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grimme-lab / xtb

Semiempirical Extended Tight-Binding Program Package
https://xtb-docs.readthedocs.io/
GNU Lesser General Public License v3.0
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MD run ends in SIGSEGV in xtb_topology_mp_ #837

Open pierre-24 opened 1 year ago

pierre-24 commented 1 year ago

Describe the bug

While running a MD using --omd, the calculation fails with:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
libpthread-2.28.s  000014AC6390DCF0  Unknown               Unknown  Unknown
libifcore.so.5     000014AC6D1F3CA0  Unknown               Unknown  Unknown
xtb                0000000000A8EE6A  xtb_topology_mp_c          79  topology.f90
xtb                00000000005F7827  xtb_propertyoutpu         204  property.F90
xtb                000000000043CB1A  xtb_prog_main_mp_         861  main.F90
xtb                0000000000451692  MAIN__                     57  primary.f90
xtb                000000000040954D  Unknown               Unknown  Unknown
libc-2.28.so       000014AC6356FD85  __libc_start_main     Unknown  Unknown
xtb                000000000040946E  Unknown               Unknown  Unknown

To Reproduce

I used xtb sphere.xyz --input MD.inp --omd (files in archive below). The program stops after the geometry optimization and right before the MD run (probably while generating the topology, given the stacktrace above). The geometry contains a molecule solvated in 400 molecules of water, and includes $wall to keep everything together.

It ran with xtb 6.6.0, straight from the repository (compiled a few weeks ago).

Files: run.zip, including MD.log, the full output, if any.

Expected behaviour

For other systems with similar geometries, it seems to work and the MD runs smoothly.

Additional context

None

pierre-24 commented 1 year ago

There is the optimized structure: xtbopt.zip (the MD part fails after optimization). I'm then using xtb xtbopt.xyz --input input.inp --md but it results in the same error ;)

Albkat commented 1 year ago

It most likely the problem with your local environment. If you can share the meson-log.txt file (located at <build_dir>/meson-logs/meson-log.txt), we will try to resolve this issue.

marcelmbn commented 3 months ago

Could be related to this one: https://github.com/grimme-lab/xtb/issues/653.