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<p style="margin-top:0;margin-bottom:0">Thank you so much!! </p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><span style="color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: small;">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 ?</span><br>
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<p style="margin-top:0;margin-bottom:0">Hmm I was thinking of use mpirun pw.x ==> sleep command ==> touch or cat prefix.EXIT, maybe this wouldn't be a good idea. Thanks to let me know. Now I'm very confident about whole restart of QE! </p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Pietro Delugas <pdelugas@sissa.it><br>
<b>Sent:</b> Monday, July 8, 2019 5:26:52 PM<br>
<b>To:</b> users@lists.quantum-espresso.org<br>
<b>Subject:</b> Re: [QE-users] Question about restarting relaxation jobs</font>
<div> </div>
</div>
<div style="background-color:#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>
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<div class="x_moz-cite-prefix">On 08/07/19 21:22, Yeon, Jejoon wrote:<br>
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<div style="">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=""><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=""><span style="color:rgb(255,0,0)"><br>
</span></div>
<div dir="auto" style=""><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=""><span><span style="color:rgb(255,0,0)"><br>
</span></span></div>
<div dir="auto" style=""><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="">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="">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=""><br>
</div>
<div dir="auto" style="">3) do not change the prefix name ...</div>
<div dir="auto" style="">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="">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>
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</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> users
<a class="x_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="x_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_x_gmail_extra" dir="auto"><br>
<div class="x_x_gmail_quote">Il 8 lug 2019 6:43 PM, "Yeon, Jejoon" <a class="x_moz-txt-link-rfc2396E" href="mailto:jyeon@udel.edu">
<jyeon@udel.edu></a> ha scritto:<br type="attribution">
<blockquote class="x_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="">prefix.EXIT folder to the new restart folder, is this correct? </span></p>
<p style="margin-top:0; margin-bottom:0"><span style=""><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="">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 face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> users
<a class="x_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="x_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="x_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">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>
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<pre class="x_moz-quote-pre">_______________________________________________
Quantum ESPRESSO is supported by MaX (<a class="x_moz-txt-link-abbreviated" href="http://www.max-centre.eu/quantum-espresso">www.max-centre.eu/quantum-espresso</a>)
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