Re: [Wien] Few questions about initialization

[Dr. K. C. Bhamu]

Hii Dr. Tran,

I am making some automatic scripts. So for the next calculations I want to
grep -ecut (energy required to separate out core and valence states).
I have a work around (print -ecut in some file and then read from that file
for further calculations).

Regards
Bhamu

On Tue, Jun 4, 2019, 1:36 AM  wrote:

> Hi,
>
> It's not possible to use gmax in batch mode with WIEN2k version 18.
> It will be possible with version 19.
>
> Which ecut?
>
> FT
>
> On Monday 2019-06-03 20:23, Dr. K. C. Bhamu wrote:
>
> >Date: Mon, 3 Jun 2019 20:23:31
> >From: Dr. K. C. Bhamu 
> >Reply-To: A Mailing list for WIEN2k users <
> wien@zeus.theochem.tuwien.ac.at>
> >To: A Mailing list for WIEN2k users 
> >Subject: [Wien] Few questions about initialization
> >
> >Dear Wien2k Experts,
> >I have some queries about initialization
> >
> >1. how to use gmax in batch mode ?
> >2. How to grep ecut ?
> >
> >3. This may be not for Wien2k related issue but  any experienced use may
> help or it may be related with Wien2k.
> >
> >When my the  PC is working for last few days and I want to do
> initialization then I face segmentation fault error (see below) and if I
> restart the PC,
> >everything goes well. Is there any workaround so that I do not need to
> restart the PC all the time?
> >
> > next is kgen
> >Segmentation fault
> > n stop error n
> >
> > So this is particular when kgen starts it means "x kgen" does not work.
> >x(_lapw) kgen gives
> >
> >Segmentation fault
> >0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
> >error: command   /home/kcbhamu/WIEN2k_18.2/kgen kgen.def   failed
> >I do not see that this is related to "x" as I faced the issue where my
> "x" was from some other Linux code.
> >
> >
> >Regards
> >Bhamu
> >
> >___
> 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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Re: [Wien] Regarding Band structure error

[Gavin Abo]

That in1c error should be due to a previously reported bug in version 
17.1 [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17353.html 
].  Since using the fixed band.pl and scf.pl files in the mailing list 
archive will not fix all the other problems with 17.1, I recommend that 
you use WIEN2k 18.2 as it has all the fixes and improvements mentioned 
on the WIEN2k updates webpage [ 
http://susi.theochem.tuwien.ac.at/reg_user/updates/ ].  You will also 
want to patch 18.2 based on past mailing list archive posts.  Some of 
them I have compiled in a README file at:


https://github.com/gsabo/WIEN2k-Patches/tree/master/18.2

On 6/3/2019 6:51 AM, Arvind Kumar wrote:

Dear Sir,
   I am running Wien2K 17.1 in my laptop (configured with 
ubuntu 18.4 with RAM 16GB). I am facing following error in band 
structure with all the compounds.

Commandline:*x lapw1 -band *

Program input is:*""*

forrtl: severe (24): end-of-file during read, unit 5, file 
/home/arvind/arvind.in1c
Image  PCRoutineLineSource
lapw1c 0046C05E  Unknown   Unknown  Unknown
lapw1c 0049F585  Unknown   Unknown  Unknown
lapw1c 00442690  parallel_mp_init_  75  
modules_tmp_.F
lapw1c 00416972  gtfnam_89  
gtfnam_tmp_.F
lapw1c 004331E9  MAIN__ 35  lapw1_tmp_.F
lapw1c 0040457E  Unknown   Unknown  Unknown
libc-2.27.so  14DD2EDC0B97  __libc_start_main  
   Unknown  Unknown
lapw1c 0040446A  Unknown   Unknown  Unknown
0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /home/arvind/Wien2K/lapw1c lapw1.def   failed


Please suggest me accordingly.

with regards,
Dr. Arvind Kumar
Assistant Professor
Department of Physics
Atma Ram Sanatan Dharma College
(University of Delhi)
Dhaula Kuan, New Delhi-110021
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Re: [Wien] Few questions about initialization

[tran]

Hi,

It's not possible to use gmax in batch mode with WIEN2k version 18.
It will be possible with version 19.

Which ecut?

FT

On Monday 2019-06-03 20:23, Dr. K. C. Bhamu wrote:


Date: Mon, 3 Jun 2019 20:23:31
From: Dr. K. C. Bhamu 
Reply-To: A Mailing list for WIEN2k users 
To: A Mailing list for WIEN2k users 
Subject: [Wien] Few questions about initialization

Dear Wien2k Experts,
I have some queries about initialization

1. how to use gmax in batch mode ?
2. How to grep ecut ?

3. This may be not for Wien2k related issue but  any experienced use may help 
or it may be related with Wien2k.

When my the  PC is working for last few days and I want to do initialization 
then I face segmentation fault error (see below) and if I restart the PC,
everything goes well. Is there any workaround so that I do not need to restart 
the PC all the time?

 next is kgen
Segmentation fault
 n stop error n

 So this is particular when kgen starts it means "x kgen" does not work.
x(_lapw) kgen gives

Segmentation fault
0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /home/kcbhamu/WIEN2k_18.2/kgen kgen.def   failed
I do not see that this is related to "x" as I faced the issue where my "x" was 
from some other Linux code.


Regards
Bhamu

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[Wien] Few questions about initialization

[Dr. K. C. Bhamu]

Dear Wien2k Experts,
I have some queries about initialization

1. how to use gmax in batch mode ?
2. How to grep ecut ?

3. This may be not for Wien2k related issue but  any experienced use may
help or it may be related with Wien2k.

When my the  PC is working for last few days and I want to do
initialization then I face segmentation fault error (see below) and if I
restart the PC, everything goes well. Is there any workaround so that I do
not need to restart the PC all the time?

 next is kgen
Segmentation fault
 n stop error n

 So this is particular when kgen starts it means "x kgen" does not work.
x(_lapw) kgen gives

Segmentation fault
0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /home/kcbhamu/WIEN2k_18.2/kgen kgen.def   failed
I do not see that this is related to "x" as I faced the issue where my "x"
was from some other Linux code.


Regards
Bhamu
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[Wien] Regarding Band structure error

[Arvind Kumar]

Dear Sir,
   I am running Wien2K 17.1 in my laptop (configured with ubuntu
18.4 with RAM 16GB). I am facing following error in band structure with all
the compounds.

Commandline: *x lapw1 -band *

Program input is: *""*

forrtl: severe (24): end-of-file during read, unit 5, file
/home/arvind/arvind.in1c
Image  PCRoutineLine
Source
lapw1c 0046C05E  Unknown   Unknown  Unknown
lapw1c 0049F585  Unknown   Unknown  Unknown
lapw1c 00442690  parallel_mp_init_  75
modules_tmp_.F
lapw1c 00416972  gtfnam_89
gtfnam_tmp_.F
lapw1c 004331E9  MAIN__ 35  lapw1_tmp_.F
lapw1c 0040457E  Unknown   Unknown
Unknownlibc-2.27.so   14DD2EDC0B97  __libc_start_main
Unknown  Unknown
lapw1c 0040446A  Unknown   Unknown  Unknown
0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /home/arvind/Wien2K/lapw1c lapw1.def   failed



Please suggest me accordingly.

with regards,
Dr. Arvind Kumar
Assistant Professor
Department of Physics
Atma Ram Sanatan Dharma College
(University of Delhi)
Dhaula Kuan, New Delhi-110021
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Re: [Wien] Can someone share the MPI parallel script using on LSF job management system with me ?

[Gavin Abo]

Yes, for both k-point parallel and mpi parallel you need "-p".

Do not use "mpirun run_lapw ." in your job script.?0?2 Use "run_lapw -p 
." which will itself run the "mpirun" or another mpi launcher that 
you have set in siteconfig.


For mpi parallel [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00985.html 
, http://www.wien2k.at/reg_user/faq/ecss_hliu_051012.pdf (slide 7)], you 
need to change your job script to output for example:


granularity:1
lapw0:c021:28
1:c021:28
extrafine:1

You might try the LSF job script or program your script based on the 
script in the post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01612.html


On 6/3/2019 2:45 AM, ?? wrote:

Dear wien2k experts,

I am using version 18.2 of wien2k on computer cluster of our group 
(LSF job?0?2management), the installation of wien2k is OK (including 
the?0?2fine grained parallelization) because of no error message in 
compile.msg. Now, I can run K-point parallel, I am lack of 
the?0?2knowledge about shell and?0?2the script is asking from good-hearted 
person.


The "on the fly" .machines file is generated by the following in the 
script:


#make .machines file

echo'granularity:1'>.machines

echo"lapw0:"`echo$LSB_HOSTS|cut -d""-f1`>>.machines

fori in`echo$LSB_HOSTS`

do

echo"1:"$i>>.machines

done

echo'extrafine:1'>>.machines


As a?0?2example, if I use one node (28 core),?0?2the .machines file is 
as?0?2following:



granularity:1

lapw0:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

1:c021

extrafine:1


The K-point parallel is OK.


Now I have to use the MPI parallel, I can not find the?0?2corresponding 
script using on LSF?0?2job?0?2management system. After reading?0?2the 
5.5?0?2chapter of UG several times and?0?2the GAQ page 
(http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html), I was 
really confused. I don't?0?2know what the content should be in 
.machines?0?2files, not to mention the script. Unluckily, I get no help 
from the cluster engineer.



Does the command "mpirun run_lapw ." ?0?2launch the job? 
?0?2Should?0?2the?0?2"-p" option be used ?



I believe that there is no big?0?2differences on same job?0?2management 
system. I?0?2can't?0?2find the?0?2script using on LSF?0?2job?0?2management system?0?2in 
mail-listing and I know that prof.?0?2Peter Blaha is bored with similar 
questions.



Here, I just want someone can share MPI parallel?0?2script 
on?0?2LSF?0?2job?0?2management system with me, I highly?0?2appreciated that.



Looking forward to your reply.


regards,

Min Lin,
phd student in China, Xiamen university, department of chemistry.
E-mail address: 2236673...@qq.com
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[Wien] Can someone share the MPI parallel script using on LSF job management system with me ?

[??????]

Dear wien2k experts,


I am using version 18.2 of wien2k on computer cluster of our group (LSF job 
management), the installation of wien2k is OK (including the fine grained 
parallelization) because of no error message in compile.msg. Now, I can run 
K-point parallel, I am lack of the knowledge about shell and the script is 
asking from good-hearted person.


The "on the fly" .machines file is generated by the following in the script:



#make .machines file
 
echo 'granularity:1' >.machines
 
echo "lapw0:"`echo $LSB_HOSTS |cut -d" " -f1` >> .machines
 
for i in `echo $LSB_HOSTS`
 
do
 
 echo "1:"$i >> .machines
 
done
 
echo 'extrafine:1' >>.machines




As a example, if I use one node (28 core), the .machines file is as following:




granularity:1
 
lapw0:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
1:c021
 
extrafine:1




The K-point parallel is OK.




Now I have to use the MPI parallel, I can not find the corresponding script 
using on LSF job management system. After reading the 5.5 chapter of UG several 
times and the GAQ page 
(http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html), I was really 
confused. I don't know what the content should be in .machines files, not to 
mention the script. Unluckily, I get no help from the cluster engineer.




Does the command "mpirun run_lapw ."  launch the job?  Should the "-p" 
option be used ?




I believe that there is no big differences on same job management system. I 
can't find the script using on LSF job management system in mail-listing and I 
know that prof. Peter Blaha is bored with similar questions.




Here, I just want someone can share MPI parallel script on LSF job management 
system with me, I highly appreciated that. 




Looking forward to your reply.



regards,


Min Lin, 
phd student in China, Xiamen university, department of chemistry.
E-mail address: 2236673...@qq.com___
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