in it ?

raback · Post by **raback** » 21 Feb 2024, 18:07

Hi,

Linear solver setting are needed when solving for linear system. Usually this relates only to PDE's but it also relates to some postprocessing solvers where, for example, B=Curl(A) is also solved using the finite element method.

No nonlinear system setting are needed for this since the primary solver finds the solution and the material parameters are evaluated using that solution.

-Peter

Matrixrifle · Post by **Matrixrifle** » 22 Feb 2024, 15:02

Hi Peter,
Thanks for the explanation. makes sense now.

aevanch · Post by **aevanch** » 07 Mar 2024, 00:11

Hi all,

I was wondering if anyone knows what _bulk could be.

I have never seen this before and am trying to figure out what it is.

In my elmersolver.log file I am getting the following errors:

_bulk: cannot open shared object file: No such file or directory
_bulk.so: cannot open shared object file: No such file or directory
./_bulk: cannot open shared object file: No such file or directory
./_bulk.so: cannot open shared object file: No such file or directory
/home/aevanch/scilib/share/elmersolver/lib/_bulk: cannot open shared object file: No such file or directory
/home/aevanch/scilib/share/elmersolver/lib/_bulk.so: cannot open shared object file: No such file or directory

Any help would be appreciated!!

Thanks,
Anna

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Elmer-elmag example throws error

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