<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<ul>
<li><font size="-1">yes you can create the exit file just with a
touch command<br>
</font></li>
</ul>
<ul>
<li><font size="-1">no don't create it in the submission script,
there is no sensible reason to create it with the submission
script, maybe I have not been clear, the program stops as soon
as it finds the exit file, if you created it with the
submission file, the program would stop just after starting
without doing nothing. what for ? <br>
</font></li>
</ul>
<ul>
<li><font size="-1">if you have doubts about the reliability of
your saved data it is probably better to copy the last
positions obtained by you previous run in the input and
restart from scratch from those coordinates. <br>
</font></li>
<li><font size="-1">if you really want to change prefix (this is
another thing which is not very frequently needed actually)
just copy the whole prefix.save directory into new_prefix.save
directory <br>
</font></li>
</ul>
<p><font size="-1"><br>
</font></p>
<p><font size="-1"><br>
</font></p>
<p><font size="-1"> <br>
</font></p>
<p><br>
</p>
<div class="moz-cite-prefix">On 08/07/19 21:22, Yeon, Jejoon wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BN7PR10MB2531BBA189BFAC801D64907CCFF60@BN7PR10MB2531.namprd10.prod.outlook.com">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;"
dir="ltr">
<div style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
1) no it's not correct. prefix.EXIT is a file that the user
creates to make the program stop before completion. When the
program finds this file in the outdir or in the working
directory the program stops writes the restart files and
deletes prefix.EXIT, so the file is practically never present
after the program has stopped unless something has gone wrong.
To restart a relaxation you just need the files contained in
the prefix.save directory and possibly the restart files.</div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
<span style="color: rgb(255, 0, 0);">>> Thanks to let me
know. </span><span style="color: rgb(255, 0, 0);">May I ask
how to create</span><span style="color: rgb(255, 0, 0);">
prefix.EXIT file? Is this an empty file just with that name,
that I can make from shell command in </span><span
style="color: rgb(255, 0, 0);">submission script? </span></div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
<span style="color: rgb(255, 0, 0);"><br>
</span></div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
<span style="color: rgb(255, 0, 0);">Also, I think </span><span
style="color: rgb(255, 0, 0);">my previous
</span><span style="color: rgb(255, 0, 0);">jobs</span><span
style="color: rgb(255, 0, 0);"> w</span><span style="color:
rgb(255, 0, 0);">ere</span><span style="color: rgb(255, 0,
0);"> not "</span><span><span style="color: rgb(255, 0, 0);">cleanly
stopped", because </span><span style="color: rgb(255, 0,
0);">I didn't used "max_seconds" neither I created any
prefix.EXIT file at any moment</span><span style="color:
rgb(255, 0, 0);">. So that is why I think my stopped jobs
cannot be continued. </span></span></div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
<span><span style="color: rgb(255, 0, 0);"><br>
</span></span></div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
<span><span style="color: rgb(255, 0, 0);">But let me try to
continue this one. </span></span><span style="color:
rgb(255, 0, 0);">Inside the prefix.save folder of
corresponding job, I can only find 3
files: charge-density.dat, data-file-schema.xml, and
paw.txt. So, I need to copy those files to outdir location,
and submit restart job with different name of .in and .out
file in the same folder, and set restart_mode to restart.
Right? </span><span><span style="color: rgb(255, 0, 0);">
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</span></span></div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
2) max_seconds uses the same time as printed in the WALL_TIME
which is the time elapsed since the job has started CPU_TIME
is the time actually used by the CPU they differ because a CPU
usage is not always 100%, may be less but if you use
multithreading may also be much larger than 100%. Consider
only WALL time to keep things simple. <br>
</div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
Just look at the seconds the program takes to make an scf loop
and set smax_seconds to one week minus that time. This already
very conservative, no need to use a longer time. </div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
<br>
</div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
3) do not change the prefix name ...</div>
<div dir="auto" style="color: rgb(33, 33, 33); font-family:
wf_segoe-ui_normal, "Segoe UI", "Segoe
WP", Tahoma, Arial, sans-serif, serif, EmojiFont;
font-size: 15px;">
To restart the program will look for a directory called
prefix.save if you change the prefix the program will not be
able to read anything...</div>
<br>
<p style="margin-top:0;margin-bottom:0"><font
face="wf_segoe-ui_normal, Segoe UI, Segoe WP, Tahoma, Arial,
sans-serif, serif, EmojiFont" color="#ff0000"><span
style="font-size: 15px;">>> Thank you so much for
the answers. Are there any links which explained of how to
restart QE jobs in detail? I searched in user manual and
i</span></font><span style="font-size: 15px; color:
rgb(255, 0, 0); font-family: wf_segoe-ui_normal, "Segoe
UI", "Segoe WP", Tahoma, Arial, sans-serif,
serif, EmojiFont;">nput file description webpage but I
couldn't find any useful info...</span><font
face="wf_segoe-ui_normal, Segoe UI, Segoe WP, Tahoma, Arial,
sans-serif, serif, EmojiFont" color="#ff0000"><span
style="font-size: 15px;"></span></font></p>
<font face="wf_segoe-ui_normal, Segoe UI, Segoe WP, Tahoma,
Arial, sans-serif, serif, EmojiFont" color="#ff0000">
<div><br>
</div>
<div>Thank you again!! </div>
</font><br>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> users
<a class="moz-txt-link-rfc2396E" href="mailto:users-bounces@lists.quantum-espresso.org"><users-bounces@lists.quantum-espresso.org></a> on behalf of
SISSA <a class="moz-txt-link-rfc2396E" href="mailto:pdelugas@sissa.it"><pdelugas@sissa.it></a><br>
<b>Sent:</b> Monday, July 8, 2019 2:38:00 PM<br>
<b>To:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Question about restarting
relaxation jobs</font>
<div> </div>
</div>
<div>
<div dir="auto">
<div>1) no it's not correct. prefix.EXIT is a file that the
user creates to make the program stop before completion.
When the program finds this file in the outdir or in the
working directory the program stops writes the restart files
and deletes prefix.EXIT, so the file is practically never
present after the program has stopped unless something has
gone wrong. To restart a relaxation you just need the files
contained in the prefix.save directory and possibly the
restart files.</div>
<div dir="auto"><br>
</div>
<div dir="auto">2) max_seconds uses the same time as printed
in the WALL_TIME which is the time elapsed since the job has
started CPU_TIME is the time actually used by the CPU they
differ because a CPU usage is not always 100%, may be less
but if you use multithreading may also be much larger than
100%. Consider only WALL time to keep things simple. </div>
<div dir="auto">Just look at the seconds the program takes to
make an scf loop and set smax_seconds to one week minus that
time. This already very conservative, no need to use a
longer time. </div>
<div dir="auto"><br>
</div>
<div dir="auto">3) do not change the prefix name ...</div>
<div dir="auto">To restart the program will look for a
directory called prefix.save if you change the prefix the
program will not be able to read anything...<br>
<div class="x_gmail_extra" dir="auto"><br>
<div class="x_gmail_quote">Il 8 lug 2019 6:43 PM, "Yeon,
Jejoon" <a class="moz-txt-link-rfc2396E" href="mailto:jyeon@udel.edu"><jyeon@udel.edu></a> ha scritto:<br
type="attribution">
<blockquote class="x_quote" style="margin:0 0 0 .8ex;
border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div dir="ltr" style="font-size:12pt; color:#000000;
font-family:'calibri' ,'helvetica' ,sans-serif">
<p style="margin-top:0; margin-bottom:0">Thank you
so much Pietro </p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">May I ask
one more question? </p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-size:12pt">1) This is just double
checking question. I checked the folder where
the relaxation was stopped by cluster due to
wall time limit (I didn't set max seconds). In
the output folder, I can see prefix.save/
folder and pwscf.save/ folder, and
prefix.update and prefix.bfgs file. But
because I have no prefix.EXIT folder neither
prefix.EXIT file, I cannot restart this
simulation. Is this correct? </span></p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-size:12pt"><br>
</span></p>
<p style="margin-top:0; margin-bottom:0">2) <span
style="font-size:12pt">Now I'm setting "</span><span
style="font-size:12pt">max_seconds" to all my
QE DFT works. But I found that CPU time and
wall time is slightly different. From my
recent finished calculation, it is written at
the end of the output file: </span></p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-size:12pt"></span></p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-size:12pt"></span></p>
<div><span style="font-size:12pt">PWSCF :
4d21h44m CPU 4d22h12m WALL</span><br>
</div>
<div><span style="font-size:12pt"> This run was
terminated on: 21:27:26 1Jul2019</span><br>
</div>
<p style="margin-top:0; margin-bottom:0">I used 30
cores, and set 7 days of wall time. Simulation
finished before wall time, but I'm not sure why
this slight difference of CPU time and wall time
occur. <br>
<span style="font-size:12pt">In this case, what
would be the good </span><span
style="font-size:12pt">time of max seconds CPU
time when compared to wall time? If I request
7 days of wall time </span><span
style="font-size:12pt">to cluster, then would
it be more "safe" to set 6 days or 6.5 days of
CPU time for max seconds? </span><span
style="font-size:12pt"> </span><br>
</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">3) This
is also double checking question. If I wish to
start the restart in same folder, I would better
to change prefix from "SimulatinoA" to
"SimulationA_restart1", would it be OK? Also,
if I wish to use different folder, I need to
copy entire files inside <span
style="font-family:'calibri' ,'helvetica'
,sans-serif ,'emojifont' ,'apple color emoji'
,'segoe ui emoji' ,'notocoloremoji' ,'segoe ui
symbol' ,'android emoji' ,'emojisymbols';
font-size:16px">prefix.EXIT folder to the new
restart folder, is this correct? </span></p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-family:'calibri' ,'helvetica'
,sans-serif ,'emojifont' ,'apple color emoji'
,'segoe ui emoji' ,'notocoloremoji' ,'segoe ui
symbol' ,'android emoji' ,'emojisymbols';
font-size:16px"><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-family:'calibri' ,'helvetica'
,sans-serif ,'emojifont' ,'apple color emoji'
,'segoe ui emoji' ,'notocoloremoji' ,'segoe ui
symbol' ,'android emoji' ,'emojisymbols';
font-size:16px">Thank you so much for friendly
answers to beginner question!! </span></p>
<p style="margin-top:0; margin-bottom:0"><span
style="font-size:12pt"></span></p>
</div>
<hr style="display:inline-block; width:98%">
<div dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
users
<a class="moz-txt-link-rfc2396E" href="mailto:users-bounces@lists.quantum-espresso.org"><users-bounces@lists.quantum-espresso.org></a>
on behalf of Pietro Davide Delugas
<a class="moz-txt-link-rfc2396E" href="mailto:pdelugas@sissa.it"><pdelugas@sissa.it></a><br>
<b>Sent:</b> Monday, July 8, 2019 4:14:06 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br>
<b>Subject:</b> Re: [QE-users] Question about
restarting relaxation jobs</font>
<div> </div>
</div>
<div style="background-color:#ffffff">
<div>Hello <br>
</div>
<div><br>
</div>
<div>1) and 2) PW writes the restart files only
when it terminates before convergence is reached
either because the max number of steps (and the
max number may be either the number of
electronic steps during scf of number of ionic
steps during structural relaxation) or the the
execution time exceed max_seconds specified in
input or because the user has stopped the
calculation creating a file in the outdir called
prefix.EXIT.
<br>
</div>
<div><br>
</div>
<div>If restart_mode in &control is set to
"restart" pw will try to restart the relaxation
from the last POSITIONS which have been saved
in the prefix.save directory using the last
saved charge density and wave functions. If it
finds the restart files it will use them also.
This mechanism works fine if positions, charge
density and wave functions data have been saved
regularly, but if the calculation is going to
be stopped abruptly, for example by the job
manager, there is no way to prevent that the
stop arrives when the program is writing these
data. The safer way to go when you are using a
job manager is to set the max_seconds variable
to a number consistently lower than the time
allocated by the job manager, the difference
between these two times should be enough to
allow to the program to pass through one of the
check_points at which, during execution, it
checks if the execution time has exceeded the
max_seconds s or if the user has created a
prefix.EXIT file. To estimate how long should be
the difference between max_seconds and the
scheduled execution time check how long it takes
to the program to make an scf loop, this one
will a very safe estimate, you could reduce
this time significantly and things should be
working.
<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>3) I don't understans what you want to do.
You create the prefix.EXIT file when you want to
stop your calculation and you want the
calculation to finish smoothly saving all
restart information so that it can resatart from
more or less the same point when it was
interrupted. It is completely senseless to
rename the output file as prefix.EXIT because
it will make the program to stop as soon as a
check_point detects the file and the file will
be deleted. The only thing that you have to do
when restarting a calculation is <br>
</div>
<div>
<ul>
<li> Specify restart_mode = 'restart' in the
input.in file </li>
</ul>
<ul>
<li> take care that the information saved in
output.out is not rewritten by the new
execution just use something as
<tt>mpirun pw.x < input.in >>
output.out </tt>which appends the new
output to the old one or redirect the output
to files with different names
</li>
</ul>
<p>4) outdir must be the same or if you want
to use a different one you have to create the
new outdir befor restarting and copy there all
the data of the previous calculation i.e. the
prefix.save directory.
<br>
</p>
<p><br>
</p>
<p>5) don't complicate things too much</p>
<p><br>
</p>
<p><br>
</p>
<p>Pietro <br>
</p>
<p><br>
</p>
</div>
<div><br>
</div>
<div>On 7/6/19 3:59 PM, Yeon, Jejoon wrote:<br>
</div>
<blockquote>
<div dir="ltr" style="font-size:12pt;
color:#000000; font-family:'calibri'
,'helvetica' ,sans-serif">
<p style="margin-top:0; margin-bottom:0">Hello </p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I
have very small amount of experience
using QE, so please excuse my beginner
question. <span style="font-size:12pt">I'm
about to start relaxation of big crystal
structure, and I
</span><span style="font-size:12pt">wish to
make my QE relaxation jobs ready for
restart. Here are my questions: </span></p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">1) According
to "restarting" section from manual, (<a
href="https://www.quantum-espresso.org/Doc/pw_user_guide/node20.html"
moz-do-not-send="true">https://www.quantum-espresso.org/Doc/pw_user_guide/node20.html</a>)
it seems that QE does not creates the
dedicated restart file, is this correct? </p>
<br>
<div>2) If I set up "<span
style="font-size:12pt">max_seconds</span><span
style="font-size:12pt">" option as 604800
seconds (1 week), and request wall time to
server 1 week, do my calculation jobs are
ready to restart after 1 week? (1 week is
just example but our server cluster have
maximum some walltime limitation, and I
don't think any of my relaxation works
will be finished within that time. ) Also,
does this "max_seconds" option must be
required to restart? </span></div>
<div><span style="font-size:12pt"><br>
</span></div>
<div><span style="font-size:12pt">3) When I
execute QE in the submit script, I use
something similar as: </span></div>
<div>mpirun pw.x < input.in >
output.out</div>
<div>In this case, if the relaxation job is
killed due to wall time limit (without
setting max_seconds), can I just change the
name of the output.out to prefix.EXIT, (of
course I set up prefix in the input file) <span
style="font-size:12pt">and then include
restart_mode = "restart" in the input
file, then submit a job for restart? </span></div>
<div><span style="font-size:12pt">I have old
files which are finished after reaching
wall time limit without "max_seconds"
option, and I'm curious if I can use those
files to restart. </span></div>
<div><span style="font-size:12pt"><br>
</span></div>
<div><span style="font-size:12pt">4) I also
use outdir option in the input file, does
the outdir option should be the same when
restart? </span></div>
<div><br>
</div>
<div><span style="font-size:12pt">5) Are there
any other things or useful hints that I
need to consider when restart? </span></div>
<div><span style="font-size:12pt"><br>
</span></div>
<div><span style="font-size:12pt">Thank you </span></div>
<div><br>
</div>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" moz-do-not-send="true">www.max-centre.eu/quantum-espresso</a>)
users mailing list <a href="mailto:users@lists.quantum-espresso.org" moz-do-not-send="true">users@lists.quantum-espresso.org</a>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
</blockquote>
<p><br>
</p>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</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/quantum-espresso">www.max-centre.eu/quantum-espresso</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>