Segmentation Fault during STRING calculation

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Segmentation Fault during STRING calculation

Postby woffermans » Wed Jan 09, 2019 4:43 pm

Dear ABINIT friends,

During a STRING calculation and right after STRING METHOD - TIME STEP 3, a segmentation fault occurred. See below for snippet.
The endings of the output and log files look reasonable. See below for output. From the log file I conclude that the error occurred while or after writing the HIST netCDF file. Probably just thereafter, since the calculation could be restarted and continued at STRING METHOD - TIME STEP 4.

If someone wants to take a look, I can provide the input and output files. But you have to react/respond reasonably in time, otherwise I will delete the files.


<snip>
...
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libifcoremt.so.5 00002ADA94D8C46C for__signal_handl Unknown Unknown
libpthread-2.17.s 00002ADA92E505D0 Unknown Unknown Unknown
abinit 00000000004301F5 Unknown Unknown Unknown
abinit 000000000041B4C1 Unknown Unknown Unknown
abinit 000000000040C578 Unknown Unknown Unknown
abinit 0000000000409B8E Unknown Unknown Unknown
libc-2.17.so 00002ADA96C683D5 __libc_start_main Unknown Unknown
abinit 0000000000409AA9 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libifcoremt.so.5 00002B646AFAF46C for__signal_handl Unknown Unknown
libpthread-2.17.s 00002B64690735D0 Unknown Unknown Unknown
abinit 00000000004301F5 Unknown Unknown Unknown
abinit 000000000041B4C1 Unknown Unknown Unknown
abinit 000000000040C578 Unknown Unknown Unknown
abinit 0000000000409B8E Unknown Unknown Unknown
libc-2.17.so 00002B646CE8B3D5 __libc_start_main Unknown Unknown
abinit 0000000000409AA9 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
...
</snip>

$ tail pd.txt
-4.22739500702405E-01 -4.22736781594062E-01 4.28610665313322E-01
8.02052238864168E-01 -9.28770692370097E-02 1.59018377693708E+00
-9.29396009610619E-02 8.02816497587862E-01 1.59246687719083E+00
5.37769003792507E-02 5.37617571431841E-02 1.03266347307147E-01
-3.58996217718412E-01 -3.59819432230984E-01 -3.39596420762159E+00
3.58996217718412E-01 3.59819432230984E-01 3.39596420762159E+00
-Cartesian components of stress tensor (GPa) [Pressure= 2.9449E+00 GPa]
- sigma(1 1)= -2.25663927E+00 sigma(3 2)= -7.60621037E-01
- sigma(2 2)= -3.94469528E+00 sigma(3 1)= -1.31394586E+00
- sigma(3 3)= -2.63332473E+00 sigma(2 1)= 1.45814166E+00
^C

$ tail pd.log
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 6.00000000E+01 degrees
Unit cell volume ucvol= 8.6602540E-01 bohr^3
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 6.00000000E+01 degrees
Unit cell volume ucvol= 8.6602540E-01 bohr^3
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 6.00000000E+01 degrees
Unit cell volume ucvol= 8.6602540E-01 bohr^3
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 6.00000000E+01 degrees
Unit cell volume ucvol= 8.6602540E-01 bohr^3
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 6.00000000E+01 degrees
Write iteration in HIST netCDF file
woffermans
 
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