[Wien] Segmentation Fault after CORE END
Gavin Abo
gsabo at crimson.ua.edu
Fri Oct 5 04:26:53 CEST 2018
Also, what compiler and version are you using? Errors like that seem
common among the 2016/2017/2018 Intel Fortran compilers [
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17542.html
]. You could possibly try gfortran or the pre-built executables just to
see if it caused by your compiler [
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17982.html
].
For example, I'm using the 2013 Intel Fortran compiler:
username at computername:~/Desktop$ ifort -v
ifort version 14.0.1
I don't know for sure, but it looks like your error message does not
come from WIEN2k 18.2 but an older version. If so, the latest version
might resolve the error.
I'm using WIEN2k 18.2:
username at computername:~/Desktop$ cat $WIENROOT/WIEN2k_VERSION
WIEN2k_18.2 (Release 17/7/2018)
My version also has the ScaleDiag.F fixes to the mixer (i.e.,
ScaleDiag.patch [
https://github.com/gsabo/WIEN2k-Patches/tree/master/18.2 ]).
I tried a quick test calculation with the structure parameters you gave
for a couple scf cycles, and it seems to run fine:
username at computername:~/wiendata$ mkdir NaMnO2
username at computername:~/wiendata$ cd NaMnO2
username at computername:~/wiendata/NaMnO2$ makestruct_lapw
...
TITLE :NaMnO2
...
Would you like to enter Spacegroup or Lattice (S/L)(def=S)? S
SPACE GROUP: (type ENTER or give first LETTER for a list)
give SPACE GROUP as SYMBOL or NUMBER: B2/m
Info: space group is : 12 Cxz B2/m -B2x
Units of lattice parameters (Bohr/Angstrom) (b/A) (def=ANG):b
Lattice PARAMETERS as a b c (1 or 3 numbers - if you specify only 1
number, a cubic system is assumed):
10.720416 11.929841 5.397058
ANGLES BETWEEN lattice vectors, as alpha beta gamma (def=90.0 90.0
90.0):90 90 122.34
NUMBER INEQUEVALENT ATOMS :3
ATOM 1 (ELEMENT): Na
POSITION OF ATOM Na as X,Y,Z (def=0 0 0) :0.5 0.5 0.5
ATOM 2 (ELEMENT): Mn
POSITION OF ATOM Mn as X,Y,Z (def=0 0 0) :0 0 0
ATOM 3 (ELEMENT): O
POSITION OF ATOM O as X,Y,Z (def=0 0 0) :0.5017 0.2294 0
...
SPECIFY possible REDUCTION of SPHERE RADII in % (def=0)
2
...
rerun setrmt ?(y,N) (def=N):
N
...
The file init.struct has been created
for modifications of your input you can also edit file datastruct and run
Tmaker / setrmt init -r X individually
username at computername:~/wiendata/NaMnO2$ cp init.struct NaMnO2.struct
username at computername:~/wiendata/NaMnO2$ init_lapw -b
...
init_lapw finished ok
username at computername:~/wiendata/NaMnO2$ run_lapw -ec 0.001
hup: Command not found.
LAPW0 END
LAPW1 END
LAPW2 END
CORE END
MIXER END
ec cc and fc_conv 0 1 1
in cycle 2 ETEST: 0 CTEST: 0
hup: Command not found.
LAPW0 END
LAPW1 END
LAPW2 END
CORE END
MIXER END
ec cc and fc_conv 0 1 1
in cycle 3 ETEST: 0 CTEST: 0
hup: Command not found.
LAPW0 END
LAPW1 END
LAPW2 END
CORE END
MIXER END
ec cc and fc_conv 0 1 1
...
On 10/4/2018 3:38 PM, Laurence Marks wrote:
> 1) What version of Wien2k are you using?
> 2) What does "cat *.error" show?
>
> This almost certainly has nothing to do with -ec, k-points. Changing
> ulimit is obsolete (unless you are using an obsolete version of
> Wien2k). This might be an error in mixer, but is more likely to be a
> setup error. However, without more information it is not possible to
> say (yet).
>
> On Thu, Oct 4, 2018 at 4:32 PM Eric Kenney <kenneyef at bc.edu
> <mailto:kenneyef at bc.edu>> wrote:
>
> I'm having an issue with segmentation faults during LAPW cycles.
> I keep getting segmentation faults after running a standard
> run_lapw command:
>
> run_lapw -ec 0.001
> LAPW0 END
> LAPW1 END
> LAPW2 END
> CORE END
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> mixer 00000000004827DD Unknown Unknown
> Unknown
> libpthread-2.12.s 00000032F8C0F7E0 Unknown Unknown
> Unknown
> mixer 0000000000415054 MAIN__ 999
> mixer.F
> mixer 000000000040475E Unknown Unknown
> Unknown
> libc-2.12.so
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__libc-2D2.12.so&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=_GDrA5gqSzwOUAk1SVsST692GzqxkO1n72mdGQGj3Yg&s=5C-9xGUj4eezgpBLcDSWyPjOahdmBgTkuZNTguIq8YQ&e=>
> 00000032F841ED1D __libc_start_main Unknown Unknown
> mixer 0000000000404669 Unknown Unknown
> Unknown
>
> > stop error
>
>
> Naturally, I've been going through the mailing list and trying to
> deduce what the issue here is. The error occurs for a large range
> of RKmax values (5-8) and a large range of K mesh values
> (1000-10000). It occurs for -ec 0.001 to -ec 0.0000001, giving a
> large range on convergences. I've tried ulimit, but my cluster
> does not appear to have that command installed, nor do I think it
> is the issue.
>
> Interestingly, I haven't had this issue in the past with other
> lattices. This lattice is NaMnO2 in the B2/m setting; imported
> straight from a .cif file from Springer Materials. I've done x
> nn, x sgroup and, x symmetry all manually, and there seems to be
> no obvious issues here. For reference, the lattice parameters are
> as follows:
>
> a=10.720416 b=11.929841 c=5.397058 90.000000 90.000000 122.340000
> NA X=0.50000000 Y=0.50000000 Z=0.50000000
> Mn X=0.00000000 Y=0.00000000 Z=0.00000000
> O X=0.50170000 Y=0.22940000 Z=0.00000000
> 4 atoms per unit cell.
>
> Thank you, and have a nice day!
>
>
>
> --
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu <http://www.numis.northwestern.edu> ;
> Corrosion in 4D: MURI4D.numis.northwestern.edu
> <http://MURI4D.numis.northwestern.edu>
> Partner of the CFW 100% program for gender equity,
> www.cfw.org/100-percent <http://www.cfw.org/100-percent>
> Co-Editor, Acta Cryst A
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