[Wien] error in SCF calculation

Fri Sep 23 17:07:43 CEST 2016

It also says "Segmentation fault (core dumped)"  just before the error and
Yes I commented out the W2kinit call. But it did not generate case.scfm
files. Shall I send the lapack path that I have provided in my .bashrc
files ? Or If any other information you need I can provide to detect the
problem.

Kind Regards,
Paresh

On Fri, Sep 23, 2016 at 8:27 PM, Laurence Marks <L-marks at northwestern.edu>
wrote:

> Does the error have any other information, or is it exactly the same. Did
> you comment out the W2kinit call as I asked?
>
> I suspect that there is something wrong with the lapack calls on your HPC
> system, but I don't have enough information to say -- I am guessing.
>
> On Fri, Sep 23, 2016 at 9:44 AM, Paresh Chandra Rout <
> pareshchandra at iiserb.ac.in> wrote:
>
>> Hello Sir,
>>
>> I recompiled through new SRC.mixer as per your suggestion but getting the
>> same error.  I also noticed one thing in that It does not generate
>> case.scfm file during the calculation. Could that be a problem ?  The error
>> occurs  only in wien2k which has installed in the HPC . But, when I tried
>> the same system on single workstation, it works fine without any problem.
>>
>> On Fri, Sep 23, 2016 at 5:36 PM, Laurence Marks <laurence.marks at gmail.com
>> > wrote:
>>
>>> That will work. Afterwards change the compile options back but don't
>>> Recompile.
>>>
>>> ---
>>> Professor Laurence Marks
>>> "Research is to see what everybody else has seen, and to think what
>>> nobody else has thought", Albert Szent-Gyorgi
>>> http://www.numis.northwestern.edu
>>> Corrosion in 4D http://MURI4D.numis.northwestern.edu
>>> Partner of the CFW 100% gender equity project, www.cfw.org/100-percent
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cfw.org_100-2Dpercent&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=Rq4H3KvOqrLf-LaERB-GYxiNnQDYyEvesHg8dYbwtR8&s=3hQH-I9CIpeY9nbLmO2ftPpfY_DW_zG4SZCEBj0xC8s&e=>
>>> Co-Editor, Acta Cryst A
>>>
>>>
>>> On Sep 23, 2016 05:36, "Paresh Chandra Rout" <pareshchandra at iiserb.ac.in>
>>> wrote:
>>>
>>>> Hello Sir,
>>>>
>>>> Would you please tell me how to compile *only mixe*r with
>>>> the compilation options removing -assume buffered_io . Shall
>>>> I remove it from compilation options while doing ./siteconfig_lapw and
>>>> then  only compile mixer ?
>>>>
>>>> Kind Regards
>>>> Paresh
>>>>
>>>> On Fri, Sep 23, 2016 at 3:03 PM, Paresh Chandra Rout <
>>>> pareshchandra at iiserb.ac.in> wrote:
>>>>
>>>>> Thank you very much. I will go through your suggestions and let you
>>>>> know .
>>>>>
>>>>> On Fri, Sep 23, 2016 at 3:41 AM, Laurence Marks <
>>>>> L-marks at northwestern.edu> wrote:
>>>>>
>>>>>> I used your BFO file (some comments later) with the same
>>>>>> anti-ferromagnetic starting point. I can get essentially the same :DIS
>>>>>> values as you have, but I do not get an error. Suggestions:
>>>>>>
>>>>>> 1) Download SRC_mixer from the main Wien2k web page. There might be a
>>>>>> bug that has already been fixed.
>>>>>> 2) Edit mixer.F as I suggested and comment out the W2kinit call.
>>>>>> 3) Change (just for mixer) the compilation options and remove the
>>>>>> -assume buffered_io as this will give more information about the location
>>>>>> in case.scfm and case.outputm.
>>>>>> 4) Remove all the files except BFO.struct (or the other) and
>>>>>> initialize, accepting all changes to the structure.
>>>>>>
>>>>>> **********************
>>>>>> Other comments.
>>>>>>
>>>>>> a) You clearly did not accept all the suggestions during init_lapw
>>>>>> for BFO, as it will find that you have a rhombohedral group and use that.
>>>>>> For special cases where you have deliberately created a superstructure
>>>>>> (e.g. for phonons) you want to remain in a low-symmetry group but in
>>>>>> general you should use all the available symmetry.
>>>>>>
>>>>>> b) I do not know how you are creating your structures, but you need
>>>>>> to be careful about the atomic positions unless you are deliberately
>>>>>> perturbing them. It appears that CaRuO3_SP came from Xcrygen, perhaps your
>>>>>> version is not that accurate. You have positions such as "Z=0.24999997"
>>>>>> which almost certainly should be 0.25, and axes of 90.000001 which I assume
>>>>>> should be 90.0. When I correct these sgroup converts it to Pnma which is
>>>>>> the known structure.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Sep 22, 2016 at 11:29 AM, Paresh Chandra Rout <
>>>>>> pareshchandra at iiserb.ac.in> wrote:
>>>>>>
>>>>>>> Hello Sir,
>>>>>>> Here I have attached my case.struct files.
>>>>>>>
>>>>>>> On Thu, Sep 22, 2016 at 8:57 PM, Paresh Chandra Rout <
>>>>>>> pareshchandra at iiserb.ac.in> wrote:
>>>>>>>
>>>>>>>> Yes . It was reproducible when I started runsp_lapw after rm
>>>>>>>> *.broy* . But to check for the actual error I had started from the
>>>>>>>> beginning again. Here, I faced the problem. These calculation were done
>>>>>>>> successfully before. Suddenly, I start facing the problem. I also
>>>>>>>> checked  case.clmvalup/dn but there is no NANs.  Also, I checked the
>>>>>>>> K-parallelisation in a single node  (If I understand it properly ) but
>>>>>>>> facing the same error.
>>>>>>>>
>>>>>>>> K-point parallelisation
>>>>>>>>  .machines file
>>>>>>>> #
>>>>>>>> granularity:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> 1:n66:1
>>>>>>>> extrafine:1
>>>>>>>>
>>>>>>>> Is this ok for k-point parallelisation.
>>>>>>>>
>>>>>>>> On Thu, Sep 22, 2016 at 7:42 PM, Peter Blaha <
>>>>>>>> pblaha at theochem.tuwien.ac.at> wrote:
>>>>>>>>
>>>>>>>>> It happened in cycle 2 or 3 for the 2 examples !
>>>>>>>>>
>>>>>>>>> Is this reproducible when you start another runsp_lapw after
>>>>>>>>>
>>>>>>>>> rm *.broy*
>>>>>>>>>
>>>>>>>>> -------------
>>>>>>>>>
>>>>>>>>> Is it reproducible when using only k-parallel setup, but no mpi ??
>>>>>>>>>
>>>>>>>>> ------------
>>>>>>>>>
>>>>>>>>> Examine case.clmvalup/dn if you see any   NANs in this file.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 09/22/2016 02:50 PM, Paresh Chandra Rout wrote:
>>>>>>>>>
>>>>>>>>>> Dear w2k users and developers,
>>>>>>>>>>
>>>>>>>>>> I am facing an error as follows
>>>>>>>>>>
>>>>>>>>>> error: command   WIEN2k_14.2_TGZ/mixer mixer.def   failed
>>>>>>>>>>
>>>>>>>>>>   stop error
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I did not encounter this error before. All my calculation was
>>>>>>>>>> running fine
>>>>>>>>>> with this version of wien2k . I tried to run single point
>>>>>>>>>> calculation on
>>>>>>>>>> three
>>>>>>>>>> different system, but in all cases I am getting the same error as
>>>>>>>>>> above
>>>>>>>>>> just after the scf cycle-3. I have attached my  case.dayfile for
>>>>>>>>>> different system. Any help to resolve this issue would be highly
>>>>>>>>>> appreciated .
>>>>>>>>>>
>>>>>>>>>> Kind Regards,
>>>>>>>>>> Paresh Chandra Rout
>>>>>>>>>> Research Scholar
>>>>>>>>>> Indian institute of Science Education and Research Bhopal
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Wien mailing list
>>>>>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
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>>>>>>>>>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>>>>>>>>>> en at zeus.theochem.tuwien.ac.at/index.html
>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=vULT25X71weKH68hPg-yj2au-8PWplKr9jBAztX_nKk&s=o3U_avGQyGQH3UYw-WVWoABuSzIzrRPlFwvOcjBuMfI&e=>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>>                                       P.Blaha
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> --------------
>>>>>>>>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>>>>>>>>> Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
>>>>>>>>> Email: blaha at theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.wien2k.at&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=vULT25X71weKH68hPg-yj2au-8PWplKr9jBAztX_nKk&s=oianLaIET4gOaPqUOlipK9qvogXj2lDdgo9ULWFLW7I&e=>
>>>>>>>>> WWW:   http://www.imc.tuwien.ac.at/TC_Blaha
>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imc.tuwien.ac.at_TC-5FBlaha&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=vULT25X71weKH68hPg-yj2au-8PWplKr9jBAztX_nKk&s=m3OSV5kmIkEc9rFkkC0Ip0vB-EesXVktYOykJvv8bh0&e=>
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> --------------
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Wien mailing list
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>>>>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=vULT25X71weKH68hPg-yj2au-8PWplKr9jBAztX_nKk&s=wEQNQEZ3v7KzFr2Qq3v_-whFFNA9BrToDqVZ11epN9o&e=>
>>>>>>>>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>>>>>>>>> en at zeus.theochem.tuwien.ac.at/index.html
>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=vULT25X71weKH68hPg-yj2au-8PWplKr9jBAztX_nKk&s=o3U_avGQyGQH3UYw-WVWoABuSzIzrRPlFwvOcjBuMfI&e=>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cfw.org_100-2Dpercent&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=kQcagraMLCrFdqjQVAzQvHFwtbxSaqaj8on6PLAY3dI&s=5Ab62Y0m_LFqX4CF2CZs2KR9UP40YtaHv2hR_oPDW8g&e=>
>>>>>> Co-Editor, Acta Cryst A
>>>>>>
>>>>>> _______________________________________________
>>>>>> Wien mailing list
>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=kQcagraMLCrFdqjQVAzQvHFwtbxSaqaj8on6PLAY3dI&s=URvSXO7ZFuoEZ34ms88qiSlYJ52UbmYWDgNYOy6x1HQ&e=>
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>>>>>>
>>>>>>
>>>>>
>>>>
>>> _______________________________________________
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>>>
>>>
>>
>
>
> --
> 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
>
> _______________________________________________
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