<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>Dear Lorenzo,</div><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><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" <paulatz@gmail.com><br><b>To: </b>"users" <users@lists.quantum-espresso.org><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">
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<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>
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<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"><paulatz@gmail.com></a><br>
<b>To: </b>"users" <a class="moz-txt-link-rfc2396E" href="mailto:users@lists.quantum-espresso.org" target="_blank"><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">
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font-size: 12pt; color: #000000">
<div><br>
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<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;
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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;
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#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"><paulatz@gmail.com></a>_<br>
<b>To: </b>"users" <a class="moz-txt-link-rfc2396E" href="mailto:users@lists.quantum-espresso.org" target="_blank"><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>
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<pre class="moz-quote-pre">_______________________________________________
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_______________________________________________<br>
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<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">www.max-centre.eu</a>)
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<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu" target="_blank">www.max-centre.eu</a>)<br>
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<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">www.max-centre.eu</a>)
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