DAMASK3.0.0 when chosse mesh_solver something wrong with "FEM_mech init"

[Karoaro]

Hello DAMASK teams:
I want to do simulations with non-periodic situations so I choose to use mesh solver.
And I used the examples to test, many combinations was choosed:
DAMASK_mesh --load tensionY_mono.yaml --geom monocrystal.msh --material material.yaml --jobname job6.1
DAMASK_mesh --load tensionZ_5g.yaml --geom disk_5grains.msh --material material.yaml --jobname job6.2
.......
Output like:

<<<+- parallelization init -+>>>

MPICH Version: 4.1.1
MPICH Release date: Mon Mar 6 14:14:15 CST 2023
MPICH ABI: 15:0:3
MPICH Device: ch3:sock
MPICH configure: --prefix=/root/petsc-3.19.6/arch-linux-c-opt MAKE=/usr/bin/make --libdir=/root/petsc-3.19.6/arch-linux-c-opt/lib CC=/usr/bin/gcc CFLAGS=-fPIC -Wno-lto-type-mismatch -g -O0 AR=/usr/bin/ar ARFLAGS=cr CXX=/usr/bin/g++ CXXFLAGS=-Wno-lto-type-mismatch -Wno-psabi -g -O0 -std=c++11 -fPIC FFLAGS=-fPIC -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 FC=/usr/bin/gfortran F77=/usr/bin/gfortran FCFLAGS=-fPIC -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 --enable-shared --with-pm=hydra --disable-java --with-hwloc=embedded --enable-fast=no --enable-error-messages=all --with-device=ch3:sock --enable-g=meminit PYTHON=/usr/bin/python3 --disable-maintainer-mode --disable-dependency-tracking
MPICH CC: /usr/bin/gcc -fPIC -Wno-lto-type-mismatch -g -O0 -O0
MPICH CXX: /usr/bin/g++ -Wno-lto-type-mismatch -Wno-psabi -g -O0 -std=c++11 -fPIC -O0
MPICH F77: /usr/bin/gfortran -fPIC -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 -O0
MPICH FC: /usr/bin/gfortran -fPIC -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 -O0

MPI standard: 4.0
OpenMP version: 201511

MPI processes: 1
Could not get $OMP_NUM_THREADS, using default
OMP_NUM_THREADS: 4

<<<+- CLI init -+>>>

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/ / //// _/ / / //// // // //
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/// _/ _/ _/ _/ _/ / /// _/ / ///
Mesh solver

F. Roters et al., Computational Materials Science 158:420–478, 2019
https://doi.org/10.1016/j.commatsci.2018.04.030

S. Balay et al., PETSc/TAO User Manual Revision 3.19
https://doi.org/10.2172/1968587

Version: v3.0.0

Compiled with: GCC version 9.4.0
Compiled on: Linux-5.10.16.3-microsoft-standard-WSL2
Compiler options: -cpp -I /root/petsc-3.19.6/include -I /root/petsc-3.19.6/arch-linux-c-opt/include -I /root/petsc-3.19.6/arch-linux-c-opt/include -I /root/petsc-3.19.6/arch-linux-c-opt/include -imultiarch x86_64-linux-gnu -D_REENTRANT -D CMAKE_SYSTEM="Linux-5.10.16.3-microsoft-standard-WSL2" -D DAMASKVERSION="v3.0.0" -D MESH -D PETSC --param l1-cache-size=48 --param l1-cache-line-size=64 --param l2-cache-size=30720 -mtune=generic -march=x86-64 -auxbase-strip CMakeFiles/DAMASK_mesh.dir/CLI.f90.o -g -O -O2 -Wno-lto-type-mismatch -pedantic-errors -Wall -Wextra -Wcharacter-truncation -Wunderflow -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wconversion-extra -Wimplicit-procedure -Wunused-parameter -std=f2018 -ffree-line-length-none -ffree-line-length-0 -fopenmp -fPIE -ffree-line-length-none -fimplicit-none -ffpe-summary=all -fpre-include=/usr/include/finclude/math-vector-fortran.h

Compiled on: Apr 22 2025 at 21:41:04

PETSc version: 3.19.6
.......
.......
.......
<<<+- DAMASK_mesh init -+>>>

load case: 1
drop guessing along trajectory
Field mechanical
Face 1 Component 1 Value 0.0000000
Face 1 Component 2 Value 0.0000000
Face 1 Component 3 Value 0.0000000
Face 2 Component 1 Value 0.0000000
Face 2 Component 2 Value 0.0000000
Face 2 Component 3 Value 0.0025000
time: 0.800000
increments: 80
output frequency: 1

<<<+- FEM_utilities init -+>>>

<<<+- FEM_mech init -+>>>
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer
[0]PETSC ERROR: Null Pointer: Parameter # 1
[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-mechanical_ksp_max_it value: 25 source: code
[0]PETSC ERROR: Option left: name:-mechanical_ksp_type value: gmres source: code
[0]PETSC ERROR: Option left: name:-mechanical_pc_type value: eisenstat source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_ksp_ew (no value) source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_ksp_ew_rtol0 value: 0.01 source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_ksp_ew_rtolmax value: 0.01 source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_type value: newtonls source: code
[0]PETSC ERROR: Option left: name:-petscds_force_quad value: 0 source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.19.6, Sep 28, 2023
[0]PETSC ERROR: DAMASK_mesh on a arch-linux-c-opt named DESKTOP-OOMIH54 by root Wed Apr 23 13:36:39 2025
[0]PETSC ERROR: Configure options --with-fc=/usr/bin/gfortran --with-cc=/usr/bin/gcc --with-cxx=/usr/bin/g++ --download-mpich --download-fftw --download-hdf5 --download-fblaslapack --download-chaco --download-hypre --download-metis --download-ml --download-mumps --download-parmetis --download-scalapack --download-suitesparse --download-superlu --download-superlu_dist --download-triangle --download-zlib --download-cmake --with-cxx-dialect=C++11 --with-c2gtml=0 --with-debugging=1 --with-ssl=0 --with-x=0 PETSC_DIR=/root/petsc-3.19.6 --with-hdf5-fortran-bindings
[0]PETSC ERROR: #1 PetscQuadratureGetNumComponents() at /root/petsc-3.19.6/src/dm/dt/interface/dt.c:252
[0]PETSC ERROR: #2 PetscFESetQuadrature() at /root/petsc-3.19.6/src/dm/dt/fe/interface/fe.c:651
[0]PETSC ERROR: #3 PetscDSSetUp() at /root/petsc-3.19.6/src/dm/dt/interface/dtds.c:446
[0]PETSC ERROR: #4 DMCreateDS() at /root/petsc-3.19.6/src/dm/interface/dm.c:6003
[0]PETSC ERROR: #5 /root/damask-3.0.0/src/mesh/mesh_mech_FEM.f90:200

... saving initial configuration ..........................................

###########################################################################
Time 1.00000E-02s: Increment 1/80-1/1 of load case 1/1
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Invalid pointer
[0]PETSC ERROR: Invalid Pointer to PetscObject: Argument 'x' (parameter # 1)
[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-mechanical_ksp_max_it value: 25 source: code
[0]PETSC ERROR: Option left: name:-mechanical_ksp_type value: gmres source: code
[0]PETSC ERROR: Option left: name:-mechanical_pc_type value: eisenstat source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_ksp_ew (no value) source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_ksp_ew_rtol0 value: 0.01 source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_ksp_ew_rtolmax value: 0.01 source: code
[0]PETSC ERROR: Option left: name:-mechanical_snes_type value: newtonls source: code
[0]PETSC ERROR: Option left: name:-petscds_force_quad value: 0 source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.19.6, Sep 28, 2023
[0]PETSC ERROR: DAMASK_mesh on a arch-linux-c-opt named DESKTOP-OOMIH54 by root Wed Apr 23 13:36:39 2025
[0]PETSC ERROR: Configure options --with-fc=/usr/bin/gfortran --with-cc=/usr/bin/gcc --with-cxx=/usr/bin/g++ --download-mpich --download-fftw --download-hdf5 --download-fblaslapack --download-chaco --download-hypre --download-metis --download-ml --download-mumps --download-parmetis --download-scalapack --download-suitesparse --download-superlu --download-superlu_dist --download-triangle --download-zlib --download-cmake --with-cxx-dialect=C++11 --with-c2gtml=0 --with-debugging=1 --with-ssl=0 --with-x=0 PETSC_DIR=/root/petsc-3.19.6 --with-hdf5-fortran-bindings
[0]PETSC ERROR: #1 VecCopy() at /root/petsc-3.19.6/src/vec/vec/interface/vector.c:1678
[0]PETSC ERROR: #2 /root/damask-3.0.0/src/mesh/mesh_mech_FEM.f90:743
Segmentation fault

I had changed the version of PETSC from 3.22 to 3.19.6, but it still didn't work.
Also I tried to add "ulilmit -s unlimited" before I run DAMASK_mesh, didn't work.
But my grid solver works well, so it makes me confused.
I want to know what's the problem and how to solve it.
Thank you!

[MarDiehl]

the mesh solver is not as thoroughly tested as the grid solver. Could you try to use a recent compiler in addition to a recent PETSc version?

[Karoaro]

Same problem happened in DAMASK-3.0.1 with compiler version 9.5
and DAMASK-3.0.0 with compiler version 11.4
And the two error message are the same.

<<<+- FEM_mech init -+>>>
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
:
system msg for write_line failure : Bad file descriptor

[dmentock]

Could you share your input files?

[MarDiehl]

and/or use a recent gfortran version (current version is 15.1, so 11.4 is a bugfix version of a version that is 4 years old)