CREST v3.0 Pre release SIGSEGV, segmentation fault occurred

[Rintontin]

Hi
I am using crest Version 3.0pre, Sat Jan 20 21:44:12 UTC 2024
commit (fafd635) compiled by 'runner@fv-az1423-259'
I tried to tautomerize a L-histidine molecule as a test and I got the following error.

manager@pc-1:~/programs/xtb$ crest test.xyz -tautomerize > test.out
forrtl: warning (768): Internal file write-to-self; undefined results
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
crest 00000000026244D0 Unknown Unknown Unknown
crest 000000000246193F Unknown Unknown Unknown
crest 000000000241BB75 Unknown Unknown Unknown
crest 000000000241B8D7 Unknown Unknown Unknown
crest 0000000000619EE9 protens_ 485 tautomerize.f90
crest 000000000253265F Unknown Unknown Unknown
crest 00000000025383C9 Unknown Unknown Unknown
crest 000000000258E246 Unknown Unknown Unknown
crest 0000000002592C5B Unknown Unknown Unknown
crest 00000000024C4D1F Unknown Unknown Unknown
crest 000000000061A28D protens_ 500 tautomerize.f90
crest 00000000025481D3 Unknown Unknown Unknown
crest 00000000024FC12E Unknown Unknown Unknown
crest 00000000024FB132 Unknown Unknown Unknown
crest 0000000002548E99 Unknown Unknown Unknown
crest 000000000261E709 Unknown Unknown Unknown
crest 00000000026AA4E3 Unknown Unknown Unknown

I am using the latest pre release version of xtb commit grimme-lab/xtb@0fb151d

My operating system is Linux Ubuntu 22.04.3 LTS 64bit
AMD® Ryzen threadripper 2990wx 32-core processor × 64
Memory: 128.0 GiB
gfortrand and gcc version 11.4.0
Python 3.10.12

test.zip

[pprcht]

#253 should do it.
Please not that the protonation tools are one part of the code I have yet to update to the new calculation interfaces.

[JayTheDog]

Hey, from what I see the protonation tool still introduces some errors (in this case via calling it with --tautomerize:

    __________________________________________
     |                                          |
     |     automated tautomerization script     |
     |__________________________________________|
Universitaet Bonn, MCTC
P.Pracht, Wed 28. Nov 13:11:52 CEST 2018

Cite as:
P.Pracht, R.Wilcken, A.Udvarhelyi, S.Rodde, S.Grimme
JCAMD, 2018, 32, 1139-1149.


******************************************************************************************
**                   P R O T O N A T I O N   C Y C L E     1 of 2                       **
******************************************************************************************

forrtl: severe (124): Invalid command supplied to EXECUTE_COMMAND_LINE
Image              PC                Routine            Line        Source             
crest              00000000006E9E3D  iomod_mp_command_        1018  iomod.F90
crest              00000000005FBEC7  xtblmo_                   226  protonate.f90
crest              000000000062199E  protsmall_                225  tautomerize.f90
crest              0000000000617C5E  tautomerize_               88  tautomerize.f90
crest              0000000000403CC7  MAIN__                    151  crest_main.f90
crest              000000000040334D  Unknown               Unknown  Unknown
crest              00000000026279A0  Unknown               Unknown  Unknown
crest              000000000040322E  Unknown               Unknown  Unknown

Also there seems to be a typo in line 572 of src/legacy_algos/tautomerize.f90.

Thanks for looking into it!

[pprcht]

Yes, thanks!