Has anyone else had trouble with LAMMPS on Centos8? It appears that LAMMPS may have been broken by one of the recent updates to centos8 or its repositories.
I was installing some new software on our centos8 workstation and as part of the process I ran a “$ yum update” command for maintenance purposes. Several days later another user on the workstation reported to me that they were getting “segmentation 11” faults running LIGGGHTS scripts they had run previously without error.
I attempted to run example scripts getting the same error. Then I downloaded a fresh clone of LIGGGHTS and recompiled with no improvement. Finally, tonight, I reinstalled Centos8 from scratch and installed LIGGGHTS and continued getting the same error.
At this point I decided to test LAMMPS to see if the failure was deeper than LIGGGHTS and found I am getting the same segmentation fault.
I am running a clean most recent stable LAMMPS distro. I compiled with make mpi, and attempted to run the granular example, in.pour.drum, with a single processor.
Here is my output:
$ mpirun -np 1 lmp_mpi in in.pour.drum
[mfg-67:74816:0:74816] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f7211277768)
==== backtrace ====
0 /lib64/libucs.so.0(+0x18bb0) [0x7f7210c0abb0]
1 /lib64/libucs.so.0(+0x18d8a) [0x7f7210c0ad8a]
2 /lib64/libuct.so.0(+0x1655b) [0x7f721233e55b]
3 /lib64/ld-linux-x86-64.so.2(+0xfd0a) [0x7f72202c3d0a]
4 /lib64/ld-linux-x86-64.so.2(+0xfe0a) [0x7f72202c3e0a]
5 /lib64/ld-linux-x86-64.so.2(+0x13def) [0x7f72202c7def]
6 /lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f721ef93ab7]
7 /lib64/ld-linux-x86-64.so.2(+0x1365e) [0x7f72202c765e]
8 /lib64/libdl.so.2(+0x11ba) [0x7f721e6ed1ba]
9 /lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f721ef93ab7]
10 /lib64/libc.so.6(_dl_catch_error+0x33) [0x7f721ef93b53]
11 /lib64/libdl.so.2(+0x1939) [0x7f721e6ed939]
12 /lib64/libdl.so.2(dlopen+0x4a) [0x7f721e6ed25a]
13 /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f721e95df05]
14 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f721e93bb16]
15 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f721e93aa5a]
16 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f721e9463ce]
17 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f721e9468b2]
18 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f721e946915]
19 /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f721fdbe494]
20 /usr/lib64/openmpi/lib/libmpi.so.40(MPI_Init+0x72) [0x7f721fdee6b2]
21 lmp_mpi() [0x40721b]
22 /lib64/libc.so.6(__libc_start_main+0xf3) [0x7f721ee7e873]
23 lmp_mpi() [0x4072ae]