Segmentation fault

GP

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Feb 1, 2021, 5:20:41 AM2/1/21

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Dear Users,

I just installed USPEX v10.4. After some compilation issues due to mismatches between my enviroment and USPEX/Matlab ones, I think I have a working code.

However, running EX01, I'm getting this error:

....

Structure 26 built with topology 830
Structure 27 built with topology 1845
Structure 28 built with topology 1022
Structure 29 built with topology 1234
Structure 30 built with topology 1490

Read Seeds ...

Read AntiSeeds ...
vasp_std > log: Segmentation fault

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

Backtrace for this error:
#0 0x7FF57EB41437
#1 0x7FF57EB41A4E
#2 0x7FF57DE1A4BF
#3 0x7FF57EBFDCBB
#4 0x7FF57EBFE66D
#5 0xD3B9ED in wforce_
#6 0xD25D3E in MAIN__ at main.f90:?
/bin/bash: line 1: 56372 Segmentation fault (core dumped) vasp_std > log

Structure1 step1 at CalcFold1
===== USPEX WARNING @ 11:12:1 01-Feb-2021 =====
Read_VASP : VASP 1st SCF is not Done!

....

Of couse, vasp_std code works if lauched interactively from CalcFold1/ .

In the _original_ INPUT.txt file I just changed these lines:

% commandExecutable
vasp_std > log
% EndExecutable

0 : whichCluster (0: no-job-script, 1: local submission, 2: remote submission)
1 : numParallelCalcs

I thank you in adavnce for any hints.

Best.

G.

Hubert Okadome Valencia

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Feb 1, 2021, 9:45:39 PM2/1/21

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Dear GP,

I think I might have encounter the same problem once.

If it is the same problem, it was related to the fact that the vasp_std command launch interactively have the current bash environment, while the vasp_std command launch by USPEX got his environment from Matlab (for example using the Matlab 'unix' command can default to /bin/sh).

By any chance, is the USPEX job working when you change your commandExecutable to the following:

% commandExecutable

bash -c "vasp_std > log"

% EndExecutable

In that case, you might have to change the environment definition by setting ~/.bashrc or the likes*.

Sincerely,

*In my case, I end up writing a script for launching vasp, then directly use that script as commandExecutable.

Dmitry Volkov

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Feb 10, 2021, 5:13:28 AM2/10/21

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Dear Users,

One possible reason for segmentation fault is a stack overflow on your particular machine during the VASP calculation. Initially, I recommend you to check the allowed size issuing command ulimit -s.

Then either you can increase it ulimit -s 8192 or made it's even unlimited issuing command ulimit -s unlimited.

Good luck and best wishes!

GP

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Feb 11, 2021, 9:29:10 AM2/11/21

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Thank you very much for the information.

However, in my specific case, the stack overflow error only appears when I run vasp through USPEX.

If I just run the same executable from the shell it works perfectly.

Still trying to guess what is happening....

Cheers.

G. P.

Kee Choon Wee

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Aug 7, 2021, 8:29:34 AM8/7/21

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This happens to me if I use more than one thread for the OpenMP version of VASP 6.2.0. The problem goes away if I set OMP_NUM_THREADS=1

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