Hi all,
I'm running into issues with a transient HO run, was wondering if anyone had advice. At first, I got this error:
[2]PETSC ERROR: ------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[2]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[2]PETSC ERROR: to get more information on the crash.
[2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[2]PETSC ERROR: Signal received
[2]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.14.6, Mar 30, 2021
[2]PETSC ERROR: C:\Users\domjon\Desktop\ISSM-SourceCode\bin/issm.exe on a named MWS-1048532 by domjon Mon Mar 11 09:55:25 2024
[2]PETSC ERROR: Configure options --prefix=/c/Users/jenkins/Jenkins/workspace/Windows-Binaries-MATLAB/externalpackages/petsc/install --PETSC_DIR=/c/Users/jenkins/Jenkins/workspace/Windows-Binaries-MATLAB/externalpackages/petsc/src --PETSC_ARCH=arch-mswin-c-opt --CFLAGS="-fPIC -Wl,-static -Wno-error=implicit-function-declaration" --CXXFLAGS="-fPIC -Wl,-static" --FFLAGS="-fPIC -Wl,-static -fallow-argument-mismatch -fallow-invalid-boz" --with-shared-libraries=0 --with-debugging=0 --with-valgrind=0 --with-x=0 --with-ssl=0 --with-proc-filesystem=0 --with-mpiexec=/c/PROGRA~1/MICROS~2/Bin/mpiexec.exe --with-mpi-lib="-L/c/Users/jenkins/Jenkins/workspace/Windows-Binaries-MATLAB/externalpackages/msmpi/install/lib -lmsmpi" --with-mpi-include=/c/Users/jenkins/Jenkins/workspace/Windows-Binaries-MATLAB/externalpackages/msmpi/install/include --download-fblaslapack=1 --download-metis=1 --download-metis-cmake-arguments="-G "MSYS Makefiles"" --download-parmetis=1 --download-parmetis-cmake-arguments="-G "MSYS Makefiles"" --download-scalapack=1 --download-scalapack-cmake-arguments="-G "MSYS Makefiles"" --download-mumps=1
[2]PETSC ERROR: #1 User provided function() line 0 in unknown file
[2]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
job aborted:
[ranks] message
[0-1] terminated
[2] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 50176059, comm rank 2
[3] terminated
In a previous post on this forum, @mathieumorlighem recommended turning verbose on to get a better sense of what's going on:
checking model consistency
marshalling file KNS.bin
Ice-sheet and Sea-level System Model (ISSM) version 4.24
(website: http://issm.jpl.nasa.gov forum: https://issm.ess.uci.edu/forum/)
starting model processor
creating datasets for analysis StressbalanceAnalysis
creating datasets for analysis StressbalanceVerticalAnalysis
creating datasets for analysis L2ProjectionBaseAnalysis
creating datasets for analysis ExtrudeFromBaseAnalysis
creating datasets for analysis DepthAverageAnalysis
creating datasets for analysis MasstransportAnalysis
Input updates from constant
creating datasets for analysis SmbAnalysis
creating datasets for analysis ExtrudeFromBaseAnalysis
creating datasets for analysis ExtrudeFromTopAnalysis
creating datasets for analysis FreeSurfaceBaseAnalysis
creating datasets for analysis FreeSurfaceTopAnalysis
creating datasets for analysis L2ProjectionBaseAnalysis
updating elements and materials for control parameters
creating output definitions
done with model processor
Processing finite element model of analysis StressbalanceAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
detecting active vertices
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis StressbalanceVerticalAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis L2ProjectionBaseAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis ExtrudeFromBaseAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis DepthAverageAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis MasstransportAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis SmbAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis ExtrudeFromBaseAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Processing finite element model of analysis ExtrudeFromTopAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis FreeSurfaceBaseAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis FreeSurfaceTopAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
Renumbering degrees of freedom
Processing finite element model of analysis L2ProjectionBaseAnalysis:
configuring element and loads
Configuring elements...
Configuring loads...
Configuring materials...
Configuring inputs...
resolving node constraints
creating nodal degrees of freedom
call computational core:
iteration 1/1000 time [yr]: 1.00 (time step: 1.00)
computing smb
computing new velocity
Updating constraints and active domain of analysis StressbalanceAnalysis for time: 1
Get solution from inputs
Reduce vector from g to f set
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=4.1601e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 136.117 > 1 %
Convergence criterion: norm(du)/norm(u) 637.021 > 10 %
Convergence criterion: max(du) 0.0018624
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=7.67226e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 28.0999 > 1 %
Convergence criterion: norm(du)/norm(u) 1099.82 > 10 %
Convergence criterion: max(du) 0.0187442
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=6.07673e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 14.9805 > 1 %
Convergence criterion: norm(du)/norm(u) 477.213 > 10 %
Convergence criterion: max(du) 0.121952
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=6.56402e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 8.89602 > 1 %
Convergence criterion: norm(du)/norm(u) 227.812 > 10 %
Convergence criterion: max(du) 0.380895
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=7.34655e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 5.46876 > 1 %
Convergence criterion: norm(du)/norm(u) 121.972 > 10 %
Convergence criterion: max(du) 0.720169
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=7.86054e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 3.41319 > 1 %
Convergence criterion: norm(du)/norm(u) 70.5308 > 10 %
Convergence criterion: max(du) 0.967164
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=7.01286e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 2.14748 > 1 %
Convergence criterion: norm(du)/norm(u) 42.8578 > 10 %
Convergence criterion: max(du) 1.03043
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=6.83749e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 1.35776 > 1 %
Convergence criterion: norm(du)/norm(u) 26.888 > 10 %
Convergence criterion: max(du) 0.939427
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=7.51688e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 0.861283 < 1 %
Convergence criterion: norm(du)/norm(u) 17.2225 > 10 %
Convergence criterion: max(du) 0.771512
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=6.53884e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 0.547675 < 1 %
Convergence criterion: norm(du)/norm(u) 11.1822 > 10 %
Convergence criterion: max(du) 0.590866
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
Allocating matrices (Kff stiffness matrix size: 5832 x 5832)
Assembling matrices
Create nodal constraints
Dirichlet lifting applied to load vector
Solving matrix system
solver residue: norm(KU-F)/norm(F)=6.41181e-15
Merging solution vector from fset to gset
checking convergence
mechanical equilibrium convergence criterion 0.348928 < 1 %
Convergence criterion: norm(du)/norm(u) 7.32551 < 10 %
Convergence criterion: max(du) 0.431906
Input updates from constant
Updating inputs from solution for StressbalanceAnalysis
number of unstable constraints: 0
total number of iterations: 11
computing basal mass balance
computing vertical velocities
Updating constraints and active domain of analysis StressbalanceVerticalAnalysis for time: 1
job aborted:
[ranks] message
[0] process exited without calling finalize
[1-3] terminated
Thanks for any help you can provide!
