<div dir="ltr"><div><div>Are you sure you need that many k-points and such a big cell in the z direction?<br></div>Attached a quick-and-dirty test. Parameters are likely far from yielding converged values, but it takes 50' on a single processor of my 2007 vintage PC. Before starting a full-fledged calculation at convergence, you should experiment a bit. Also, tuning the parallelism may make a significant difference.<br><br></div>Paolo<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 25, 2016 at 5:13 PM, Abualnaja, Faris <span dir="ltr"><<a href="mailto:f.abualnaja15@imperial.ac.uk" target="_blank">f.abualnaja15@imperial.ac.uk</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">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Dear all,</p>
<p><br>
</p>
<p>I am running phonon calculations on graphene, and the calculations are taking days to complete! The calculations are run on a supercomputer and are running in parallel. I am using QE version 4.3.1, the amount of k-points that are calculated are 12x12x1 for
an MP-grid which reduces down to 19 irreducible symmetry points. My phonon input is below:</p>
<p><br>
</p>
<p></p>
<p><span style="background-color:rgb(190,190,190)">Phonon Dispersion of graphene</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> &inputph</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> recover=.true.</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> tr2_ph=1.0d-16</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> ldisp=.true.</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> nq1=12 nq2=12 nq3=1</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> prefix='graphene'</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> amass(1)=12.01</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> fildyn='graphene.dyn'</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> /</span></p>
<br>
<p></p>
<p>and part of the output is shown here:</p>
<p><br>
</p>
<p></p>
<p><span style="background-color:rgb(190,190,190)">Parallel version (MPI), running on 48 processors</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> K-points division: npool = 3</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> R & G space division: proc/pool = 16</span></p>
<p></p>
<p><span style="background-color:rgb(190,190,190)"> :</span></p>
<p><span style="background-color:rgb(190,190,190)"> :</span></p>
<p></p>
<p><span style="background-color:rgb(190,190,190)">Computing dynamical matrix for</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> q = ( 0.0000000 0.0000000 0.0000000 )</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span><span style="background-color:rgb(190,190,190)"> </span><span style="background-color:rgb(190,190,190)"> 25 Sym.Ops. (with q -> -q+G )</span></span></p>
<p><span></span></p>
<p><span style="background-color:rgb(190,190,190)"> G cutoff = 245.0079 ( 16214 G-vectors) FFT grid: ( 32, 32,600)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> number of k points= 217 Methfessel-Paxton smearing, width (Ry)= 0.0100</span></p>
<span style="background-color:rgb(190,190,190)"> :</span>
<div><span style="background-color:rgb(190,190,190)"> :<span style="background-color:rgb(255,255,255)"> </span></span></div>
<div><br>
</div>
<div>
<p><span style="background-color:rgb(190,190,190)">There are 4 irreducible representations</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Representation 1 1 modes -B_2g To be done</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Representation 2 2 modes -E_2g To be done</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Representation 3 1 modes -A_2u To be done</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span><span style="background-color:rgb(190,190,190)"> Representation 4 2 modes -E_1u To b</span><span style="background-color:rgb(190,190,190)">e done</span></span></p>
<span style="font-family:Calibri,Arial,Helvetica,sans-serif,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols;font-size:16px;background-color:rgb(190,190,190)"> :</span>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols;font-size:16px">
<span style="background-color:rgb(190,190,190)"> :<span style="background-color:rgb(255,255,255)"> </span></span></div>
<p><span style="background-color:rgb(190,190,190)">G cutoff = 245.0079 ( 259459 G-vectors) FFT grid: ( 32, 32,600)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Largest allocated arrays est. size (Mb) dimensions</span></p>
<p><span><span style="background-color:rgb(190,190,190)"> </span><span style="background-color:rgb(190,190,190)"> Kohn-Sham Wavefunctions 0.34 Mb ( 2220, 10)</span></span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> NL pseudopotentials 0.07 Mb ( 2220, 2)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Each V/rho on FFT grid 0.59 Mb ( 38912)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Each G-vector array 0.12 Mb ( 16224)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> G-vector shells 0.05 Mb ( 6856)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Largest temporary arrays est. size (Mb) dimensions</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Auxiliary wavefunctions 1.35 Mb ( 2220, 40)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Each subspace H/S matrix 0.02 Mb ( 40, 40)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Each <psi_i|beta_j> matrix 0.00 Mb ( 2, 10)</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> The potential is recalculated from file :</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> ./_ph0/graphene.save/charge-density.dat</span></p>
<p><span></span><br>
</p>
<p><span> <span style="background-color:rgb(190,190,190)"> Starting wfc are 8 atomic + 2 random wfc</span></span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> total cpu time spent up to now is 2.64
</span><span style="background-color:rgb(190,190,190)">secs</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> per-process dynamical memory: 15.0 Mb</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Band Structure Calculation</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> Davidson diagonalization with overlap</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> c_bands: 1 eigenvalues not converged</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> c_bands: 1 eigenvalues not converged</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> c_bands: 1 eigenvalues not converged</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> c_bands: 1 eigenvalues not converged</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> c_bands: 1 eigenvalues not converged</span></p>
<p><span></span><br>
</p>
<p><span><span style="background-color:rgb(190,190,190)"> </span><span style="background-color:rgb(190,190,190)"> ethr = 1.25E-10, avg # of iterations = 63.7</span></span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> total cpu time spent up to now is 4392.92
</span><span style="background-color:rgb(190,190,190)">secs</span></p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span></span><br>
</p>
<span style="background-color:rgb(190,190,190)"></span>
<p><span style="background-color:rgb(190,190,190)"> End of band structure calculation</span></p>
<br>
</div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols;font-size:16px;background-color:rgb(190,190,190)"> :</span>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols;font-size:16px">
<span style="background-color:rgb(190,190,190)"> :<span style="background-color:rgb(255,255,255)"> </span></span></div>
<div><br>
</div>
Any suggestions on how to speed up the process and if I am missing something?! Thank you in advance for all your kind help and time.</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Faris</div>
<div>Imperial<br>
<p></p>
<p><br>
</p>
</div>
</div>
</div>
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