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<p>Thanks, Gerhard. I actually read about the bus error but I was confused because</p>
<p>different reasons are suggested including error in executable. But I sent a</p>
<p>message to our cluster administrator to check if the error is related to hardware.</p>
<p><br>
</p>
<p><br>
</p>
<p>Regards,</p>
<p>Fhokrul</p>
<p><br>
</p>
<br>
<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Wien <wien-bounces@zeus.theochem.tuwien.ac.at> on behalf of Fecher, Gerhard <fecher@uni-mainz.de><br>
<b>Sent:</b> Tuesday, March 7, 2017 11:28 AM<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] lapwsopara error</font>
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<div class="PlainText">maybe this helps<br>
<br>
from Wikipedia<br>
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.<br>
<br>
more is found from google<br>
<br>
Ciao<br>
Gerhard<br>
<br>
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:<br>
"I think the problem, to be quite honest with you,<br>
is that you have never actually known what the question is."<br>
<br>
====================================<br>
Dr. Gerhard H. Fecher<br>
Institut of Inorganic and Analytical Chemistry<br>
Johannes Gutenberg - University<br>
55099 Mainz<br>
and<br>
Max Planck Institute for Chemical Physics of Solids<br>
01187 Dresden<br>
________________________________________<br>
Von: Wien [wien-bounces@zeus.theochem.tuwien.ac.at] im Auftrag von Md. Fhokrul Islam [fislam@hotmail.com]<br>
Gesendet: Dienstag, 7. März 2017 12:21<br>
An: A Mailing list for WIEN2k users<br>
Betreff: Re: [Wien] lapwsopara error<br>
<br>
Hi Gavin,<br>
<br>
<br>
You are right, there are .timeso files (but no .stdoutso) for each k-point and the ones that fail to complete<br>
<br>
have an error message:<br>
<br>
<br>
-cn0130 Bus error<br>
<br>
Considering that this error occurs due to a specific choice of spin direction, can it be due to software bug?<br>
<br>
<br>
Thanks,<br>
Fhokrul<br>
<br>
<br>
<br>
________________________________<br>
From: Wien <wien-bounces@zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <gsabo@crimson.ua.edu><br>
Sent: Tuesday, March 7, 2017 12:52 AM<br>
To: A Mailing list for WIEN2k users<br>
Subject: Re: [Wien] lapwsopara error<br>
<br>
For example, in the lapwsopara_lapw file on line 292 there is<br>
<br>
>& .stdoutso_$loop<br>
<br>
and on line 297 there is<br>
<br>
>>.timeso_$loop<br>
<br>
So, some errors that occur might be redirected into these dot files<br>
(which are usually hidden unless ls -a is used or show hidden is<br>
selected in a graphic file manager [<br>
<a href="http://askubuntu.com/questions/94780/what-are-dot-files" id="LPlnk191983" previewremoved="true">http://askubuntu.com/questions/94780/what-are-dot-files</a> ]). So if you
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<a id="LPImageAnchor_14888900572860.6685797921484418" href="http://askubuntu.com/questions/94780/what-are-dot-files" target="_blank" style="display: table-cell; text-align: center;"><img aria-label="Preview image with link selected. Double-tap to open the link." id="LPThumbnailImageID_14888900572860.36378881622087644" width="250" height="250" style="display: inline-block; max-width: 250px; max-height: 250px; height: 250px; width: 250px; border-width: 0px; vertical-align: bottom;" src="https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-icon@2.png?v=c492c9229955"></a></div>
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<a id="LPUrlAnchor_14888900572860.6045573612679889" href="http://askubuntu.com/questions/94780/what-are-dot-files" target="_blank" style="text-decoration: none;">What are dot-files? - Ask Ubuntu</a></div>
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askubuntu.com</div>
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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!</div>
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<br>
[<a href="https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-icon@2.png?v=c492c9229955]<http://askubuntu.com/questions/94780/what-are-dot-files" id="LPlnk916024" previewremoved="true">https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-icon@2.png?v=c492c9229955]<http://askubuntu.com/questions/94780/what-are-dot-files</a>><br>
<br>
What are dot-files? - Ask Ubuntu<<a href="http://askubuntu.com/questions/94780/what-are-dot-files" id="LPlnk101252" previewremoved="true">http://askubuntu.com/questions/94780/what-are-dot-files</a>>
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<a id="LPUrlAnchor_14888901162220.880443754772755" href="http://askubuntu.com/questions/94780/what-are-dot-files" target="_blank" style="text-decoration: none;">What are dot-files? - Ask Ubuntu</a></div>
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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!</div>
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<br>
askubuntu.com<br>
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!<br>
<br>
<br>
<br>
haven't already done so, I suggest also checking the .timeso_* and<br>
.stdoutso_* files if they exist.<br>
<br>
On 3/6/2017 8:04 AM, Peter Blaha wrote:<br>
> All this info does not help.<br>
> There must be somewhere an info why some of the lapwso calculations<br>
> crash.<br>
> What is in the error files, or in the STDOUT of your batch job.<br>
><br>
> Eventually try to put my lapwso uplapwso_1.def line at the end of<br>
> your job, or add ls -als /path-to-vector-file/*vector*<br>
><br>
><br>
><br>
> On 03/06/2017 02:29 PM, Md. Fhokrul Islam wrote:<br>
>> Hi Prof Blaha,<br>
>><br>
>><br>
>> Thank you for your reply. Here is some more info about this calculation.<br>
>><br>
>><br>
>> I am using Wien2k16 which is compiled using intel/2017.<br>
>><br>
>><br>
>> I have checked the output files from lapw1c which look correct to<br>
>> me. Unfortunately,<br>
>><br>
>> I couldn't check vector* files since it was in temporary scratch<br>
>> directory which are<br>
>><br>
>> automatically deleted after the job exits form the queue. But the<br>
>> corresponding energyup/dn<br>
>><br>
>> files are ok. For each k-point it writes out all eigenvalues for the<br>
>> corresponding k-point:<br>
>><br>
>><br>
>> (more lines above)<br>
>><br>
>> 200.20204200.20204198.22381 0.20204 0.20204 0.20204 0.20204 0.20204<br>
>> 0.20204 0.20204 0.20204 0.20204 0.20204 0.00000<br>
>> 0.20204 0.20204 -1.77619999.00000997.00000997.00000<br>
>> 0.60204999.00000999.00000999.00000999.00000999.00000<br>
>> 1.666666666667E-01 1.666666666667E-01 5.000000000000E-01 1<br>
>> 9481 7160 1.0<br>
>> 1 -2.97772569684435<br>
>> 2 -2.97708536428630<br>
>> 3 -2.97619544771632<br>
>> 4 -2.30343486814166<br>
>> .....<br>
>> So I think lapw1 works fine. But the problem is in lapwso. Here is the<br>
>> k-mesh that I am using for 001 (same for 110 direction<br>
>> which works fine):<br>
>><br>
>> 1 1 1 3 6 1.0 -7.0 1.5<br>
>> 16 k, div: ( 3 3 1)<br>
>> 2 1 3 3 6 1.0<br>
>> 3 1 5 3 6 1.0<br>
>> 4 3 1 3 6 1.0<br>
>> 5 3 3 3 6 1.0<br>
>> 6 3 5 3 6 1.0<br>
>> 7 5 1 3 6 1.0<br>
>> 8 5 3 3 6 1.0<br>
>> 9 5 5 3 6 1.0<br>
>> END<br>
>><br>
>> For k-points 2,3,4, 6 and 9 it created all energyso* and outputso* files<br>
>> correctly. But for the remaining k-points<br>
>> it didn't. The supercell has 135 atoms and it is supposed to write<br>
>> parameters for each atoms for both spins and<br>
>> then write out the energy. But it turns out the file ends after writing<br>
>> the parameters for atoms upto 133 spin 1.<br>
>> Here is how the end of the outputso_1 file looks like (the same for<br>
>> other 3 incomplete files)<br>
>><br>
>> outputso_1:<br>
>><br>
>> relativistic lo: 1 0.300000000000000 2<br>
>> 4<br>
>> -0.420088705696323<br>
>> RLO COEFFICIENT: l,A,B,C 1 10.38893 0.00000 -11.18331<br>
>><br>
>> ATOMIC PARAMETERS FOR ** SPIN=1<br>
>><br>
>> ENERGY PARAMETERS ARE 0.20 0.20 -1.78 0.20 0.20<br>
>> 0.20 0.20<br>
>> for lo:<br>
>> 0.20 0.20 -1.78 999.00<br>
>> 997.00 997.00 0.60 999.00<br>
>> 999.00 999.00 999.00 999.00<br>
>><br>
>> energysoup_1 (last few lines):<br>
>><br>
>> 200.20204200.20204198.22005 0.20204 0.20204 0.20204 0.20204 0.20204<br>
>> 0.20204 0.20204 0.20204 0.20204 0.20204 0.00000<br>
>> 0.20204 0.20204 -1.77995999.00000997.00000997.00000<br>
>> 0.60204999.00000999.00000 0.30000999.00000999.00000<br>
>> 200.20204200.20204198.22192 0.20204 0.20204 0.20204 0.20204 0.20204<br>
>> 0.20204 0.20204 0.20204 0.20204 0.20204 0.00000<br>
>> 0.20204 0.20204 -1.77808999.00000997.00000997.00000<br>
>> 0.60204999.00000999.00000 0.30000999.00000999.00000<br>
>><br>
>> Clearly both of these files are incomplete. I think memory is not an<br>
>> issue as I am using about 9GB/core and also have<br>
>> 500 GB disk space available. System doesn't have any symmetry for both<br>
>> in-plane and out-of-plane calculations.<br>
>><br>
>> By the way, there seems to be a formatting problem in outputso files.<br>
>> After writing out parameters for 99 atoms<br>
>> it places an asterisk in place of atom index as shown in the above.<br>
>><br>
>> ATOMIC PARAMETERS FOR ** SPIN=1<br>
>><br>
>><br>
>> Kind regards,<br>
>> Fhokrul<br>
>><br>
>><br>
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