<div dir="ltr"><div><div><div><div><div><div><div>Dear Dr. Andea Thank you so much.<br><br></div>Dear Dr. Lorenzo, YES I read your mail, and I replied with thanks as well.<br><br></div>I am facing a new problem with <b>QE-6.2</b> on my supercomputer account.<br><br></div>I had run a SCF for doped graphene structure with 48 atoms, and then tried to run NSCF calculation (I wanted to calculate DOS ultimately).<br></div>The NSCF calculation stopped in between because the calculation has already<b> consumed 80 GB</b> and the disk ran out of memory.<br></div>I am a bit surprised... because I have never seen an NSCF calculation taking too much of memory before. <br></div>I am not getting why this case has happened. <br><br></div><div>Can any of u plz suggest.<br><br></div><div>I am very thankful for your precious time and knowledge.<br><br><br></div><div>Sincerely,<br></div><div>B S Bhushan<br></div><div>ABV-IIITM Gwalior, India.<br><br></div><div><div><div><div><div><div><div><br></div></div></div></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Nov 7, 2017 at 4:10 PM, Lorenzo Paulatto <span dir="ltr"><<a href="mailto:paulatz@gmail.com" target="_blank">paulatz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>Dear BS, </div><div dir="auto">Did you read my email? Was it not clear at some point? </div><div dir="auto"><br></div><div dir="auto">Kind regards <span class="HOEnZb"><font color="#888888"><br><br><div data-smartmail="gmail_signature" dir="auto">-- <br>Lorenzo Paulatto<br>Written on a virtual keyboard with real fingers</div></font></span><div><div class="h5"><div class="gmail_extra" dir="auto"><br><div class="gmail_quote">On 7 Nov 2017 10:37 a.m., "B S Bhushan" <<a href="mailto:ecebhushan@gmail.com" target="_blank">ecebhushan@gmail.com</a>> wrote:<br type="attribution"><blockquote class="m_-7638545686268666740quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Seems like the dos.x of QE-6.2 can not find xml data from NSCF produced using QE-6.1.<br></div>The following error was shown,<br><br>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<br> Program DOS v.6.2 (svn rev. 13949:13950) starts on 7Nov2017 at 13:22:50 <br><div class="m_-7638545686268666740quoted-text"><br> This program is part of the open-source Quantum ESPRESSO suite<br> for quantum simulation of materials; please cite<br> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br></div> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);<div class="m_-7638545686268666740quoted-text"><br> URL <a href="http://www.quantum-espresso.org" target="_blank">http://www.quantum-espresso.or<wbr>g</a>", <br> in publications or presentations arising from this work. More details at<br> <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.or<wbr>g/quote</a><br><br></div> Parallel version (MPI), running on 1 processors<br><br> MPI processes distributed on 1 nodes<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%<br> Error in routine pw_readschemafile (1):<br> xml data file not found<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br>------------------------------<wbr>------------------------------<wbr>--------------<br>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>with errorcode 1.<br><br>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>You may or may not see output from other processes, depending on<br>exactly when Open MPI kills them.<br>------------------------------<wbr>------------------------------<wbr>--------------<br>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------<br><br><br></div><b><font size="4">should I do the VC-relax and NSCF again using QE-6.2 ??????????????</font></b><br><div><br></div><div>Please Suggest...</div><div><br></div><div>Thank you very much for your kind support.</div><div class="m_-7638545686268666740quoted-text"><div><br></div><div>Sincerely,</div><div>B S Bhushan</div><div>Ph.D Scholar,</div><div>ABV-IIITM Gwalior, India.<br></div><div><br></div></div></div><div class="m_-7638545686268666740elided-text"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Nov 7, 2017 at 11:41 AM, B S Bhushan <span dir="ltr"><<a href="mailto:ecebhushan@gmail.com" target="_blank">ecebhushan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thank you very very much Dr. Andrea.<div><br></div><div>I have a question sir...</div><div>If I install the QE-6.2 on my supercomputer and run dos.x directly on the NSCF outputs produced using QE-6.1 will it work properly. </div><div>Or I have to do VC-relax and NSCF again using QE-6.2.</div><div><br></div><div>Please suggest... Your answer will save a lot of time for time.</div><div><br></div><div>Thank you so so much for your precious time and knowledge.</div><div> </div><div>Sincerely,</div><div>B S Bhushan</div></div><div class="m_-7638545686268666740m_64394283556743969HOEnZb"><div class="m_-7638545686268666740m_64394283556743969h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <span dir="ltr"><<a href="mailto:vh261281@dal.ca" target="_blank">vh261281@dal.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space">
I think the input to dos.x (I call it <a href="http://dos.in" target="_blank">dos.in</a>) looks like this:
<div><br>
</div>
<div> &DOS<br>
outdir='./'<br>
prefix=‘graphene'<br>
fildos=‘graphene.dos',<br>
Emin=-10.0, Emax=16, DeltaE=0.002<br>
/</div>
<div><br>
</div>
<div>You run dos.x after the nscf run. I think the <a href="http://nscf.in" target="_blank">nscf.in</a> should contain the relaxed structure.</div>
<div><br>
</div>
<div>For the definition of Emin, Emax and DeltaE, see the online dos.x manual.</div>
<div><br>
</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Vahid</div>
<div><br>
</div>
<div>Vahid Askarpour<br>
Department of Physics and Atmospheric Science<br>
Dalhousie University,<br>
Halifax, NS, Canada</div>
<div><br>
<div>
<blockquote type="cite"><div><div class="m_-7638545686268666740m_64394283556743969m_-5923798252834930914h5">
<div>On Nov 6, 2017, at 4:19 PM, B S Bhushan <<a href="mailto:ecebhushan@gmail.com" target="_blank">ecebhushan@gmail.com</a>> wrote:</div>
<br class="m_-7638545686268666740m_64394283556743969m_-5923798252834930914m_7435531516736988890Apple-interchange-newline">
</div></div><div><div><div class="m_-7638545686268666740m_64394283556743969m_-5923798252834930914h5">
<div dir="ltr">Dear Experts,
<div><br>
</div>
<div>I am trying to extract the DOS profiles for some graphene systems using Supercomputing facility.<br>
</div>
<div><br>
</div>
<div>First, I performed VC-relax and then NSCF (I have not manually updated the relaxed coordinates in the nscf input file, since nscf automatically reads them from previous scf run). Then I tried to execute dos.x, however I am getting segmentation
fault error as shown below.</div>
<div><br>
</div>
<div>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%</div>
<div>
<div> Program DOS v.6.1 (svn rev. 13369) starts on 6Nov2017 at 23:32:32</div>
<div><br>
</div>
<div> This program is part of the open-source Quantum ESPRESSO suite</div>
<div> for quantum simulation of materials; please cite</div>
<div> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);</div>
<div> URL <a href="http://www.quantum-espresso.org/" target="_blank">http://www.quantum-espresso.or<wbr>g</a>",</div>
<div> in publications or presentations arising from this work. More details at</div>
<div> <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.o<wbr>rg/quote</a></div>
<div><br>
</div>
<div> Parallel version (MPI), running on 16 processors</div>
<div> R & G space division: proc/nbgrp/npool/nimage = 16</div>
<div><br>
</div>
<div> Info: using nr1, nr2, nr3 values from input</div>
<div><br>
</div>
<div> Info: using nr1, nr2, nr3 values from input</div>
<div>forrtl: severe (174): SIGSEGV, segmentation fault occurred</div>
<div>Image PC Routine Line Source</div>
<div>dos.x 000000000073A4B1 qexml_module_mp_q 3753 qexml.f90</div>
<div>dos.x 000000000055AD27 pw_restart_mp_rea 2101 pw_restart.f90</div>
<div>dos.x 00000000005579E4 pw_restart_mp_pw_ 1057 pw_restart.f90</div>
<div>dos.x 000000000040A828 read_xml_file_ 240 read_file.f90</div>
<div>dos.x 0000000000406331 MAIN__ 95 dos.f90</div>
<div>dos.x 000000000040621C Unknown Unknown Unknown</div>
<div>libc.so.6 0000003FF541ECDD Unknown Unknown Unknown</div>
<div>dos.x 0000000000406119 Unknown Unknown Unknown</div>
</div>
<div>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%</div>
<div><br>
</div>
<div><br>
</div>
<div>I am not getting any error, if I run dos.x directly after vc-relax. However, If I run dos.x after NSCF the error appears.</div>
<div><br>
</div>
<div>The input script for vc-relax, nscf are attached with the mail here.</div>
<div><br>
</div>
<div>I thank you very much for your precious time and knowledge.</div>
<div><br>
</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>B S Bhushan</div>
<div>Ph.D Scholar,</div>
<div>ABV-IIITM Gwalior, India.</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div></div><span id="m_-7638545686268666740m_64394283556743969m_-5923798252834930914m_7435531516736988890cid:A4E30279-FA14-46BB-8E02-CEFEABC41D9D"><<a href="http://graphene.in" target="_blank">graphene.in</a>></span><span id="m_-7638545686268666740m_64394283556743969m_-5923798252834930914m_7435531516736988890cid:75617D83-8A3A-4958-B99C-36D907D8EC3B"><<a href="http://graphene_nscf.in" target="_blank">graphene_nscf.in</a><wbr>></span>_____________________________<wbr>__________________<br>
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