Using GFN-FF on HKUST-1 Segfault but Works if Using Valgrind

[williamyxl]

xtb version:

xtb --version
      -----------------------------------------------------------
     |                   =====================                   |
     |                           x T B                           |
     |                   =====================                   |
     |                         S. Grimme                         |
     |          Mulliken Center for Theoretical Chemistry        |
     |                    University of Bonn                     |
      -----------------------------------------------------------

   * xtb version 6.7.1 (edcfbbe) compiled by 'conda@afd1a870197c' on 2025-04-11

normal termination of xtb

I have tested the same xtb version on Materials Project mp-66 diamond and qmof-0b5e989, worked without SegFault.

HKUST-1 vasp file: https://github.com/WMD-group/Crystal_structures/blob/master/MOFs/HKUST-1/HKUST1.vasp

Commands to reproduce SegFault:

export OMP_STACKSIZE=5G
export OMP_NUM_THREADS=1
xtb --gfnff HKUST1.vasp --opt

Output:

      -----------------------------------------------------------
     |                   =====================                   |
     |                           x T B                           |
     |                   =====================                   |
     |                         S. Grimme                         |
     |          Mulliken Center for Theoretical Chemistry        |
     |                    University of Bonn                     |
      -----------------------------------------------------------

   * xtb version 6.7.1 (edcfbbe) compiled by 'conda@afd1a870197c' on 2025-04-11

...
...
...

 * started run on 2025/04/21 at 03:59:53.086
   ID    Z sym.   atoms
    1    8 O      1-48
    2    6 C      49-120
    3    1 H      121-144
    4   29 Cu     145-156

           -------------------------------------------------
          |                Calculation Setup                |
           -------------------------------------------------

          program call               : xtb --gfnff HKUST1.vasp --opt
          coordinate file            : HKUST1.vasp
          omp threads                :                     1


molecular fragmentation (1/2 indicates fragments):
111111111111111111111111111111111111111111111111111111111111111111111111
111111111111111111111111111111111111111111111111111111111111111111111111
211111211111
# atoms in fragment 1/2:   154     2
 fragment masses (1/2) :     2292.40      127.09
CMA distance (Bohr)    :   0.000
constraining FC (au)   :  0.0500

          ==================== Thresholds ====================
          CN  :   150.00000
          rep :   500.00000
          disp:  2500.00000
          HB1 :   250.00000
          HB2 :   450.00000

          Pauling EN used:
          Z : 1  EN :  2.20
          Z : 6  EN :  2.55
          Z : 8  EN :  3.44
          Z :29  EN :  1.90
          electric field strengths (au): 0.000

           -------------------------------------------------
          |           Force Field Initialization            |
           -------------------------------------------------

          distances ...
          ----------------------------------------
          generating topology and atomic info file ...

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7f0b3778c51f in ???
        at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#1  0x55d16f2417f0 in ???
#2  0x55d16f223d25 in ???
#3  0x55d16f24979d in ???
#4  0x55d16f1f9dd2 in ???
#5  0x55d16f289489 in ???
#6  0x55d16f1cad6f in ???
#7  0x55d16f1b8244 in ???
#8  0x7f0b37773d8f in __libc_start_call_main
        at ../sysdeps/nptl/libc_start_call_main.h:58
#9  0x7f0b37773e3f in __libc_start_main_impl
        at ../csu/libc-start.c:392
#10  0x55d16f1b82e6 in ???
#11  0xffffffffffffffff in ???
Segmentation fault (core dumped)

seems like a SegFault happened during generating the topology file.

So I added Valgrind:

valgrind xtb --gfnff HKUST1.vasp --opt

Output:

==63678== Memcheck, a memory error detector
==63678== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==63678== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==63678== Command: xtb --gfnff HKUST1.vasp --opt
==63678==
      -----------------------------------------------------------
     |                   =====================                   |
     |                           x T B                           |
     |                   =====================                   |
     |                         S. Grimme                         |
     |          Mulliken Center for Theoretical Chemistry        |
     |                    University of Bonn                     |
      -----------------------------------------------------------

   * xtb version 6.7.1 (edcfbbe) compiled by 'conda@afd1a870197c' on 2025-04-11

...
...
...

 * started run on 2025/04/21 at 03:59:59.686
   ID    Z sym.   atoms
    1    8 O      1-48
    2    6 C      49-120
    3    1 H      121-144
    4   29 Cu     145-156

           -------------------------------------------------
          |                Calculation Setup                |
           -------------------------------------------------

          program call               : xtb --gfnff HKUST1.vasp --opt
          coordinate file            : HKUST1.vasp
          omp threads                :                     1


molecular fragmentation (1/2 indicates fragments):
111111111111111111111111111111111111111111111111111111111111111111111111
111111111111111111111111111111111111111111111111111111111111111111111111
211111211111
# atoms in fragment 1/2:   154     2
 fragment masses (1/2) :     2292.40      127.09
CMA distance (Bohr)    :   0.000
constraining FC (au)   :  0.0500

          ==================== Thresholds ====================
          CN  :   150.00000
          rep :   500.00000
          disp:  2500.00000
          HB1 :   250.00000
          HB2 :   450.00000

          Pauling EN used:
          Z : 1  EN :  2.20
          Z : 6  EN :  2.55
          Z : 8  EN :  3.44
          Z :29  EN :  1.90
          electric field strengths (au): 0.000

           -------------------------------------------------
          |           Force Field Initialization            |
           -------------------------------------------------

==63678== Conditional jump or move depends on uninitialised value(s)
==63678==    at 0x1B7787: __xtb_gfnff_neighbor_MOD_gettransvec (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1883B5: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==
==63678== Conditional jump or move depends on uninitialised value(s)
==63678==    at 0x1B7789: __xtb_gfnff_neighbor_MOD_gettransvec (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1883B5: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==
          distances ...
          ----------------------------------------
          generating topology and atomic info file ...
==63678== Invalid read of size 4
==63678==    at 0x1A77B0: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Address 0x1087545c is 4 bytes before a block of size 707,616 alloc'd
==63678==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1BB018: __xtb_gfnff_neighbor_MOD_get_nb (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1A66FF: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==
          pair mat ...
          computing topology distances matrix with Floyd-Warshall algo ...
          making topology EEQ charges ...
          #fragments for EEQ constrain: 1
          ----------------------------------------
          generating topology and atomic info file ...
==63678== Invalid read of size 16
==63678==    at 0x1A77F0: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Address 0x108753b8 is 97,864 bytes inside a block of size 97,968 free'd
==63678==    at 0x484B27F: free (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1A7650: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Block was alloc'd at
==63678==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1A4C47: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==
==63678== Invalid read of size 4
==63678==    at 0x1A7840: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Address 0x108753c8 is 97,880 bytes inside a block of size 97,968 free'd
==63678==    at 0x484B27F: free (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1A7650: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Block was alloc'd at
==63678==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1A4C47: __xtb_gfnff_ini2_MOD_gfnff_neigh (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x189D25: __xtb_gfnff_ini_MOD_gfnff_ini (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1AF79D: __xtb_gfnff_setup_MOD_gfnff_setup (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15FDD2: __xtb_gfnff_calculator_MOD_newgffcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1EF489: __xtb_main_setup_MOD_newcalculator (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130D6F: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==
          pair mat ...
          computing topology distances matrix with Floyd-Warshall algo ...
          making topology EEQ charges ...
          #fragments for EEQ constrain: 1
          rings ...
          # BATM   2688
          # H in HB   24
          doing iterative Hueckel for 8 subsystem(s) ...
 perfect biradical detected at FT-HMO level. Breaking the symmetry
 because its assumed to be an anit-aromatic system like COT or CB.
 ...
 ... same mesaage for many many times
 ...
 perfect biradical detected at FT-HMO level. Breaking the symmetry
 because its assumed to be an anit-aromatic system like COT or CB.

  atom   neighbors  erfCN metchar sp-hybrid imet pi  qest     coordinates
    1  O       2    1.82   0.00         2    0    1  -0.316   41.869297    6.849388   17.608664
    2  O       2    1.82   0.00         2    0    1  -0.316   24.716591   31.594048   14.097603
 ...
 atom coords, yada yada yada ...
 ...
  156  Cu      5    3.76   0.16         0    2    0   0.378   25.209011    5.733307   16.216225

          #atoms :   156
          #bonds :   198
          #angl  :   384
          #tors  :   456
          #nmol  :   1
          #optfrag :   1
           -------------------------------------------------
          |                   G F N - F F                   |
          |          A general generic force-field          |
          |                  Version 1.0.3                  |
           -------------------------------------------------
          Number of HB bonds (bound hydrogen)     348624
          Number of HB bonds (unbound hydrogen)   33696
          Number of XB bonds                      0
==63678== Invalid read of size 8
==63678==    at 0x5AF78F2: dgemv_kernel_4x1 (in /home/xyan11/miniforge3/envs/mofa2/lib/libopenblasp-r0.3.29.so)
==63678==    by 0x5AF837C: dgemv_n_HASWELL (in /home/xyan11/miniforge3/envs/mofa2/lib/libopenblasp-r0.3.29.so)
==63678==    by 0x49E5B91: dgemv_ (in /home/xyan11/miniforge3/envs/mofa2/lib/libopenblasp-r0.3.29.so)
==63678==    by 0x1F50D1: __xtb_mctc_blas_level2_MOD_mctc_dgemv (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1F6B62: __xtb_mctc_blas_wrap2_MOD_mctc_dgemv312 (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x18451B: __xtb_gfnff_eg_MOD_gfnff_eg (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15CE22: __xtb_gfnff_calculator_MOD_singlepoint (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130FB5: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Address 0x10922ce0 is 0 bytes after a block of size 1,248 alloc'd
==63678==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1B0DC7: __xtb_gfnff_neighbourlist_MOD_newgffneighbourlist (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x180B43: __xtb_gfnff_eg_MOD_gfnff_eg (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15CE22: __xtb_gfnff_calculator_MOD_singlepoint (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130FB5: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==
==63678== Invalid read of size 8
==63678==    at 0x5AF8644: dgemv_n_HASWELL (in /home/xyan11/miniforge3/envs/mofa2/lib/libopenblasp-r0.3.29.so)
==63678==    by 0x49E5B91: dgemv_ (in /home/xyan11/miniforge3/envs/mofa2/lib/libopenblasp-r0.3.29.so)
==63678==    by 0x1F50D1: __xtb_mctc_blas_level2_MOD_mctc_dgemv (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1F6B62: __xtb_mctc_blas_wrap2_MOD_mctc_dgemv312 (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x1845CA: __xtb_gfnff_eg_MOD_gfnff_eg (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15CE22: __xtb_gfnff_calculator_MOD_singlepoint (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130FB5: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==  Address 0x10922ce0 is 0 bytes after a block of size 1,248 alloc'd
==63678==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==63678==    by 0x1B0DC7: __xtb_gfnff_neighbourlist_MOD_newgffneighbourlist (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x180B43: __xtb_gfnff_eg_MOD_gfnff_eg (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x15CE22: __xtb_gfnff_calculator_MOD_singlepoint (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x130FB5: __xtb_prog_main_MOD_xtbmain (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==    by 0x11E244: main (in /home/xyan11/miniforge3/envs/mofa2/bin/xtb)
==63678==

 E+G (total)                   0 d,  0 h,  0 min, 15.896 sec
 distance/D3 list               ...        0 min,  0.007 sec (  0.043%)
 non bonded repulsion           ...        0 min,  0.108 sec (  0.680%)
 dCN                            ...        0 min,  0.532 sec (  3.346%)
 EEQ energy and q               ...        0 min,  3.066 sec ( 19.287%)
                                ...        0 min,  0.000 sec (  0.000%)
 EEQ gradient                   ...        0 min,  6.832 sec ( 42.982%)
 bonds                          ...        0 min,  0.036 sec (  0.228%)
 bend and torsion               ...        0 min,  0.023 sec (  0.144%)
 bonded ATM                     ...        0 min,  0.016 sec (  0.098%)
 HB/XB (incl list setup)        ...        0 min,  4.764 sec ( 29.967%)

         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         ::                     SUMMARY                     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         :: total energy             -33.027972249873 Eh    ::
         :: gradient norm              0.207495326239 Eh/a0 ::
         ::.................................................::
         :: bond energy              -32.526862666540 Eh    ::
         :: angle energy               0.016633335953 Eh    ::
         :: torsion energy             0.009206915749 Eh    ::
         :: repulsion energy           2.080937847509 Eh    ::
         :: electrostat energy        -2.302577382193 Eh    ::
         :: dispersion energy         -0.247125829557 Eh    ::
         :: HB energy                 -0.015126272096 Eh    ::
         :: XB energy                  0.000000000000 Eh    ::
         :: bonded atm energy         -0.043058198698 Eh    ::
         :: external energy            0.000000000000 Eh    ::
         :: add. restraining           0.000000000000 Eh    ::
         :: total charge               0.000000000000 e     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::


........................................................................
.............................. CYCLE    1 ..............................
........................................................................

I used ctrl+c to exit valgrind, and the files: gfnff_charges and gfnff_topo are there! Then, I ran without valgraind:

xtb --gfnff HKUST1.vasp --opt

Output:

      -----------------------------------------------------------
     |                   =====================                   |
     |                           x T B                           |
     |                   =====================                   |
     |                         S. Grimme                         |
     |          Mulliken Center for Theoretical Chemistry        |
     |                    University of Bonn                     |
      -----------------------------------------------------------

   * xtb version 6.7.1 (edcfbbe) compiled by 'conda@afd1a870197c' on 2025-04-11

...
...
...

 * started run on 2025/04/21 at 04:07:51.500
   ID    Z sym.   atoms
    1    8 O      1-48
    2    6 C      49-120
    3    1 H      121-144
    4   29 Cu     145-156

           -------------------------------------------------
          |                Calculation Setup                |
           -------------------------------------------------

          program call               : xtb --gfnff HKUST1.vasp --opt
          coordinate file            : HKUST1.vasp
          omp threads                :                     1


molecular fragmentation (1/2 indicates fragments):
111111111111111111111111111111111111111111111111111111111111111111111111
111111111111111111111111111111111111111111111111111111111111111111111111
211111211111
# atoms in fragment 1/2:   154     2
 fragment masses (1/2) :     2292.40      127.09
CMA distance (Bohr)    :   0.000
constraining FC (au)   :  0.0500
          GFN-FF topology read from file successfully!
           -------------------------------------------------
          |                   G F N - F F                   |
          |          A general generic force-field          |
          |                  Version 1.0.3                  |
           -------------------------------------------------
          Number of HB bonds (bound hydrogen)     348624
          Number of HB bonds (unbound hydrogen)   33696
          Number of XB bonds                      0

 E+G (total)                   0 d,  0 h,  0 min,  0.514 sec
 distance/D3 list               ...        0 min,  0.000 sec (  0.073%)
 non bonded repulsion           ...        0 min,  0.004 sec (  0.800%)
 dCN                            ...        0 min,  0.019 sec (  3.695%)
 EEQ energy and q               ...        0 min,  0.072 sec ( 14.065%)
                                ...        0 min,  0.000 sec (  0.000%)
 EEQ gradient                   ...        0 min,  0.226 sec ( 43.919%)
 bonds                          ...        0 min,  0.001 sec (  0.175%)
 bend and torsion               ...        0 min,  0.000 sec (  0.023%)
 bonded ATM                     ...        0 min,  0.000 sec (  0.056%)
 HB/XB (incl list setup)        ...        0 min,  0.179 sec ( 34.815%)

         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         ::                     SUMMARY                     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         :: total energy             -33.027972249873 Eh    ::
         :: gradient norm              0.207495326239 Eh/a0 ::
         ::.................................................::
         :: bond energy              -32.526862666540 Eh    ::
         :: angle energy               0.016633335953 Eh    ::
         :: torsion energy             0.009206915749 Eh    ::
         :: repulsion energy           2.080937847509 Eh    ::
         :: electrostat energy        -2.302577382193 Eh    ::
         :: dispersion energy         -0.247125829557 Eh    ::
         :: HB energy                 -0.015126272096 Eh    ::
         :: XB energy                  0.000000000000 Eh    ::
         :: bonded atm energy         -0.043058198698 Eh    ::
         :: external energy            0.000000000000 Eh    ::
         :: add. restraining           0.000000000000 Eh    ::
         :: total charge               0.000000000000 e     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::


........................................................................
.............................. CYCLE    1 ..............................
........................................................................
     iter. time                 ...        0 min,  0.506 sec
          total energy         -33.027972249872548 Eh
            energy change       -0.18+309 Eh

          gradient norm          0.213240622767545 Eh/a0
            max. gradient        0.030157411030399 Eh/a0

            step length          0.000000000000000 a0
            max. step            0.000000000000000 a0

       unit cell volume       4546.399375090608373 A^3

       current lattice:
       35.139151938390995       -0.000066566808652        0.000094139683600
       17.569518322653124       30.431574628036522        0.000108753317208
       17.569633615737885       10.143894176147619       28.691221597433103

........................................................................
.............................. CYCLE    2 ..............................
........................................................................
     iter. time                 ...        0 min,  0.490 sec
          total energy         -33.057885354491511 Eh
            energy change       -0.30E-01 Eh

          gradient norm          0.087634616894103 Eh/a0
            max. gradient        0.023795707468652 Eh/a0

            step length          0.213240622767545 a0
            max. step            0.030157411030399 a0

       unit cell volume       4533.648144155040427 A^3

       current lattice:
       35.109243542666576       -0.001237631416174        0.009042055379507
       17.569516210641609       30.406263613614328        0.009053685970966
       17.569631258329331       10.143894798519629       28.664376769570371

........................................................................
.............................. CYCLE    3 ..............................
........................................................................
     iter. time                 ...        0 min,  0.486 sec
          total energy         -33.066747463450994 Eh
            energy change       -0.89E-02 Eh

          gradient norm          0.056702622961371 Eh/a0
            max. gradient        0.012047659746873 Eh/a0

            step length          0.153738632257075 a0
            max. step            0.023795707468652 a0

       unit cell volume       4517.417779430395967 A^3

       current lattice:
       35.070012929232234       -0.001895333980354        0.017556122480569
       17.569565734757411       30.372534363491980        0.017597656235278
       17.566248444642831       10.141631359109956       28.630856615173762

It seems charge and topology are read from the files. It seems interesting that Valgrind helped preventing the SegFault from happening when xtb trying to generate topology from the input vasp file. More interestingly, this only happens on HKUST-1.

[williamyxl]

nvm, it's not a reproducible bug. Changed computer, segfault disappeared.