mikekryjak
commented
3 days ago Hi @Theosaurus2. I've never considered running 1D with vorticity. I wonder if it's supported/possible since one physical interpretation of vorticity is rotation which is not a 1D phenomenon, but that is something that we would need @bendudson to answer. Your error kind of sounds like the component is expecting more dimensions...
Are you on the Slack channel? If not, let me know what your email is and I can add you. And sorry for the late response.
Hi,
I was trying to setup a 1D simulation with evolving density, pressure and momentum for AR,AR+ and e with a simple sheath boundary, collisions, and vorticity to evolve the potential. I've attached my BOUT.inp file bellow. BOUT.txt
I used -DCHECK=3 to get the bellow errors:
Run started at : Tue Oct 29 14:57:06 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default)
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 sheath exited on signal 11 (Segmentation fault).
As for using DCHECK=3 i have two separate errors that might help.
Error encountered: Assertion failed in /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/region.hxx, line 288: std::abs(dy) < ny====== Exception path ====== [bt] #13 ./hermes-3() [0x574e9e] _start at ??:? [bt] #12 /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xf3) [0x7fcae0581083] libc_start_main at /build/glibc-LcI20x/glibc-2.31/csu/../csu/libc-start.c:342 [bt] #11 ./hermes-3() [0x578c3d] main at /scratch/tc1447/hermes2/hermes-3/hermes-3.cxx:375 (discriminator 15) [bt] #10 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN6Solver5solveEid+0x783) [0x7fcae847c715] Solver::solve(int, double) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/solver/solver.cxx:548 (discriminator 7) [bt] #9 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN6Solver7run_rhsEdb+0x319) [0x7fcae848237b] Solver::run_rhs(double, bool) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/solver/solver.cxx:1398 [bt] #8 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN12PhysicsModel6runRHSEdb+0x3d) [0x7fcae83fe24d] PhysicsModel::runRHS(double, bool) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/physics/physicsmodel.cxx:114 [bt] #7 ./hermes-3(_ZN12PhysicsModel3rhsEdb+0x36) [0x5972d0] PhysicsModel::rhs(double, bool) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/physicsmodel.hxx:271 [bt] #6 ./hermes-3() [0x577823] Hermes::rhs(double) at /scratch/tc1447/hermes2/hermes-3/hermes-3.cxx:265 [bt] #5 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/libhermes-3-lib.so(_ZN18ComponentScheduler9transformER7Options+0xeb) [0x7fcae8a8d315] ComponentScheduler::transform(Options&) at /scratch/tc1447/hermes2/hermes-3/src/component_scheduler.cxx:57 (discriminator 3) [bt] #4 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/libhermes-3-lib.so(_ZN9Vorticity7finallyERK7Options+0xd1c) [0x7fcae8bd955c] Vorticity::finally(Options const&) at /scratch/tc1447/hermes2/hermes-3/src/vorticity.cxx:702 (discriminator 3) [bt] #3 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN2FV15Div_a_GradperpERK7Field3DS2+0x818) [0x7fcae81fb9c7] FV::Div_a_Grad_perp(Field3D const&, Field3D const&) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/mesh/fv_ops.cxx:111 (discriminator 3) [bt] #2 ./hermes-3(_ZNK11SpecificIndIL8IND_TYPE0EE2ypEi+0x5a) [0x68a8b8] SpecificInd<(IND_TYPE)0>::yp(int) const at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/region.hxx:288 (discriminator 3) [bt] #1 ./hermes-3(_ZN13BoutExceptionC2IA42_cJA75_ciA18_cEEERKTDpRKT0+0x10a) [0x68ae74] BoutException::BoutException<char [42], char [75], int, char [18]>(char const (&) [42], char const (&) [75], int const&, char const (&) [18]) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/boutexception.hxx:23 (discriminator 4) ====== Back trace ====== -> virtual void Vorticity::finally(const Options&) on line 636 of '/scratch/tc1447/hermes2/hermes-3/src/vorticity.cxx'
====== Exception thrown ====== Assertion failed in /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/region.hxx, line 288: std::abs(dy) < ny
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0 with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 43.79 sec
The following tests FAILED: 6 - vorticity (Failed) Errors while running CTest
Error encountered: Field3D: (-1, 2, 0) operator out of bounds (1, 260, 1)====== Exception path ====== [bt] #12 ./hermes-3() [0x574e9e] _start at ??:? [bt] #11 /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xf3) [0x7f5a11dda083] libc_start_main at /build/glibc-LcI20x/glibc-2.31/csu/../csu/libc-start.c:342 [bt] #10 ./hermes-3() [0x578c3d] main at /scratch/tc1447/hermes2/hermes-3/hermes-3.cxx:375 (discriminator 15) [bt] #9 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN6Solver5solveEid+0x783) [0x7f5a19cd5715] Solver::solve(int, double) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/solver/solver.cxx:548 (discriminator 7) [bt] #8 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN6Solver7run_rhsEdb+0x319) [0x7f5a19cdb37b] Solver::run_rhs(double, bool) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/solver/solver.cxx:1398 [bt] #7 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/external/BOUT-dev/lib/libbout++.so.5.1.0(_ZN12PhysicsModel6runRHSEdb+0x3d) [0x7f5a19c5724d] PhysicsModel::runRHS(double, bool) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/src/physics/physicsmodel.cxx:114 [bt] #6 ./hermes-3(_ZN12PhysicsModel3rhsEdb+0x36) [0x5972d0] PhysicsModel::rhs(double, bool) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/physicsmodel.hxx:271 [bt] #5 ./hermes-3() [0x577823] Hermes::rhs(double) at /scratch/tc1447/hermes2/hermes-3/hermes-3.cxx:265 [bt] #4 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/libhermes-3-lib.so(_ZN18ComponentScheduler9transformER7Options+0x6c) [0x7f5a1a2e6296] ComponentScheduler::transform(Options&) at /scratch/tc1447/hermes2/hermes-3/src/component_scheduler.cxx:53 (discriminator 3) [bt] #3 /scratch/tc1447/hermes2/hermes-3/build-petsc-debug/libhermes-3-lib.so(_ZN9Vorticity9transformER7Options+0x12e2) [0x7f5a1a42e3da] Vorticity::transform(Options&) at /scratch/tc1447/hermes2/hermes-3/src/vorticity.cxx:381 (discriminator 1) [bt] #2 ./hermes-3(_ZN7Field3DclEiii+0xf7) [0x596221] Field3D::operator()(int, int, int) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/field3d.hxx:364 [bt] #1 ./hermes-3(_ZN13BoutExceptionC1IA70_cJiiiiiiEEERKTDpRKT0+0x157) [0x5a73b1] BoutException::BoutException<char [70], int, int, int, int, int, int>(char const (&) [70], int const&, int const&, int const&, int const&, int const&, int const&) at /scratch/tc1447/hermes2/hermes-3/external/BOUT-dev/include/bout/boutexception.hxx:23 (discriminator 4) ====== Back trace ====== -> virtual void Vorticity::transform(Options&) on line 222 of '/scratch/tc1447/hermes2/hermes-3/src/vorticity.cxx'
====== Exception thrown ====== Field3D: (-1, 2, 0) operator out of bounds (1, 260, 1)
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0 with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.
I'm not sure if I've set something up wrong or if this is a bug