Re: [Wien] SOC DOS Error

[Paresh Chandra Rout]

Thank you sir. I have not followed that step. I will do it and write you
back .

On Tue, Sep 29, 2015 at 12:00 PM, Peter Blaha 
wrote:

> After lapw1  and BEFORE lapw2 you need:
>
> x lapwso -up -p
>
> On 09/29/2015 06:30 AM, Paresh Chandra Rout wrote:
>
>> First of all thank you very much sir for replying me  . I have run lapw1
>> -up -p and  lapw1 -dn -p before entering into the lapw2  as you per your
>> suggestion in archive. Still I am facing the same problem . But I would
>> like to let you know that
>> I have run x *lapw1 -up -p *and**x*lapw1 -dn -p *through job script
>> first then enter into the lapw2 .
>> Kindly help me sir.
>>
>> Kind regards
>> Paresh
>>
>> On Tue, Sep 29, 2015 at 4:24 AM, Gavin Abo > > wrote:
>>
>> Did you run the lapw1 steps before that [
>>
>> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11340.html
>> ]?
>>
>>
>> On 9/28/2015 8:01 AM, Paresh Chandra Rout wrote:
>>
>>> Dear all,
>>> While doing *DOS* calculation in *spin-orbit  coupling *case, I
>>> encounter with an error with message
>>> running LAPW2 in parallel mode
>>> *calculating QTL's from parallel vectors*
>>> *FERMI - Error*
>>> 0.201u 0.051s 0:00.39 64.1%0+0k 0+8io 0pf+0w
>>>
>>> I ran all the command prompt  systematically but for
>>> *x lapw2 -p -up -so -qtl * case I am face the above error.
>>>
>>>
>>> Is there any mistake that I am making or am I missing something ?
>>> Kindly give me some suggestion .
>>>
>>> Thanking you in advance !
>>>
>>> Kind Regards
>>> Paresh Chandra Rout
>>> Research Scholar
>>> Indian Institute of Science Education and Reseach Bhopal
>>>
>>
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>>
>>
>>
>>
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>>
> --
>
>   P.Blaha
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
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Re: [Wien] time difference among nodes

[Elias Assmann]

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On 09/28/2015 01:58 PM, Luis Ogando wrote:
> The problem is solved ! The solution was one suggested by Lyudmila 
> Dobysheva : reboot the nodes. We will never know the origin of the 
> problem, but, honestly, I do not care !

Good to hear that!  So, how did you get the admins to reboot them?

> "There are more things in heaven and earth, Horatio, Than are
> dreamt of in your philosophy."

That is an apt quote for people working on clusters ;-).


Elias

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Re: [Wien] afm calculation - error in LAPW1 - during SCF cycle of AFM Calculation

[Lyudmila Dobysheva]

28.09.2015 19:45, Krishnaveni. S wrote:

Error in LAPW1
  'SELECT' - no energy limits found for atom   1  L= 1
  'SELECT' - E-bottom   -5.18127   E-top -200.0
  Can some one suggest what I should be doing in this case please?


You should make a search in the mailing archive of WIEN2k with the key 
words: 'SELECT' - no energy limits found for atom;

carefully read the discussions;
try to solve your problem yourself;
if you fail - write a letter with much more information. Attentive 
reading the discussions will suggest you which information is necessary 
for solving the problem.


Best wishes
  Lyudmila Dobysheva
--
Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
426001 Izhevsk, ul.Kirova 132
RUSSIA
--
Tel.:7(3412) 432045(office), 722529(Fax)
E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office)
lyuk...@gmail.com (home)
Skype:  lyuka17 (home), lyuka18 (office)
http://ftiudm.ru/content/view/25/103/lang,english/
--
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Re: [Wien] time difference among nodes

[Luis Ogando]

Hi Lyudmila,

   Thanks again !
   I will ask them.
   All the best,
  Luis


2015-09-29 10:37 GMT-03:00 Lyudmila Dobysheva :

> 29.09.2015 14:57, Laurence Marks wrote:
>
>> If it happens again, one thing to ask them to check is swap usage and
>> how much memory is cached.
>>
> ...
>
>> Alternatively it was something else, a zombie, big log files or other
>> things. Rebooting gets rid of a lot of system caches and helps
>>
>
> I stand for losing parallelization on that node due to unclear reason
> (maybe this bad swapping/caching threw away parallel options from the
> memory and all jobs had been sent to only one processor of the node).
>
> I would like to know what had administrator seen in the "1" mode of top
> command.
>
> Best wishes
>   Lyudmila Dobysheva
> --
> Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
> 426001 Izhevsk, ul.Kirova 132
> RUSSIA
> --
> Tel.:7(3412) 432045(office), 722529(Fax)
> E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office)
> lyuk...@gmail.com (home)
> Skype:  lyuka17 (home), lyuka18 (office)
> http://ftiudm.ru/content/view/25/103/lang,english/
> --
> ___
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Re: [Wien] SOC DOS Error

[Peter Blaha]

After lapw1  and BEFORE lapw2 you need:

x lapwso -up -p

On 09/29/2015 06:30 AM, Paresh Chandra Rout wrote:

First of all thank you very much sir for replying me  . I have run lapw1
-up -p and  lapw1 -dn -p before entering into the lapw2  as you per your
suggestion in archive. Still I am facing the same problem . But I would
like to let you know that
I have run x *lapw1 -up -p *and**x*lapw1 -dn -p *through job script
first then enter into the lapw2 .
Kindly help me sir.

Kind regards
Paresh

On Tue, Sep 29, 2015 at 4:24 AM, Gavin Abo > wrote:

Did you run the lapw1 steps before that [
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11340.html
]?


On 9/28/2015 8:01 AM, Paresh Chandra Rout wrote:

Dear all,
While doing *DOS* calculation in *spin-orbit  coupling *case, I
encounter with an error with message
running LAPW2 in parallel mode
*calculating QTL's from parallel vectors*
*FERMI - Error*
0.201u 0.051s 0:00.39 64.1%0+0k 0+8io 0pf+0w

I ran all the command prompt  systematically but for
*x lapw2 -p -up -so -qtl * case I am face the above error.


Is there any mistake that I am making or am I missing something ?
Kindly give me some suggestion .

Thanking you in advance !

Kind Regards
Paresh Chandra Rout
Research Scholar
Indian Institute of Science Education and Reseach Bhopal


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--

  P.Blaha
--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] time difference among nodes

[Lyudmila Dobysheva]

29.09.2015 14:57, Laurence Marks wrote:

If it happens again, one thing to ask them to check is swap usage and
how much memory is cached.

...

Alternatively it was something else, a zombie, big log files or other
things. Rebooting gets rid of a lot of system caches and helps


I stand for losing parallelization on that node due to unclear reason 
(maybe this bad swapping/caching threw away parallel options from the 
memory and all jobs had been sent to only one processor of the node).


I would like to know what had administrator seen in the "1" mode of top 
command.


Best wishes
  Lyudmila Dobysheva
--
Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
426001 Izhevsk, ul.Kirova 132
RUSSIA
--
Tel.:7(3412) 432045(office), 722529(Fax)
E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office)
lyuk...@gmail.com (home)
Skype:  lyuka17 (home), lyuka18 (office)
http://ftiudm.ru/content/view/25/103/lang,english/
--
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Re: [Wien] Im_eps

[Peter Blaha]

Broadening.

On 09/29/2015 12:12 PM, emami seyyed amir abbas wrote:

ِDear users

I am trying to obtain imaginary and real part of Dielectric function. As
i know these information can be find in case.joint and case.epsilon but
the  Im_eps_xx which is in both file have a different value. What is the
reason of this discrepancy?

Regards


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--

  P.Blaha
--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] time difference among nodes

[Gavin Abo]

From the top's sent before, it looks like the administrators might have 
configured the system with no swap:


r1i1n2

Swap:0M total,0M used,0M free,10563M cached

r1i1n3

Swap:0M total,0M used,0M free,23089M cached

Keep in mind that having swap might mean the difference between hurt 
performance and a hard crash under low memory [ 
http://unix.stackexchange.com/questions/190398/do-i-need-swap-space-if-i-have-more-than-enough-amount-of-ram 
].


On 9/29/2015 5:57 AM, Laurence Marks wrote:


If it happens again, one thing to ask them to check is swap usage and 
how much memory is cached. On some of my nodes I have noticed that 
they do not always release cached memory, and can start swapping. If 
this happens the job will get very slow. The commands to use to clear 
the cache can be found at
http://www.tecmint.com/clear-ram-memory-cache-buffer-and-swap-space-on-linux/ 
or similar. (Needs root access.) Top can also show memory use.


While there should be no need to do this, I have noticed that I need 
to do it every 3hrs on 4 nodes - the other 20 don't need it. It is an 
issue mainly for big calculations.


Alternatively it was something else, a zombie, big log files or other 
things. Rebooting gets rid of a lot of system caches and helps -- even 
on my Android tablet every week or two. It's murky waters.


---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
http://www.numis.northwestern.edu
Corrosion in 4Dhttp://MURI4D.numis.northwestern.edu 


Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what 
nobody else has thought"

Albert Szent-Gyorgi

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[Wien] Need your attention please

[sikander Azam]

Resp. All
I am a bit confused with some logic, please clear me on the following
questions

   1. what are the strengths and weaknesses of the DFT in contrast to the
   more traditional wave function approach
   2. What are the properties of this “gas” I mean the “homogeneous
   electron gas” which is used as a model to obtain the LDA
   exchange-correlation energy? It is the same electron gas as used, say, in
   Drude- Sommerfeld model?


Regards
Sikander
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Re: [Wien] Can we perform layered AFM calculations with Wien2k?

[pieper]

Hello Krishnaveni Parthasarathy

Yes you can - though admittedly I did not look up your reference, and I 
might misinterprete your idea of 'layered AFM'. And I suppose you 
consider collinear magnetic moments. If that is not the case you might 
look into the (unsupported) WienNCM.


In general, study the UG, especially the chapters on AFM calculations.

You can think of any collinear AFM as ferromagnetic layers stacked along 
one particular crystalographic direction, the direction to the nearest 
antiparallel neighbor. For calculations with Wien2k you need a .strcut 
with a unit cell that has at least two magnetic atoms along that 
direction (perhaps from supercell if the crystalografic primitve cell is 
not large enough).


Since you want them to be magnetically inequivalent the two have to be 
on inequievalent crystalografic sites. If they are on crystalografic 
equivalent positions you have to split the position and number the atoms 
to tell Wien2k that they are not same (perhaps Mn1 and Mn2). Note that 
this results in a different symmetry of your structure.


If you want to compare total energies for different magnetic structures 
be careful to calculate all of them on the same crystalographic unit 
cell, changing only in the initialization which magnetic atom belongs to 
the group pointing 'up' and which one to the group pointing 'down'. If 
you have, for example, constructed a supercell with four inequivalent 
Mn-sites Mn1 .. Mn4, you can calculate AFM structures corresponding to 
Mn1, Mn2 up and Mn3, Mn4 down, or Mn1,3 up and Mn2,4 down, or ... This 
will correspond to ferromagnetic layers of Mn1, Mn2 stacked with 
antiparallel ferromagnetic layers Mn3,4, or ferromagnetic layers of 
Mn1,3 ... Not all of these arrangements are necessarily different. If 
the direction Mn1 - Mn2 is symmetry related to the one Mn1-Mn3 in the 
underlying crystalografic lattice, then there is no need to calculate 
with the stacking in these two equivalent directions. And obviously, for 
a complicated AF wave vector (the direction of the stacking), you will 
need large supercells so think, before you start.


Good luck,

Martin Pieper


---
Dr. Martin Pieper
Karl-Franzens University
Institute of Physics
Universitätsplatz 5
A-8010 Graz
Austria
Tel.: +43-(0)316-380-8564


Am 28.09.2015 18:43, schrieb Krishnaveni. S:

Ref: Electronic Structure, Chemical Bonding, and Finite-Temperature
Magnetic Properties of Full Heusler Alloys

Authors: YASEMIN KURTULUS, MICHAEL GILLEßEN, RICHARD DRONSKOWSKI*

DOI 10.1002/jcc.20308

online in Wiley InterScience (www.interscience.wiley.com [1]).

Ref to the article (Page 93) mentioned above, I understand that one
can perform layered calculation in AFM calculations.

In page 93, the authors have mentioned as below: “Here, the symmetry
has been slightly reduced to obtain a model in which the Mn planes can
be treated separately. This particular alignment is characterized by
alternating planes along (001) of spin-up and spin-down manganese
moments, and the identically oriented manganese moments within each
plane are coupled by the p orbitals of the Z elements. An alternative
anti ferromagnetic model with alternating magnetic planes along (111)
is also thinkable, but earlier total-energycalculations11 have already
clarified that the (001) model is characterized by lower energies in
almost all cases.”

 The author has specified that these calculations have been done in
VASP. Can some one help me understand if it is possible to perform
similar type of calculations in Wien2k?

--

Thanks and regards

Krishnaveni Parthasarathy
8939675012

Links:
--
[1] http://www.interscience.wiley.com

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Re: [Wien] time difference among nodes

[Luis Ogando]

Hi Lyudmila,

   Unfortunately, they do not have "top mode 1" output corresponding to the
problem period.
   Thanks again.
   All the best,
 Luis


2015-09-29 10:37 GMT-03:00 Lyudmila Dobysheva :

> 29.09.2015 14:57, Laurence Marks wrote:
>
>> If it happens again, one thing to ask them to check is swap usage and
>> how much memory is cached.
>>
> ...
>
>> Alternatively it was something else, a zombie, big log files or other
>> things. Rebooting gets rid of a lot of system caches and helps
>>
>
> I stand for losing parallelization on that node due to unclear reason
> (maybe this bad swapping/caching threw away parallel options from the
> memory and all jobs had been sent to only one processor of the node).
>
> I would like to know what had administrator seen in the "1" mode of top
> command.
>
> Best wishes
>   Lyudmila Dobysheva
> --
> Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
> 426001 Izhevsk, ul.Kirova 132
> RUSSIA
> --
> Tel.:7(3412) 432045(office), 722529(Fax)
> E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office)
> lyuk...@gmail.com (home)
> Skype:  lyuka17 (home), lyuka18 (office)
> http://ftiudm.ru/content/view/25/103/lang,english/
> --
> ___
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> 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
>
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Re: [Wien] time difference among nodes

[Luis Ogando]

Dear Prof. Marks,

   Thanks !
   I will send your message to the administrators !
   All the best,
   Luis


2015-09-29 8:57 GMT-03:00 Laurence Marks :

> If it happens again, one thing to ask them to check is swap usage and how
> much memory is cached. On some of my nodes I have noticed that they do not
> always release cached memory, and can start swapping. If this happens the
> job will get very slow. The commands to use to clear the cache can be found
> at
>
> http://www.tecmint.com/clear-ram-memory-cache-buffer-and-swap-space-on-linux/
> or similar. (Needs root access.) Top can also show memory use.
>
> While there should be no need to do this, I have noticed that I need to do
> it every 3hrs on 4 nodes - the other 20 don't need it. It is an issue
> mainly for big calculations.
>
> Alternatively it was something else, a zombie, big log files or other
> things. Rebooting gets rid of a lot of system caches and helps -- even on
> my Android tablet every week or two. It's murky waters.
>
> ---
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> http://www.numis.northwestern.edu
> Corrosion in 4D http://MURI4D.numis.northwestern.edu
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought"
> Albert Szent-Gyorgi
> Hi Elias,
>
>There were no other jobs in the specific queue I was using and the
> nodes are dedicated to that queue, so, it was the opportunity to reboot
> them without furious reactions from other users.
>After trying everything suggested by the Wien2k community, the
> administrators resignedly remembered the words of wisdom given by the
> cluster guru, Shakespeare, and followed the suggestion given by Lyudmila
> Dobysheva. In other words, they killed my job, restarted all the nodes and
> I resubmitted the calculation
>All the best,
>  Luis
>
>
> 2015-09-29 3:50 GMT-03:00 Elias Assmann :
>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> On 09/28/2015 01:58 PM, Luis Ogando wrote:
>> > The problem is solved ! The solution was one suggested by Lyudmila
>> > Dobysheva : reboot the nodes. We will never know the origin of the
>> > problem, but, honestly, I do not care !
>>
>> Good to hear that!  So, how did you get the admins to reboot them?
>>
>> > "There are more things in heaven and earth, Horatio, Than are
>> > dreamt of in your philosophy."
>>
>> That is an apt quote for people working on clusters ;-).
>>
>>
>> Elias
>>
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v1
>> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>>
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>> QDT7WZ/DqG+KpcVTRmnz
>> =JtdF
>> -END PGP SIGNATURE-
>> ___
>> 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
>>
>
>
> ___
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> SEARCH the MAILING-LIST at:
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Re: [Wien] time difference among nodes

[Luis Ogando]

Hi Elias,

   There were no other jobs in the specific queue I was using and the nodes
are dedicated to that queue, so, it was the opportunity to reboot them
without furious reactions from other users.
   After trying everything suggested by the Wien2k community, the
administrators resignedly remembered the words of wisdom given by the
cluster guru, Shakespeare, and followed the suggestion given by Lyudmila
Dobysheva. In other words, they killed my job, restarted all the nodes and
I resubmitted the calculation
   All the best,
 Luis


2015-09-29 3:50 GMT-03:00 Elias Assmann :

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> On 09/28/2015 01:58 PM, Luis Ogando wrote:
> > The problem is solved ! The solution was one suggested by Lyudmila
> > Dobysheva : reboot the nodes. We will never know the origin of the
> > problem, but, honestly, I do not care !
>
> Good to hear that!  So, how did you get the admins to reboot them?
>
> > "There are more things in heaven and earth, Horatio, Than are
> > dreamt of in your philosophy."
>
> That is an apt quote for people working on clusters ;-).
>
>
> Elias
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1
> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>
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> QDT7WZ/DqG+KpcVTRmnz
> =JtdF
> -END PGP SIGNATURE-
> ___
> 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
>
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[Wien] Im_eps

[emami seyyed amir abbas]

ِDear users 

I am trying to obtain imaginary and real part of Dielectric function. As i know 
these information can be find in case.joint and case.epsilon but the  Im_eps_xx 
which is in both file have a different value. What is the reason of this 
discrepancy?

Regards
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Re: [Wien] time difference among nodes

[Laurence Marks]

If it happens again, one thing to ask them to check is swap usage and how
much memory is cached. On some of my nodes I have noticed that they do not
always release cached memory, and can start swapping. If this happens the
job will get very slow. The commands to use to clear the cache can be found
at
http://www.tecmint.com/clear-ram-memory-cache-buffer-and-swap-space-on-linux/
or similar. (Needs root access.) Top can also show memory use.

While there should be no need to do this, I have noticed that I need to do
it every 3hrs on 4 nodes - the other 20 don't need it. It is an issue
mainly for big calculations.

Alternatively it was something else, a zombie, big log files or other
things. Rebooting gets rid of a lot of system caches and helps -- even on
my Android tablet every week or two. It's murky waters.

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
Hi Elias,

   There were no other jobs in the specific queue I was using and the nodes
are dedicated to that queue, so, it was the opportunity to reboot them
without furious reactions from other users.
   After trying everything suggested by the Wien2k community, the
administrators resignedly remembered the words of wisdom given by the
cluster guru, Shakespeare, and followed the suggestion given by Lyudmila
Dobysheva. In other words, they killed my job, restarted all the nodes and
I resubmitted the calculation
   All the best,
 Luis


2015-09-29 3:50 GMT-03:00 Elias Assmann :

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> On 09/28/2015 01:58 PM, Luis Ogando wrote:
> > The problem is solved ! The solution was one suggested by Lyudmila
> > Dobysheva : reboot the nodes. We will never know the origin of the
> > problem, but, honestly, I do not care !
>
> Good to hear that!  So, how did you get the admins to reboot them?
>
> > "There are more things in heaven and earth, Horatio, Than are
> > dreamt of in your philosophy."
>
> That is an apt quote for people working on clusters ;-).
>
>
> Elias
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1
> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>
> iQIcBAEBAgAGBQJWCjTGAAoJEE/4gtQZfOqPhFAQAKZmda0t9FGgfAsk9UjymogK
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> QDT7WZ/DqG+KpcVTRmnz
> =JtdF
> -END PGP SIGNATURE-
> ___
> 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
>
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