Re: [Wien] Query regarding wien2k_scratch directory

2024-04-26 Thread shamik chakrabarti 
In that case, after deleting the case directory, the space in hd of Linux
should be recovered. But the space is decreasing every time, I ran some
calculations and after copying delete the whole directory.

On Sat, 27 Apr 2024, 01:48 Tomas Kana,  wrote:

> The dot and slash ./ means your current directory
>
>
> Dear Sir,
>
>   After echo $SCRATCH the output is:   ./
>
>
> Any comments
>
>
>
> On Fri, 26 Apr 2024 at 22:14, Peter Blaha 
> wrote:
>
>
>
>
>
>
>
> During   userconfig  you have specified a SCRATCH directory. Only
>   you can know what you did there.
>
> PS:   echo $SCRATCH   will tell you, what you specified.
>
>
>
>
>
> Am 26.04.2024 um 13:30 schrieb shamik
>   chakrabarti:
>
>
>
>
>
>
> Dear Wien2k users,
>
>
>
>
>
>  After running calculations I am saving
>   the data in external hdd while deleting the same from linux.
>   However, at each time, after deleting data, I have found that
>   some amount of spaces are not recovered. Wien2k is saving some
>   files in Linux which I am not able to delete.
>
> My query is where are those extra files are stored? Whether
>   there is some directory called as _scratch but then I am not
>   able to find it either?
>
>
>
>
>
> Any response is eagerly awaited.
>
>
>
>
>
> with regards,
>
>
>
>
>
> --
>
>
>
>
>
>
>
>
>   Dr. Shamik
> Chakrabarti
>
>   Research Fellow
>
>   Department of Physics
>
>   Indian Institute of
> Technology Patna
>
>   Bihta-801103
>
>   Patna
>
>   Bihar, India
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>   ___
> Wien mailing list
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> 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
>
>
> --
> ---
> Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-158801165300
> Email: peter.bl...@tuwien.ac.at
> WWW:   http://www.imc.tuwien.ac.at  WIEN2k: http://www.wien2k.at
> -
>
>
>
> ___
>
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>
> SEARCH the MAILING-LIST at:
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>
>
>
>
>
>
>
>
> ___
>
> Wien mailing list
>
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>
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
> SEARCH the MAILING-LIST at:
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Re: [Wien] w2web xcrysden problem

2024-04-26 Thread Straus, Daniel B 
Hi Gavin,

I am using ver 23.2.

Modifying viewxcrys.pl in the way you suggested fixed the problem.

Thanks for the help.

Daniel Straus
Assistant Professor
Department of Chemistry
Tulane University
5088 Percival Stern Hall
6400 Freret Street
New Orleans, LA 70118
(504) 862-3585
http://straus.tulane.edu/


From: Gavin Abo 
Sent: Tuesday, April 23, 2024 10:34 PM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] w2web xcrysden problem


What WIEN2k version are you using?

Could you provide what XCRYSDEN_TOPDIR is?

It looks like the Perl code in WIEN2k 23.2 is implemented differently between 
that of "view structure" and that of the "Calculate density with XCrysDen" and 
"View density with XCrysDen" in w2web.

For "view structure", in SRC_w2web/htdocs/util/viewxcrys.pl, it looks like 
XCRYSDEN_TOPDIR runs through some regular expressions [1] before getting stored 
in the XCRYSDENDIR variable before it executes the XCrysDen command:

${XCRYSDENDIR}xcrysden --wien_struct $DIR

On the other hand, "Calculate density with XCrysDen" and "View density with 
XCrysDen" in SRC_w2web/htdocs/util/rhoxcrys.pl executes XCrysDen commands, 
respectively, as:

xcrysden --wien_density $DIR

xcrysden --wien_renderdensity $DIR

Since the above two calls work fine on your computer system, you could maybe 
find "${XCRYSDENDIR}xcrysden --wien_struct $DIR" in viewxcrys.pl and try 
removing the ${XCRYSDENDIR} to make the XCrysDen command similar:

xcrysden --wien_struct $DIR"

[1] https://en.wikipedia.org/wiki/Regular_expression
Kind Regards,
Gavin
WIEN2k user

On 4/23/2024 9:35 AM, Straus, Daniel B wrote:
I am having a problem where only some of the xcrysden functionality works in 
w2web.

Execution-->view structure does not work. The following message is printed:
View structure with XCrysDen
Requires X-Windows system ...

However, if I go to Tasks-->El. Dens. and click either the Calculate density 
with XCrysDen or View density with XCrysDen, xcrysden opens and works fine.

The XCRYSDEN_TOPDIR environment variable is set correctly.

Any suggestions?

Thank you!


Daniel Straus
Assistant Professor
Department of Chemistry
Tulane University
5088 Percival Stern Hall
6400 Freret Street
New Orleans, LA 70118
(504) 862-3585
http://straus.tulane.edu/
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Re: [Wien] SLURM cluster issues

2024-04-26 Thread Straus, Daniel B 
Hi Peter,

Thanks for the response. In case this is helpful to anyone in the future:

To get w2web working on the cluster and not get banned for accidentally running 
things on the login node, I modified the w2web source so it does not create a 
new configuration for every node by fixing the host name in the configuration 
part of the script. I then run w2web on a compute node using an interactive job 
with port forwarding enabled. This way, everything will either run on the 
compute node running w2web or it will get submitted as a batch job to the queue 
if I use a submission script.


Daniel Straus
Assistant Professor
Department of Chemistry
Tulane University
5088 Percival Stern Hall
6400 Freret Street
New Orleans, LA 70118
(504) 862-3585
http://straus.tulane.edu/


From: Peter Blaha 
Sent: Tuesday, April 16, 2024 1:58 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] SLURM cluster issues


Hi,


I am trying to set up WIEN2k ver 23.2 to run on a SLURM cluster. I have gotten 
it to work with SCALAPACK, runnning with a slurm batch submission script 
through w2web by following the examples.

I have two issues.

1.   Is it possible to make the “x dstart” button in the initialize web 
interface submit its job with a script like is possible for running SCF? Right 
now, it runs on the w2web node, and I can’t use a preexisting .machines file 
because all jobs are submitted through SLURM so the .machines needs to be 
generated on the fly.

If you really want to run this in parallel on a compute node (makes only sense 
for really big cases with 100 or more atoms/unit cell), you have to do it 
similar as with the scf calculation and execute it via a script.

A user could activate the   -nodstart   option in the initialization and run 
dstart as "single program" with the submission method.

1.

2.   I cannot seem to get ELPA to work. It compiles fine and passes the 
ELPA make check tests. However, when I try to run the TiC example in the 
usersguide, I always get an error. I have a feeling that ELPA is not using the 
correct kernel—is there a way to specify that though WIEN2k, or should I set a 
default ELPA kernel through ELPA ./configure?

Here is a link to a zip file with what I hope are the relevant files: 
https://tulane.box.com/s/ozohfwe0xyoipb8jzxeh3ec15imq1eam. My email got blocked 
when I attached them directly.


I guess the only problem is that the TiC case is too small to run in mpi 
parallel.

In WIEN2k one has to adapt the parallelization to the case one is studying.

The openMP parallelization (on one node) works always, but is efficient only up 
to 4 nodes. It should always be used.

The k-point parallelization is the second option, it is helpful if one has many 
k-points in the input and the lapw1 step takes more than eg. 20 seconds.

The last parllelization is via mpi using SCALAPACK and/or ELPA. The latter is 
much more efficient, but works only if the problem size (number of atoms ---> 
size of the eigenvalue problem) exceeds a few thousands. Even with such 
intermediate sizes (NMAT between 3000 -2) the number of cores should not be 
too large, otherwise communication wins and it takes longer than on fewer cores.

For really large problems (NMAT up to 10x10) many cores (eg. 512) can 
be used efficiently.



PS: I always compile ELPA without machine specific options and let it decide on 
runtime what is available on the specific hardware).



PPS: I'd also suggest to run the w2web interface ONLY on a local workstation 
and setting up a case there. Only after the initialization I'd migrate 
(migrate_lapw) this to a supercomputer and run the scf there.



Best regards

--

---

Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna

Phone: +43-158801165300

Email: peter.bl...@tuwien.ac.at

WWW:   http://www.imc.tuwien.ac.at  WIEN2k: http://www.wien2k.at

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Re: [Wien] Query regarding wien2k_scratch directory

2024-04-26 Thread Tomas Kana 
The dot and slash ./ means your current directory


Dear Sir,
 
  After echo $SCRATCH the output is:   ./


Any comments



On Fri, 26 Apr 2024 at 22:14, Peter Blaha  wrote:



  

  
  
During   userconfig  you have specified a SCRATCH directory. Only
  you can know what you did there.

PS:   echo $SCRATCH   will tell you, what you specified.





Am 26.04.2024 um 13:30 schrieb shamik
  chakrabarti:




  
  
Dear Wien2k users,





 After running calculations I am saving
  the data in external hdd while deleting the same from linux.
  However, at each time, after deleting data, I have found that
  some amount of spaces are not recovered. Wien2k is saving some
  files in Linux which I am not able to delete.

My query is where are those extra files are stored? Whether
  there is some directory called as _scratch but then I am not
  able to find it either?





Any response is eagerly awaited.





with regards,  





-- 


  

  

  

  Dr. Shamik
Chakrabarti

  Research Fellow 

  Department of Physics

  Indian Institute of
Technology Patna

  Bihta-801103

  Patna

  Bihar, India



  



  



  



  

  

  

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-- 
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email: peter.bl...@tuwien.ac.at  
WWW:   http://www.imc.tuwien.ac.at  WIEN2k: http://www.wien2k.at
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-- 
Dr. Shamik Chakrabarti
Research Fellow 
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India








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Re: [Wien] Query regarding wien2k_scratch directory

2024-04-26 Thread Peter Blaha 

Guess what  ./ means.

Wien2k stores files ONLY in your "case" directories.

Am 26.04.2024 um 20:05 schrieb shamik chakrabarti:

Dear Sir,
  After echo $SCRATCH the output is:   ./

Any comments

On Fri, 26 Apr 2024 at 22:14, Peter Blaha  
wrote:


During   userconfig  you have specified a SCRATCH directory. Only
you can know what you did there.

PS:   echo $SCRATCH   will tell you, what you specified.


Am 26.04.2024 um 13:30 schrieb shamik chakrabarti:

Dear Wien2k users,

 After running calculations I am saving the
data in external hdd while deleting the same from linux. However,
at each time, after deleting data, I have found that some amount
of spaces are not recovered. Wien2k is saving some files in Linux
which I am not able to delete.
My query is where are those extra files are stored? Whether there
is some directory called as _scratch but then I am not able to
find it either?

Any response is eagerly awaited.

with regards,

-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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at:http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html


-- 
---

Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

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--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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--
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

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Re: [Wien] Query regarding wien2k_scratch directory

2024-04-26 Thread shamik chakrabarti 
Dear Sir,

  After echo $SCRATCH the output is:   ./

Any comments

On Fri, 26 Apr 2024 at 22:14, Peter Blaha  wrote:

> During   userconfig  you have specified a SCRATCH directory. Only you can
> know what you did there.
>
> PS:   echo $SCRATCH   will tell you, what you specified.
>
>
> Am 26.04.2024 um 13:30 schrieb shamik chakrabarti:
>
> Dear Wien2k users,
>
>  After running calculations I am saving the data in
> external hdd while deleting the same from linux. However, at each time,
> after deleting data, I have found that some amount of spaces are not
> recovered. Wien2k is saving some files in Linux which I am not able to
> delete.
> My query is where are those extra files are stored? Whether there is some
> directory called as _scratch but then I am not able to find it either?
>
> Any response is eagerly awaited.
>
> with regards,
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>
> ___
> Wien mailing 
> listw...@zeus.theochem.tuwien.ac.athttp://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
>
> --
> ---
> Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-158801165300
> Email: peter.bl...@tuwien.ac.at
> WWW:   http://www.imc.tuwien.ac.at  WIEN2k: http://www.wien2k.at
> -
>
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>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Query regarding wien2k_scratch directory

2024-04-26 Thread Peter Blaha 
During   userconfig  you have specified a SCRATCH directory. Only you 
can know what you did there.


PS:   echo $SCRATCH   will tell you, what you specified.


Am 26.04.2024 um 13:30 schrieb shamik chakrabarti:

Dear Wien2k users,

 After running calculations I am saving the data 
in external hdd while deleting the same from linux. However, at each 
time, after deleting data, I have found that some amount of spaces are 
not recovered. Wien2k is saving some files in Linux which I am not 
able to delete.
My query is where are those extra files are stored? Whether there is 
some directory called as _scratch but then I am not able to find it 
either?


Any response is eagerly awaited.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

___
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at:http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html


--
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

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[Wien] Query regarding wien2k_scratch directory

2024-04-26 Thread shamik chakrabarti 
Dear Wien2k users,

 After running calculations I am saving the data in
external hdd while deleting the same from linux. However, at each time,
after deleting data, I have found that some amount of spaces are not
recovered. Wien2k is saving some files in Linux which I am not able to
delete.
My query is where are those extra files are stored? Whether there is some
directory called as _scratch but then I am not able to find it either?

Any response is eagerly awaited.

with regards,

-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
___
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