<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<br>
<blockquote type="cite"
cite="mid:2024184708.2260168.1607340281041.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif; font-size:
12pt; color: #000000">
<div><br data-mce-bogus="1">
</div>
<div>The qq2rr code is serial right? After running in /scratch
(for memory issue) it shows Bus error!</div>
<div><br data-mce-bogus="1">
</div>
<div>
<div>/var/spool/slurm/slurmd.spool/job3829394/slurm_script:
line 38: 179584 Done ls anh*</div>
<div> 179585 Bus error |
/gpfs/home/kghosh/kanka/qe-6.5/bin/d3_qq2rr.x 1 1 1</div>
<div>Job finished</div>
</div>
<div><br>
</div>
<div>Any specific reason for this error?</div>
</div>
</blockquote>
<p>It is parallelized with openmp (not MPI), although I have not
tested it in a while. I do not know what causes a bus error, it is
not something I had seen since the nineties. Maybe out of memory ?
If you are running it on a cluster, it may be better to submit it
as a job even if it is serial<br>
</p>
<p><br>
</p>
<blockquote type="cite"
cite="mid:2024184708.2260168.1607340281041.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif; font-size:
12pt; color: #000000">
<div><br data-mce-bogus="1">
</div>
<div>Regards,</div>
<div>Kanka</div>
<div><br>
</div>
<div data-marker="__SIG_PRE__"><br data-mce-bogus="1">
</div>
<div data-marker="__SIG_PRE__">Kanka Ghosh<br>
Postdoctoral Researcher<br>
I2M-Bordeaux<br>
University of Bordeaux, CNRS UMR 5295<br>
Site: Ecole Nationale Supérieure des Arts et Métiers<br>
Bordeaux-Talence 33400</div>
<div><br>
</div>
<hr id="zwchr" data-marker="__DIVIDER__">
<div data-marker="__HEADERS__"><b>From: </b>"Lorenzo Paulatto"
<a class="moz-txt-link-rfc2396E" href="mailto:paulatz@gmail.com"><paulatz@gmail.com></a><br>
<b>To: </b>"users" <a class="moz-txt-link-rfc2396E" href="mailto:users@lists.quantum-espresso.org"><users@lists.quantum-espresso.org></a><br>
<b>Sent: </b>Friday, December 4, 2020 1:12:09 PM<br>
<b>Subject: </b>Re: [QE-users] D3Q code stopped due to davcio
error<br>
</div>
<div><br>
</div>
<div data-marker="__QUOTED_TEXT__"><br>
<blockquote
cite="mid:1889012996.738225.1607082668582.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt; color: #000000">
<div><br>
</div>
<div>Yes it took little more than 5 days to compute only
the first q-point. anyway it seems that I should use
1x1x1 grid instead of 2x2x2. But are you suggesting to
do the single mode calculation with 1x1x1 grid or the
"mode=full" using the 1x1x1 grid?</div>
</div>
</blockquote>
<p>Yes, but no need to do it: you have done it already. You
can just call d3_qq2rr and specify "1 1 1" as the grid size:</p>
<p>ls anh*| d3_qq2rr.x 1 1 1</p>
<p>and it will automatically compute the force constants from
the calculation at (0,0,0). This way you can immediately
test how it works. <br>
</p>
<p>If you want to try the 2x2x2 grid, I would use 10 pools and
maybe try with *fewer* CPUs per pool: at the moment you are
using 128 which requires a lot of communications. If the
calculation fits in RAM, I would recommend keeping each pool
on a single computing node.</p>
<p>You may try to use some local scratch in order to avoid
running out of disk space (ask the cluster managers what to
use).<br>
</p>
<p>Finally, if you manage to get everything running, you can
run al the q-points triplet simultaneously as different
batch jobs by setting "first" and "last". You can have the
same outdir and prefix, as long as they work on different
triplets, they will not interfere (this is true for d3q, but
not in general for other linear response codes)<br>
</p>
<p>hth<br>
</p>
<blockquote
cite="mid:1889012996.738225.1607082668582.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt; color: #000000">
<div><br>
</div>
<div>Regards,</div>
<div>Kanka </div>
<div><br>
</div>
<div>Kanka Ghosh<br>
Postdoctoral Researcher<br>
I2M-Bordeaux<br>
University of Bordeaux, CNRS UMR 5295<br>
Site: Ecole Nationale Supérieure des Arts et Métiers<br>
Bordeaux-Talence 33400</div>
<div><br>
</div>
<hr id="zwchr">
<div><b>From: </b>"Lorenzo Paulatto" <a
class="moz-txt-link-rfc2396E"
href="mailto:paulatz@gmail.com" target="_blank"
moz-do-not-send="true"><paulatz@gmail.com></a><br>
<b>To: </b>"users" <a class="moz-txt-link-rfc2396E"
href="mailto:users@lists.quantum-espresso.org"
target="_blank" moz-do-not-send="true"><users@lists.quantum-espresso.org></a><br>
<b>Sent: </b>Friday, December 4, 2020 9:09:50 AM<br>
<b>Subject: </b>Re: [QE-users] D3Q code stopped due to
davcio error<br>
</div>
<div><br>
</div>
<div>
<blockquote
cite="mid:1857405677.309805.1607037269563.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt; color: #000000">Thanks for pointing
out the storage issue. Yes, I am running it at the
French computing centre (University of Bordeaux's
cluster system (curta, mcia)). Here I am attaching
the d3q output file. Indeed, it was in the process
of computing the second q-point triplet.</div>
</blockquote>
<p>I do not have access to Bordeaux cluster, but I
could ask it if you need that I look at the code. That
said, I see that to compute the first q-point it took
about 5 days, it will take at least a month to do the
second point ! Because it has less symmetry the code
needs to compute 2x more k-points and 3x more
perturbations. <br>
</p>
<blockquote
cite="mid:1857405677.309805.1607037269563.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt; color: #000000">
<div><br>
</div>
<div>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;">"Maybe
for such a large system you can get some decent
force-constants already from (0,0,0) alone"<br>
</p>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;"><br>
</p>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;">In
that case, you mean to implement the
"mode=gamma-only" tag?</p>
</div>
</div>
</blockquote>
<p>Not really, the triple (0,0,0) is in itself the 1x1x1
grid, and you can threat it as such. Thanks to some
Fourier interpolation trickery, you can use it to get
the D3 matrices at any point. Also, the d3_qq2rr code
is not particularly optimized, and is not parallelized
I'm not sure you would manage to compute the Fourier
transform of the 2x2x2 grid anyway.</p>
<p>You have to keep in mind that the 3-body force
constant become huge very quickly with the number of
atoms and the size of the grid: each D3 matrix has
(3*nat)^3 complex elements, and a grid n x n x n
contains n^6 power triplets</p>
<p>In your case, the 2x2x2 grid would use about 2.2GB of
RAM, which is probably still feasible, but i would try
the 1x1x1 first.</p>
<p><br>
</p>
<p>cheers<br>
</p>
<blockquote
cite="mid:1857405677.309805.1607037269563.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt; color: #000000">
<div>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;"><br>
</p>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;"><br>
</p>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;">Regards,</p>
<p style="color: rgb(0, 0, 0); font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; margin: 0px;">Kanka</p>
<span style="color: #000000; font-family: arial,
helvetica, sans-serif; font-size: 16px;
font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight:
400; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
background-color: #ffffff;
text-decoration-thickness: initial;
text-decoration-style: initial;
text-decoration-color: initial; display: inline
!important; float: none;"></span>
<div style="clear: both;"><br>
</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Kanka Ghosh<br>
Postdoctoral Researcher<br>
I2M-Bordeaux<br>
University of Bordeaux, CNRS UMR 5295<br>
Site: Ecole Nationale Supérieure des Arts et
Métiers<br>
Bordeaux-Talence 33400</div>
<div><br>
</div>
<hr id="zwchr">
<div><b>From: </b>"Lorenzo Paulatto" <a
class="moz-txt-link-rfc2396E"
href="mailto:paulatz@gmail.com" target="_blank"
moz-do-not-send="true"><paulatz@gmail.com></a>_<br>
<b>To: </b>"users" <a
class="moz-txt-link-rfc2396E"
href="mailto:users@lists.quantum-espresso.org"
target="_blank" moz-do-not-send="true"><users@lists.quantum-espresso.org></a><br>
<b>Sent: </b>Thursday, December 3, 2020 11:23:58
PM<br>
<b>Subject: </b>Re: [QE-users] D3Q code stopped
due to davcio error<br>
</div>
<div><br>
</div>
<div> task # 71
<blockquote
cite="mid:1454603361.227824.1607028128135.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica,
sans-serif; font-size: 12pt; color: #000000">
<div>
<div>
<div> from davcio : error # 5011</div>
<div> error while writing from file
".//D3_Q1.0_0_0_Q2.0_0_-1o2_Q3.0_0_1o2/scf.d1.dq1pq1.72"</div>
</div>
</div>
<br>
</div>
</blockquote>
<p><br>
</p>
<p>I guess it may have run out of space, d3q uses
a ton of disk space and there is not easy way to
avoid this. If you are running on any of the
French computing centers I can try to have a
look directly.</p>
<p>I do not think the change in number of CPUs
could cause this problem, but if you provide the
full output I can check. Also, 44 atoms is a lot
for the d3q code, it seems like you're running
the second q-point triplet, which is of kind
(0,q,-q), it takes much more time and disk space
than the triplet (0,0,0). Maybe for such a large
system you can get some decent force-constants
already from (0,0,0) alone<br>
</p>
cheers<br>
<br>
<blockquote
cite="mid:1454603361.227824.1607028128135.JavaMail.zimbra@u-bordeaux.fr">
<div style="font-family: arial, helvetica,
sans-serif; font-size: 12pt; color: #000000">
<div><br>
</div>
<div>Kanka Ghosh<br>
Postdoctoral Researcher<br>
I2M-Bordeaux<br>
University of Bordeaux, CNRS UMR 5295<br>
Site: Ecole Nationale Supérieure des Arts et
Métiers<br>
Bordeaux-Talence 33400</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre">_______________________________________________
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu" target="_blank" moz-do-not-send="true">www.max-centre.eu</a>)
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org" target="_blank" moz-do-not-send="true">users@lists.quantum-espresso.org</a>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
</blockquote>
<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a
class="moz-txt-link-abbreviated"
href="http://www.max-centre.eu" target="_blank"
moz-do-not-send="true">www.max-centre.eu</a>)<br>
users mailing list <a
class="moz-txt-link-abbreviated"
href="mailto:users@lists.quantum-espresso.org"
target="_blank" moz-do-not-send="true">users@lists.quantum-espresso.org</a><br>
<a class="moz-txt-link-freetext"
href="https://lists.quantum-espresso.org/mailman/listinfo/users"
target="_blank" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre">_______________________________________________
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu" target="_blank" moz-do-not-send="true">www.max-centre.eu</a>)
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org" target="_blank" moz-do-not-send="true">users@lists.quantum-espresso.org</a>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
</blockquote>
<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a
class="moz-txt-link-abbreviated"
href="http://www.max-centre.eu" target="_blank"
moz-do-not-send="true">www.max-centre.eu</a>)<br>
users mailing list <a class="moz-txt-link-abbreviated"
href="mailto:users@lists.quantum-espresso.org"
target="_blank" moz-do-not-send="true">users@lists.quantum-espresso.org</a><br>
<a class="moz-txt-link-freetext"
href="https://lists.quantum-espresso.org/mailman/listinfo/users"
target="_blank" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre">_______________________________________________
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu" target="_blank" moz-do-not-send="true">www.max-centre.eu</a>)
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org" target="_blank" moz-do-not-send="true">users@lists.quantum-espresso.org</a>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
</blockquote>
<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu">www.max-centre.eu</a>)<br>
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu">www.max-centre.eu</a>)
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
</blockquote>
</body>
</html>