I prepared a very simple case from a more complex one that has problems to run in parallel. The case consist of a coil, a copper plate, and air. The serial run works with no problems. Any insight into what could be happening?
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
WARNING:: ReadTargetNames: Could not map name to Body nor BC: bnry5
WARNING:: ReadTargetNames: Could not map name to Body nor BC: bnry5
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
ComputeChange: NS (ITER=1) (NRM,RELC): ( 0.59847995 2.0000000 ) :: coilsolver
ComputeChange: NS (ITER=2) (NRM,RELC): ( 0.57031824 0.48189182E-01 ) :: coilsolver
#0 0x7fddfa8c0d21 in ???
#1 0x7fddfa8bfef5 in ???
#2 0x7fddfa6f10bf in ???
#3 0x7fddfafa1b48 in __parallelutils_MOD_parallelsumvectorint
at /home/fjimenez/git/elmerfem/fem/src/ParallelUtils.F90:716
#4 0x7fddfaba0e65 in choosefixedbulknodesnarrow
at /home/fjimenez/git/elmerfem/fem/src/modules/CoilSolver.F90:1212
#5 0x7fddfaba8834 in coilsolver_
at /home/fjimenez/git/elmerfem/fem/src/modules/CoilSolver.F90:374
#6 0x7fddfae4a19a in __mainutils_MOD_singlesolver
at /home/fjimenez/git/elmerfem/fem/src/MainUtils.F90:5250
#7 0x7fddfae5f53b in __mainutils_MOD_solveractivate
at /home/fjimenez/git/elmerfem/fem/src/MainUtils.F90:5493
#8 0x7fddfb0bd9f0 in execsimulation
at /home/fjimenez/git/elmerfem/fem/src/ElmerSolver.F90:2348
#9 0x7fddfb0c401d in elmersolver_
at /home/fjimenez/git/elmerfem/fem/src/ElmerSolver.F90:593
#10 0x55e31320a3cd in solver
at /home/fjimenez/git/elmerfem/fem/src/Solver.F90:57
#11 0x55e31320a13e in main
at /home/fjimenez/git/elmerfem/fem/src/Solver.F90:34
I first did
ElmerGrid 8 2 copper_and_coil -partdual -metiskway 4
Then
mpirun -np 4 ElmerSolver_mpi copper_and_coil.sif
received Error
ReadTargetNames: Requested the use of entity names but this file does not exits: ./copper_and_coil/mesh.names
ElmerGrid did not create mesh.names file
Edited sif to remove use meh names
! Use Mesh Names = True
Thanks for taking a quick look at the case kevinarden, I should've investigated the problem a little more before posting. It turned out that
my conda mpi library was incompatible with my system one. I hadn't had this problem before so I thought that the problem was Elmer related.
It is now working as normal when I deactivate my conda environment. Not sure what happened, I have done tons of parallel runs with this setup so far with no problems.
ssnestinger@PC:~/Desktop/test$ mpirun -np 8 ElmerSolver_mpi copper_and_coil.sif
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:17:44
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
MAIN: OMP_NUM_THREADS not set. Using only 1 thread per task.
MAIN: ParCommInit: Initialize #PEs: 8
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: e5b2b7b8d, Compiled: 2023-11-03)
MAIN: Running in parallel using 8 tasks.
MAIN: Running with just one thread per task.
MAIN: MUMPS library linked in.
MAIN: Zoltan library linked in.
MAIN: =============================================================
MAIN:
MAIN:
MAIN: -------------------------------------
MAIN: Reading Model: copper_and_coil.sif
LoadInputFile: Scanning input file: copper_and_coil.sif
LoadInputFile: Scanning only size info
LoadInputFile: First time visiting
LoadInputFile: Reading base load of sif file
LoadInputFile: Loading input file: copper_and_coil.sif
LoadInputFile: Reading base load of sif file
CheckKeyword: Unlisted keyword: [save coil set] in section: [solver 1]
CheckKeyword: Unlisted keyword: [save coil index] in section: [solver 1]
CheckKeyword: Unlisted keyword: [single coil cut] in section: [solver 1]
CheckKeyword: Unlisted keyword: [a re {e}] in section: [boundary condition 1]
CheckKeyword: Unlisted keyword: [a im {e}] in section: [boundary condition 1]
CheckKeyword: Unlisted keyword: [jfix] in section: [boundary condition 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: 2
LoadInputFile: Number of Solvers: 5
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
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
BiCGStabl: 55 0.5942E-08 0.5621E-08
ComputeChange: NS (ITER=1) (NRM,RELC): ( 0.57594313 2.0000000 ) :: coilsolver
BiCGStabl: 57 0.1046E-07 0.9895E-08
ComputeChange: NS (ITER=2) (NRM,RELC): ( 0.59854992 0.38496239E-01 ) :: coilsolver
BiCGStabl: 5 0.7412E-08 0.6728E-08
BiCGStabl: 6 0.4098E-08 0.3687E-08
BiCGStabl: 6 0.1043E-07 0.8717E-08
#0 0x7f7ec5223970 in ???
#1 0x7f7ec5222ad5 in ???
#2 0x7f7ec4e3c45f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f7ec5a752e8 in __parallelutils_MOD_parallelsumvectorint
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ParallelUtils.F90:839
#4 0x7f7df54e941d in choosefixedbulknodesnarrow
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:1266
#5 0x7f7df54f32dc in coilsolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:381
#6 0x7f7ec58efbfd in __mainutils_MOD_singlesolver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5256
#7 0x7f7ec590556c in __mainutils_MOD_solveractivate
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5531
#8 0x7f7ec5ba6517 in execsimulation
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:2616
#9 0x7f7ec5bafec7 in elmersolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:662
#10 0x55aeba00a3f0 in solver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:57
#11 0x55aeba00a15e in main
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:34
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node PC exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
The same error can be reproduced using the elmer-elmag/TEAM7 example:
ssnestinger@PC:~/Desktop/elmer-elmag/TEAM7$ mpirun -np 2 ElmerSolver_mpi steady.sif
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 12:54:22
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 12:54:22
ParCommInit: Initialize #PEs: 2
MAIN: OMP_NUM_THREADS not set. Using only 1 thread per task.
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: e5b2b7b8d, Compiled: 2023-11-03)
MAIN: Running in parallel using 2 tasks.
MAIN: Running with just one thread per task.
MAIN: MUMPS library linked in.
MAIN: Zoltan library linked in.
MAIN: =============================================================
ParCommInit: Initialize #PEs: 2
MAIN:
MAIN:
MAIN: -------------------------------------
MAIN: Reading Model: steady.sif
LoadInputFile: Scanning input file: steady.sif
LoadInputFile: Scanning only size info
LoadInputFile: First time visiting
LoadInputFile: Reading base load of sif file
LoadInputFile: Loading input file: steady.sif
LoadInputFile: Reading base load of sif file
WARNING:: LoadInputFile: Entry missing for: Body Force 1
CheckKeyword: Unlisted keyword: [jfix] in section: [boundary condition 1]
CheckKeyword: Unlisted keyword: [gmsh format] in section: [solver 4]
LoadInputFile: Number of BCs: 1
LoadInputFile: Number of Body Forces: 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
LoadInputFile: Number of Initial Conditions: 0
LoadInputFile: Number of Materials: 2
LoadInputFile: Number of Equations: 2
LoadInputFile: Number of Solvers: 5
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: [CoilSolver]...[CoilSolver_Init0]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver_Init0]
WhitneyAVSolver_Init0: Setting element type to: "n:0 e:1"
Loading user function library: [MagnetoDynamics]...[MagnetoDynamicsCalcFields_Init0]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_Init0]
Loading user function library: [SaveData]...[SaveLine_Init0]
ElmerAsciiMesh: Base mesh name: ./TEAM7
PermuteNodeNumbering: Performing node mapping
ReadTargetNames: Reading names info from file: ./TEAM7/mesh.names
WARNING:: ReadTargetNames: Could not map name to Body nor BC: coilskin
WARNING:: ReadTargetNames: Could not map name to Body nor BC: plateskin
MapBodiesAndBCs: Minimum initial body index: 2
MapBodiesAndBCs: Maximum initial body index: 3
MapBodiesAndBCs: Minimum initial boundary index: 5
MapBodiesAndBCs: Maximum initial boundary index: 6
LoadMesh: Elapsed REAL time: 0.6834 (s)
MeshStabParams: Computing stabilization parameters
MeshStabParams: Elapsed REAL time: 0.0054 (s)
MAIN: -------------------------------------
Loading user function library: [CoilSolver]...[CoilSolver_Init]
Loading user function library: [CoilSolver]...[CoilSolver_bulk]
Loading user function library: [CoilSolver]...[CoilSolver]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver_Init]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver_bulk]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver]
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: mgdynamics transient
OptimizeBandwidth: Initial bandwidth for mgdynamics transient: 82825
OptimizeBandwidth: Optimized bandwidth for mgdynamics transient: 3994
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: mgdynamicscalc
OptimizeBandwidth: Initial bandwidth for mgdynamicscalc: 12177
OptimizeBandwidth: Optimized bandwidth for mgdynamicscalc: 1267
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: [SaveData]...[SaveLine_Init]
Loading user function library: [SaveData]...[SaveLine_bulk]
Loading user function library: [SaveData]...[SaveLine]
MAIN: Number of timesteps to be saved: 1
CoilSolver: --------------------------------------
CoilSolver: Solving current distribution in a coil
CoilSolver: --------------------------------------
CoilSolver: Assuming that all coils are closed!
CoilSolver: Coil volume: 1.5886E-03
CoilSolver: Coil center: 1.9400E-01 1.0000E-01 9.9000E-02
CoilSolver: Choosing narrow fixing nodes for set: 1
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
CoilSolver: Choosing narrow fixing nodes for set: 2
CoilSolver: Coil system consists of 1 coils
CoilSolver: Set1 : 33 +nodes and 33 -nodes
CoilSolver: Set2 : 33 +nodes and 33 -nodes
CoilSolver: Computing the dummy potential field
CutInterfaceConnections: Number of connections cut: 210
EnforceDirichletConditions: Dirichlet conditions enforced for dofs: 66
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 11757
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
SolveLinearSystem: Calculating nodal loads for: coiltmp
ComputeChange: NS (ITER=1) (NRM,RELC): ( 0.58632456 2.0000000 ) :: coil solver
CoilSolver: Discrepancy of start and end coil currents: 7.4300E-07
CoilSolver: Initial coil current for coil 1: 4.2911E-03
CoilSolver: Coil potential multiplier: -6.3899E+05
CutInterfaceConnections: Number of connections cut: 210
EnforceDirichletConditions: Dirichlet conditions enforced for dofs: 66
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 11757
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
SolveLinearSystem: Calculating nodal loads for: coiltmp
ComputeChange: NS (ITER=2) (NRM,RELC): ( 0.58161669 0.80618347E-02 ) :: coil solver
CoilSolver: Discrepancy of start and end coil currents: 3.8524E-08
CoilSolver: Initial coil current for coil 1: 4.2912E-03
CoilSolver: Coil potential multiplier: -6.3898E+05
CoilSolver: Computing current component: 1
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 11757
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
CoilSolver: Computing current component: 2
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 11757
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
CoilSolver: Computing current component: 3
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 11757
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
#0 0x7fcf91e23970 in ???
#1 0x7fcf91e22ad5 in ???
#2 0x7fcf91a3c45f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7fcf926752e8 in __parallelutils_MOD_parallelsumvectorint
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ParallelUtils.F90:839
#4 0x7fcf7d13441d in choosefixedbulknodesnarrow
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:1266
#5 0x7fcf7d13e2dc in coilsolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:381
#6 0x7fcf924efbfd in __mainutils_MOD_singlesolver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5256
#7 0x7fcf9250556c in __mainutils_MOD_solveractivate
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5531
#8 0x7fcf927a6517 in execsimulation
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:2616
#9 0x7fcf927afec7 in elmersolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:662
#10 0x5647b5ad03f0 in solver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:57
#11 0x5647b5ad015e in main
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:34
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node PC exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
ssnestinger@PC:~/Desktop/elmer-elmag/TEAM7$ mpirun -np 8 ElmerSolver_mpi steady.sif
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ELMER SOLVER (v 9.0) STARTED AT: 2023/11/03 13:05:07
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
MAIN: OMP_NUM_THREADS not set. Using only 1 thread per task.
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
ParCommInit: Initialize #PEs: 8
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: e5b2b7b8d, Compiled: 2023-11-03)
MAIN: Running in parallel using 8 tasks.
MAIN: Running with just one thread per task.
MAIN: MUMPS library linked in.
MAIN: Zoltan library linked in.
MAIN: =============================================================
WARNING:: LoadInputFile: Entry missing for: Body Force 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
MAIN:
MAIN:
MAIN: -------------------------------------
MAIN: Reading Model: steady.sif
LoadInputFile: Scanning input file: steady.sif
LoadInputFile: Scanning only size info
LoadInputFile: First time visiting
LoadInputFile: Reading base load of sif file
LoadInputFile: Loading input file: steady.sif
LoadInputFile: Reading base load of sif file
CheckKeyword: Unlisted keyword: [jfix] in section: [boundary condition 1]
WARNING:: LoadInputFile: Entry missing for: Body Force 1
CheckKeyword: Unlisted keyword: [gmsh format] in section: [solver 4]
LoadInputFile: Number of BCs: 1
LoadInputFile: Number of Body Forces: 1
WARNING:: LoadInputFile: Entry missing for: Body Force 1
LoadInputFile: Number of Initial Conditions: 0
LoadInputFile: Number of Materials: 2
LoadInputFile: Number of Equations: 2
LoadInputFile: Number of Solvers: 5
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: [CoilSolver]...[CoilSolver_Init0]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver_Init0]
WhitneyAVSolver_Init0: Setting element type to: "n:0 e:1"
Loading user function library: [MagnetoDynamics]...[MagnetoDynamicsCalcFields_Init0]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_Init0]
Loading user function library: [SaveData]...[SaveLine_Init0]
ElmerAsciiMesh: Base mesh name: ./TEAM7
PermuteNodeNumbering: Performing node mapping
ReadTargetNames: Reading names info from file: ./TEAM7/mesh.names
WARNING:: ReadTargetNames: Could not map name to Body nor BC: coilskin
WARNING:: ReadTargetNames: Could not map name to Body nor BC: plateskin
MapBodiesAndBCs: Minimum initial body index: 1
MapBodiesAndBCs: Maximum initial body index: 3
MapBodiesAndBCs: Minimum initial boundary index: 4
MapBodiesAndBCs: Maximum initial boundary index: 6
LoadMesh: Elapsed REAL time: 0.1849 (s)
MeshStabParams: Computing stabilization parameters
MeshStabParams: Elapsed REAL time: 0.0022 (s)
MAIN: -------------------------------------
Loading user function library: [CoilSolver]...[CoilSolver_Init]
Loading user function library: [CoilSolver]...[CoilSolver_bulk]
Loading user function library: [CoilSolver]...[CoilSolver]
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: coil solver
OptimizeBandwidth: Initial bandwidth for coil solver: 45
OptimizeBandwidth: Optimized bandwidth for coil solver: 26
OptimizeBandwidth: ---------------------------------------------------------
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver_Init]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver_bulk]
Loading user function library: [MagnetoDynamics]...[WhitneyAVSolver]
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: mgdynamics transient
OptimizeBandwidth: Initial bandwidth for mgdynamics transient: 21281
OptimizeBandwidth: Optimized bandwidth for mgdynamics transient: 1969
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: mgdynamicscalc
OptimizeBandwidth: Initial bandwidth for mgdynamicscalc: 3224
OptimizeBandwidth: Optimized bandwidth for mgdynamicscalc: 399
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: [SaveData]...[SaveLine_Init]
Loading user function library: [SaveData]...[SaveLine_bulk]
Loading user function library: [SaveData]...[SaveLine]
MAIN: Number of timesteps to be saved: 1
CoilSolver: --------------------------------------
CoilSolver: Solving current distribution in a coil
CoilSolver: --------------------------------------
CoilSolver: Assuming that all coils are closed!
CoilSolver: Coil volume: 1.5886E-03
CoilSolver: Coil center: 1.9400E-01 1.0000E-01 9.9000E-02
CoilSolver: Choosing narrow fixing nodes for set: 1
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
CoilSolver: Choosing narrow fixing nodes for set: 2
CoilSolver: Coil system consists of 1 coils
CoilSolver: Set1 : 33 +nodes and 33 -nodes
CoilSolver: Set2 : 33 +nodes and 33 -nodes
CoilSolver: Computing the dummy potential field
CutInterfaceConnections: Number of connections cut: 222
EnforceDirichletConditions: Dirichlet conditions enforced for dofs: 66
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 501
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
10 0.2540E+00
20 0.7284E-02
30 0.3627E-02
40 0.1131E-01
50 0.1152E-06
Idrs: 54 0.2338E-08
SolveLinearSystem: Calculating nodal loads for: coiltmp
ComputeChange: NS (ITER=1) (NRM,RELC): ( 0.58632455 2.0000000 ) :: coil solver
CoilSolver: Discrepancy of start and end coil currents: 3.3290E-08
CoilSolver: Initial coil current for coil 1: 4.2912E-03
CoilSolver: Coil potential multiplier: -6.3899E+05
CutInterfaceConnections: Number of connections cut: 220
EnforceDirichletConditions: Dirichlet conditions enforced for dofs: 66
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 501
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
10 0.1543E-01
20 0.8769E-02
30 0.7585E-03
40 0.4167E-02
50 0.5455E-05
Idrs: 57 0.2917E-08
SolveLinearSystem: Calculating nodal loads for: coiltmp
ComputeChange: NS (ITER=2) (NRM,RELC): ( 0.58161645 0.80622181E-02 ) :: coil solver
CoilSolver: Discrepancy of start and end coil currents: 2.3996E-08
CoilSolver: Initial coil current for coil 1: 4.2912E-03
CoilSolver: Coil potential multiplier: -6.3898E+05
CoilSolver: Computing current component: 1
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 501
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
10 0.4327E-06
Idrs: 13 0.4439E-08
CoilSolver: Computing current component: 2
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 501
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
10 0.2101E-03
Idrs: 15 0.6847E-08
CoilSolver: Computing current component: 3
CRS_IncompleteLU: ILU(0) (Real), Performing Factorization:
CRS_IncompleteLU: ILU(0) (Real), NOF nonzeros: 501
CRS_IncompleteLU: ILU(0) (Real), filling (%) : 100
CRS_IncompleteLU: ILU(0) (Real), Factorization ready at (s): 0.00
10 0.2714E-03
Idrs: 18 0.2657E-08
#0 0x7f64f0423970 in ???
#1 0x7f64f0422ad5 in ???
#2 0x7f64f003c45f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f64f0c752e8 in __parallelutils_MOD_parallelsumvectorint
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ParallelUtils.F90:839
#4 0x7f64282be41d in choosefixedbulknodesnarrow
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:1266
#5 0x7f64282c82dc in coilsolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:381
#6 0x7f64f0aefbfd in __mainutils_MOD_singlesolver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5256
#7 0x7f64f0b0556c in __mainutils_MOD_solveractivate
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5531
#8 0x7f64f0da6517 in execsimulation
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:2616
#9 0x7f64f0dafec7 in elmersolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:662
#10 0x5587b20793f0 in solver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:57
#11 0x5587b207915e in main
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:34
#0 0x7f6306823970 in ???
#1 0x7f6306822ad5 in ???
#2 0x7f630643c45f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f63070752e8 in __parallelutils_MOD_parallelsumvectorint
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ParallelUtils.F90:839
#4 0x7f62fe50841d in choosefixedbulknodesnarrow
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:1266
#5 0x7f62fe5122dc in coilsolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/modules/CoilSolver.F90:381
#6 0x7f6306eefbfd in __mainutils_MOD_singlesolver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5256
#7 0x7f6306f0556c in __mainutils_MOD_solveractivate
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/MainUtils.F90:5531
#8 0x7f63071a6517 in execsimulation
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:2616
#9 0x7f63071afec7 in elmersolver_
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/ElmerSolver.F90:662
#10 0x55aab70193f0 in solver
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:57
#11 0x55aab701915e in main
at /home/ssnestinger/opt/elmer/elmerfem/fem/src/Solver.F90:34
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 5 with PID 0 on node PC exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Debugging Effort:
With some debugging, it looks like CoilSolver is attempting to process the Solver % Matrix for a PE partition without any coil elements. Since the partition has no coil, no initial Matrix is associated with the Solver which gives an Invalid Memory Reference at elmerfem/fem/src/ParallelUtils.F90:839: