[Wien] lapwsopara error

Md. Fhokrul Islam fislam at hotmail.com
Tue Mar 7 13:39:06 CET 2017


Thanks, Gerhard. I actually read about the bus error but I was confused because

different reasons are suggested including error in executable. But I sent a

message to our cluster administrator to check if the error is related to hardware.



Regards,

Fhokrul



________________________________
From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Fecher, Gerhard <fecher at uni-mainz.de>
Sent: Tuesday, March 7, 2017 11:28 AM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] lapwsopara error

maybe this helps

from Wikipedia
In computing, a bus error is a fault raised by hardware, notifying an operating system (OS) that a process is trying to access memory that the CPU cannot physically address: an invalid address for the address bus, hence the name. In modern use on most architectures these are much rarer than segmentation faults, which occur primarily due to memory access violations: problems in the logical address or permissions.

more is found from google

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."

====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden
________________________________________
Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von Md. Fhokrul Islam [fislam at hotmail.com]
Gesendet: Dienstag, 7. März 2017 12:21
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] lapwsopara error

Hi Gavin,


You are right, there are .timeso files (but no .stdoutso) for each k-point and the ones that fail to complete

have an error message:


-cn0130 Bus error

Considering that this error occurs due to a specific choice of spin direction, can it be due to software bug?


Thanks,
Fhokrul



________________________________
From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <gsabo at crimson.ua.edu>
Sent: Tuesday, March 7, 2017 12:52 AM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] lapwsopara error

For example, in the lapwsopara_lapw file on line 292 there is

 >& .stdoutso_$loop

and on line 297 there is

 >>.timeso_$loop

So, some errors that occur might be redirected into these dot files
(which are usually hidden unless ls -a is used or show hidden is
selected in a graphic file manager [
http://askubuntu.com/questions/94780/what-are-dot-files ]).  So if you
[https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-icon@2.png?v=c492c9229955]<http://askubuntu.com/questions/94780/what-are-dot-files>

What are dot-files? - Ask Ubuntu<http://askubuntu.com/questions/94780/what-are-dot-files>
askubuntu.com
I am having a hard time grasping what dot-files are or what they are for. Are they directories? How do I navigate to them? Thank you!



[https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-icon@2.png?v=c492c9229955]<http://askubuntu.com/questions/94780/what-are-dot-files>

What are dot-files? - Ask Ubuntu<http://askubuntu.com/questions/94780/what-are-dot-files>
[https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-icon@2.png?v=c492c9229955]<http://askubuntu.com/questions/94780/what-are-dot-files>

What are dot-files? - Ask Ubuntu<http://askubuntu.com/questions/94780/what-are-dot-files>
askubuntu.com
I am having a hard time grasping what dot-files are or what they are for. Are they directories? How do I navigate to them? Thank you!



askubuntu.com
I am having a hard time grasping what dot-files are or what they are for. Are they directories? How do I navigate to them? Thank you!



haven't already done so, I suggest also checking the .timeso_* and
.stdoutso_* files if they exist.

On 3/6/2017 8:04 AM, Peter Blaha wrote:
> All this info does not help.
> There must be somewhere an info why some of the lapwso calculations
> crash.
> What is in the error files, or in the STDOUT of your batch job.
>
> Eventually try to put my   lapwso uplapwso_1.def   line at the end of
> your job, or add   ls -als /path-to-vector-file/*vector*
>
>
>
> On 03/06/2017 02:29 PM, Md. Fhokrul Islam wrote:
>> Hi Prof Blaha,
>>
>>
>> Thank you for your reply. Here is some more info about this calculation.
>>
>>
>> I am using Wien2k16 which is compiled using intel/2017.
>>
>>
>> I have checked the output files from lapw1c which look correct to
>> me. Unfortunately,
>>
>> I couldn't check vector* files since it was in temporary scratch
>> directory which are
>>
>> automatically deleted after the job exits form the queue. But the
>> corresponding energyup/dn
>>
>> files are ok. For each k-point it writes out all eigenvalues for the
>> corresponding k-point:
>>
>>
>> (more lines above)
>>
>> 200.20204200.20204198.22381  0.20204  0.20204  0.20204  0.20204 0.20204
>>  0.20204  0.20204  0.20204  0.20204  0.20204  0.00000
>>   0.20204  0.20204 -1.77619999.00000997.00000997.00000
>>  0.60204999.00000999.00000999.00000999.00000999.00000
>>  1.666666666667E-01 1.666666666667E-01 5.000000000000E-01         1
>>  9481  7160  1.0
>>            1  -2.97772569684435
>>            2  -2.97708536428630
>>            3  -2.97619544771632
>>            4  -2.30343486814166
>>            .....
>> So I think lapw1 works fine. But the problem is in lapwso. Here is the
>> k-mesh that I am using for 001 (same for 110 direction
>> which works fine):
>>
>>          1         1         1         3         6  1.0 -7.0 1.5
>>  16 k, div: (  3  3  1)
>>          2         1         3         3         6  1.0
>>          3         1         5         3         6  1.0
>>          4         3         1         3         6  1.0
>>          5         3         3         3         6  1.0
>>          6         3         5         3         6  1.0
>>          7         5         1         3         6  1.0
>>          8         5         3         3         6  1.0
>>          9         5         5         3         6  1.0
>> END
>>
>> For k-points 2,3,4, 6 and 9 it created all energyso* and outputso* files
>> correctly. But for the remaining k-points
>> it didn't. The supercell has 135 atoms and it is supposed to write
>> parameters for each atoms for both spins and
>> then write out the energy. But it turns out the file ends after writing
>> the parameters for atoms upto 133 spin 1.
>> Here is how the end of the outputso_1 file looks like (the same for
>> other 3 incomplete files)
>>
>> outputso_1:
>>
>>  relativistic lo:           1  0.300000000000000 2
>>     4
>>  -0.420088705696323
>> RLO COEFFICIENT: l,A,B,C   1         10.38893     0.00000 -11.18331
>>
>>           ATOMIC PARAMETERS FOR **  SPIN=1
>>
>>            ENERGY PARAMETERS ARE   0.20   0.20  -1.78   0.20 0.20
>> 0.20   0.20
>>  for lo:
>>                0.20     0.20    -1.78   999.00
>>              997.00   997.00     0.60   999.00
>>              999.00   999.00   999.00   999.00
>>
>> energysoup_1 (last few lines):
>>
>> 200.20204200.20204198.22005  0.20204  0.20204  0.20204  0.20204 0.20204
>>  0.20204  0.20204  0.20204  0.20204  0.20204  0.00000
>>   0.20204  0.20204 -1.77995999.00000997.00000997.00000
>>  0.60204999.00000999.00000  0.30000999.00000999.00000
>> 200.20204200.20204198.22192  0.20204  0.20204  0.20204  0.20204 0.20204
>>  0.20204  0.20204  0.20204  0.20204  0.20204  0.00000
>>   0.20204  0.20204 -1.77808999.00000997.00000997.00000
>>  0.60204999.00000999.00000  0.30000999.00000999.00000
>>
>> Clearly both of these files are incomplete. I think memory is not an
>> issue as I am using about 9GB/core and also have
>> 500 GB disk space available. System doesn't have any symmetry for both
>> in-plane and out-of-plane calculations.
>>
>> By the way, there seems to be a formatting problem in outputso files.
>> After writing out parameters for 99 atoms
>> it places an asterisk in place of atom index as shown in the above.
>>
>>          ATOMIC PARAMETERS FOR **  SPIN=1
>>
>>
>> Kind regards,
>> Fhokrul
>>
>>
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