schrummy14 / liggghts_flexible_fibers Goto Github PK

I am running a test case create by me and in some part of the program I receive segmentation fault.

The simulation crash when some bonds are broken.

The execution command:
$ mpiexec -n 2 liggghts -in in.insert_particles

The problem seems to be caused by the method unpack_exchange of the class AtomVecBondGraN. The file backtrace.txt shows the backtrace reported by gbd 8.2.1 running in debian 10, kernel 4.19.0-6-amd64.

The problem occur when the program execute the instruction:

bond_hist[nlocal][k][l] = buf[m++];

I think the program is trying to write a value outside array bond_hist.

I see that the method grow of the class AtomVecBondGran make the memory allocation for the array bond_hist. Can this method be allocating less memory than is necessary by the program?

The file study.tar.gz has the backtrace.txt and the simulation files.

study.tar.gz

Thank you.

Hi
I have re-installed LIGGGHTS-flexible fibers version (https://github.com/schrummy14/LIGGGHTS_Flexible_Fibers.git) on my win10 pc using Ubuntu app. After compilation I am able to run the tutorial examples, however, when I try to run model for my problem, I get the following error.
Strange thing is that I was able to run the same code before. Also, my PC has 12 cores but I am not able to allocate more than 6
cores for the run. All the above problems were not there previously.
I have attached a minimum working example and an example which is not working but was working previously. To run each example, please first run in.insert_particles first, and then run in.settle_particles.

Requesting to please help

Thanks
Shubham
Attachments:
Working.zip
Not Working.zip

ERROR
[APSD-CDW-MECH76:01120] 3 more processes have sent help message help-btl-vader.txt / cma-permission-denied
[APSD-CDW-MECH76:01120] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[APSD-CDW-MECH76:01126] *** Process received signal ***
[APSD-CDW-MECH76:01126] Signal: Segmentation fault (11)
[APSD-CDW-MECH76:01126] Signal code: Address not mapped (1)
[APSD-CDW-MECH76:01126] Failing at address: 0x7faca700b000
[APSD-CDW-MECH76:01126] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x153c0)[0x7faff2e923c0]
[APSD-CDW-MECH76:01126] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x18e984)[0x7faff2dfe984]
[APSD-CDW-MECH76:01126] [ 2] liggghts(+0x7b9141)[0x7faff4b0b141]
[APSD-CDW-MECH76:01126] [ 3] liggghts(+0x1f77c9)[0x7faff45497c9]
[APSD-CDW-MECH76:01126] [ 4] liggghts(+0x7adf4c)[0x7faff4afff4c]
[APSD-CDW-MECH76:01126] [ 5] liggghts(+0x6bbba3)[0x7faff4a0dba3]
[APSD-CDW-MECH76:01126] [ 6] liggghts(+0x6b96e6)[0x7faff4a0b6e6]
[APSD-CDW-MECH76:01126] [ 7] liggghts(+0x6b9e85)[0x7faff4a0be85]
[APSD-CDW-MECH76:01126] [ 8] liggghts(+0xba981)[0x7faff440c981]
[APSD-CDW-MECH76:01126] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7faff2c970b3]
[APSD-CDW-MECH76:01126] [10] liggghts(+0xbc33e)[0x7faff440e33e]
[APSD-CDW-MECH76:01126] *** End of error message ***

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

SIGINT/SIGTERM caught - Writing restart on next occasion and quitting after that.
SIGINT/SIGTERM caught - Writing restart on next occasion and quitting after that.
SIGINT/SIGTERM caught - Writing restart on next occasion and quitting after that
.--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 0 on node APSD-CDW-MECH76 exited on signal 11 (Segmentation fault).

I am using your code to run a study case and I receive this error:

ERROR on proc 0: Failed to operate on granular bond history during copy i2 (../fix_bond_propagate_gran.cpp:125)

What can I do to resolve the issue?

I did some improvement in the code too and would like to share it with you.

Thank you very much.

The nonlinear damping equations are time step dependent. As long as you calibrate the damping at the time step you wish to use, this shouldn't be an issue. Work is being done to determine the best way to make the damping not dependent on the time step.

Tests using restart files are causing particles to disappear after 5 steps. This only happens when coupling with openFOAM and I believe the error is in the coupling files.
Workaround is to not read in restart files.

Hi @schrummy14

I would like to contribute to your code.
There is something I can do to help?

Regards.

The current code that added molecule tags during insertion has broken the multisphere atom_type.
Work is being done to address this to have both working.
Worst case scenario will be that you WILL NOT be able to use atom type bond/gran with multisphere particles.

Particles that are heavily overlapped (atoms that can bond through to another atom to another atom).

Example script that reproduces the error is attached.
in.straw_drop.txt

Critical bug found in which during the coupling, the bond histories are reset to zero.
Current work is to find where and why the bond history values are being reset and to fix this issue.