[Wien] Segmentation fault (core dumped) error in w2w with spin-orbit
Md. Fhokrul Islam
fislam at hotmail.com
Fri Jul 26 15:48:07 CEST 2019
Dear Kyohoon,
Thank you for your time to help me fix the problem. I started from the scratch and used joinvec to create single file vector and energy files as you suggested but unfortunately, it is still giving me the same error "Segmentation fault (core dumped)". I noticed that the case.eigup/dn files, which is created during the 'x w2w' from case.enegysoup/dn files have some problem. I tried different k-mesh and each case the eigenvalues at the last k-point of the case.klist file is incomplete. I checked the case.energysoup/dn files but there is nothing wrong in those files.
I checked in google that core dumped problem is associated with program trying to access memory that is not there. But I am not sure why the problem appears only in this particular case.
Regards,
Fhokrul
________________________________
From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Kyohoon Ahn <butz1004 at korea.ac.kr>
Sent: Friday, July 26, 2019 7:05 AM
To: A Mailing list for WIEN2k users <wien at zeus.theochem.tuwien.ac.at>
Subject: Re: [Wien] Segmentation fault (core dumped) error in w2w with spin-orbit
Dear Fhokrul,
Thank you for your kind response :)
Then,,, Shall we try to use "x joinvec" ..?
In my case, the following procedure works fine for me. (without inversion case)
########################################
### PART 1. WIEN2K ###
########################################
\cp case.vns case.vnsup
\cp case.vns case.vnsdn
\cp case.vsp case.vspup
\cp case.vsp case.vspdn
x kgen -fbz (no shift)
x lapw1 -up -c -p
x lapw1 -dn -c -p
x lapwso -up -c -p
x joinvec -up -so
x joinvec -dn -so
# Now we can delete the useless vector files:
# rm *.vectorup* -f
# rm *.vectordn* -f
# rm *.vectorsoup_* -f
# rm *.vectorsodn_* -f
########################################
### PART 2. WIEN2WANNIER & WANNIER90 ###
########################################
write_inwf -up
write_inwf -dn
write_win -up
write case.fermiup and case.fermidn
x wannier90 -pp
x w2w -up -c -so (Please note that, here should be no "-p" with joinvec)
x w2w -dn -c -so
x wannier90 -so
Have a nice day.!
Best regards,
- Kyohoon
2019년 7월 26일 (금) 오전 1:10, Md. Fhokrul Islam <fislam at hotmail.com<mailto:fislam at hotmail.com>>님이 작성:
Hi Kyohoon,
1) I think -c switch is default for spin-orbit calculation but I tried both with/without -c. Doesn't make any difference.
2) No, there is no case.in1 file, onle case.in1c
3) I did rerun calculation the same way you did but it still doesn't create case.amn* or case.mmn* files (these files are empty). It creates the error file upw2w.error file right away with single message: "Error in W2W". Again -c switch doesn't make any difference.
By the way, these are parallel calculation so I have -p switch in all steps of the calculation.
Thanks,
Fhokrul
________________________________
From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>> on behalf of Kyohoon Ahn <butz1004 at korea.ac.kr<mailto:butz1004 at korea.ac.kr>>
Sent: Thursday, July 25, 2019 8:12 PM
To: A Mailing list for WIEN2k users <wien at zeus.theochem.tuwien.ac.at<mailto:wien at zeus.theochem.tuwien.ac.at>>
Subject: Re: [Wien] Segmentation fault (core dumped) error in w2w with spin-orbit
Dear Fhokrul,
Your procedure looks fine.
Here I have some questions:
(1) Is there no [-c] in your lapwso ..?
(2) Are there both of [in1] and [in1c] in your directory?
If yes, could you delete the [in1], before the [lapw1~lapwso] ?
(3) Could you try to do [x wannier90 -pp], just before [x w2w] ?
And could you try to use [x w2w -up -c -so], instead of [x w2w -up -so] ?
(<<< I think they are the same,,, but just for checking ...)
Best regards,
- Kyohoon
2019년 7월 25일 (목) 오후 6:49, Md. Fhokrul Islam <fislam at hotmail.com<mailto:fislam at hotmail.com>>님이 작성:
Dear Kyohoon,
Thank you for your reply. Our procedure are almost the same. First I use prepare_w2wdir [dirrecotry name] and then I initialize the calculation with init_w2w -up, so it does all the steps you mentioned both for DFT part and Wannier90.
After initialization I run:
x lapw1 -c -up (my system doesn't have inversion symmetry)
x lapw1 -c -dn
x lapwso -up
x w2w -up -so ---> job crashes here with core dumped error
x w2w -dn -so
x wannier90 -so
I have used this procedure for several other calculation with different systems
and it worked. But for some reason, for this system it is works only up to lapwso.
I will check if they problem goes away with smaller k-mesh.
Regards,
Fhokrul
________________________________
From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>> on behalf of Kyohoon Ahn <butz1004 at korea.ac.kr<mailto:butz1004 at korea.ac.kr>>
Sent: Thursday, July 25, 2019 3:53 PM
To: A Mailing list for WIEN2k users <wien at zeus.theochem.tuwien.ac.at<mailto:wien at zeus.theochem.tuwien.ac.at>>
Subject: Re: [Wien] Segmentation fault (core dumped) error in w2w with spin-orbit
Dear Fhokrul,
I also usually do some calculations with [run_lapw -so].
(i.e., not runsp_lapw)
So I may be I can share my experiences.
In my case, the procedure is following:
########################################
### PART 1. WIEN2K ###
########################################
\cp case.vns case.vnsup
\cp case.vns case.vnsdn
\cp case.vsp case.vspup
\cp case.vsp case.vspdn
x kgen -fbz (no shift)
x lapw1 -up (and with the additional options from the dayfile)
x lapw1 -dn
x lapwso -up
########################################
### PART 2. WIEN2WANNIER & WANNIER90 ###
########################################
write_inwf -up
write_inwf -dn
write_win -up
write case.fermiup and case.fermidn
x wannier90 -pp
x w2w -so -up
x w2w -so -dn
wannier90 -so
The above procedure works fine for me.
Is there any difference from yours?
Have a nice day.!
Best regards,
- Kyohoon
2019년 7월 23일 (화) 오후 3:04, Md. Fhokrul Islam <fislam at hotmail.com<mailto:fislam at hotmail.com>>님이 작성:
Hi Wien2k users and developers,
I encountered couple of problems running w2w with SO for a tetragonal Cd3As2 (with some impurity). I am using Wien2k18.2.
1. This is a non-magnetic system so I did run spin unpolarized calculations (x lapw1, x lapwso) following a note by Elias Assmann but it crashes when starts
x w2w -so -up
x w2w -so -dn
It asks for spin-polarized files vspup and vspdn files etc. I have done several non-magnetic calculations with exactly the same approach but I didn't have any problem before. But for some reason, in this case the upw2w.def and dnw2w.def files are just like the way it creates def files for spin-polarized calculations. I tried copying .vsp file to vspup and vspdn, and also other files to corresponding spin-polarized extension but it didn't work.
2. Because of this problem in (1) I rerun the DFT calculations with spin-polarized setting but this time it crashed with the error:
Segmentation fault (core dumped)
Segmentation fault (core dumped)
There are some segmentation fault in 'w2w -so' reported in mailing list in 2016 but I understood the issue is resolved for later version of w2w. So I am not sure why I am getting the error. There is no other error message.
Note that the bandstructure calculation works fine for this system, so the problem is something to do with w2w. I am wondering if anyone has encountered similar problem or has any suggestion on how to fix it.
Thanks,
Fhokrul
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SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
_______________________________________________
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