Hi,
I was testing the CAD-based geometry example using OpenMC version 0.15.0. The examples run successfully as provided. However, when enabling geometry debug mode by executing openmc.run(geometry_debug=True), the simulations terminate with errors related to overlapping cells in the geometry. This issue occurs across all three geometries in the notebook.
Is this behavior expected?
For reference, I’ve included the output messages for the cylinder case below. Thank you for your time and assistance.
Best,
Sharp
===========================================================
| The OpenMC Monte Carlo Code
Copyright | 2011-2024 MIT, UChicago Argonne LLC, and contributors
License | License Agreement — OpenMC Documentation
Version | 0.15.0
Git SHA1 | 84fb85977f46e162fea8f5a20ea653a3ec62ac24
Date/Time | 2025-02-12 10:16:53
MPI Processes | 1
OpenMP Threads | 22
Reading model XML file ‘model.xml’ …
WARNING: Other XML file input(s) are present. These files may be ignored in
favor of the model.xml file.
Reading cross sections XML file…
Loading file dagmc.h5m
Initializing the GeomQueryTool…
Using faceting tolerance: 0.0001
Building acceleration data structures…
Reading U235 from /home/sharp/openmc-data/endfb-viii.0-hdf5/neutron/U235.h5
Reading H1 from /home/sharp/openmc-data/endfb-viii.0-hdf5/neutron/H1.h5
Reading O16 from /home/sharp/openmc-data/endfb-viii.0-hdf5/neutron/O16.h5
Reading c_H_in_H2O from
/home/sharp/openmc-data/endfb-viii.0-hdf5/neutron/c_H_in_H2O.h5
Minimum neutron data temperature: 294 K
Maximum neutron data temperature: 294 K
Preparing distributed cell instances…
Reading plot XML file…
Writing summary.h5 file…
WARNING: Cell overlap checking is ON.
Maximum neutron transport energy: 20000000 eV for H1
Initializing source particles…
====================> K EIGENVALUE SIMULATION <====================
Bat./Gen. k Average k
========= ======== ====================
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 2, 3 on universe 1
ERROR: Overlapping cells detected: 2, 3 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 2, 3 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
Overlapping cells detected: 2, 3 on universe 1
ERROR: Overlapping cells detected: 1, 2 on universe 1
ERROR: Overlapping cells detected: 2, 3 on universe 1
ERROR: Overlapping cells detected: 2, 3 on universe 1
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
Sorry! You were supposed to get help about:
help-mpi-api.txt
from the file:
mpi-abort
But I couldn’t find that topic in the file. Sorry!
Sorry! You were supposed to get help about:
help-mpi-api.txt
from the file:
mpi-abort
But I couldn’t find that topic in the file. Sorry!
fatal flex scanner internal error–end of buffer missed
t-#
ERROR: Overlapping cells detected: 1, 2 on universe 1
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
Proc: [[10141,0],0]
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.
fatal flex scanner internal error–end of buffer missed
fatal flex scanner internal error–end of buffer missed
ERROR: [1739355414.076168] [sharp-Precision-3490:12478:0] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 8 was not set in ucs
[1739355414.076175] [sharp-Precision-3490:12478:0] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
Overlapping cells detected: 1, 2 on universe 1[sharp-Precision-3490:12478:0:12519] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[1739355414.076176] [sharp-Precision-3490:12478:1] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 1 was not set in ucs
[1739355414.076184] [sharp-Precision-3490:12478:0] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[sharp-Precision-3490:12478:1:12525] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))