On a RHEL 9 cluster with VTK installed, why would this seg fault? I just used 'make auto' and OpenMPI 5.0.2.
mpirun -np 4 lmp_auto< in.chute_wear
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2024-02-20-15:56:33 by me, git commit bbd23c8521fe0a4f3f5bfd0d3dc9a7dddd68d90b)
Created orthogonal box = (-0.5 -0.2 -0.4) to (0.1 0.2 0.15)
2 by 1 by 2 MPI processor grid
Reading STL file 'meshes/simple_chute.stl' (mesh processing step 1/3)
Reading STL file 'meshes/insertion_face.stl' (mesh processing step 1/3)
Fix particledistribution/discrete (id pdd1): distribution based on mass%:
pts1: d=3.000000e-03 (max. bounding sphere) mass%=30.000000%
pts2: d=5.000000e-03 (max. bounding sphere) mass%=70.000000%
Fix particledistribution/discrete (id pdd1): distribution based on number%:
pts1: d=3.000000e-03 (max. bounding sphere) number%=66.489362%
pts2: d=5.000000e-03 (max. bounding sphere) number%=33.510638%
0 atoms in group nve_group
Setting up run at Tue Feb 20 17:17:53 2024
Import and parallelization of mesh cad containing 1616 triangle(s) successful
Import and parallelization of mesh inface containing 2 triangle(s) successful
INFO: Particle insertion ins: 12.766349 particles every 1000 steps - particle rate 1276.634850 (mass rate 1.000000e-01)
6000 particles (mass 4.699856e-01) within 469000 steps
Memory usage per processor = 10.2945 Mbytes
Step Atoms KinEng 1 Volume
0 0 0 0 0.132
INFO: Particle insertion ins: inserted 13 particle templates (mass 1.100866e-03) at step 1
- a total of 13 particle templates (mass 1.100866e-03) inserted so far.
1 13 0.00055043321 0 0.132
Loop time of 0.00863524 on 4 procs for 1 steps with 13 atoms, finish time Tue Feb 20 17:17:53 2024
Pair time (%) = 1.8675e-06 (0.0216265)
Neigh time (%) = 0.000459823 (5.32495)
Comm time (%) = 7.43025e-06 (0.0860457)
Outpt time (%) = 1.19235e-05 (0.13808)
Other time (%) = 0.0081542 (94.4293)
Nlocal: 3.25 ave 13 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
[ournode:909573] *** Process received signal ***
[ournode:909573] Signal: Segmentation fault (11)
[ournode:909573] Signal code: Address not mapped (1)
[ournode:909573] Failing at address: 0x33
[ournode:909573] [ 0] /lib64/libc.so.6(+0x54db0)[0x150b27454db0]
[ournode:909573] [ 1] /usr/lib64/openmpi/lib/paraview/libvtkCommonCore.so.1(_ZNK9vtkObject13GetObjectNameB5cxx11Ev+0x13)[0x150b298c6533]
[ournode:909573] [ 2] lmp_auto[0x5493b6]
[ournode:909573] [ 3] lmp_auto[0x54a880]
[ournode:909573] [ 4] lmp_auto[0x507b5e]
[ournode:909573] [ 5] lmp_auto[0x9a68af]
[ournode:909573] [ 6] lmp_auto[0x6b6d9b]
[ournode:909573] [ 7] lmp_auto[0x6b72f9]
[ournode:909573] [ 8] lmp_auto[0x4150cb]
[ournode:909573] [ 9] /lib64/libc.so.6(+0x3feb0)[0x150b2743feb0]
[ournode:909573] [10] /lib64/libc.so.6(__libc_start_main+0x80)[0x150b2743ff60]
[ournode:909573] [11] lmp_auto[0x415315]
[ournode:909573] *** End of error message ***
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.
--------------------------------------------------------------------------
prterun noticed that process rank 0 with PID 909573 on ournode exited on
signal 11 (Segmentation fault).
-------------------------------------------
Edit: backtrace from the core:
arning: Unexpected size of section `.reg-xstate/909497' in core file.
#0 0x00001531ce6c6533 in vtkObject::GetObjectName[abi:cxx11]() const ()
from /usr/lib64/openmpi/lib/paraview/libvtkCommonCore.so.1
[Current thread is 1 (Thread 0x1531cdd45b00 (LWP 909497))]
Missing separate debuginfos, use: dnf debuginfo-install double-conversion-3.1.5-6.el9.x86_64 expat-2.5.0-1.el9.x86_64 glibc-2.34-83.el9_3.7.x86_64 hwloc-libs-2.4.1-5.el9.x86_64 jbigkit-libs-2.1-23.el9.x86_64 libevent-2.1.12-6.el9.x86_64 libfabric-1.18.0-1.el9.x86_64 libgcc-11.4.1-2.1.el9.x86_64 libibverbs-46.0-1.el9.x86_64 libjpeg-turbo-2.0.90-6.el9_1.x86_64 libnl3-3.7.0-1--Type for more, q to quit, c to continue without paging--
.el9.x86_64 libpng-1.6.37-12.el9.x86_64 libpsm2-11.2.230-1.el9.x86_64 libstdc++-11.4.1-2.1.el9.x86_64 libtiff-4.4.0-10.el9.x86_64 libuuid-2.37.4-15.el9.x86_64 libwebp-1.2.0-8.el9_3.x86_64 libzstd-1.5.1-2.el9.x86_64 lz4-libs-1.9.3-5.el9.x86_64 munge-libs-0.5.13-13.el9.x86_64 numactl-libs-2.0.16-1.el9.x86_64 openmpi-4.1.1-7.el9.x86_64 openmpi-devel-4.1.1-7.el9.x86_64 paraview-openmpi-5.11.1-1.el9.x86_64 pugixml-1.13-1.el9.x86_64 xz-libs-5.2.5-8.el9_0.x86_64 zlib-1.2.11-40.el9.x86_64
(gdb)
(gdb) bt full
#0 0x00001531ce6c6533 in vtkObject::GetObjectName[abi:cxx11]() const ()
from /usr/lib64/openmpi/lib/paraview/libvtkCommonCore.so.1
No symbol table info available.
#1 0x00000000005493b6 in LAMMPS_NS::DumpParticle::reset_vtk_data_containers() ()
No symbol table info available.
#2 0x000000000054a880 in LAMMPS_NS::DumpParticle::parse_parameters(int, char const* const*, bool, std::__cxx11::list, std::allocator >, std::allocator, std::allocator > > >) ()
No symbol table info available.
#3 0x0000000000507b5e in LAMMPS_NS::DumpCustomVTK::DumpCustomVTK(LAMMPS_NS::LAMMPS*, int, char**) ()
No symbol table info available.
#4 0x00000000009a68af in LAMMPS_NS::Output::add_dump(int, char**) ()
No symbol table info available.
#5 0x00000000006b6d9b in LAMMPS_NS::Input::execute_command() ()
No symbol table info available.
#6 0x00000000006b72f9 in LAMMPS_NS::Input::file() ()
No symbol table info available.
#7 0x00000000004150cb in main ()
No symbol table info available.