Re: [Wien] Segmentation Fault after CORE END

[Laurence Marks]

Everything indicates that there are errors in what you are doing. Based
upon the case.scfm and case.outputm files, the prior error was not in the
mixer, it was a general failure due to incorrect useage.

As one example, you cannot just "change" the potential. At a minimum you
must save the prior version, change case.in0 then run.

On Fri, Oct 5, 2018, 17:36 Eric Kenney  wrote:

> Based on the recommendation of Gavin Abo, I entered the struct file by
> hand.  I got the system to run properly for a bit and did some
> calculations.  But, upon attempting to change the potential from PBE to
> LDA, the mixer began crashing again.  Now it's crashing even using PBE.
>
> I'm using version 18.1; I'll look into seeing if I can get it patched.
>
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] Segmentation Fault after CORE END

[Eric Kenney]

Based on the recommendation of Gavin Abo, I entered the struct file by
hand.  I got the system to run properly for a bit and did some
calculations.  But, upon attempting to change the potential from PBE to
LDA, the mixer began crashing again.  Now it's crashing even using PBE.

I'm using version 18.1; I'll look into seeing if I can get it patched.
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] Segmentation Fault after CORE END

[Gavin Abo]

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@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@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@computername:~/wiendata$ mkdir NaMnO2
username@computername:~/wiendata$ cd NaMnO2
username@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@computername:~/wiendata/NaMnO2$ cp init.struct NaMnO2.struct
username@computername:~/wiendata/NaMnO2$ init_lapw -b
...
  init_lapw finished ok
username@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 > 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  004827DD Unknown   Unknown 
Unknown
libpthread-2.12.s  0032F8C0F7E0 Unknown   Unknown 
Unknown
mixer  00415054 MAIN__    999 
mixer.F
mixer  0040475E Unknown   Unknown 
Unknown
libc-2.12.so


0032F841ED1D  __libc_start_main Unknown  Unknown
mixer  00404669 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
(1000-1).  It occurs for -ec 0.001 to -ec 0.001, 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 

Re: [Wien] Segmentation Fault after CORE END

[Laurence Marks]

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  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  PCRoutineLine
> Source
> mixer  004827DD  Unknown   Unknown  Unknown
> libpthread-2.12.s  0032F8C0F7E0  Unknown   Unknown  Unknown
> mixer  00415054  MAIN__999  mixer.F
> mixer  0040475E  Unknown   Unknown  Unknown
> libc-2.12.so
> 
> 0032F841ED1D  __libc_start_main Unknown  Unknown
> mixer  00404669  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 (1000-1).  It occurs for -ec
> 0.001 to -ec 0.001, 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 90.00 90.00  122.34
> NA X=0.5000 Y=0.5000 Z=0.5000
> Mn X=0. Y=0. Z=0.
> O X=0.5017 Y=0.2294 Z=0.
> 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 ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html