Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Hessian calculation runs into segmentation fault when atoms are frozen #475

Closed
TamasFoldes opened this issue May 5, 2021 · 4 comments · Fixed by #1175
Closed

Hessian calculation runs into segmentation fault when atoms are frozen #475

TamasFoldes opened this issue May 5, 2021 · 4 comments · Fixed by #1175
Labels
bug Something isn't working

Comments

@TamasFoldes
Copy link

TamasFoldes commented May 5, 2021 •
edited by awvwgk
Loading

Describe the bug
I attempted to calculate the Hessian of a system with several atoms frozen. The calculation terminated with an error showing segmentation fault:

writing file \<hessian>.

 projected vibrational frequencies (cm⁻¹)

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

Backtrace for this error:
#0  0x153a79b5fd01 in ???
#1  0x153a79b5eed5 in ???
#2  0x153a797e720f in ???
#3  0x556310f7e468 in ???
#4  0x556310e711a8 in ???
#5  0x556310e6bf98 in ???
#6  0x153a797c80b2 in ???
#7  0x556310e6bffd in ???
#8  0xffffffffffffffff in ???
Segmentation fault (core dumped)

To Reproduce
Input and output files are attached.

Expected behaviour
Normal termination with the results printed out.

Additional context
output.txt
structure.txt
xcontrol.txt
@TamasFoldes TamasFoldes added the unconfirmed This report has not yet been confirmed by the developers label May 5, 2021
@awvwgk awvwgk added bug Something isn't working and removed unconfirmed This report has not yet been confirmed by the developers labels May 5, 2021
@awvwgk
Copy link
Member

awvwgk commented May 5, 2021

Thanks for reporting, this looks indeed faulty. I'll have to investigate what is throwing up here.

@jiachenchem
Copy link

jiachenchem commented Aug 30, 2021 •
edited
Loading

A little bit more detail for this issue. xtb 6.4.1 seems to work if number of freezing atoms is smaller than 7. Control and output files are attached. When number of freezing atoms are larger, then I have the segmantation fault.
xcontrol_2.txt
output_2.txt

@TamasFoldes
Copy link
Author

Thank you for the notification! I tested v 6.4.1 when it came out and noticed the limitation. Is there a plan to further extend the number of frozen atoms possible in a single calculation?

@lxsep
Copy link

lxsep commented Apr 11, 2024

Hello, I am trying to do the same in version 6.6.1 and having the same error as in here. I already tried to extend the memory for the calculation and it is not working.

This was referenced Feb 4, 2025
Open
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Fix hessian with fixed atoms foxtran/xtb
4 participants
@jiachenchem @awvwgk @TamasFoldes @lxsep