Error when Robin boundary condition is applied

ASPECT
1

Hi all,

I am trying to use the Boundary convective heating model.

However, I face the segmentation error as below:

In debug mode:

/software/compilers/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:1149: std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator const [with _Tp = dealii::Tensor<1, 2>; _Alloc = std::allocator<dealii::Tensor<1, 2> >; const_reference = const dealii::Tensor<1, 2>&; size_type = long unsigned int]: Assertion ‘__n < this->size()’ failed.

SIGABRT received

--------------------------------------------------------------------------

prterun detected that one or more processes exited with non-zero status,

thus causing the job to be terminated. The first process to do so was:

Process name: [prterun-node209-1547542@1,26]

Exit code: 1

--------------------------------------------------------------------------

in release mode:

/home/college/2921731K/aspect/build/aspect-release(_ZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS_14AdvectionFieldE+0x582)[0x132f9c2]

[node203:543915] [ 5] /home/college/2921731K/aspect/build/aspect-release(_ZN6aspect9SimulatorILi2EE30assemble_and_solve_temperatureERKdPd+0x2d8)[0xf17af8]

[node203:543915] [ 6] /home/college/2921731K/aspect/build/aspect-release(_ZN6aspect9SimulatorILi2EE35solve_iterated_advection_and_stokesEv+0x2c5)[0xf1cd25]

[node203:543915] [ 7] /home/college/2921731K/aspect/build/aspect-release(_ZN6aspect9SimulatorILi2EE14solve_timestepEv+0x190)[0x1314d00]

[node203:543915] [ 8] /home/college/2921731K/aspect/build/aspect-release(_ZN6aspect9SimulatorILi2EE3runEv+0x2f7)[0x13448f7]

[node203:543915] [ 9] /home/college/2921731K/aspect/build/aspect-release[0x1a985d5]

[node203:543915] [10] /home/college/2921731K/aspect/build/aspect-release(main+0x33f3)[0xb84083]

[node203:543915] [11] /lib64/libc.so.6(__libc_start_main+0xe5)[0x7fd1aa45b7e5]

[node203:543915] [12] /home/college/2921731K/aspect/build/aspect-release(_start+0x2e)[0xb8573e]

[node203:543915] *** End of error message ***

--------------------------------------------------------------------------

prterun noticed that process rank 99 with PID 543999 on node node203 exited on

signal 11 (Segmentation fault).

--------------------------------------------------------------------------

Is this related to the versions of packages I am using?

Could I get advice to solve this problem?

However, the HPC server I am using already has error with multi-node jobs. It may be related to configuration of server.

Thanks for your help!

Cheers,

Hyunseong

2

@hyunseong96 Is this with a single-processor job (one only 1 MPI rank)? If so, can you run it in a debugger to get a backtrace to see which line of which function this happens in. Separately, can you post the input file you use?

Best

W.

3

Hi @bangerth ,

It was mpirun with 128 cores. I just put the last repetitive part of error message.

I ran debugging in simpler geometry quickly, and the exception happened at line 2121 of dealii-candi/deal.II-v9.6.1/include/deal.II/base/tensor.h

Exception has occurred.

EXC_BAD_ACCESS (code=1, address=0x0)

europa_chunk_45_ref_newE_20_dis_coarse5_heating2.prm (9.2 KB)

This is the prm file I am using!

Cheers,

Hyunseong

4

@hyunseong96 I can’t run your input file without the plugins. But in any case, can you run your model on a single processor in debug mode, and in a debugger? This should pinpoint the exact place where this happens, and perhaps why. If you’re new to using debuggers, you may want to watch lectures 25 and/or 41.25 at Wolfgang Bangerth's video lectures to see the basic techniques of using a debugger.

Best

W.

5

@bangerth I removed the additional plugin as:

europa_chunk_45_ref_newE_20_dis_coarse5_heating_no_additional_plugin.prm (8.9 KB)

With this prm file, I get

image
image4108×2348 1.77 MB

error is

--------------------------------------------------------

An error occurred in line <406> of file </Users/h.kim.6/dealii-candi/tmp/unpack/deal.II-v9.7.0/source/base/timer.cc> in function

void dealii::TimerOutput::enter_subsection(const std::string &)

The violated condition was:

std::find(active_sections.begin(), active_sections.end(), section_name) == active_sections.end()

Additional information:

Cannot enter the already active section <Assemble temperature system>.

Stacktrace:

-----------

#0 2 libdeal_II.g.9.7.0.dylib 0x0000000114236fd8 _ZN6dealii11TimerOutput16enter_subsectionERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE + 876: 2 libdeal_II.g.9.7.0.dylib 0x0000000114236fd8 _ZN6dealii11TimerOutput16enter_subsectionERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE

#1 3 aspect-debug 0x0000000100509b7c _ZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS_14AdvectionFieldE + 196: 3 aspect-debug 0x0000000100509b7c _ZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS_14AdvectionFieldE

#2 4 aspect-debug 0x00000001001406f4 _ZN6aspect9SimulatorILi2EE30assemble_and_solve_temperatureERKdPd + 928: 4 aspect-debug 0x00000001001406f4 _ZN6aspect9SimulatorILi2EE30assemble_and_solve_temperatureERKdPd

#3 5 aspect-debug 0x0000000100146a60 _ZN6aspect9SimulatorILi2EE35solve_iterated_advection_and_stokesEv + 308: 5 aspect-debug 0x0000000100146a60 _ZN6aspect9SimulatorILi2EE35solve_iterated_advection_and_stokesEv

#4 6 ??? 0x000000010980c1b0 0x0 + 4454400432: 6 ??? 0x000000010980c1b0 0x0

#5 7 aspect-debug 0x0000000100b8a194 main + 0: 7 aspect-debug 0x0000000100b8a194 main

#6 8 aspect-debug 0x0000000100509204 _ZN6aspect9SimulatorILi2EE31local_assemble_advection_systemERKNS_14AdvectionFieldERKN6dealii6VectorIdEERKNS5_18TriaActiveIteratorINS5_15DoFCellAccessorILi2ELi2ELb0EEEEERNS_8internal8Assembly7Scratch15AdvectionSystemILi2EEERNSH_8CopyData15AdvectionSystemILi2EEE + 3760: 8 aspect-debug 0x0000000100509204 _ZN6aspect9SimulatorILi2EE31local_assemble_advection_systemERKNS_14AdvectionFieldERKN6dealii6VectorIdEERKNS5_18TriaActiveIteratorINS5_15DoFCellAccessorILi2ELi2ELb0EEEEERNS_8internal8Assembly7Scratch15AdvectionSystemILi2EEERNSH_8CopyData15AdvectionSystemILi2EEE

#7 9 aspect-debug 0x00000001005a87b8 _ZN6dealii10WorkStream8internal10sequential3runIZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS4_14AdvectionFieldEEUlRKNS_18TriaActiveIteratorINS_15DoFCellAccessorILi2ELi2ELb0EEEEERNS4_8internal8Assembly7Scratch15AdvectionSystemILi2EEERNSH_8CopyData15AdvectionSystemILi2EEEE_ZNS6_25assemble_advection_systemES9_EUlRKSO_E_NS_16FilteredIteratorISD_EESK_SO_EEvRKT1_RKNS_9std_cxx2013type_identityISW_E4typeET_T0_RKT2_RKT3_ + 196: 9 aspect-debug 0x00000001005a87b8 _ZN6dealii10WorkStream8internal10sequential3runIZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS4_14AdvectionFieldEEUlRKNS_18TriaActiveIteratorINS_15DoFCellAccessorILi2ELi2ELb0EEEEERNS4_8internal8Assembly7Scratch15AdvectionSystemILi2EEERNSH_8CopyData15AdvectionSystemILi2EEEE_ZNS6_25assemble_advection_systemES9_EUlRKSO_E_NS_16FilteredIteratorISD_EESK_SO_EEvRKT1_RKNS_9std_cxx2013type_identityISW_E4typeET_T0_RKT2_RKT3_

#8 10 aspect-debug 0x000000010050c78c _ZN6dealii10WorkStream3runIZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS2_14AdvectionFieldEEUlRKNS_18TriaActiveIteratorINS_15DoFCellAccessorILi2ELi2ELb0EEEEERNS2_8internal8Assembly7Scratch15AdvectionSystemILi2EEERNSF_8CopyData15AdvectionSystemILi2EEEE_ZNS4_25assemble_advection_systemES7_EUlRKSM_E_NS_16FilteredIteratorISB_EESI_SM_EEvRKT1_RKNS_9std_cxx2013type_identityISU_E4typeET_T0_RKT2_RKT3_jj + 220: 10 aspect-debug 0x000000010050c78c _ZN6dealii10WorkStream3runIZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS2_14AdvectionFieldEEUlRKNS_18TriaActiveIteratorINS_15DoFCellAccessorILi2ELi2ELb0EEEEERNS2_8internal8Assembly7Scratch15AdvectionSystemILi2EEERNSF_8CopyData15AdvectionSystemILi2EEEE_ZNS4_25assemble_advection_systemES7_EUlRKSM_E_NS_16FilteredIteratorISB_EESI_SM_EEvRKT1_RKNS_9std_cxx2013type_identityISU_E4typeET_T0_RKT2_RKT3_jj

#9 11 aspect-debug 0x000000010050a018 _ZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS_14AdvectionFieldE + 1376: 11 aspect-debug 0x000000010050a018 _ZN6aspect9SimulatorILi2EE25assemble_advection_systemERKNS_14AdvectionFieldE

#10 12 aspect-debug 0x00000001001406f4 _ZN6aspect9SimulatorILi2EE30assemble_and_solve_temperatureERKdPd + 928: 12 aspect-debug 0x00000001001406f4 _ZN6aspect9SimulatorILi2EE30assemble_and_solve_temperatureERKdPd

#11 13 aspect-debug 0x0000000100146a60 _ZN6aspect9SimulatorILi2EE35solve_iterated_advection_and_stokesEv + 308: 13 aspect-debug 0x0000000100146a60 _ZN6aspect9SimulatorILi2EE35solve_iterated_advection_and_stokesEv

#12 14 aspect-debug 0x00000001005327d4 _ZN6aspect9SimulatorILi2EE14solve_timestepEv + 300: 14 aspect-debug 0x00000001005327d4 _ZN6aspect9SimulatorILi2EE14solve_timestepEv

#13 15 aspect-debug 0x0000000100534f24 _ZN6aspect9SimulatorILi2EE3runEv + 956: 15 aspect-debug 0x0000000100534f24 _ZN6aspect9SimulatorILi2EE3runEv

#14 16 aspect-debug 0x0000000100b8c060 main + 7884: 16 aspect-debug 0x0000000100b8c060 main

#15 17 dyld 0x000000018607ab98 start + 6076: 17 dyld 0x000000018607ab98 start

--------------------------------------------------------

Abort() was called during dealing with an assertion or exception.

Traceback functionality not available

This happens at line 1163 of aspect/source/simulator/assemply.cc about local_assemble_advection_system.

image
image1812×638 113 KB

Hope this is the right one.

Cheers,

Hyunseong

6

Hi Hyunseong,

You forgot to specify which boundary heat flux plugin you want to use in the Boundary convective heating model section. Adding

set List of boundary heat flux model names = function

fixed it for me.
No idea why this error is the result; but it’s good to know and will hopefully allow us to catch this problem earlier and give a more useful error message.

Cheers,
Juliane

7

@jdannberg

Yes, this did fix the error! Ugh sorry it was my mistake to write same line (coefficient) twice, thinking I wrote all needed :frowning:

Thank you!!

Cheers,

Hyunseong

8

I added a patch in Do some error checking to avoid accessing invalid vector elements. by bangerth · Pull Request #6687 · geodynamics/aspect · GitHub that makes sure we get a better error message, rather than just accessing the invalid vector elements.

Best

W.