Elmer-elmag example throws error
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Re: Elmer-elmag example throws error
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.
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Re: Elmer-elmag example throws error
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:
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
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
-Peter
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Re: Elmer-elmag example throws error
...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
-Peter
Re: Elmer-elmag example throws error
Hi,
Is this the full case that would be helpful?
Thank you,
Anna
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
Anna
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Re: Elmer-elmag example throws error
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.
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.
Re: Elmer-elmag example throws error
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
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Re: Elmer-elmag example throws error
What if you change
Linear System Iterative Method = CG
Linear System Preconditioning = ILU3
to
Linear System Iterative Method = BiCGStab
Linear System Preconditioning = ILU1
Linear System Iterative Method = CG
Linear System Preconditioning = ILU3
to
Linear System Iterative Method = BiCGStab
Linear System Preconditioning = ILU1
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Re: Elmer-elmag example throws error
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
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
Re: Elmer-elmag example throws error
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
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
Re: Elmer-elmag example throws error
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
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