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crest-lab / crest

CREST - A program for the automated exploration of low-energy molecular chemical space.
https://crest-lab.github.io/crest-docs/
GNU Lesser General Public License v3.0
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CREST v3.0 Pre release SIGSEGV, segmentation fault occurred #252

Open Rintontin opened 5 months ago

Rintontin commented 5 months ago

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 https://github.com/grimme-lab/xtb/commit/0fb151dceb19b8df9f6012789cf7d2dd6e4a6cd2

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 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

Yes, thanks!