In my opinion 93 Ry is a lot. You may use a lower cutoff for optimizing the structure, refining it later (discovering maybe that very little changes). Also note that convergence thresholds etot_conv_thr = 1.0D-5 , forc_conv_thr = 1.95D-6 are very strict (too much in my opinion: the code will go on forever performing tiny steps very close to convergence). Also scf convergence threshold conv_thr = 1D-10 is too strict in my opinion: the code reduces it anyway while approaching convergence.
For parallelism: make tests with a single scf iteration, experiment with different parallelization levels, and do not assume that using all available processors is always the best choice. Mixed MPI-OpenMP parallelization might work better than an all-MPI one.. Paolo On Wed, Sep 2, 2015 at 9:55 PM, Bang C. Huynh <[email protected]> wrote: > Dear Pascal & Paolo, > > Thank you for your replies. Although it's true that I'm using USPP, > there's uranium involved and the pseudopotential file (generated from the > PSlibrary > for the ld1.x atomic code) suggests a minimum value of 93 for Ecutwfc, > hence the high Ecutwfc used in my input. I'm a bit hesitant to lower this, > as I'm not sure how much accuracy will be compromised. > > I'll play around with the k-grid to see if I can use a coarser one, > perhaps 2x2x1. Currently with 4x4x2 there are 18 non-equivalent k-points in > total, which I do agree are a bit much. > > If you are interested here's the output file (incomplete): > https://dl.dropboxusercontent.com/u/21657676/skutU0.125_vc.vc2.out > > > > Regards, > --- > > > *Bang C. Huynh*Peterhouse > University of Cambridge > CB2 1RD > The United Kingdom > > On 02-09-2015 12:00, [email protected] wrote: > > > > Message: 6 > Date: Tue, 1 Sep 2015 22:03:49 +0200 > From: Pascal Boulet <[email protected]> > Subject: Re: [Pw_forum] Effective parallel implementation? > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="windows-1252" > > Hello Bang, > > For comparison, in my case I have been able to run a vc-relax job on 92 > atoms, 48 cores in 12 hours. I am using USPP, gamma point calculation and no > symmetry. This is a slab. I am using a basic command line: mpirun -np 40 pw.x > < input > output. > > Of course, I do not know if our computers are comparable, but it seems that > your performance could be improved, probably through compilation > optimization. I am using national supercomputer facility and QE was installed > by a system manager, so I cannot give compilation details. > > I have noted a few things in your input that I (personally) would change: > Energy convergence=1d-7 > Force convergence=1d-4 eventually 1d-5 if you plan to compute phonons (in any > case it should not be smaller than energy convergence) > conv_thr=1d-8 (or smaller ? 1d-9, 1d-10 -- in case of phonon calculations > only) > It seems that your are using USPP, so in this case I think you can reduce > Ecutwfc to between 30-50, but you have to test this, and Ecutrho should be > between 8 and 12 times Ecutwfc. > Check also if you can reduce the number of k-points: your cell seems to be > rather large. > > HTH > Pascal > > > Le 1 sept. 2015 ? 21:18, Bang C. Huynh <[email protected]> a ?crit : > > Dear all, I am currently attempting to perform several structural > relaxation calculations on supercells that contain at least ~70 atoms (and > even more, say hundreds). My calculations are being done on a single node > with 40 cores, 2.4 GHz, Intel Xeon E5-2676v3 and 160 GiB memory > (m4.10xlarge Amazon EC2). I am just wondering if my implementation for > parallelism is 'reasonable' in the sense that the resources are fully > utilised, and not in some way underutilised or poorly distributed. I'm > pretty new to this so I'm not sure what to expect... Should I be happy with > the current performance, can it be better, or should I consider deploying > more resources and is it worth it? Currently one scf iteration takes around > 5-7 minutes. Scf-convergence is achieved after around 50 scf iterations, > and I'm not sure how long it's going to take for the vc-relax iterations to > converge... The input file is shown below. I use this command to initiate > the job: > > mpirun -np 40 pw.x -npool 2 -ndiag 36 < skutU0.125_vc.vc2 > > skutU0.125_vc.vc2.out > > Thank you for your help. Regards, -- Bang C. Huynh Peterhouse University > of Cambridge CB2 1RD The United Kingdom ========input======= > > &CONTROL title = skutterudite-U-doped , calculation = 'vc-relax' , outdir > = './' , wfcdir = './' , pseudo_dir = '../pseudo/' , prefix = > 'skutU0.125_vc' , etot_conv_thr = 1.0D-5 , forc_conv_thr = 1.95D-6 , nstep > = 250 , dt = 150 , / &SYSTEM ibrav = 6, celldm(1) = 17.06 celldm(3) = 2, > nat = 66, ntyp = 3, ecutwfc = 93 , ecutrho = 707 , occupations = 'smearing' > , starting_spin_angle = .false. , degauss = 0.02 , smearing = > 'methfessel-paxton' , / &ELECTRONS conv_thr = 1D-10 , / &IONS / &CELL > cell_dynamics = 'damp-w' , cell_dofree = 'all' , / ATOMIC_SPECIES Co > 58.93000 Co.pz-nd-rrkjus.UPF Sb 121.76000 Sb.pz-bhs.UPF U 238.02891 > U.pz-spfn-rrkjus_psl.1.0.0.UPF ATOMIC_POSITIONS crystal Co 0.250000000 > 0.250000000 0.125000000 0 0 0 Co 0.250000000 0.250000000 0.625000000 0 0 0 > Co 0.750000000 0.750000000 0.375000000 0 0 0 Co 0.750000000 0.750000000 > 0.875000000 0 0 0 Co 0.750000000 0.750000000 0.125000000 0 0 0 Co > 0.750000000 0.750000000 0.625000000 0 0 0 Co 0.250000000 0.250000000 > 0.375000000 0 0 0 Co 0.250000000 0.250000000 0.875000000 0 0 0 Co > 0.750000000 0.250000000 0.375000000 0 0 0 Co 0.750000000 0.250000000 > 0.875000000 0 0 0 Co 0.250000000 0.750000000 0.125000000 0 0 0 Co > 0.250000000 0.750000000 0.625000000 0 0 0 Co 0.250000000 0.750000000 > 0.375000000 0 0 0 Co 0.250000000 0.750000000 0.875000000 0 0 0 Co > 0.750000000 0.250000000 0.125000000 0 0 0 Co 0.750000000 0.250000000 > 0.625000000 0 0 0 Sb 0.000000000 0.337592989 0.078553498 Sb 0.000000000 > 0.337592989 0.578553498 Sb 0.000000000 0.662407041 0.421446502 Sb > 0.000000000 0.662407041 0.921446502 Sb 0.000000000 0.662407041 0.078553498 > Sb 0.000000000 0.662407041 0.578553498 Sb 0.000000000 0.337592989 > 0.421446502 Sb 0.000000000 0.337592989 0.921446502 Sb 0.157106996 > 0.000000000 0.168796495 Sb 0.157106996 0.000000000 0.668796480 Sb > 0.842893004 0.000000000 0.331203520 Sb 0.842893004 0.000000000 0.831203520 > Sb 0.157106996 0.000000000 0.331203520 Sb 0.157106996 0.000000000 > 0.831203520 Sb 0.842893004 0.000000000 0.168796495 Sb 0.842893004 > 0.000000000 0.668796480 Sb 0.337592989 0.157106996 0.000000000 Sb > 0.337592989 0.157106996 0.500000000 Sb 0.662407041 0.842893004 0.000000000 > Sb 0.662407041 0.842893004 0.500000000 Sb 0.662407041 0.157106996 > 0.000000000 Sb 0.662407041 0.157106996 0.500000000 Sb 0.337592989 > 0.842893004 0.000000000 Sb 0.337592989 0.842893004 0.500000000 Sb > 0.500000000 0.837592959 0.328553498 Sb 0.500000000 0.837592959 0.828553498 > Sb 0.500000000 0.162407011 0.171446502 Sb 0.500000000 0.162407011 > 0.671446502 Sb 0.500000000 0.162407011 0.328553498 Sb 0.500000000 > 0.162407011 0.828553498 Sb 0.500000000 0.837592959 0.171446502 Sb > 0.500000000 0.837592959 0.671446502 Sb 0.657106996 0.500000000 0.418796480 > Sb 0.657106996 0.500000000 0.918796480 Sb 0.342893004 0.500000000 > 0.081203505 Sb 0.342893004 0.500000000 0.581203520 Sb 0.657106996 > 0.500000000 0.081203505 Sb 0.657106996 0.500000000 0.581203520 Sb > 0.342893004 0.500000000 0.418796480 Sb 0.342893004 0.500000000 0.918796480 > Sb 0.837592959 0.657106996 0.250000000 Sb 0.837592959 0.657106996 > 0.750000000 Sb 0.162407011 0.342893004 0.250000000 Sb 0.162407011 > 0.342893004 0.750000000 Sb 0.162407011 0.657106996 0.250000000 Sb > 0.162407011 0.657106996 0.750000000 Sb 0.837592959 0.342893004 0.250000000 > Sb 0.837592959 0.342893004 0.750000000 U 0.000000000 0.000000000 > 0.000000000 U 0.000000000 0.000000000 0.500000000 K_POINTS automatic 4 4 2 > 0 0 0 > > _______________________________________________ Pw_forum mailing list > [email protected] http://pwscf.org/mailman/listinfo/pw_forum > > -- > Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE > Aix-Marseille Universit? - ST JEROME - Avenue Escadrille Normandie Niemen - > 13013 Marseille > T?l: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > Site : http://allos.up.univ-mrs.fr/pascal - Email : [email protected] > Afin de respecter l'environnement, merci de n'imprimer cet email que si > n?cessaire. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150901/e196c6be/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Tue, 1 Sep 2015 22:41:53 +0200 > From: Paolo Giannozzi <[email protected]> > Subject: Re: [Pw_forum] Effective parallel implementation? > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCuVHov+w+7sG=iynz7lff441p+urr5nm5nqer6mm7g...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Tue, Sep 1, 2015 at 9:18 PM, Bang C. Huynh <[email protected]> wrote: > > The input file is shown below > > performances are better estimated from the output, rather than the input. > What is useful in particular is the final printout with timings. It is > sufficient to do it for a single scf step. > > Paolo > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
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