Elmer-elmag example throws error

[kevinarden]

It is looking for a library file named _bulk and cannot find it. I have no library file named bulk on my system. You need to post you case file for further help.

[raback]

Hi

There have been different flavors of solver modules over the years. The standard solver does quite a bit of things that could be left for library. You could just provide rules for bulk and boundary assembly etc. The code in MainUtils.F90 around line 1250 checks this possibility:

Code: Select all

        AssProc = GetProcAddr( TRIM(proc_name)//'_bulk', abort=.FALSE. )
        CALL Info('AddEquationBasics','Checking for _bulk solver',Level=12)
        IF ( AssProc /= 0 ) THEN
          CALL Info('AddEquationBasics','Solver will be be performed in steps',Level=8)
          Solver % SolverMode = SOLVER_MODE_STEPS
        END IF        
      END IF

You just see this as your verbosity is >=12. The are some tests like ModelPDEslitted that follows this ideology but it never really caught popularity.

-Peter

[raback]

...your error probably has nothing to do with this. There are ~1000 tests that don't have _bulk defined but pass. As you see in the code there is no "procname" so somehow you have come here without giving the Procedure. Sharing the full case would indeed be helpful.

-Peter

[aevanch]

Hi,

Is this the full case that would be helpful?

Code: Select all

ELMER SOLVER (v 9.0) STARTED AT: 2024/03/06 15:33:26
--------------------------------------------------------------------------
The library attempted to open the following supporting CUDA libraries,
but each of them failed.  CUDA-aware support is disabled.
libcuda.so.1: cannot open shared object file: No such file or directory
libcuda.dylib: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.so.1: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.dylib: cannot open shared object file: No such file or directory
If you are not interested in CUDA-aware support, then run with
--mca opal_warn_on_missing_libcuda 0 to suppress this message.  If you are interested
in CUDA-aware support, then try setting LD_LIBRARY_PATH to the location
of libcuda.so.1 to get passed this issue.
--------------------------------------------------------------------------
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: 416941d5, Compiled: 2022-05-11)
MAIN:  Running one task without MPI parallelization.
MAIN:  Running in parallel with 2 threads per task.
MAIN: =============================================================
LoadInputFile: Trying to read "Run Control" section only
MAIN: 
MAIN: 
MAIN: -------------------------------------
MAIN: Reading Model: case.sif
LoadInputFile: Scanning input file: case.sif
LoadInputFile: Scanning only size info
LoadInputFile: First time visiting
LoadInputFile: Reading base load of sif file
LoadInputFile: Loading input file: case.sif
LoadInputFile: Reading base load of sif file
LoadInputFile: Number of BCs: 2
LoadInputFile: Number of Body Forces: 0
LoadInputFile: Number of Initial Conditions: 1
LoadInputFile: Number of Materials: 3
LoadInputFile: Number of Equations: 1
LoadInputFile: Number of Solvers: 4
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
ElmerAsciiMesh: Base mesh name: ./.
MAIN: -------------------------------------
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: statcurrentsolver...done.
OptimizeBandwidth: Half bandwidth without optimization: 24
OptimizeBandwidth: 
OptimizeBandwidth: Bandwidth Optimization ...done.
OptimizeBandwidth: Half bandwidth after optimization: 16
OptimizeBandwidth: ---------------------------------------------------------
_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

Thank you,
Anna

[kevinarden]

The library attempted to open the following supporting CUDA libraries,
but each of them failed. CUDA-aware support is disabled.
libcuda.so.1: cannot open shared object file: No such file or directory
libcuda.dylib: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.so.1: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.dylib: cannot open shared object file: No such file or directory

You can start by attaching your sif file.

[aevanch]

Hi, here is the sif file.

Code: Select all

Header
  CHECK KEYWORDS "Warn"
  Mesh DB "." "."
End

Simulation
  Max Output Level = 4
  Coordinate System = Cartesian 3D
  Simulation Type = Steady state
  Steady State Max Iterations = 30
End

Constants
  Stefan Boltzmann = 5.6704e-08
End

! equations
Equation 1
  Active Solvers(3) = 3 2 1   ! ThermalSolverPartThree, ThermalSolverPartTwo, ThermalSolverPartOne, 
End


! ThermalSolverPartOne
Solver 1
  Equation = StatCurrentSolver
  Procedure = "StatCurrentSolve" "StatCurrentSolver"
  Variable = Potential
  Variable DOFs = 1
  Calculate Volume Current = Logical True
  Calculate Electric Conductivity = Logical True
  Linear System Solver = Iterative
  Linear System Iterative Method = CG
  Linear System Preconditioning = ILU3
  Linear System Max Iterations = 300
  Linear System Convergence Tolerance = 1e-09
  Nonlinear System Max Iterations = 1
  Nonlinear System Convergence Tolerance = 1e-07
  Nonlinear System Newton After Iterations = 3
  Nonlinear System Newton After Tolerance = 1e-13
  Nonlinear System Relaxation Factor = 1
  Steady State Convergence Tolerance = 1e-07
End

! ThermalSolverPartTwo
Solver 2
  Equation = HeatEquation
  Variable = Temperature
  Variable DOFs = 1
  Linear System Solver = Iterative
  Linear System Iterative Method = BiCGStab
  Linear System Preconditioning = ILU1
  Linear System Max Iterations = 350
  Linear System Convergence Tolerance = 1e-09
  Nonlinear System Max Iterations = 1
  Nonlinear System Convergence Tolerance = 1e-07
  Nonlinear System Newton After Iterations = 3
  Nonlinear System Newton After Tolerance = 1e-12
  Nonlinear System Relaxation Factor = 0.5
  Steady State Convergence Tolerance = 1e-07
End

! ThermalSolverPartThree
Solver 3
  Exec Solver = After All
  Equation = StressAnalysis
  Variable = Displacement
  Variable DOFs = 3
  Linear System Solver = Direct
  Linear System Direct Method = Banded
  Nonlinear System Max Iterations = 1
  Nonlinear System Convergence Tolerance = 1e-06
  Nonlinear System Newton After Iterations = 3
  Nonlinear System Newton After Tolerance = 1e-12
  Nonlinear System Relaxation Factor = 1.0
  Steady State Convergence Tolerance = 1e-06
End

! ResultOutputSolver
Solver 4
  Exec Solver = After timestep
  Equation = ResultOutputSolver
  Procedure = "ResultOutputSolve" "ResultOutputSolver"
  VTU Format = True
  Save Geometry Ids = Logical True
End


! material_3
Material 1
  Density = 135
  Heat Capacity = 4
  Heat Conductivity = 3.622
  Heat Expansion Coefficient = 0.03
  Youngs Modulus = 90
  Poisson Ratio = 0.62
  Relative Permeability = 1.3
  Relative Permittivity = 1
  Solid = Logical True
  Electric Conductivity = 2.3
End

! material_2
Material 2
  Density = 123
  Heat Capacity = 2
  Heat Conductivity = 222
  Heat Expansion Coefficient = 3
  Youngs Modulus = 122
  Poisson Ratio = 0.42
  Relative Permeability = 1.3
  Relative Permittivity = 12
  Solid = Logical True
  Electric Conductivity = 1.7
End

! material_1
Material 3
  Density = 1234
  Heat Capacity = 123
  Heat Conductivity = 0.5
  Heat Expansion Coefficient = 2.9e-05
  Youngs Modulus = 169
  Poisson Ratio = 0.22
  Relative Permeability = 1
  Relative Permittivity = 1
  Solid = Logical True
  Electric Conductivity = 1.3
End


! material_1
Body 1
  Target Bodies(1) = 1
  Equation = 1  ! equations
  Initial Condition = 1  ! condition_0
  Material = 3  ! material_1
End

! material_2
Body 2
  Target Bodies(1) = 2
  Equation = 1  ! equations
  Initial Condition = 1  ! condition_0
  Material = 2  ! material_2
End

! material_3
Body 3
  Target Bodies(1) = 3
  Equation = 1  ! equations
  Initial Condition = 1  ! condition_0
  Material = 1  ! material_3
End


! bottom
Boundary Condition 1
  Target Boundaries(1) = 4
  Potential = 14
  Temperature = 298
End

! top
Boundary Condition 2
  Target Boundaries(1) = 5
  Potential = 7
  Temperature = 298
End




! condition_0
Initial Condition 1
  Temperature = 273.15
  Potential = 0
End

[kevinarden]

What if you change

Linear System Iterative Method = CG
Linear System Preconditioning = ILU3

to

Linear System Iterative Method = BiCGStab
Linear System Preconditioning = ILU1

[raback]

Hi,

can you solve anything with success? CUDA does not like DLL so that could be the culprint. However, in that case you should not be able to run most cases. There is something fishy since the code should be looking for "ProcName_bulk" and not just "_bulk".

What is you setup and how did you install Elmer?

-Peter

[aevanch]

Hi,

Yes I can solve the first solver only with success. When I try to run the last two solvers on their own, they give the _bulk error.

Kevin, I am going to try your suggestion, and I will report back.

Thank you,
Anna

[aevanch]

I am running my code in Jupyter Notebook using open on demand on the Palmetto Cluster. (I am a university student).

Could you provide more information on what "ProcName_bulk" is or what it's function and or/what it stores?

I installed elmer using linux on the jupyter notebook terminal in our cluster.



Kevin,
The change in the simulation allowed me to still run the first solver with success, however no change was seen for being able to run all three in succession.

Thank you,
Anna