March 2018 - Nek5000-users - mailman3.cels.anl.gov

'comp_vort3' in 2D
by nek5000-users＠lists.mcs.anl.gov 01 Apr '18

01 Apr '18

Hello neks, I am using 'comp_vort3' for a 2D flow, with a forcing in x direction, call comp_vort3 (vort, w1, w2, vx, vy, vz) call outpost (vort(1,1), vort(1,2), vort(1,3), pr, t, 'vrt') In this case, the x and y component of vorticity should be trivial, and only z component should remain. However I am getting a non-zero component of x-component, vort(1,1) while vort(1,2) and vort(1,3) are zero. However if I add a z-direction, comp_vort3 returns a non-zero value of vort(1,3) and the x and y-components are zero, which should be the case. So my question is, in 2D, does comp_vort3 return only one value which is in vort(1,1)? The vorticity fields in both cases look sort of similar. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech.

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Re: [Nek5000-users] Guidelines for Tolerances
by nek5000-users＠lists.mcs.anl.gov 31 Mar '18

31 Mar '18

Your tolerances look good to me. Typically 1e-5 for pressure is accurate enough. Note, in the Pn/Pn-2 formulation the tolerance is equivalent to the desired divergence error. This is in contract to Pn/Pn where such a relation does not exists. In most cases the divergence error is dominated by the spatial resolution. That's something you can try - just lower the tol to say 1e-5. If you'll get a similiar divergence error (compared to 1e-8) try to lower it even further. -- Stefan -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Saturday 31st March 2018 11:07 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Guidelines for Tolerances > > Dear Nek experts, > > sorry, my first mail was incomplete. I will start again. > > I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. > The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. > > In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. > > The log for one timestep is given below (sorry about the formatting). > As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. > Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? > > Best regards, > Steffen > > > Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 > Solving for Hmholtz scalars > 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 > 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 > 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 > 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 > 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 > 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 > 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 > 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 > 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 > 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 > 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 > 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 > 99999 Scalars done 8.5000E+02 1.7601E-01 > Solving for fluid > 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 > 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 > 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 > 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 > 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 > 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 > 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 > 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 > 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 > 99999 Fluid done 8.5000E+02 1.2875E-01 > ________________________________________ > Von: Straub, Steffen (ISTM) > Gesendet: Samstag, 31. März 2018 10:45 > An: nek5000-users(a)lists.mcs.anl.gov > Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 > > Dear Nek experts, > > I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. > The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. > > > ________________________________________ > Von: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> im Auftrag von nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> > Gesendet: Freitag, 30. März 2018 17:02 > An: nek5000-users(a)lists.mcs.anl.gov > Betreff: Nek5000-users Digest, Vol 109, Issue 32 > > Send Nek5000-users mailing list submissions to > nek5000-users(a)lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) > 4. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Mar 2018 15:34:49 +0200 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > Subject: Re: [Nek5000-users] logfile > Message-ID: > <mailman.12194.1522416912.19102.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset=utf-8 > > That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: > > * Specify the parameters below in usrdat3 of your usr file. > * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure > > -- > Stefan > > -----Original message----- > > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > > Sent: Friday 30th March 2018 14:19 > > To: nek5000-users(a)lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > Thanks, Paul, > > Could you please tell me the parameters in terms of ###.par file. > > I am using the latest version. > > > > Thank you > > > > On Fri, Mar 30, 2018 at 5:35 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > > > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > > orders of magnitude reduction in residual and are working only with 16 > > > significant digits. It seems like you might need to change your .rea file in > > > the following way: > > > > > > > > > set p21 and p22 to 0 > > > > > > > > > set p24, tolrel , to 1.e-3 > > > > > > set p25, tolabs, to 1.e-3 > > > > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > > analytic convergence study where you know the answer to an infinite number > > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > > residual tolerances are set conservatively based on these input values. > > > > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > > > > You have 17 iterations for the moment equations. > > > > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > > for the pressure residual tolerance). > > > > > > > > > hth, > > > > > > Paul > > > > > > > > > ________________________________ > > > From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > > > nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > > > Sent: Friday, March 30, 2018 4:52:26 AM > > > To: nek5000-users(a)lists.mcs.anl.gov > > > Subject: Re: [Nek5000-users] logfile > > > > > > The following is my logfile entry (sample lines). The first line is > > > understandable. What do the values in the third and following lines > > > denote? > > > > > > > > > ------------------------------------------------------ > > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > > 3.5403E+00 > > > Solving for Hmholtz scalars > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > > Solving for fluid > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > > -------------------------------------------------------- > > > > > > On Fri, Mar 30, 2018 at 3:05 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > >> I am not sure what you are talking about? > > >> > > >> -----Original message----- > > >>> From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > > >>> Sent: Friday 30th March 2018 10:30 > > >>> To: nek5000-users(a)lists.mcs.anl.gov > > >>> Subject: [Nek5000-users] logfile > > >>> > > >>> Hi Neks, > > >>> > > >>> What are the entries in the logfile that is output from running > > >>> the code. Please let me know where the entries are determined in the > > >>> code. > > >>> > > >>> Thanks > > >>> Swarandeep > > >>> _______________________________________________ > > >>> Nek5000-users mailing list > > >>> Nek5000-users(a)lists.mcs.anl.gov > > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >>> > > >> _______________________________________________ > > >> Nek5000-users mailing list > > >> Nek5000-users(a)lists.mcs.anl.gov > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users(a)lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users(a)lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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Guidelines for Tolerances
by nek5000-users＠lists.mcs.anl.gov 31 Mar '18

31 Mar '18

Dear Nek experts, sorry, my first mail was incomplete. I will start again. I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. The log for one timestep is given below (sorry about the formatting). As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? Best regards, Steffen Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 Solving for Hmholtz scalars 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 99999 Scalars done 8.5000E+02 1.7601E-01 Solving for fluid 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 99999 Fluid done 8.5000E+02 1.2875E-01 ________________________________________ Von: Straub, Steffen (ISTM) Gesendet: Samstag, 31. März 2018 10:45 An: nek5000-users(a)lists.mcs.anl.gov Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 Dear Nek experts, I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. ________________________________________ Von: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> im Auftrag von nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Gesendet: Freitag, 30. März 2018 17:02 An: nek5000-users(a)lists.mcs.anl.gov Betreff: Nek5000-users Digest, Vol 109, Issue 32 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) 2. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) 3. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) 4. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 30 Mar 2018 15:34:49 +0200 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] logfile Message-ID: <mailman.12194.1522416912.19102.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset=utf-8 That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: * Specify the parameters below in usrdat3 of your usr file. * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure -- Stefan -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 30th March 2018 14:19 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks, Paul, > Could you please tell me the parameters in terms of ###.par file. > I am using the latest version. > > Thank you > > On Fri, Mar 30, 2018 at 5:35 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > orders of magnitude reduction in residual and are working only with 16 > > significant digits. It seems like you might need to change your .rea file in > > the following way: > > > > > > set p21 and p22 to 0 > > > > > > set p24, tolrel , to 1.e-3 > > > > set p25, tolabs, to 1.e-3 > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > analytic convergence study where you know the answer to an infinite number > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > residual tolerances are set conservatively based on these input values. > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > You have 17 iterations for the moment equations. > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > for the pressure residual tolerance). > > > > > > hth, > > > > Paul > > > > > > ________________________________ > > From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > > nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > > Sent: Friday, March 30, 2018 4:52:26 AM > > To: nek5000-users(a)lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > The following is my logfile entry (sample lines). The first line is > > understandable. What do the values in the third and following lines > > denote? > > > > > > ------------------------------------------------------ > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > 3.5403E+00 > > Solving for Hmholtz scalars > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > Solving for fluid > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > -------------------------------------------------------- > > > > On Fri, Mar 30, 2018 at 3:05 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > >> I am not sure what you are talking about? > >> > >> -----Original message----- > >>> From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > >>> Sent: Friday 30th March 2018 10:30 > >>> To: nek5000-users(a)lists.mcs.anl.gov > >>> Subject: [Nek5000-users] logfile > >>> > >>> Hi Neks, > >>> > >>> What are the entries in the logfile that is output from running > >>> the code. Please let me know where the entries are determined in the > >>> code. > >>> > >>> Thanks > >>> Swarandeep > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users(a)lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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Re: [Nek5000-users] Nek5000-users Digest, Vol 109, Issue 32
by nek5000-users＠lists.mcs.anl.gov 31 Mar '18

31 Mar '18

Dear Nek experts, I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. ________________________________________ Von: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> im Auftrag von nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Gesendet: Freitag, 30. März 2018 17:02 An: nek5000-users(a)lists.mcs.anl.gov Betreff: Nek5000-users Digest, Vol 109, Issue 32 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) 2. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) 3. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) 4. Re: logfile (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 30 Mar 2018 15:34:49 +0200 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] logfile Message-ID: <mailman.12194.1522416912.19102.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset=utf-8 That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: * Specify the parameters below in usrdat3 of your usr file. * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure -- Stefan -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 30th March 2018 14:19 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks, Paul, > Could you please tell me the parameters in terms of ###.par file. > I am using the latest version. > > Thank you > > On Fri, Mar 30, 2018 at 5:35 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > orders of magnitude reduction in residual and are working only with 16 > > significant digits. It seems like you might need to change your .rea file in > > the following way: > > > > > > set p21 and p22 to 0 > > > > > > set p24, tolrel , to 1.e-3 > > > > set p25, tolabs, to 1.e-3 > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > analytic convergence study where you know the answer to an infinite number > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > residual tolerances are set conservatively based on these input values. > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > You have 17 iterations for the moment equations. > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > for the pressure residual tolerance). > > > > > > hth, > > > > Paul > > > > > > ________________________________ > > From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > > nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > > Sent: Friday, March 30, 2018 4:52:26 AM > > To: nek5000-users(a)lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > The following is my logfile entry (sample lines). The first line is > > understandable. What do the values in the third and following lines > > denote? > > > > > > ------------------------------------------------------ > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > 3.5403E+00 > > Solving for Hmholtz scalars > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > Solving for fluid > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > -------------------------------------------------------- > > > > On Fri, Mar 30, 2018 at 3:05 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > >> I am not sure what you are talking about? > >> > >> -----Original message----- > >>> From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > >>> Sent: Friday 30th March 2018 10:30 > >>> To: nek5000-users(a)lists.mcs.anl.gov > >>> Subject: [Nek5000-users] logfile > >>> > >>> Hi Neks, > >>> > >>> What are the entries in the logfile that is output from running > >>> the code. Please let me know where the entries are determined in the > >>> code. > >>> > >>> Thanks > >>> Swarandeep > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users(a)lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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pretex error when reading BC from file with no velocity field and passive scalars
by nek5000-users＠lists.mcs.anl.gov 30 Mar '18

30 Mar '18

Dear Neks, I am constructing a mesh for conjugate heat transfer simulations. My temperature is a passive scalar and I want to add more passive scalars. However, when I am combining fluid-solid rea files with pretex (choosing option 3), I get the following error while reading boundary conditions of solids (only the relevant part is pasted here, I can upload the whole output if necessary): > Showing only 90 elements of 142912 > input name of new .rea file > walls_gen > Found 0 curve sides. > IFLD: 2 3 F T > ***** THERMAL BOUNDARY CONDITIONS ***** > ***** THERMAL BOUNDARY CONDITIONS *****$ > I 11 0.00000 0.00000 0.00000 0.00000 0.00000 > I 11 0.00000 0.00000 0.00000 0.00000 0.00000$ > made it to: 10640 6 > nelin,ifld: 10640 3 > Error reading boundary conditions. Returning. > start locglob_lexico: 8 142912 1143296 2.00000009E-03 > locglob: 1 1 1143296 > locglob: 2 137 1143296 > locglob: 3 5287 1143296 > locglob: 1 153323 1143296 > locglob: 2 153323 1143296 > locglob: 3 153323 1143296 > locglob: 1 153323 1143296 > locglob: 2 153323 1143296 > locglob: 3 153323 1143296 > Performing unique_vertex2 self_chk 1143296 > done locglob_lexico: 153323 153323 1143296 8 > Performing makecell self_chk 1143296 > > *** MIDWAY BREAK MENU *** Note the two lines that end with $, which I think are the indication of the problem. My solid walls have exactly 10640 elements. I think the issue is in the file build.f at line https://github.com/Nek5000/Nek5000/blob/f0a6dd029cd2116fbfdbb1f6e7bfbfdd180… which IMHO should be executed outside of the do loop that starts a line before. The header for no fluid BCs should not be read in the do loop, because this field is not processed. The header of currently processed field is read inside imp_bc function at line https://github.com/Nek5000/Nek5000/blob/f0a6dd029cd2116fbfdbb1f6e7bfbfdd180… and printed after that. In the output above, these are the four lines with two of them ending with $. The third and fourth of those lines should be 'PASSIVE SCALAR 1 BOUNDARY CONDITIONS', not the boundary condition for the first element itself. After rotating lines 1282 and 1283 my mesh gets properly constructed. However, I am not aware of other use cases that would require dummy reading inside the loop if the velocity field is not present. Should I open an issue about this in the github repository or maybe provide a simplified example? Best regards, Jure Oder

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Re: [Nek5000-users] logfile
by nek5000-users＠lists.mcs.anl.gov 30 Mar '18

30 Mar '18

Some random observations/comments from the logfile: - Please use the latest offical replease (available as a tarball) instead of the master branch on GitHub - Your're using a dimensional setup with (unreasonably) tight tolerances (as discussed) - Is your flow incompressible? -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 30th March 2018 15:33 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Please find the attached link with permissions enabled > logfile <https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=…>or try the link: > > https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=… <https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=…> > > On Fri, Mar 30, 2018 at 6:54 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > Can you please change the permissions such that everyone with the link can read it. Thanks! > > -----Original message----- > > From:[email protected] <mailto:From%[email protected]> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> > > Sent: Friday 30th March 2018 13:42 > > To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > > Subject: Re: [Nek5000-users] logfile > > > > Please find the link for the logfile > > logfile <https://drive.google.com/file/d/17OwfMBxok-h5Uy2QWtKGnQUYVBEiG5wC/view?usp=… <https://drive.google.com/file/d/17OwfMBxok-h5Uy2QWtKGnQUYVBEiG5wC/view?usp=…>> > > > > On Fri, Mar 30, 2018 at 4:59 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > Can you please attach your logfile? > > > > > > -----Original message----- > > > From:[email protected] <mailto:From%[email protected]> <mailto:From%[email protected] <mailto:From%[email protected]>> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > Sent: Friday 30th March 2018 13:21 > > > To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > Subject: Re: [Nek5000-users] logfile > > > > > > Thanks for the information. > > > > > > In my calculation, I am using a variable viscosity formulation. The > > > viscosity depends on the temperature. As the run proceeds the initial > > > residual for the TEMP gradually rises from 1E+03 until at around at > > > the value 6E+07, the logfile shows an error for non-positive > > > diffusivity. I have checked the temperature distribution which has no > > > such value so as to make the diffusivity negative (or zero). Please > > > indicate what I may be doing wrong. > > > > > > Thank you > > > Swarandeep > > > > > > On Fri, Mar 30, 2018 at 3:30 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > > > > > > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 > > > > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration > > > > > > > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance > > > > > > > > ... > > > > > > > > > > > > -----Original message----- > > > >> From:[email protected] <mailto:From%[email protected]> <mailto:From%[email protected] <mailto:From%[email protected]>> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > >> Sent: Friday 30th March 2018 11:52 > > > >> To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > >> Subject: Re: [Nek5000-users] logfile > > > >> > > > >> The following is my logfile entry (sample lines). The first line is > > > >> understandable. What do the values in the third and following lines > > > >> denote? > > > >> > > > >> > > > >> ------------------------------------------------------ > > > >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > > >> 3.5403E+00 > > > >> Solving for Hmholtz scalars > > > >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > >> 1520 Scalars done 7.6000E-02 8.3823E-02 > > > >> Solving for fluid > > > >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > > >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > > >> 1.0000E-10 7.8799E-01 3.0171E+00 > > > >> 1520 Fluid done 7.6000E-02 3.3650E+00 > > > >> -------------------------------------------------------- > > > >> > > > >> On Fri, Mar 30, 2018 at 3:05 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > > >> > I am not sure what you are talking about? > > > >> > > > > >> > -----Original message----- > > > >> >> From:[email protected] <mailto:From%[email protected]> <mailto:From%[email protected] <mailto:From%[email protected]>> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > >> >> Sent: Friday 30th March 2018 10:30 > > > >> >> To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > >> >> Subject: [Nek5000-users] logfile > > > >> >> > > > >> >> Hi Neks, > > > >> >> > > > >> >> What are the entries in the logfile that is output from running > > > >> >> the code. Please let me know where the entries are determined in the > > > >> >> code. > > > >> >> > > > >> >> Thanks > > > >> >> Swarandeep > > > >> >> _______________________________________________ > > > >> >> Nek5000-users mailing list > > > >> >> Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > >> >> > > > >> > _______________________________________________ > > > >> > Nek5000-users mailing list > > > >> > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > >> _______________________________________________ > > > >> Nek5000-users mailing list > > > >> Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > >> > > > > _______________________________________________ > > > > Nek5000-users mailing list > > > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Re: [Nek5000-users] logfile
by nek5000-users＠lists.mcs.anl.gov 30 Mar '18

30 Mar '18

That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: * Specify the parameters below in usrdat3 of your usr file. * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure -- Stefan -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 30th March 2018 14:19 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks, Paul, > Could you please tell me the parameters in terms of ###.par file. > I am using the latest version. > > Thank you > > On Fri, Mar 30, 2018 at 5:35 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > orders of magnitude reduction in residual and are working only with 16 > > significant digits. It seems like you might need to change your .rea file in > > the following way: > > > > > > set p21 and p22 to 0 > > > > > > set p24, tolrel , to 1.e-3 > > > > set p25, tolabs, to 1.e-3 > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > analytic convergence study where you know the answer to an infinite number > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > residual tolerances are set conservatively based on these input values. > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > You have 17 iterations for the moment equations. > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > for the pressure residual tolerance). > > > > > > hth, > > > > Paul > > > > > > ________________________________ > > From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > > nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > > Sent: Friday, March 30, 2018 4:52:26 AM > > To: nek5000-users(a)lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > The following is my logfile entry (sample lines). The first line is > > understandable. What do the values in the third and following lines > > denote? > > > > > > ------------------------------------------------------ > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > 3.5403E+00 > > Solving for Hmholtz scalars > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > Solving for fluid > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > -------------------------------------------------------- > > > > On Fri, Mar 30, 2018 at 3:05 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > >> I am not sure what you are talking about? > >> > >> -----Original message----- > >>> From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > >>> Sent: Friday 30th March 2018 10:30 > >>> To: nek5000-users(a)lists.mcs.anl.gov > >>> Subject: [Nek5000-users] logfile > >>> > >>> Hi Neks, > >>> > >>> What are the entries in the logfile that is output from running > >>> the code. Please let me know where the entries are determined in the > >>> code. > >>> > >>> Thanks > >>> Swarandeep > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users(a)lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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Re: [Nek5000-users] logfile
by nek5000-users＠lists.mcs.anl.gov 30 Mar '18

30 Mar '18

>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration >1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 timestep, solve type, iteration counter, final residual, initial residual, solver tolerance ... -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 30th March 2018 11:52 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > The following is my logfile entry (sample lines). The first line is > understandable. What do the values in the third and following lines > denote? > > > ------------------------------------------------------ > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > 3.5403E+00 > Solving for Hmholtz scalars > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > 1520 Scalars done 7.6000E-02 8.3823E-02 > Solving for fluid > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > 1.0000E-10 7.8799E-01 3.0171E+00 > 1520 Fluid done 7.6000E-02 3.3650E+00 > -------------------------------------------------------- > > On Fri, Mar 30, 2018 at 3:05 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > I am not sure what you are talking about? > > > > -----Original message----- > >> From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > >> Sent: Friday 30th March 2018 10:30 > >> To: nek5000-users(a)lists.mcs.anl.gov > >> Subject: [Nek5000-users] logfile > >> > >> Hi Neks, > >> > >> What are the entries in the logfile that is output from running > >> the code. Please let me know where the entries are determined in the > >> code. > >> > >> Thanks > >> Swarandeep > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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logfile
by nek5000-users＠lists.mcs.anl.gov 30 Mar '18

30 Mar '18

Hi Neks, What are the entries in the logfile that is output from running the code. Please let me know where the entries are determined in the code. Thanks Swarandeep

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Re: [Nek5000-users] Maximum number of history points using hpts()
by nek5000-users＠lists.mcs.anl.gov 30 Mar '18

30 Mar '18

A Nek5000 run on NP ranks with (in total) 359640 history points requires lhis >= 359640/NP + 1. I don't see why with lhis = 359641 you need more than 1 MPI ranks. At least from a history point memory perspective. -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 30th March 2018 10:30 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > > I have increased the number of MPI ranks and it worked just fine. > Thank you, > > Best regards, > > Arnold > > > Le 30/03/2018 à 09:48, > nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> a écrit : > Hi so lhis is equal to 359641 and I'm using 7 ranks.. However I > can try and increase that value (which I will try immediately). > > Best, > Arnold > > Le 29/03/2018 à 17:57, nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> a > écrit : > What's your lhis? How many MPI ranks are you using? > -----Original message----- > From:[email protected] <mailto:From:[email protected]> <nek5000-users(a)lists.mcs.anl.gov> <mailto:[email protected]>Sent: Thursday 29th March 2018 17:54 > To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > I'm executing 9 times nek5000 to call hpts (using different > case.his files containing each 39960 points, using a shell script) > because I need When I'm using 359640=9*39660 points > This works perfectly fine. However when I'm trying to use a > single file in order to execute nek5000 once, it gives the > following error following error when the number of points is equal > to 359640 : > dump history points > reading history points > found 359640 points > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > (signal 11) > I guess I'm encountering some memory problems.. > Best regards, > Arnold > Le 29/03/2018 à 17:27, > nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> a écrit : > What do you mean with doesn't work anymore. How does it manifest itself? > -----Original message----- > From:[email protected] <mailto:From:[email protected]> <mailto:From:[email protected]> <mailto:From:[email protected]> <nek5000-users(a)lists.mcs.anl.gov> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]>Sent: Thursday 29th March 2018 17:23 > To: nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]>Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > Hello Pierre, > In my case my case.his file contains 39960 points and lhis=39961, > however when I increased the first value and the lhis variable > accordingly it doesn't work anymore. Is there something I'm > missing? > Best, > Arnold > Le 29/03/2018 à 16:30, > nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> a écrit : > Hi > Arnold, > You can set it in the SIZE file: > param(lhis=100) ! # of pts a proc reads from hpts.in > ! Note: lhis*np > npoints in > hpts.in > best, > Pierre > On 2018-03-29 16:14, nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> wrote: > Hi Neks, > I was wondering if there is any maximum number of history points > one should put in the case.his file. If someone could help me > regarding that topic, I haven't found any information yet. > Thank you for your time, > Best, > Arnold > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>-- > Arnold Wakim > Ph.D. Student > Département Aérodynamique, Aéroélasticité, Acoustique > INST > Tél: +33 1 46 23 51 83 > ONERA - The French Aerospace Lab - Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > Nous suivre sur : www.onera.fr <http://www.onera.fr> <http://www.onera.fr> <http://www.onera.fr> <http://www.onera.fr> <http://www.onera.fr> <http://www.onera.fr> <http://www.onera.fr> | Twitter <http://www.twitter.com/@onera_fr> <http://www.twitter.com/@onera_fr> <http://www.twitter.com/@onera_fr> <http://www.twitter.com/@onera_fr> | LinkedIn <http://www.linkedin.com/company/onera> <http://www.linkedin.com/company/onera> <http://www.linkedin.com/company/onera> <http://www.linkedin.com/company/onera> | Facebook <http://www.facebook.fr/thefrenchaerospacelab> <http://www.facebook.fr/thefrenchaerospacelab> <http://www.facebook.fr/thefrenchaerospacelab> <http://www.facebook.fr/thefrenchaerospacelab> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en /emails- terms> <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en/emails-terms>_______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]>https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>_______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected]> <mailto:[email protected]>https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>-- > Arnold Wakim > Ph.D. Student > Département Aérodynamique, Aéroélasticité, Acoustique > INST > Tél: +33 1 46 23 51 83 > ONERA - The French Aerospace Lab - Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > Nous suivre sur : www.onera.fr <http://www.onera.fr> <http://www.onera.fr> <http://www.onera.fr> | Twitter <http://www.twitter.com/@onera_fr> <http://www.twitter.com/@onera_fr> | LinkedIn <http://www.linkedin.com/company/onera> <http://www.linkedin.com/company/onera> | Facebook <http://www.facebook.fr/thefrenchaerospacelab> <http://www.facebook.fr/thefrenchaerospacelab> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en/emails-terms> <http://www.onera.fr/onera-en/emails-terms>_______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>_______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > -- > Arnold Wakim > Ph.D. Student > Département Aérodynamique, Aéroélasticité, Acoustique > INST > Tél: +33 1 46 23 51 83 > > ONERA - The French Aerospace Lab - Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur : www.onera.fr <http://www.onera.fr> | Twitter <http://www.twitter.com/@onera_fr> | > LinkedIn <http://www.linkedin.com/company/onera> | Facebook <http://www.facebook.fr/thefrenchaerospacelab> > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms <http://www.onera.fr/onera-en/emails-terms> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > -- > Arnold Wakim > Ph.D. Student > Département Aérodynamique, Aéroélasticité, Acoustique > INST > Tél: +33 1 46 23 51 83 > > ONERA - The French Aerospace Lab - Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur : www.onera.fr <http://www.onera.fr> | Twitter <http://www.twitter.com/@onera_fr> | LinkedIn <http://www.linkedin.com/company/onera> | Facebook <http://www.facebook.fr/thefrenchaerospacelab> > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms <http://www.onera.fr/onera-en/emails-terms>_______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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