From nek5000-users at lists.mcs.anl.gov Thu Nov 4 10:07:47 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 4 Nov 2010 10:07:47 -0500 Subject: [Nek5000-users] cfill with temperature Message-ID: Neks, I am attempting to reset the temperature of a certain part of my flow domain to a constant value using cfill. I have had success doing this with the x, y, and z velocities, but temperature doesn't seem to work. I have attached the pertinent code from my usrchk, I would appreciate any help! Thanks, Josh nxyz = nx1*ny1*nz1 n = nxyz*nelv if (istep.eq.0.and.time.lt.1.0) then do e=1,nelv if (xm1(2,2,2,e).gt.0.9) then call cfill(vx(1,1,1,e),1.0,nxyz) call cfill(vy(1,1,1,e),4.0,nxyz) call cfill(vz(1,1,1,e),0.0,nxyz) endif if (zm1(2,2,2,e).ge.0) then call cfill(t(1,1,1,e,1),980,nxyz) else call cfill(t(1,1,1,e,1),327,nxyz) endif if (xm1(2,2,2,e).le.-1.3) then call cfill(t(1,1,1,e,1),980,nxyz) endif enddo endif -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 4 11:45:48 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 5 Nov 2010 00:45:48 +0800 Subject: [Nek5000-users] Rayleigh Benard convection in cylindrical container In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bofu wang Date: 2010/11/5 Subject: Rayleigh Benard convection in cylindrical container To: nek5000-users at lists.mcs.anl.gov Dear all I am trying to use nek5000 to simulate Rayleigh Benard convection in a vertical cylinder with heated bottom cooled top and insulated sidewall. All the wall boundaries are set no slip. The hight to radius ratio is 1.0. The Prandtl number is 0.02 and Ra=4000. The .rea and .usr file are changed from ray_dd.rea and ray.usr in $HOME/nek5_svn/examples/benard/. The files are attached. My problem is with these files I can't get right result. Could any one help to find out where the problem is? Regards, Bofuwang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: attach00 Type: application/octet-stream Size: 15755 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 4 14:20:19 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 4 Nov 2010 14:20:19 -0500 Subject: [Nek5000-users] Laplacian as a forcing function and stability issues Message-ID: Hi, I am trying to implement a LES model which requires a term like c . Sij* to be added to the existing unfiltered viscous term. I am computing Sij* by filtering the velocity and calling comp_gije() twice. This is then included in the forcing function. This seems to work for few steps but the solution starts to blow up afterwards. I am wondering if this would be due to stability issues since the laplacian here is not calculated by any of the splitting methods. I would like to know if it would be possible to add this term to the Navier Stokes formulation that is solved each step. Any other ideas/ thoughts would be helpful. Thanks. Regards Shriram -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 4 16:28:17 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 4 Nov 2010 16:28:17 -0500 (CDT) Subject: [Nek5000-users] Rayleigh Benard convection in cylindrical container In-Reply-To: References: Message-ID: Bofuwang, We can't look at your attachment. Can you send in another format (e.g., tarfile)? Paul On Fri, 5 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > ---------- Forwarded message ---------- > From: bofu wang > Date: 2010/11/5 > Subject: Rayleigh Benard convection in cylindrical container > To: nek5000-users at lists.mcs.anl.gov > > > Dear all > I am trying to use nek5000 to simulate Rayleigh Benard convection in a > vertical cylinder with heated bottom cooled top and insulated sidewall. > All the wall boundaries are set no slip. > The hight to radius ratio is 1.0. > The Prandtl number is 0.02 and Ra=4000. > The .rea and .usr file are changed from ray_dd.rea and ray.usr in > $HOME/nek5_svn/examples/benard/. > The files are attached. > > My problem is with these files I can't get right result. > Could any one help to find out where the problem is? > > Regards, > Bofuwang > From nek5000-users at lists.mcs.anl.gov Thu Nov 4 16:30:14 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 4 Nov 2010 16:30:14 -0500 (CDT) Subject: [Nek5000-users] Laplacian as a forcing function and stability issues In-Reply-To: References: Message-ID: Hi Shriram, Do you want to send .rea/.usr/SIZE in a tarfile? I can take a look... I've been having good luck w/ dyn. smag. of late. Paul On Thu, 4 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > I am trying to implement a LES model which requires a term like c . Sij* to > be added to the existing unfiltered viscous term. I am computing Sij* by > filtering the velocity and calling comp_gije() twice. This is then included > in the forcing function. This seems to work for few steps but the solution > starts to blow up afterwards. I am wondering if this would be due to > stability issues since the laplacian here is not calculated by any of the > splitting methods. I would like to know if it would be possible to add this > term to the Navier Stokes formulation that is solved each step. Any other > ideas/ thoughts would be helpful. Thanks. > > Regards > Shriram > From nek5000-users at lists.mcs.anl.gov Thu Nov 4 17:52:50 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 4 Nov 2010 17:52:50 -0500 Subject: [Nek5000-users] Laplacian as a forcing function and stability issues In-Reply-To: References: Message-ID: Hi Paul, Thanks for offering to look into this. I have e-mailed you the files. Regards Shriram On 4 November 2010 16:30, wrote: > > Hi Shriram, > > Do you want to send .rea/.usr/SIZE in a tarfile? > > I can take a look... I've been having good luck w/ dyn. smag. > of late. > > Paul > > > > On Thu, 4 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > Hi, >> >> I am trying to implement a LES model which requires a term like c . Sij* >> to >> be added to the existing unfiltered viscous term. I am computing Sij* by >> filtering the velocity and calling comp_gije() twice. This is then >> included >> in the forcing function. This seems to work for few steps but the solution >> starts to blow up afterwards. I am wondering if this would be due to >> stability issues since the laplacian here is not calculated by any of the >> splitting methods. I would like to know if it would be possible to add >> this >> term to the Navier Stokes formulation that is solved each step. Any other >> ideas/ thoughts would be helpful. Thanks. >> >> Regards >> Shriram >> >> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 5 13:03:40 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 6 Nov 2010 02:03:40 +0800 Subject: [Nek5000-users] Rayleigh Benard convection in cylindrical problem In-Reply-To: References: Message-ID: Hello Sorry for the mistake of the attachment. The files are can be download from following link, http://email.ustc.edu.cn/coremail/XPS/nf/doGetFile.jsp?mid=1%3a1tbiAQEHDkqSNDZrHwABsm&mode=download&sid=BAStgQKKdACJYVuJdaKKVOTseaNubgzy The problem is I don't know how to set Prandtl number and Rayleigh number correctly. Would anyone help to have a check of the session files? Regards Bofuwang -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 5 13:50:15 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 5 Nov 2010 13:50:15 -0500 (CDT) Subject: [Nek5000-users] Rayleigh Benard convection in cylinder In-Reply-To: References: Message-ID: Hi Bofuwang, We are still having problems with downloading your files -- this time there was an error message "Cookie not matched!" A tarfile would be more preferable. As far as Rayleigh and Prandtl number is concerned you can modify the the variables Ra and Pr (that is currently set to viscosity, namely parameter 2 out of 123 of ray1.rea) in subroutine rayleigh_const of ray0.usr. Best, Aleks On Sat, 6 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hello > > Sorry for the mistake of the attachment. > The files are can be download from following link, > http://email.ustc.edu.cn/coremail/XPS/nf/doGetFile.jsp?mid=1%3a1tbiAQEHDkqSNDZrHwABsm&mode=download&sid=BAStgQKKdACJYVuJdaKKVOTseaNubgzy > > The problem is I don't know how to set Prandtl number and Rayleigh number > correctly. > Would anyone help to have a check of the session files? > > Regards > Bofuwang > From nek5000-users at lists.mcs.anl.gov Mon Nov 8 07:12:14 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 Nov 2010 21:12:14 +0800 Subject: [Nek5000-users] Rayleigh Benard convection in cylinder Message-ID: Hi, Aleks Thank you very much for your concern! I know how to set the parameters now. I should also thank Paul for his example files. Regards, Bofuwang -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 8 13:44:04 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 Nov 2010 14:44:04 -0500 (EST) Subject: [Nek5000-users] A small bug Message-ID: <51014.172.24.182.45.1289245444.squirrel@webmail01.uottawa.ca> Hi, in the subroutine prepost.f, line 1156 (the sixth in the following piece of code) the format for the last item in the list (i.e. " 4 NELT,NX,NY,N") should be A15 and not A12 because of the additional spaces in the string corresponding to " 4 ". Is this correct?. WRITE(24,'(4I4,1pe14.7,I5,1X,30A1,1X,A12)') $ NELGT,NX1,NY1,NZ1,TIME,ikstep,(EXCODE1(I),I=1,30), $ 'NELT,NX,NY,N' else if (nelgt.lt.10000) then WRITE(fhdfle,'(4I4,1pe14.7,I5,1X,30A1,1X,A12)') $ NELGT,NX1,NY1,NZ1,TIME,ikstep,(EXCODE1(I),I=1,30), $ ' 4 NELT,NX,NY,N' Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Mon Nov 8 13:49:41 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 Nov 2010 13:49:41 -0600 (CST) Subject: [Nek5000-users] A small bug In-Reply-To: <51014.172.24.182.45.1289245444.squirrel@webmail01.uottawa.ca> References: <51014.172.24.182.45.1289245444.squirrel@webmail01.uottawa.ca> Message-ID: Yes - good eye! I've changed this and it will be folded into the next svn update. Thanks! Paul On Mon, 8 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > in the subroutine prepost.f, line 1156 (the sixth in the following piece > of code) the format for the last item in the list (i.e. " 4 NELT,NX,NY,N") > should be A15 and not A12 because of the additional spaces in the string > corresponding to " 4 ". Is this correct?. > > WRITE(24,'(4I4,1pe14.7,I5,1X,30A1,1X,A12)') > $ NELGT,NX1,NY1,NZ1,TIME,ikstep,(EXCODE1(I),I=1,30), > $ 'NELT,NX,NY,N' > else > if (nelgt.lt.10000) then > WRITE(fhdfle,'(4I4,1pe14.7,I5,1X,30A1,1X,A12)') > $ NELGT,NX1,NY1,NZ1,TIME,ikstep,(EXCODE1(I),I=1,30), > $ ' 4 NELT,NX,NY,N' > > > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Nov 9 10:51:12 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 9 Nov 2010 10:51:12 -0600 Subject: [Nek5000-users] Conversion from .f???? to .fld Message-ID: Neks, I am trying my hand at interpolating data from an old geometry onto a new geometry (using a routine that one of the developers, Aleks, sent me). To do this, I need to be able to convert a .f????? file to a .fld file. Is this a relatively straightforward process, and if so, can someone post how to do it or send me a basic routine that does it? Thanks, Josh -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 9 11:03:36 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 9 Nov 2010 11:03:36 -0600 (CST) Subject: [Nek5000-users] Conversion from .f???? to .fld In-Reply-To: References: Message-ID: Josh, In usrdat(), set nsteps=0 param(67) = 6 ! read .f format param(66) = 4 ! write .fld format Paul On Tue, 9 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Neks, > > I am trying my hand at interpolating data from an old geometry onto a new > geometry (using a routine that one of the developers, Aleks, sent me). To > do this, I need to be able to convert a .f????? file to a .fld file. Is > this a relatively straightforward process, and if so, can someone post how > to do it or send me a basic routine that does it? Thanks, > > Josh > From nek5000-users at lists.mcs.anl.gov Tue Nov 9 14:08:46 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 9 Nov 2010 14:08:46 -0600 (CST) Subject: [Nek5000-users] cfill with temperature In-Reply-To: References: Message-ID: Sorry, I didn't see this till just now... Is it still unresolved? Paul I would propose using 980. and 327. instead of integers as the input value. Paul On Thu, 4 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Neks, > > I am attempting to reset the temperature of a certain part of my flow domain > to a constant value using cfill. I have had success doing this with the x, > y, and z velocities, but temperature doesn't seem to work. I have attached > the pertinent code from my usrchk, I would appreciate any help! Thanks, > > Josh > > nxyz = nx1*ny1*nz1 > n = nxyz*nelv > > > if (istep.eq.0.and.time.lt.1.0) then > do e=1,nelv > if (xm1(2,2,2,e).gt.0.9) then > call cfill(vx(1,1,1,e),1.0,nxyz) > call cfill(vy(1,1,1,e),4.0,nxyz) > call cfill(vz(1,1,1,e),0.0,nxyz) > endif > if (zm1(2,2,2,e).ge.0) then > call cfill(t(1,1,1,e,1),980,nxyz) > else > call cfill(t(1,1,1,e,1),327,nxyz) > endif > if (xm1(2,2,2,e).le.-1.3) then > call cfill(t(1,1,1,e,1),980,nxyz) > endif > enddo > > endif > From nek5000-users at lists.mcs.anl.gov Tue Nov 9 14:11:55 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 9 Nov 2010 14:11:55 -0600 Subject: [Nek5000-users] cfill with temperature In-Reply-To: References: Message-ID: We figured it out, we think it had something to do with our if statements. We corrected it by just setting everything to 980.0, since it's a very small portion of the domain that needed 327.0. Thanks! Josh On Tue, Nov 9, 2010 at 2:08 PM, wrote: > > Sorry, > > I didn't see this till just now... > > Is it still unresolved? > > Paul > > > I would propose using 980. and 327. instead of integers > as the input value. > > Paul > > > > On Thu, 4 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > Neks, >> >> I am attempting to reset the temperature of a certain part of my flow >> domain >> to a constant value using cfill. I have had success doing this with the >> x, >> y, and z velocities, but temperature doesn't seem to work. I have >> attached >> the pertinent code from my usrchk, I would appreciate any help! Thanks, >> >> Josh >> >> nxyz = nx1*ny1*nz1 >> n = nxyz*nelv >> >> >> if (istep.eq.0.and.time.lt.1.0) then >> do e=1,nelv >> if (xm1(2,2,2,e).gt.0.9) then >> call cfill(vx(1,1,1,e),1.0,nxyz) >> call cfill(vy(1,1,1,e),4.0,nxyz) >> call cfill(vz(1,1,1,e),0.0,nxyz) >> endif >> if (zm1(2,2,2,e).ge.0) then >> call cfill(t(1,1,1,e,1),980,nxyz) >> else >> call cfill(t(1,1,1,e,1),327,nxyz) >> endif >> if (xm1(2,2,2,e).le.-1.3) then >> call cfill(t(1,1,1,e,1),980,nxyz) >> endif >> enddo >> >> endif >> >> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke (probably) -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 10 15:23:15 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 10 Nov 2010 14:23:15 -0700 Subject: [Nek5000-users] solver tolerances and norm of residual Message-ID: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> Hello Neks. I'm wondering about some details regarding the solvers, namely in regard to the following two tolerances: P021 DIVERGENCE tolerance for the pressure solver P022 HELMHOLTZ tolerance for the velocity solver I assume these tolerances are for some norm on the residual of pressure/velocity. If so, what is the specific norm? Thanks. --Mike From nek5000-users at lists.mcs.anl.gov Fri Nov 12 09:21:39 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 12 Nov 2010 09:21:39 -0600 (CST) Subject: [Nek5000-users] RB convection with high Rayleigh numbers In-Reply-To: <277033905.51185.1289570216060.JavaMail.root@zimbra.anl.gov> References: <277033905.51185.1289570216060.JavaMail.root@zimbra.anl.gov> Message-ID: Let me echo Aleks' comments by pointing out that any experimentalist does the same thing. They don't just turn the heater on at full power at the start -- invariably they ramp it up. In nonlinear systems, it matters how you get to the state of interest... Otherwise they would wait forever for the system to settle down. Thus, this is a physics issue - not a numerics issue. Paul On Fri, 12 Nov 2010, Aleksandr Obabko wrote: > Hi David, > > The simulation would just blow up due to runaway CFL if I did not... And lowering timestep did not help. Plus usually it is quicker to reach statistically steady state for lower Ra/resolution and for the subsequent solutions restarted from a previous one with bumped up Ra/resolution as compared to one straight run at the target high Ra/resolution. > > Best, > Aleks > > > > ----- Original Message ----- > From: "David Goluskin" > To: "Aleksandr Obabko" > Sent: Thursday, November 11, 2010 9:32:10 PM > Subject: Re: [Nek5000-users] RB convection with high Rayleigh numbers > > Hi Aleks, > > Back in May you told Mani this: > > > > > A while back I was able to simulate 3D convection between stress-free surfaces at Rayleigh number Ra=1e6 (and Taylor number 5e5) with 4600 elements (and lx1=6) using time step 1e-5. > > I remember that to get to Ra=1e6 I had to get lower Ra solution first and then use it as initial condition. > > > I was just wondering why you had to do that. What would happen if you didn`t? > > Best, > > David > From nek5000-users at lists.mcs.anl.gov Fri Nov 12 10:32:04 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 12 Nov 2010 10:32:04 -0600 (CST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> Message-ID: Yes - p21 is the L2 norm of the divergence, which is the residual of the pressure solve. p22 is the norm of the residual for the velocity in the Helmholtz solve. If you are solving H u = ( -h1*Lap + h2) u = f, the iteration stops when \int h1^2 grad u . grad u + h2^2 u^2 dV / vol < tol = p22 Paul On Wed, 10 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hello Neks. > > I'm wondering about some details regarding the solvers, namely in regard to the following two tolerances: > > P021 DIVERGENCE tolerance for the pressure solver > P022 HELMHOLTZ tolerance for the velocity solver > > I assume these tolerances are for some norm on the residual of pressure/velocity. If so, what is the specific norm? > > Thanks. > --Mike > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Nov 16 10:40:31 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 11:40:31 -0500 (EST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> Message-ID: <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> Hi Nek users, I am new in using Nek5. I have succesfully simualted the lid-driven flow, rayleigh-b?nard in a square cavity and laminar poiseuille flow. All of them were 2d cases. I though it would be straightforward to move from 2D to 3D simualtions but I have not been able to run a 3D poiseuille channel. I am obtaining an error on Helmoltz solver even in the first iteration. Please, find output, usr and box files attached. Thanks in advance. .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering -------------- next part -------------- A non-text attachment was scrubbed... Name: 3dtest3.box Type: application/octet-stream Size: 453 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3dtest3.output Type: application/octet-stream Size: 23827 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3dtest3.usr Type: application/octet-stream Size: 2506 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 16 11:08:37 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 18:08:37 +0100 Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> Message-ID: <1289927317.5279.11.camel@localhost.localdomain> Hello Alex, I looked through your files & didn't see anything amiss (by the way, it would be best to post your *.rea file). Since it blows up on the first attempt to solve for pressure, perhaps the BC's don't satisfy conservation of mass? Cheers, Frank On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov wrote: > Hi Nek users, > > I am new in using Nek5. I have succesfully simualted the lid-driven flow, > rayleigh-b?nard in a square cavity and laminar poiseuille flow. All of > them were 2d cases. I though it would be straightforward to move from 2D > to 3D simualtions but I have not been able to run a 3D poiseuille channel. > I am obtaining an error on Helmoltz solver even in the first iteration. > > Please, find output, usr and box files attached. > Thanks in advance. > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universit?t Wien (Vienna University of Technology) Inst. f. Str?mungsmechanik und W?rme?bertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 16 11:56:17 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 12:56:17 -0500 (EST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <1289927317.5279.11.camel@localhost.localdomain> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> Message-ID: <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> Hi Frank, The rea file has been attached. Meanwhile I'll check the BC... Thanks > Hello Alex, > > I looked through your files & didn't see anything amiss (by the way, it > would be best to post your *.rea file). Since it blows up on the first > attempt to solve for pressure, perhaps the BC's don't satisfy > conservation of mass? > > Cheers, > Frank > > > > On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov > wrote: > >> Hi Nek users, >> >> I am new in using Nek5. I have succesfully simualted the lid-driven >> flow, >> rayleigh-b??nard in a square cavity and laminar poiseuille flow. All of >> them were 2d cases. I though it would be straightforward to move from 2D >> to 3D simualtions but I have not been able to run a 3D poiseuille >> channel. >> I am obtaining an error on Helmoltz solver even in the first iteration. >> >> Please, find output, usr and box files attached. >> Thanks in advance. >> >> .......................................... >> Alex Fabregat >> Post-doctoral fellow >> University of Ottawa >> Department of Mechanical Engineering >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- > Frank Herbert Muldoon, Ph.D. Mechanical Engineering > Technische Universit??t Wien (Vienna University of Technology) > Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid > Mechanics and Heat Transfer) > Resselgasse 3 > 1040 Wien > Tel: +4315880132232 > Fax: +4315880132299 > Cell:+436765203470 > fmuldoo (skype) > http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering -------------- next part -------------- A non-text attachment was scrubbed... Name: 3dtest3.rea Type: application/octet-stream Size: 43475 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 16 12:25:57 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 19:25:57 +0100 Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> Message-ID: <1289931957.5279.16.camel@localhost.localdomain> A quick look of the *rea file did not bring up anything. I recall an issue with periodic BC's, following is an email from one of the developers: Hi Frank, Yes -- we currently don't support periodic bcs for anything smaller than a 3 x 3 x 3 array of elements. There's a technical reason for this --- it can be circumvented if really needed, but it would not fit within the std. context. Sorry about that. Paul On Tue, 2010-11-16 at 12:56 -0500, nek5000-users at lists.mcs.anl.gov wrote: > Hi Frank, > > The rea file has been attached. > Meanwhile I'll check the BC... > > Thanks > > > Hello Alex, > > > > I looked through your files & didn't see anything amiss (by the way, it > > would be best to post your *.rea file). Since it blows up on the first > > attempt to solve for pressure, perhaps the BC's don't satisfy > > conservation of mass? > > > > Cheers, > > Frank > > > > > > > > On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov > > wrote: > > > >> Hi Nek users, > >> > >> I am new in using Nek5. I have succesfully simualted the lid-driven > >> flow, > >> rayleigh-b??nard in a square cavity and laminar poiseuille flow. All of > >> them were 2d cases. I though it would be straightforward to move from 2D > >> to 3D simualtions but I have not been able to run a 3D poiseuille > >> channel. > >> I am obtaining an error on Helmoltz solver even in the first iteration. > >> > >> Please, find output, usr and box files attached. > >> Thanks in advance. > >> > >> .......................................... > >> Alex Fabregat > >> Post-doctoral fellow > >> University of Ottawa > >> Department of Mechanical Engineering > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > -- > > Frank Herbert Muldoon, Ph.D. Mechanical Engineering > > Technische Universit??t Wien (Vienna University of Technology) > > Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid > > Mechanics and Heat Transfer) > > Resselgasse 3 > > 1040 Wien > > Tel: +4315880132232 > > Fax: +4315880132299 > > Cell:+436765203470 > > fmuldoo (skype) > > http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universit?t Wien (Vienna University of Technology) Inst. f. Str?mungsmechanik und W?rme?bertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html From nek5000-users at lists.mcs.anl.gov Tue Nov 16 12:50:51 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 13:50:51 -0500 (EST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <1289931957.5279.16.camel@localhost.localdomain> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> <1289931957.5279.16.camel@localhost.localdomain> Message-ID: <51031.172.24.182.149.1289933451.squirrel@webmail01.uottawa.ca> Hi, I think this is not the reason because in a previous attempt to face the 3D problems I tried to solve the 3D lid-driven cavity (no periodic BC) and I obtained the same error: NaN in Helholtz residual. Maybe I should start from the turbChannel example and simplify the problem to reach a laminar 3D poiseuille flow. Anyway, thanks a lot for your answers. > A quick look of the *rea file did not bring up anything. I recall an > issue with periodic BC's, following is an email from one of the > developers: > > > Hi Frank, > > Yes -- we currently don't support periodic bcs for > anything smaller than a 3 x 3 x 3 array of elements. > > There's a technical reason for this --- it can be > circumvented if really needed, but it would not > fit within the std. context. > > Sorry about that. > > Paul > > On Tue, 2010-11-16 at 12:56 -0500, nek5000-users at lists.mcs.anl.gov > wrote: >> Hi Frank, >> >> The rea file has been attached. >> Meanwhile I'll check the BC... >> >> Thanks >> >> > Hello Alex, >> > >> > I looked through your files & didn't see anything amiss (by the way, >> it >> > would be best to post your *.rea file). Since it blows up on the >> first >> > attempt to solve for pressure, perhaps the BC's don't satisfy >> > conservation of mass? >> > >> > Cheers, >> > Frank >> > >> > >> > >> > On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov >> > wrote: >> > >> >> Hi Nek users, >> >> >> >> I am new in using Nek5. I have succesfully simualted the lid-driven >> >> flow, >> >> rayleigh-b????nard in a square cavity and laminar poiseuille flow. >> All of >> >> them were 2d cases. I though it would be straightforward to move from >> 2D >> >> to 3D simualtions but I have not been able to run a 3D poiseuille >> >> channel. >> >> I am obtaining an error on Helmoltz solver even in the first >> iteration. >> >> >> >> Please, find output, usr and box files attached. >> >> Thanks in advance. >> >> >> >> .......................................... >> >> Alex Fabregat >> >> Post-doctoral fellow >> >> University of Ottawa >> >> Department of Mechanical Engineering >> >> _______________________________________________ >> >> Nek5000-users mailing list >> >> Nek5000-users at lists.mcs.anl.gov >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > >> > -- >> > Frank Herbert Muldoon, Ph.D. Mechanical Engineering >> > Technische Universit????t Wien (Vienna University of Technology) >> > Inst. f. Str????mungsmechanik und W????rme????bertragung (Institute of >> Fluid >> > Mechanics and Heat Transfer) >> > Resselgasse 3 >> > 1040 Wien >> > Tel: +4315880132232 >> > Fax: +4315880132299 >> > Cell:+436765203470 >> > fmuldoo (skype) >> > http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > >> >> >> .......................................... >> Alex Fabregat >> Post-doctoral fellow >> University of Ottawa >> Department of Mechanical Engineering >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- > Frank Herbert Muldoon, Ph.D. Mechanical Engineering > Technische Universit??t Wien (Vienna University of Technology) > Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid > Mechanics and Heat Transfer) > Resselgasse 3 > 1040 Wien > Tel: +4315880132232 > Fax: +4315880132299 > Cell:+436765203470 > fmuldoo (skype) > http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Tue Nov 16 13:30:00 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 13:30:00 -0600 (CST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <51031.172.24.182.149.1289933451.squirrel@webmail01.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> <1289931957.5279.16.camel@localhost.localdomain> <51031.172.24.182.149.1289933451.squirrel@webmail01.uottawa.ca> Message-ID: Hi Alex, I just tried your case - it ran w/o any difficulty. I wonder if there is an issue w/ your SIZE file? I've placed the one that I used in www.mcs.anl.gov/~fischer/SIZE which you can just grab. Then makenek 3dtest followed by the usual run process.... Let me know if this resolves the issue for you. Cheers, Paul F. On Tue, 16 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > I think this is not the reason because in a previous attempt to face the > 3D problems I tried to solve the 3D lid-driven cavity (no periodic BC) and > I obtained the same error: NaN in Helholtz residual. > > Maybe I should start from the turbChannel example and simplify the problem > to reach a laminar 3D poiseuille flow. > > Anyway, thanks a lot for your answers. > >> A quick look of the *rea file did not bring up anything. I recall an >> issue with periodic BC's, following is an email from one of the >> developers: >> >> >> Hi Frank, >> >> Yes -- we currently don't support periodic bcs for >> anything smaller than a 3 x 3 x 3 array of elements. >> >> There's a technical reason for this --- it can be >> circumvented if really needed, but it would not >> fit within the std. context. >> >> Sorry about that. >> >> Paul >> >> On Tue, 2010-11-16 at 12:56 -0500, nek5000-users at lists.mcs.anl.gov >> wrote: >>> Hi Frank, >>> >>> The rea file has been attached. >>> Meanwhile I'll check the BC... >>> >>> Thanks >>> >>>> Hello Alex, >>>> >>>> I looked through your files & didn't see anything amiss (by the way, >>> it >>>> would be best to post your *.rea file). Since it blows up on the >>> first >>>> attempt to solve for pressure, perhaps the BC's don't satisfy >>>> conservation of mass? >>>> >>>> Cheers, >>>> Frank >>>> >>>> >>>> >>>> On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov >>>> wrote: >>>> >>>>> Hi Nek users, >>>>> >>>>> I am new in using Nek5. I have succesfully simualted the lid-driven >>>>> flow, >>>>> rayleigh-b????nard in a square cavity and laminar poiseuille flow. >>> All of >>>>> them were 2d cases. I though it would be straightforward to move from >>> 2D >>>>> to 3D simualtions but I have not been able to run a 3D poiseuille >>>>> channel. >>>>> I am obtaining an error on Helmoltz solver even in the first >>> iteration. >>>>> >>>>> Please, find output, usr and box files attached. >>>>> Thanks in advance. >>>>> >>>>> .......................................... >>>>> Alex Fabregat >>>>> Post-doctoral fellow >>>>> University of Ottawa >>>>> Department of Mechanical Engineering >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>>> -- >>>> Frank Herbert Muldoon, Ph.D. Mechanical Engineering >>>> Technische Universit????t Wien (Vienna University of Technology) >>>> Inst. f. Str????mungsmechanik und W????rme????bertragung (Institute of >>> Fluid >>>> Mechanics and Heat Transfer) >>>> Resselgasse 3 >>>> 1040 Wien >>>> Tel: +4315880132232 >>>> Fax: +4315880132299 >>>> Cell:+436765203470 >>>> fmuldoo (skype) >>>> http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> >>> .......................................... >>> Alex Fabregat >>> Post-doctoral fellow >>> University of Ottawa >>> Department of Mechanical Engineering >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> -- >> Frank Herbert Muldoon, Ph.D. Mechanical Engineering >> Technische Universit??t Wien (Vienna University of Technology) >> Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid >> Mechanics and Heat Transfer) >> Resselgasse 3 >> 1040 Wien >> Tel: +4315880132232 >> Fax: +4315880132299 >> Cell:+436765203470 >> fmuldoo (skype) >> http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Nov 16 14:06:38 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 15:06:38 -0500 (EST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> <1289931957.5279.16.camel@localhost.localdomain> <51031.172.24.182.149.1289933451.squirrel@webmail01.uottawa.ca> Message-ID: <51380.172.24.182.149.1289937998.squirrel@webmail01.uottawa.ca> Hi Paul, it worked!! The crucial difference between my file and yours was: < parameter (lz2=lz1-2) > parameter (lz2=lz1 ) I am a little ashamed for not having seen it but the output was not giving me any clue. Thank you so much. > > Hi Alex, > > I just tried your case - it ran w/o any difficulty. > > I wonder if there is an issue w/ your SIZE file? I've > placed the one that I used in > > www.mcs.anl.gov/~fischer/SIZE > > which you can just grab. Then makenek 3dtest followed by > the usual run process.... Let me know if this resolves the > issue for you. > > Cheers, > > Paul F. > > > On Tue, 16 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi, >> >> I think this is not the reason because in a previous attempt to face the >> 3D problems I tried to solve the 3D lid-driven cavity (no periodic BC) >> and >> I obtained the same error: NaN in Helholtz residual. >> >> Maybe I should start from the turbChannel example and simplify the >> problem >> to reach a laminar 3D poiseuille flow. >> >> Anyway, thanks a lot for your answers. >> >>> A quick look of the *rea file did not bring up anything. I recall an >>> issue with periodic BC's, following is an email from one of the >>> developers: >>> >>> >>> Hi Frank, >>> >>> Yes -- we currently don't support periodic bcs for >>> anything smaller than a 3 x 3 x 3 array of elements. >>> >>> There's a technical reason for this --- it can be >>> circumvented if really needed, but it would not >>> fit within the std. context. >>> >>> Sorry about that. >>> >>> Paul >>> >>> On Tue, 2010-11-16 at 12:56 -0500, nek5000-users at lists.mcs.anl.gov >>> wrote: >>>> Hi Frank, >>>> >>>> The rea file has been attached. >>>> Meanwhile I'll check the BC... >>>> >>>> Thanks >>>> >>>>> Hello Alex, >>>>> >>>>> I looked through your files & didn't see anything amiss (by the way, >>>> it >>>>> would be best to post your *.rea file). Since it blows up on the >>>> first >>>>> attempt to solve for pressure, perhaps the BC's don't satisfy >>>>> conservation of mass? >>>>> >>>>> Cheers, >>>>> Frank >>>>> >>>>> >>>>> >>>>> On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov >>>>> wrote: >>>>> >>>>>> Hi Nek users, >>>>>> >>>>>> I am new in using Nek5. I have succesfully simualted the lid-driven >>>>>> flow, >>>>>> rayleigh-b????nard in a square cavity and laminar poiseuille flow. >>>> All of >>>>>> them were 2d cases. I though it would be straightforward to move >>>>>> from >>>> 2D >>>>>> to 3D simualtions but I have not been able to run a 3D poiseuille >>>>>> channel. >>>>>> I am obtaining an error on Helmoltz solver even in the first >>>> iteration. >>>>>> >>>>>> Please, find output, usr and box files attached. >>>>>> Thanks in advance. >>>>>> >>>>>> .......................................... >>>>>> Alex Fabregat >>>>>> Post-doctoral fellow >>>>>> University of Ottawa >>>>>> Department of Mechanical Engineering >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>>> -- >>>>> Frank Herbert Muldoon, Ph.D. Mechanical Engineering >>>>> Technische Universit????t Wien (Vienna University of Technology) >>>>> Inst. f. Str????mungsmechanik und W????rme????bertragung (Institute >>>>> of >>>> Fluid >>>>> Mechanics and Heat Transfer) >>>>> Resselgasse 3 >>>>> 1040 Wien >>>>> Tel: +4315880132232 >>>>> Fax: +4315880132299 >>>>> Cell:+436765203470 >>>>> fmuldoo (skype) >>>>> http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>> >>>> >>>> .......................................... >>>> Alex Fabregat >>>> Post-doctoral fellow >>>> University of Ottawa >>>> Department of Mechanical Engineering >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> -- >>> Frank Herbert Muldoon, Ph.D. Mechanical Engineering >>> Technische Universit??t Wien (Vienna University of Technology) >>> Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid >>> Mechanics and Heat Transfer) >>> Resselgasse 3 >>> 1040 Wien >>> Tel: +4315880132232 >>> Fax: +4315880132299 >>> Cell:+436765203470 >>> fmuldoo (skype) >>> http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> .......................................... >> Alex Fabregat >> Post-doctoral fellow >> University of Ottawa >> Department of Mechanical Engineering >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>_______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Tue Nov 16 14:14:03 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 14:14:03 -0600 (CST) Subject: [Nek5000-users] solver tolerances and norm of residual In-Reply-To: <51380.172.24.182.149.1289937998.squirrel@webmail01.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50785.172.24.182.149.1289930177.squirrel@webmail01.uottawa.ca> <1289931957.5279.16.camel@localhost.localdomain> <51031.172.24.182.149.1289933451.squirrel@webmail01.uottawa.ca> <51380.172.24.182.149.1289937998.squirrel@webmail01.uottawa.ca> Message-ID: Sorry - that's a check that we should add... It's now on my todo list. Paul On Tue, 16 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, > > it worked!! > > The crucial difference between my file and yours was: > > < parameter (lz2=lz1-2) >> parameter (lz2=lz1 ) > > I am a little ashamed for not having seen it but the output was not giving > me any clue. > > Thank you so much. > >> >> Hi Alex, >> >> I just tried your case - it ran w/o any difficulty. >> >> I wonder if there is an issue w/ your SIZE file? I've >> placed the one that I used in >> >> www.mcs.anl.gov/~fischer/SIZE >> >> which you can just grab. Then makenek 3dtest followed by >> the usual run process.... Let me know if this resolves the >> issue for you. >> >> Cheers, >> >> Paul F. >> >> >> On Tue, 16 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi, >>> >>> I think this is not the reason because in a previous attempt to face the >>> 3D problems I tried to solve the 3D lid-driven cavity (no periodic BC) >>> and >>> I obtained the same error: NaN in Helholtz residual. >>> >>> Maybe I should start from the turbChannel example and simplify the >>> problem >>> to reach a laminar 3D poiseuille flow. >>> >>> Anyway, thanks a lot for your answers. >>> >>>> A quick look of the *rea file did not bring up anything. I recall an >>>> issue with periodic BC's, following is an email from one of the >>>> developers: >>>> >>>> >>>> Hi Frank, >>>> >>>> Yes -- we currently don't support periodic bcs for >>>> anything smaller than a 3 x 3 x 3 array of elements. >>>> >>>> There's a technical reason for this --- it can be >>>> circumvented if really needed, but it would not >>>> fit within the std. context. >>>> >>>> Sorry about that. >>>> >>>> Paul >>>> >>>> On Tue, 2010-11-16 at 12:56 -0500, nek5000-users at lists.mcs.anl.gov >>>> wrote: >>>>> Hi Frank, >>>>> >>>>> The rea file has been attached. >>>>> Meanwhile I'll check the BC... >>>>> >>>>> Thanks >>>>> >>>>>> Hello Alex, >>>>>> >>>>>> I looked through your files & didn't see anything amiss (by the way, >>>>> it >>>>>> would be best to post your *.rea file). Since it blows up on the >>>>> first >>>>>> attempt to solve for pressure, perhaps the BC's don't satisfy >>>>>> conservation of mass? >>>>>> >>>>>> Cheers, >>>>>> Frank >>>>>> >>>>>> >>>>>> >>>>>> On Tue, 2010-11-16 at 11:40 -0500, nek5000-users at lists.mcs.anl.gov >>>>>> wrote: >>>>>> >>>>>>> Hi Nek users, >>>>>>> >>>>>>> I am new in using Nek5. I have succesfully simualted the lid-driven >>>>>>> flow, >>>>>>> rayleigh-b????nard in a square cavity and laminar poiseuille flow. >>>>> All of >>>>>>> them were 2d cases. I though it would be straightforward to move >>>>>>> from >>>>> 2D >>>>>>> to 3D simualtions but I have not been able to run a 3D poiseuille >>>>>>> channel. >>>>>>> I am obtaining an error on Helmoltz solver even in the first >>>>> iteration. >>>>>>> >>>>>>> Please, find output, usr and box files attached. >>>>>>> Thanks in advance. >>>>>>> >>>>>>> .......................................... >>>>>>> Alex Fabregat >>>>>>> Post-doctoral fellow >>>>>>> University of Ottawa >>>>>>> Department of Mechanical Engineering >>>>>>> _______________________________________________ >>>>>>> Nek5000-users mailing list >>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>>> -- >>>>>> Frank Herbert Muldoon, Ph.D. Mechanical Engineering >>>>>> Technische Universit????t Wien (Vienna University of Technology) >>>>>> Inst. f. Str????mungsmechanik und W????rme????bertragung (Institute >>>>>> of >>>>> Fluid >>>>>> Mechanics and Heat Transfer) >>>>>> Resselgasse 3 >>>>>> 1040 Wien >>>>>> Tel: +4315880132232 >>>>>> Fax: +4315880132299 >>>>>> Cell:+436765203470 >>>>>> fmuldoo (skype) >>>>>> http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>> >>>>> >>>>> .......................................... >>>>> Alex Fabregat >>>>> Post-doctoral fellow >>>>> University of Ottawa >>>>> Department of Mechanical Engineering >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> -- >>>> Frank Herbert Muldoon, Ph.D. Mechanical Engineering >>>> Technische Universit??t Wien (Vienna University of Technology) >>>> Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid >>>> Mechanics and Heat Transfer) >>>> Resselgasse 3 >>>> 1040 Wien >>>> Tel: +4315880132232 >>>> Fax: +4315880132299 >>>> Cell:+436765203470 >>>> fmuldoo (skype) >>>> http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> >>> .......................................... >>> Alex Fabregat >>> Post-doctoral fellow >>> University of Ottawa >>> Department of Mechanical Engineering >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Nov 16 15:26:14 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 Nov 2010 15:26:14 -0600 (CST) Subject: [Nek5000-users] Users Meeting, Dec. 9 & 10 Message-ID: Dear Nek Users, We're happy to confirm that Uesrmeeting2010 is on for Dec. 9 and 10. It appears that we will have ~20 participants. More detail concerning the schedule will be forthcoming in an email to registered participants in the next few days. We look forward to meeting you at Argonne next month! -- The Nek5k development group From nek5000-users at lists.mcs.anl.gov Wed Nov 17 23:21:12 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 17 Nov 2010 23:21:12 -0600 (CST) Subject: [Nek5000-users] Temperature Issue, non physical values for certain Pr num. In-Reply-To: <718908637.8734971290057591439.JavaMail.root@neo-mail-3> Message-ID: <1553684884.8735641290057672593.JavaMail.root@neo-mail-3> Hi, I am having an issue with temperature values in my domain. The domain consists of two inlets, one at a temperature of 300 and the other 100. It appears that the interface between the two is giving non-physical temperatures, but what is interesting is the magnitude of these over/under shoots is dependent on the Prandtl number.? To see the extend of this I saved the max/min temperature in the domain for several time steps. See the attached image.? The low Pr case had Pr = 0.005, where as the other case had Pr = 0.71.? Both cases show non - physical results, but the low Pr case seems to recover and approach the limits for the domain given by the boundary conditions.? In the other Pr =?0.71 case, the fluctuations and magnitudes are much larger and don't appear to stabilize and recover. Again, I have looked at fld files to confirm that these large differences occur at the interface between the hot/cold fluid.? Is there a solution to this problem? Thanks, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tempIssue.tif Type: image/tiff Size: 55834 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 18 02:08:36 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 Nov 2010 02:08:36 -0600 (CST) Subject: [Nek5000-users] =?utf-8?q?Temperature_Issue=2C=09non_physical_val?= =?utf-8?q?ues_for_certain_Pr_num=2E?= In-Reply-To: <1553684884.8735641290057672593.JavaMail.root@neo-mail-3> References: <1553684884.8735641290057672593.JavaMail.root@neo-mail-3> Message-ID: Hi Michael, Yes - this is a well-known issue when not fully resolved because the code does not preserve monotonicity, particularly at LES resolutions. It is a high-prioty item, but won't be addressed till next year. Under these circumstances I typically clip the temperature field - which is a poor man's monotonicity preservation algorithm. Although unsatisfying, it's not all that bad and we've gotten very good results in some past mixed-stream problems where there is a sharp interface. (One can, of course, always come up w/ a case where this approach doesn't work and something more robust is required, which is why we'll be looking into this soon...) Paul On Wed, 17 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > Hi, > > > > I am having an issue with temperature values in my domain. The domain consists of two inlets, one at a temperature of 300 and the other 100. It appears > > that the interface between the two is giving non-physical temperatures, but what is interesting is the magnitude of these over/under shoots is dependent on > > the Prandtl number.?? To see the extend of this I saved the max/min temperature in the domain for several time steps. > > > > See the attached image.?? The low Pr case had Pr = 0.005, where as the other case had Pr = 0.71.?? Both cases show non - physical results, but the low Pr > > case seems to recover and approach the limits for the domain given by the boundary conditions.?? In the other Pr =??0.71 case, the fluctuations and magnitudes are > > much larger and don't appear to stabilize and recover. > > > > Again, I have looked at fld files to confirm that these large differences occur at the interface between the hot/cold fluid.?? Is there a solution to this problem? > > > > Thanks, > > Michael > From nek5000-users at lists.mcs.anl.gov Thu Nov 18 03:08:09 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 Nov 2010 10:08:09 +0100 Subject: [Nek5000-users] Temperature Issue, non physical values for certain Pr num. In-Reply-To: <1553684884.8735641290057672593.JavaMail.root@neo-mail-3> References: <1553684884.8735641290057672593.JavaMail.root@neo-mail-3> Message-ID: <1290071289.5279.127.camel@localhost.localdomain> Hi Michael, This is a problem arising in the convective terms due to insufficient resolution. As a result, the convective term can create over/under shoots of a convected quantity by numerically creating anti-diffusion and steepening gradients instead of simply convecting them. This will occur where gradients of the convected quantity are high. As to the Prandtl # effect, what is happening is that the numerical problem arising in the convective term is suppressed by the increased physical diffusion in the temperature equation at lower Prandtl #. Obviously this is not good, but the only solution at present in NEK is to increase resolution. Another approach would be to use a non-linear convective scheme such as ENO, TVD, Flux Corrected Transport etc. which add diffusion only in regions of high (and under-resolved gradients), but NEK does not (at present) have such schemes, and I believe that implementing such schemes in the context of Finite element methods is not all simple. My two-cents worth would be that adding such schemes would be a great addition to NEK. I have run into the same problem you are facing. Cheers, Frank On Wed, 2010-11-17 at 23:21 -0600, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > > > I am having an issue with temperature values in my domain. The domain > consists of two inlets, one at a temperature of 300 and the other 100. > It appears > > that the interface between the two is giving non-physical > temperatures, but what is interesting is the magnitude of these > over/under shoots is dependent on > > the Prandtl number. To see the extend of this I saved the max/min > temperature in the domain for several time steps. > > > > See the attached image. The low Pr case had Pr = 0.005, where as the > other case had Pr = 0.71. Both cases show non - physical results, but > the low Pr > > case seems to recover and approach the limits for the domain given by > the boundary conditions. In the other Pr = 0.71 case, the > fluctuations and magnitudes are > > much larger and don't appear to stabilize and recover. > > > > Again, I have looked at fld files to confirm that these large > differences occur at the interface between the hot/cold fluid. Is > there a solution to this problem? > > > > Thanks, > > Michael > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universit?t Wien (Vienna University of Technology) Inst. f. Str?mungsmechanik und W?rme?bertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html From nek5000-users at lists.mcs.anl.gov Thu Nov 18 08:31:11 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 Nov 2010 08:31:11 -0600 (CST) Subject: [Nek5000-users] Temperature Issue, non physical values for certain Pr num. In-Reply-To: Message-ID: <1216781124.8778271290090671473.JavaMail.root@neo-mail-3> Thank you for the responses. Paul,? Is there an efficient way to clip the temperatures or do I need to loop through the points each time step? -Michael ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "Nekton User List" Sent: Thursday, November 18, 2010 2:08:36 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Temperature Issue,????????non physical values for certain Pr num. Hi Michael, Yes - this is a well-known issue when not fully resolved because the code does not preserve monotonicity, particularly at LES resolutions. It is a high-prioty item, but won't be addressed till next year. Under these circumstances I typically clip the temperature field - which is a poor man's monotonicity preservation algorithm. Although unsatisfying, it's not all that bad and we've gotten very good results in some past mixed-stream problems where there is a sharp interface. (One can, of course, always come up w/ a case where this approach doesn't work and something more robust is required, which is why we'll be looking into this soon...) Paul On Wed, 17 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > Hi, > > > > I am having an issue with temperature values in my domain. The domain consists of two inlets, one at a temperature of 300 and the other 100. It appears > > that the interface between the two is giving non-physical temperatures, but what is interesting is the magnitude of these over/under shoots is dependent on > > the Prandtl number.? To see the extend of this I saved the max/min temperature in the domain for several time steps. > > > > See the attached image.? The low Pr case had Pr = 0.005, where as the other case had Pr = 0.71.? Both cases show non - physical results, but the low Pr > > case seems to recover and approach the limits for the domain given by the boundary conditions.? In the other Pr =?0.71 case, the fluctuations and magnitudes are > > much larger and don't appear to stabilize and recover. > > > > Again, I have looked at fld files to confirm that these large differences occur at the interface between the hot/cold fluid.? Is there a solution to this problem? > > > > Thanks, > > Michael > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 19 12:08:42 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 13:08:42 -0500 (EST) Subject: [Nek5000-users] X11 In-Reply-To: <1289927317.5279.11.camel@localhost.localdomain> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> Message-ID: <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> Hi, i am trying to compile prenek on my MacBook: ./maketools prenek The following error appears: xdriver.c:4:22: error: X11/Xlib.h: No such file or directory xdriver.c:5:23: error: X11/Xutil.h: No such file or directory xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory The X11 folder in my case would be located at: /usr/X11R6/include/X11/ Where can i find a variable to define a path to the X11 directory?. Thanks. .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Fri Nov 19 12:32:53 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 12:32:53 -0600 (CST) Subject: [Nek5000-users] X11 In-Reply-To: <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> Message-ID: Hello Alex, You can define the X11R6 path in the variable "X" in the file /prenek/makefile. C = code L = . X = /usr/X11R6/lib HTF, Harish. On Fri, 19 Nov 2010 nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > i am trying to compile prenek on my MacBook: > ./maketools prenek > > The following error appears: > > xdriver.c:4:22: error: X11/Xlib.h: No such file or directory > xdriver.c:5:23: error: X11/Xutil.h: No such file or directory > xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory > xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory > xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory > > The X11 folder in my case would be located at: > /usr/X11R6/include/X11/ > > Where can i find a variable to define a path to the X11 directory?. > > Thanks. > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Nov 19 12:50:43 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 13:50:43 -0500 (EST) Subject: [Nek5000-users] X11 In-Reply-To: References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> Message-ID: <51028.172.24.182.197.1290192643.squirrel@webmail02.uottawa.ca> Hi Harish, I did that but the problem persists. This is the output: ---------------------- Make prenek... ---------------------- gfortran -c prenek.f gfortran -c curve.f gfortran -c edit.f gfortran -c build.f gfortran -c build1.f gfortran -c build2.f gfortran -c bound.f gfortran -c plot.f gfortran -c xinterface.f gfortran -c glomod.f glomod.f:1534.9: ja(2) = w(2,1) 1 Warning: Array reference at (1) is out of bounds gfortran -c legend.f gfortran -c vprops.f gfortran -c iolib.f gfortran -c subs.f gfortran -c zipper2.f zipper2.f:1560.20: COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3) 1 Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size zipper2.f:2816.20: COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3) 1 Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size zipper2.f:4639.20: common /ctmp2/ xp(nxm3),yp(nxm3),zp(nxm3),wk(ldw) 1 Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size zipper2.f:4640.20: common /ctmp0/ jx(nxm*3),jyt(nym*3),jzt(nzm*3) 1 Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size zipper2.f:4776.20: common /ctmp0/ xcb(2,2,2),ycb(2,2,2),zcb(2,2,2),w(ldw) 1 Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size gfortran -c postnek6.f gfortran -c screen.f gcc -c -DUNDERSCORE -Dr8 revert.c gfortran -c crs.f gfortran -c mxm.f gcc -c -DUNDERSCORE -Dr8 xdriver.c xdriver.c:4:22: error: X11/Xlib.h: No such file or directory xdriver.c:5:23: error: X11/Xutil.h: No such file or directory xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory In file included from xdriver.c:9: /usr/lib/gcc/i686-apple-darwin8/4.0.1/include/X11/Xos.h:298:23: error: X11/Xarch.h: No such file or directory xdriver.c:10:23: error: X11/Xatom.h: No such file or directory xdriver.c:11:27: error: X11/Xresource.h: No such file or directory .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Fri Nov 19 12:53:23 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 12:53:23 -0600 (CST) Subject: [Nek5000-users] X11 In-Reply-To: <51028.172.24.182.197.1290192643.squirrel@webmail02.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> <51028.172.24.182.197.1290192643.squirrel@webmail02.uottawa.ca> Message-ID: pre and post have slightly different x11 interfaces... given that post was used on a wider variety of platforms, it got more development. I'm upgrading pre right now and will see if I can remedy this issue. Paul On Fri, 19 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi Harish, > > I did that but the problem persists. This is the output: > > ---------------------- > Make prenek... > ---------------------- > gfortran -c prenek.f > gfortran -c curve.f > gfortran -c edit.f > gfortran -c build.f > gfortran -c build1.f > gfortran -c build2.f > gfortran -c bound.f > gfortran -c plot.f > gfortran -c xinterface.f > gfortran -c glomod.f > glomod.f:1534.9: > > ja(2) = w(2,1) > 1 > Warning: Array reference at (1) is out of bounds > gfortran -c legend.f > gfortran -c vprops.f > gfortran -c iolib.f > gfortran -c subs.f > gfortran -c zipper2.f > zipper2.f:1560.20: > > COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3) > 1 > Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size > zipper2.f:2816.20: > > COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3) > 1 > Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size > zipper2.f:4639.20: > > common /ctmp2/ xp(nxm3),yp(nxm3),zp(nxm3),wk(ldw) > 1 > Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size > zipper2.f:4640.20: > > common /ctmp0/ jx(nxm*3),jyt(nym*3),jzt(nzm*3) > 1 > Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size > zipper2.f:4776.20: > > common /ctmp0/ xcb(2,2,2),ycb(2,2,2),zcb(2,2,2),w(ldw) > 1 > Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size > gfortran -c postnek6.f > gfortran -c screen.f > gcc -c -DUNDERSCORE -Dr8 revert.c > gfortran -c crs.f > gfortran -c mxm.f > gcc -c -DUNDERSCORE -Dr8 xdriver.c > xdriver.c:4:22: error: X11/Xlib.h: No such file or directory > xdriver.c:5:23: error: X11/Xutil.h: No such file or directory > xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory > xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory > xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory > In file included from xdriver.c:9: > /usr/lib/gcc/i686-apple-darwin8/4.0.1/include/X11/Xos.h:298:23: error: > X11/Xarch.h: No such file or directory > xdriver.c:10:23: error: X11/Xatom.h: No such file or directory > xdriver.c:11:27: error: X11/Xresource.h: No such file or directory > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Nov 19 12:55:50 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 12:55:50 -0600 (CST) Subject: [Nek5000-users] X11 In-Reply-To: <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> Message-ID: Hi Alex, Does post compile on your macbook? Paul On Fri, 19 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > i am trying to compile prenek on my MacBook: > ./maketools prenek > > The following error appears: > > xdriver.c:4:22: error: X11/Xlib.h: No such file or directory > xdriver.c:5:23: error: X11/Xutil.h: No such file or directory > xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory > xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory > xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory > > The X11 folder in my case would be located at: > /usr/X11R6/include/X11/ > > Where can i find a variable to define a path to the X11 directory?. > > Thanks. > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Nov 19 12:56:53 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 12:56:53 -0600 (CST) Subject: [Nek5000-users] X11 In-Reply-To: References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> <51028.172.24.182.197.1290192643.squirrel@webmail02.uottawa.ca> Message-ID: Hi Alex, Are you sure you are providing the path to /usr/X11R6/lib in the makefile and not /usr/X11R6/include/X11? Harish. On Fri, 19 Nov 2010 nek5000-users at lists.mcs.anl.gov wrote: > > pre and post have slightly different x11 interfaces... given > that post was used on a wider variety of platforms, it got > more development. > > I'm upgrading pre right now and will see if I can remedy this > issue. > > Paul > > > On Fri, 19 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > Hi Harish, > > > > I did that but the problem persists. This is the output: > > > > ---------------------- > > Make prenek... > > ---------------------- > > gfortran -c prenek.f > > gfortran -c curve.f > > gfortran -c edit.f > > gfortran -c build.f > > gfortran -c build1.f > > gfortran -c build2.f > > gfortran -c bound.f > > gfortran -c plot.f > > gfortran -c xinterface.f > > gfortran -c glomod.f > > glomod.f:1534.9: > > > > ja(2) = w(2,1) > > 1 > > Warning: Array reference at (1) is out of bounds > > gfortran -c legend.f > > gfortran -c vprops.f > > gfortran -c iolib.f > > gfortran -c subs.f > > gfortran -c zipper2.f > > zipper2.f:1560.20: > > > > COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3) > > 1 > > Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size > > zipper2.f:2816.20: > > > > COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3) > > 1 > > Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size > > zipper2.f:4639.20: > > > > common /ctmp2/ xp(nxm3),yp(nxm3),zp(nxm3),wk(ldw) > > 1 > > Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size > > zipper2.f:4640.20: > > > > common /ctmp0/ jx(nxm*3),jyt(nym*3),jzt(nzm*3) > > 1 > > Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size > > zipper2.f:4776.20: > > > > common /ctmp0/ xcb(2,2,2),ycb(2,2,2),zcb(2,2,2),w(ldw) > > 1 > > Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size > > gfortran -c postnek6.f > > gfortran -c screen.f > > gcc -c -DUNDERSCORE -Dr8 revert.c > > gfortran -c crs.f > > gfortran -c mxm.f > > gcc -c -DUNDERSCORE -Dr8 xdriver.c > > xdriver.c:4:22: error: X11/Xlib.h: No such file or directory > > xdriver.c:5:23: error: X11/Xutil.h: No such file or directory > > xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory > > xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory > > xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory > > In file included from xdriver.c:9: > > /usr/lib/gcc/i686-apple-darwin8/4.0.1/include/X11/Xos.h:298:23: error: > > X11/Xarch.h: No such file or directory > > xdriver.c:10:23: error: X11/Xatom.h: No such file or directory > > xdriver.c:11:27: error: X11/Xresource.h: No such file or directory > > > > .......................................... > > Alex Fabregat > > Post-doctoral fellow > > University of Ottawa > > Department of Mechanical Engineering > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Nov 19 13:10:38 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 14:10:38 -0500 (EST) Subject: [Nek5000-users] X11 In-Reply-To: References: <2EF961D6-A4F2-4C32-9997-A0B2D521C5E3@nrel.gov> <50178.172.24.182.149.1289925631.squirrel@webmail02.uottawa.ca> <1289927317.5279.11.camel@localhost.localdomain> <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> <51028.172.24.182.197.1290192643.squirrel@webmail02.uottawa.ca> Message-ID: <51235.172.24.182.197.1290193838.squirrel@webmail01.uottawa.ca> Yes, please see the makefile... FLAGS = $(FFLAGS_IN) CFLAGS = $(CFLAGS_IN) LFLAGS = $(LFLAGS_IN) prefix = $(bin_nek_tools) C = code L = . X = /usr/X11R6/lib ...and yes, the same problem when compiling postnek. .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Fri Nov 19 13:27:24 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 13:27:24 -0600 (CST) Subject: [Nek5000-users] X11 In-Reply-To: <50931.172.24.182.197.1290190122.squirrel@webmail02.uottawa.ca> Message-ID: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> Did you check if the X11 header files exist? Make sure that X11SDK is installed on your system. -Stefan ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Friday, November 19, 2010 7:08:42 PM Subject: [Nek5000-users] X11 Hi, i am trying to compile prenek on my MacBook: ./maketools prenek The following error appears: xdriver.c:4:22: error: X11/Xlib.h: No such file or directory xdriver.c:5:23: error: X11/Xutil.h: No such file or directory xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory The X11 folder in my case would be located at: /usr/X11R6/include/X11/ Where can i find a variable to define a path to the X11 directory?. Thanks. .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Nov 19 14:44:41 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 Nov 2010 15:44:41 -0500 (EST) Subject: [Nek5000-users] X11 In-Reply-To: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> References: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> Message-ID: <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> Yes, they are in /usr/X11R6/include/X11. > Did you check if the X11 header files exist? Make sure that X11SDK is > installed on your system. > -Stefan > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Friday, November 19, 2010 7:08:42 PM > Subject: [Nek5000-users] X11 > > Hi, > > i am trying to compile prenek on my MacBook: > ./maketools prenek > > The following error appears: > > xdriver.c:4:22: error: X11/Xlib.h: No such file or directory > xdriver.c:5:23: error: X11/Xutil.h: No such file or directory > xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory > xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory > xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory > > The X11 folder in my case would be located at: > /usr/X11R6/include/X11/ > > Where can i find a variable to define a path to the X11 directory?. > > Thanks. > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Mon Nov 22 14:23:49 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 Nov 2010 15:23:49 -0500 (EST) Subject: [Nek5000-users] X11 In-Reply-To: <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> References: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> Message-ID: <49526.172.24.182.197.1290457429.squirrel@webmail02.uottawa.ca> The problem has been fixed after reinstalling and updating the X11. Now, when executing the prex/pretex: Can't open display Did you setenv DISPLAY to your localHost and xhost + on the local display? I have set the environment variable: DISPLAY=:0.0 export DISPLAY xhost + but a new error appears: xhost: unable to open display ":0.0" Is this a permission problem? Any help? > Yes, they are in /usr/X11R6/include/X11. > >> Did you check if the X11 header files exist? Make sure that X11SDK is >> installed on your system. >> -Stefan >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Friday, November 19, 2010 7:08:42 PM >> Subject: [Nek5000-users] X11 >> >> Hi, >> >> i am trying to compile prenek on my MacBook: >> ./maketools prenek >> >> The following error appears: >> >> xdriver.c:4:22: error: X11/Xlib.h: No such file or directory >> xdriver.c:5:23: error: X11/Xutil.h: No such file or directory >> xdriver.c:6:28: error: X11/cursorfont.h: No such file or directory >> xdriver.c:7:27: error: X11/Intrinsic.h: No such file or directory >> xdriver.c:8:28: error: X11/StringDefs.h: No such file or directory >> >> The X11 folder in my case would be located at: >> /usr/X11R6/include/X11/ >> >> Where can i find a variable to define a path to the X11 directory?. >> >> Thanks. >> >> .......................................... >> Alex Fabregat >> Post-doctoral fellow >> University of Ottawa >> Department of Mechanical Engineering >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Mon Nov 22 17:12:29 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 Nov 2010 00:12:29 +0100 Subject: [Nek5000-users] nelt>lelt Message-ID: <1290467549.8589.167.camel@localhost.localdomain> Hello all, Anyone have any idea what could be causing the following error (I am running 64 processes using 18432 elements)? 18422 18423 18424 18425 18426 18427 18428 18429 18430 18431 18432 done :: mapping elements to processors ABORT: nelt>lelt! 0 14179 288 My SIZE file follows. C Dimension file to be included C C HCUBE array dimensions C parameter (ldim=3) parameter (lx1=6,ly1=lx1,lz1=lx1,lelt=288,lelv=lelt) parameter (lxd=9,lyd=lxd,lzd=lxd) parameter (lelx=1,lely=1,lelz=1) c parameter (lzl=3 + 2*(ldim-3)) c parameter (lx2=lx1-2) parameter (ly2=ly1-2) parameter (lz2=lz1-2) parameter (lx3=lx1) parameter (ly3=ly1) parameter (lz3=lz1) c c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) c parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes parameter (lpx2=1,lpy2=1,lpz2=1) c c c parameter (lbelv=lelv,lbelt=lelt) ! MHD c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2) c parameter (lbelv=1,lbelt=1) ! MHD parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes parameter (lbx2=1,lby2=1,lbz2=1) c C LX1M=LX1 when there are moving meshes; =1 otherwise parameter (lx1m=lx1,ly1m=ly1,lz1m=lz1) parameter (ldimt= 11) ! 3 passive scalars + T parameter (ldimt1=ldimt+1) parameter (ldimt3=ldimt+3) parameter (lp = 64) parameter (lelg = 18432) c c Note: In the new code, LELGEC should be about sqrt(LELG) c PARAMETER (LELGEC = 1) PARAMETER (LXYZ2 = 1) PARAMETER (LXZ21 = 1) c PARAMETER (LMAXV=LX1*LY1*LZ1*LELV) PARAMETER (LMAXT=LX1*LY1*LZ1*LELT) PARAMETER (LMAXP=LX2*LY2*LZ2*LELV) PARAMETER (LXZ=LX1*LZ1) PARAMETER (LORDER=3) PARAMETER (MAXOBJ=4,MAXMBR=LELT*6,lhis=1) C C Common Block Dimensions C PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT) PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT) C C The parameter LVEC controls whether an additional 42 field arrays C are required for Steady State Solutions. If you are not using C Steady State, it is recommended that LVEC=1. C PARAMETER (LVEC=1) C C Uzawa projection array dimensions C parameter (mxprev = 20) parameter (lgmres = 30) C C Split projection array dimensions C parameter(lmvec = 1) parameter(lsvec = 1) parameter(lstore=lmvec*lsvec) c c NONCONFORMING STUFF c parameter (maxmor = lelt) C C Array dimensions C COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2 $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID $,NXD,NYD,NZD c automatically added by makenek parameter(lxo = lx1) ! max output grid size (lxo>=lx1) c automatically added by makenek parameter(lpart = 10 ) ! max number of particles c automatically added by makenek integer ax1,ay1,az1,ax2,ay2,az2 parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! running averages -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universit?t Wien (Vienna University of Technology) Inst. f. Str?mungsmechanik und W?rme?bertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 22 17:19:52 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 Nov 2010 17:19:52 -0600 (CST) Subject: [Nek5000-users] nelt>lelt In-Reply-To: <1290467549.8589.167.camel@localhost.localdomain> References: <1290467549.8589.167.camel@localhost.localdomain> Message-ID: Hello, Your actual number of elements per core, nelt, is greater than the upper bound, lelt -- to be precise, nelt=14179 > lelt=288. You should either recompile the case with larger lelt or increase number of cores your are running on (make sure you have appropriate upper bound for them, lp, in SIZE) Best, Aleks On Tue, 23 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hello all, > > Anyone have any idea what could be causing the following error (I am > running 64 processes using 18432 elements)? > > 18422 18423 18424 18425 18426 18427 18428 > 18429 > 18430 18431 18432 > done :: mapping elements to processors > > ABORT: nelt>lelt! 0 14179 288 > > > My SIZE file follows. > > > > > > > C Dimension file to be included > C > C HCUBE array dimensions > C > parameter (ldim=3) > parameter (lx1=6,ly1=lx1,lz1=lx1,lelt=288,lelv=lelt) > parameter (lxd=9,lyd=lxd,lzd=lxd) > parameter (lelx=1,lely=1,lelz=1) > c > parameter (lzl=3 + 2*(ldim-3)) > c > parameter (lx2=lx1-2) > parameter (ly2=ly1-2) > parameter (lz2=lz1-2) > parameter (lx3=lx1) > parameter (ly3=ly1) > parameter (lz3=lz1) > c > c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation > c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes > c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) > c > parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation > parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes > parameter (lpx2=1,lpy2=1,lpz2=1) > c > c > c parameter (lbelv=lelv,lbelt=lelt) ! MHD > c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes > c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2) > c > parameter (lbelv=1,lbelt=1) ! MHD > parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes > parameter (lbx2=1,lby2=1,lbz2=1) > c > C LX1M=LX1 when there are moving meshes; =1 otherwise > parameter (lx1m=lx1,ly1m=ly1,lz1m=lz1) > parameter (ldimt= 11) ! 3 passive scalars + > T > parameter (ldimt1=ldimt+1) > parameter (ldimt3=ldimt+3) > parameter (lp = 64) > parameter (lelg = 18432) > c > c Note: In the new code, LELGEC should be about sqrt(LELG) > c > PARAMETER (LELGEC = 1) > PARAMETER (LXYZ2 = 1) > PARAMETER (LXZ21 = 1) > c > PARAMETER (LMAXV=LX1*LY1*LZ1*LELV) > PARAMETER (LMAXT=LX1*LY1*LZ1*LELT) > PARAMETER (LMAXP=LX2*LY2*LZ2*LELV) > PARAMETER (LXZ=LX1*LZ1) > PARAMETER (LORDER=3) > PARAMETER (MAXOBJ=4,MAXMBR=LELT*6,lhis=1) > C > C Common Block Dimensions > C > PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT) > PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT) > C > C The parameter LVEC controls whether an additional 42 field arrays > C are required for Steady State Solutions. If you are not using > C Steady State, it is recommended that LVEC=1. > C > PARAMETER (LVEC=1) > C > C Uzawa projection array dimensions > C > parameter (mxprev = 20) > parameter (lgmres = 30) > C > C Split projection array dimensions > C > parameter(lmvec = 1) > parameter(lsvec = 1) > parameter(lstore=lmvec*lsvec) > c > c NONCONFORMING STUFF > c > parameter (maxmor = lelt) > C > C Array dimensions > C > COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2 > $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID > $,NXD,NYD,NZD > > c automatically added by makenek > parameter(lxo = lx1) ! max output grid size (lxo>=lx1) > > c automatically added by makenek > parameter(lpart = 10 ) ! max number of particles > > c automatically added by makenek > integer ax1,ay1,az1,ax2,ay2,az2 > parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! > running averages > > > -- > Frank Herbert Muldoon, Ph.D. Mechanical Engineering > Technische Universit??t Wien (Vienna University of Technology) > Inst. f. Str??mungsmechanik und W??rme??bertragung (Institute of Fluid > Mechanics and Heat Transfer) > Resselgasse 3 > 1040 Wien > Tel: +4315880132232 > Fax: +4315880132299 > Cell:+436765203470 > fmuldoo (skype) > http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html > From nek5000-users at lists.mcs.anl.gov Mon Nov 22 20:15:20 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 Nov 2010 03:15:20 +0100 Subject: [Nek5000-users] nelt>lelt In-Reply-To: References: <1290467549.8589.167.camel@localhost.localdomain> Message-ID: <1290478520.8589.188.camel@localhost.localdomain> Thanks Alex, I got it working now. Cheers, Frank On Mon, 2010-11-22 at 17:19 -0600, nek5000-users at lists.mcs.anl.gov wrote: > Hello, > > Your actual number of elements per core, nelt, is greater than the > upper bound, lelt -- to be precise, nelt=14179 > lelt=288. > > You should either recompile the case with larger lelt or increase number > of cores your are running on (make sure you have appropriate upper bound > for them, lp, in SIZE) > > Best, > Aleks > > > On Tue, 23 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > Hello all, > > > > Anyone have any idea what could be causing the following error (I am > > running 64 processes using 18432 elements)? > > > > 18422 18423 18424 18425 18426 18427 18428 > > 18429 > > 18430 18431 18432 > > done :: mapping elements to processors > > > > ABORT: nelt>lelt! 0 14179 288 > > > > > > My SIZE file follows. > > > > > > > > > > > > > > C Dimension file to be included > > C > > C HCUBE array dimensions > > C > > parameter (ldim=3) > > parameter (lx1=6,ly1=lx1,lz1=lx1,lelt=288,lelv=lelt) > > parameter (lxd=9,lyd=lxd,lzd=lxd) > > parameter (lelx=1,lely=1,lelz=1) > > c > > parameter (lzl=3 + 2*(ldim-3)) > > c > > parameter (lx2=lx1-2) > > parameter (ly2=ly1-2) > > parameter (lz2=lz1-2) > > parameter (lx3=lx1) > > parameter (ly3=ly1) > > parameter (lz3=lz1) > > c > > c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation > > c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes > > c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) > > c > > parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation > > parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes > > parameter (lpx2=1,lpy2=1,lpz2=1) > > c > > c > > c parameter (lbelv=lelv,lbelt=lelt) ! MHD > > c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes > > c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2) > > c > > parameter (lbelv=1,lbelt=1) ! MHD > > parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes > > parameter (lbx2=1,lby2=1,lbz2=1) > > c > > C LX1M=LX1 when there are moving meshes; =1 otherwise > > parameter (lx1m=lx1,ly1m=ly1,lz1m=lz1) > > parameter (ldimt= 11) ! 3 passive scalars + > > T > > parameter (ldimt1=ldimt+1) > > parameter (ldimt3=ldimt+3) > > parameter (lp = 64) > > parameter (lelg = 18432) > > c > > c Note: In the new code, LELGEC should be about sqrt(LELG) > > c > > PARAMETER (LELGEC = 1) > > PARAMETER (LXYZ2 = 1) > > PARAMETER (LXZ21 = 1) > > c > > PARAMETER (LMAXV=LX1*LY1*LZ1*LELV) > > PARAMETER (LMAXT=LX1*LY1*LZ1*LELT) > > PARAMETER (LMAXP=LX2*LY2*LZ2*LELV) > > PARAMETER (LXZ=LX1*LZ1) > > PARAMETER (LORDER=3) > > PARAMETER (MAXOBJ=4,MAXMBR=LELT*6,lhis=1) > > C > > C Common Block Dimensions > > C > > PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT) > > PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT) > > C > > C The parameter LVEC controls whether an additional 42 field arrays > > C are required for Steady State Solutions. If you are not using > > C Steady State, it is recommended that LVEC=1. > > C > > PARAMETER (LVEC=1) > > C > > C Uzawa projection array dimensions > > C > > parameter (mxprev = 20) > > parameter (lgmres = 30) > > C > > C Split projection array dimensions > > C > > parameter(lmvec = 1) > > parameter(lsvec = 1) > > parameter(lstore=lmvec*lsvec) > > c > > c NONCONFORMING STUFF > > c > > parameter (maxmor = lelt) > > C > > C Array dimensions > > C > > COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2 > > $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID > > $,NXD,NYD,NZD > > > > c automatically added by makenek > > parameter(lxo = lx1) ! max output grid size (lxo>=lx1) > > > > c automatically added by makenek > > parameter(lpart = 10 ) ! max number of particles > > > > c automatically added by makenek > > integer ax1,ay1,az1,ax2,ay2,az2 > > parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! > > running averages > > > > > > -- > > Frank Herbert Muldoon, Ph.D. Mechanical Engineering > > Technische Universit?t Wien (Vienna University of Technology) > > Inst. f. Str?mungsmechanik und W?rme?bertragung (Institute of Fluid > > Mechanics and Heat Transfer) > > Resselgasse 3 > > 1040 Wien > > Tel: +4315880132232 > > Fax: +4315880132299 > > Cell:+436765203470 > > fmuldoo (skype) > > http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html > > > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universit?t Wien (Vienna University of Technology) Inst. f. Str?mungsmechanik und W?rme?bertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.html From nek5000-users at lists.mcs.anl.gov Tue Nov 23 13:33:50 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 Nov 2010 14:33:50 -0500 (EST) Subject: [Nek5000-users] prex/pretex GUI not working In-Reply-To: <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> References: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> Message-ID: <51439.172.24.182.129.1290540830.squirrel@webmail01.uottawa.ca> Hi again, I still have a problem with prex/pretex. After reinstalling and updating "X11" for mac and setting correctly the "DISPLAY" env variable and using "xhost +", I tried to execute pre(te)x from a xterm and the following problem appears: mylaptop:~/my_grid alex$ ./pretex -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 Bus error Things seem to work better with "postx" and a GUI remains open and no "bus error" is obtained. However no menus appear and after typing the "Session Name" the terminal seems frozen: mylaptop:~/my_grid alex$ ./postx -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 NEKTON Version 2.6 Enter Session Name annular2d Any help?. .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Tue Nov 23 13:43:45 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 Nov 2010 13:43:45 -0600 (CST) Subject: [Nek5000-users] prex/pretex GUI not working In-Reply-To: <51439.172.24.182.129.1290540830.squirrel@webmail01.uottawa.ca> Message-ID: <1342310367.116800.1290541425001.JavaMail.root@zimbra.anl.gov> Hi Alex, Could you open anything else through X11 say pdf document with xpdf or gimp -- just any other graphics? Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, November 23, 2010 1:33:50 PM Subject: [Nek5000-users] prex/pretex GUI not working Hi again, I still have a problem with prex/pretex. After reinstalling and updating "X11" for mac and setting correctly the "DISPLAY" env variable and using "xhost +", I tried to execute pre(te)x from a xterm and the following problem appears: mylaptop:~/my_grid alex$ ./pretex -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 Bus error Things seem to work better with "postx" and a GUI remains open and no "bus error" is obtained. However no menus appear and after typing the "Session Name" the terminal seems frozen: mylaptop:~/my_grid alex$ ./postx -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 NEKTON Version 2.6 Enter Session Name annular2d Any help?. .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Nov 23 13:44:41 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 Nov 2010 12:44:41 -0700 Subject: [Nek5000-users] prex/pretex GUI not working In-Reply-To: <51439.172.24.182.129.1290540830.squirrel@webmail01.uottawa.ca> References: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> <51439.172.24.182.129.1290540830.squirrel@webmail01.uottawa.ca> Message-ID: Alex, I recently installed prex on my MacBook pro (10.6.4) from the latest svn distribution. It worked fine. I wonder what the differences are between our setups. I compiled prex with gfortran (from fink) and gcc version 4.2.1 (Apple Inc. build 5664). I have the SDK X11 stuff that Stefan mentioned earlier; this I got from the latest Xcode. /Developer/SDKs/MacOSX10.6.sdk/usr/X11 /Developer/SDKs/MacOSX10.5.sdk/usr/X11R6 My X11 is XQuartz 2.5.3 from http://xquartz.macosforge.org/trac/wiki Is there something else I should check on my machine that might help? --Mike On Nov 23, 2010, at 12:33 PM, wrote: > Hi again, > > I still have a problem with prex/pretex. After reinstalling and updating > "X11" for mac and setting correctly the "DISPLAY" env variable and using > "xhost +", I tried to execute pre(te)x from a xterm and the following > problem appears: > > mylaptop:~/my_grid alex$ ./pretex > > -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 > Bus error > > Things seem to work better with "postx" and a GUI remains open and no "bus > error" is obtained. However no menus appear and after typing the "Session > Name" the terminal seems frozen: > > mylaptop:~/my_grid alex$ ./postx > > -Adobe-Helvetica-Medium-R-Normal--12-120-75-75-P-67-ISO8859-1 > NEKTON Version 2.6 > Enter Session Name > annular2d > > Any help?. > > .......................................... > Alex Fabregat > Post-doctoral fellow > University of Ottawa > Department of Mechanical Engineering > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Nov 24 08:24:14 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 24 Nov 2010 09:24:14 -0500 (EST) Subject: [Nek5000-users] prex/pretex GUI not working In-Reply-To: References: <1870354299.94253.1290194844152.JavaMail.root@zimbra.anl.gov> <51500.172.24.182.197.1290199481.squirrel@webmail01.uottawa.ca> <51439.172.24.182.129.1290540830.squirrel@webmail01.uottawa.ca> Message-ID: <50089.172.24.182.20.1290608654.squirrel@webmail01.uottawa.ca> Hi, I executed the common applications to check if X11 were working correctly and some graphics stuff were being obtained: xclock, xcalc... However I am outdated with respect to the configuration you stated. My versions are: MacOSX: 10.4.11 (Tiger) gcc/gfortran: 4.0.1 X11: 1.1.3 (XFree86 4.4.0) So, maybe I should start by upgrading my OS... Thanks for your help. > Alex, > > I recently installed prex on my MacBook pro (10.6.4) from the latest svn distribution. It worked fine. I wonder what the differences are between > our setups. > > I compiled prex with gfortran (from fink) and gcc version 4.2.1 (Apple Inc. build 5664). > > I have the SDK X11 stuff that Stefan mentioned earlier; this I got from the latest Xcode. > /Developer/SDKs/MacOSX10.6.sdk/usr/X11 > /Developer/SDKs/MacOSX10.5.sdk/usr/X11R6 > > My X11 is XQuartz 2.5.3 from > http://xquartz.macosforge.org/trac/wiki > > Is there something else I should check on my machine that might help? > > --Mike .......................................... Alex Fabregat Post-doctoral fellow University of Ottawa Department of Mechanical Engineering From nek5000-users at lists.mcs.anl.gov Thu Nov 25 12:36:10 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 25 Nov 2010 19:36:10 +0100 Subject: [Nek5000-users] T and P derivatives In-Reply-To: <33551039.1337211278032681081.JavaMail.root@zimbra> References: <33551039.1337211278032681081.JavaMail.root@zimbra> Message-ID: <4CEEAC9A.6040006@lav.mavt.ethz.ch> Hi all, Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ? thank you all francesco -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 26 03:39:03 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 26 Nov 2010 03:39:03 -0600 (CST) Subject: [Nek5000-users] T and P derivatives In-Reply-To: <4CEEAC9A.6040006@lav.mavt.ethz.ch> Message-ID: <1476532248.124769.1290764343420.JavaMail.root@zimbra.anl.gov> Franceso, we just store the velocity, temperature and pressure and not the gradients. Also, we construct the time derivates based on field of interest and do not store them. hth, Stefan ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, November 25, 2010 7:36:10 PM Subject: [Nek5000-users] T and P derivatives Hi all, Sorry to bug you but i have already lost enough time looking for the temperature and pressure gradients. Does anybody knows where are they stored? And the velocity time derivatives ? thank you all francesco _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Nov 26 08:40:19 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 26 Nov 2010 08:40:19 -0600 (CST) Subject: [Nek5000-users] T and P derivatives In-Reply-To: <4CEEAC9A.6040006@lav.mavt.ethz.ch> References: <33551039.1337211278032681081.JavaMail.root@zimbra> <4CEEAC9A.6040006@lav.mavt.ethz.ch> Message-ID: Hi Francesco, Don't waste too much time looking - we're happy to answer! As Stefan commented, we don't store the gradients, we just compute them. Typical usage would be subroutine userchk include 'SIZE' include 'TOTAL' common /mystuff/ uij(lx1*ly1*lz1*lelt,ldim,ldim) $ , px(lx1*ly1,lz1*lelt) $ , py(lx1*ly1,lz1*lelt) $ , pz(lx1*ly1,lz1*lelt) call gradm1(uij(1,1,1),uij(1,1,2),uij(1,1,3),vx) call gradm1(uij(1,2,1),uij(1,2,2),uij(1,2,3),vy) call gradm1(uij(1,3,1),uij(1,3,2),uij(1,3,3),vz) if (lx2.ne.lx1) then ! use something different for mesh 2 call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) call gradm1(px,py,pz,pr) else call gradm1(px,py,pz,pr) endif --- Paul On Thu, 25 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > Hi all, > > Sorry to bug you but i have already lost enough time looking for the > temperature and pressure gradients. > Does anybody knows where are they stored? > And the velocity time derivatives ? > > thank you all > > francesco > From nek5000-users at lists.mcs.anl.gov Fri Nov 26 08:48:30 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 26 Nov 2010 08:48:30 -0600 (CST) Subject: [Nek5000-users] T and P derivatives In-Reply-To: References: <33551039.1337211278032681081.JavaMail.root@zimbra> <4CEEAC9A.6040006@lav.mavt.ethz.ch> Message-ID: PS ... slight bug in what I sent... Should read: > call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) > call gradm1(px,py,pz,pm1) On Fri, 26 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Francesco, > > Don't waste too much time looking - we're happy to answer! > > As Stefan commented, we don't store the gradients, we just > compute them. Typical usage would be > > > subroutine userchk > include 'SIZE' > include 'TOTAL' > common /mystuff/ uij(lx1*ly1*lz1*lelt,ldim,ldim) > $ , px(lx1*ly1,lz1*lelt) > $ , py(lx1*ly1,lz1*lelt) > $ , pz(lx1*ly1,lz1*lelt) > > call gradm1(uij(1,1,1),uij(1,1,2),uij(1,1,3),vx) > call gradm1(uij(1,2,1),uij(1,2,2),uij(1,2,3),vy) > call gradm1(uij(1,3,1),uij(1,3,2),uij(1,3,3),vz) > > if (lx2.ne.lx1) then ! use something different for mesh 2 > call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) > call gradm1(px,py,pz,pr) > else > call gradm1(px,py,pz,pr) > endif > > > --- Paul > > > On Thu, 25 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi all, >> >> Sorry to bug you but i have already lost enough time looking for the >> temperature and pressure gradients. >> Does anybody knows where are they stored? >> And the velocity time derivatives ? >> >> thank you all >> >> francesco >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Nov 26 12:11:47 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 26 Nov 2010 19:11:47 +0100 Subject: [Nek5000-users] T and P derivatives In-Reply-To: References: <33551039.1337211278032681081.JavaMail.root@zimbra> <4CEEAC9A.6040006@lav.mavt.ethz.ch> Message-ID: <4CEFF863.6090601@lav.mavt.ethz.ch> thank you, i was just hoping to save same operations. francesco On 11/26/2010 03:48 PM, nek5000-users at lists.mcs.anl.gov wrote: > > PS ... slight bug in what I sent... Should read: > >> call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) >> call gradm1(px,py,pz,pm1) > > > On Fri, 26 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > >> >> Hi Francesco, >> >> Don't waste too much time looking - we're happy to answer! >> >> As Stefan commented, we don't store the gradients, we just >> compute them. Typical usage would be >> >> >> subroutine userchk >> include 'SIZE' >> include 'TOTAL' >> common /mystuff/ uij(lx1*ly1*lz1*lelt,ldim,ldim) >> $ , px(lx1*ly1,lz1*lelt) >> $ , py(lx1*ly1,lz1*lelt) >> $ , pz(lx1*ly1,lz1*lelt) >> >> call gradm1(uij(1,1,1),uij(1,1,2),uij(1,1,3),vx) >> call gradm1(uij(1,2,1),uij(1,2,2),uij(1,2,3),vy) >> call gradm1(uij(1,3,1),uij(1,3,2),uij(1,3,3),vz) >> >> if (lx2.ne.lx1) then ! use something different for mesh 2 >> call mappr (pm1,pr,px,py) ! interpolate P(m2) --> P(m1) >> call gradm1(px,py,pz,pr) >> else >> call gradm1(px,py,pz,pr) >> endif >> >> >> --- Paul >> >> >> On Thu, 25 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi all, >>> >>> Sorry to bug you but i have already lost enough time looking for the >>> temperature and pressure gradients. >>> Does anybody knows where are they stored? >>> And the velocity time derivatives ? >>> >>> thank you all >>> >>> francesco >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Nov 30 19:14:23 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 Nov 2010 19:14:23 -0600 (CST) Subject: [Nek5000-users] A Restart Issue with NaNs In-Reply-To: <2008331564.11856381291165891383.JavaMail.root@neo-mail-3> Message-ID: <1004731072.11857521291166063053.JavaMail.root@neo-mail-3> Hi, I am having an issue with a simulation in which I restart using the restart options in the Rea file. At the very first time step I get NaN's in the Helmholtz VelZ .? I have done several restarts of the same simulation at earlier points to arrive at where I am at now, however I get this upon trying to continue the simulation further.? Any ideas on why this could be, or how to troubleshoot it?? I'm not sure what I could do since this is showing up on the very first time step. Thanks a lot, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 30 19:21:09 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 Nov 2010 19:21:09 -0600 (CST) Subject: [Nek5000-users] A Restart Issue with NaNs In-Reply-To: <1004731072.11857521291166063053.JavaMail.root@neo-mail-3> References: <1004731072.11857521291166063053.JavaMail.root@neo-mail-3> Message-ID: Hi Micheal, How did this computation finish on the prior run? Is the data corrupted? (i.e., are there nans in the file?) You might try setting nsteps to zero and then checking via glmin/glmax or something to see if the restart file is corrupted. Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > Hi, > > > > I am having an issue with a simulation in which I restart using the restart options in the Rea file. At the very first time step > > I get NaN's in the Helmholtz VelZ .?? I have done several restarts of the same simulation at earlier points to arrive at where I am at > > now, however I get this upon trying to continue the simulation further.?? > > > > Any ideas on why this could be, or how to troubleshoot it??? I'm not sure what I could do since this is showing up on the very > > first time step. > > > > Thanks a lot, > > Michael > From nek5000-users at lists.mcs.anl.gov Tue Nov 30 19:31:53 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 Nov 2010 19:31:53 -0600 (CST) Subject: [Nek5000-users] A Restart Issue with NaNs In-Reply-To: <1579612603.11862021291166862408.JavaMail.root@neo-mail-3> Message-ID: <799372115.11863761291167113348.JavaMail.root@neo-mail-3> I don't believe it is corrupted. I?min/max values given after the restart files load looks good, and I also just confirmed it using glmax/glmin. Also,?I have several restart files that I have tried, all resulting in the same problem. I have also looked at them in visit and everything looks consistent from what I had before, could it still be corrupted even then? I have 5?? *.f? files in increments of 4 seconds. I terminated the run to change something with 'echo -2 >ioinfo'.? Fld?files 3-5 give the problem, while number 2 worked. -Michael ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "Nekton User List" Sent: Tuesday, November 30, 2010 7:21:09 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] A Restart Issue with NaNs Hi Micheal, How did this computation finish on the prior run? Is the data corrupted? (i.e., are there nans in the file?) You might try setting nsteps to zero and then checking via glmin/glmax or something to see if the restart file is corrupted. Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > Hi, > > > > I am having an issue with a simulation in which I restart using the restart options in the Rea file. At the very first time step > > I get NaN's in the Helmholtz VelZ .? I have done several restarts of the same simulation at earlier points to arrive at where I am at > > now, however I get this upon trying to continue the simulation further.? > > > > Any ideas on why this could be, or how to troubleshoot it?? I'm not sure what I could do since this is showing up on the very > > first time step. > > > > Thanks a lot, > > Michael > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 30 20:43:53 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 Nov 2010 20:43:53 -0600 (CST) Subject: [Nek5000-users] A Restart Issue with NaNs In-Reply-To: <799372115.11863761291167113348.JavaMail.root@neo-mail-3> References: <799372115.11863761291167113348.JavaMail.root@neo-mail-3> Message-ID: Hi Michael, One of my favorite tests at this point is to reduce dt to a ridiculously low value, e.g., 1.e-6 or so... At that point, inertia should conquer all and the solution should change very little... >From your earlier email, I had the impression that you had made several runs (for this case?) with restart w/o difficulty, but now it looks like you're indicating you get the problem for any of the restart files? Has something changed in the .usr file or .rea file? Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > I don't believe it is corrupted. I??min/max values given after the restart > files load looks good, and I also > > just confirmed it using glmax/glmin. > > > > Also,??I have several restart files that I have tried, all resulting in the > same problem. I have also looked > > at them in visit and everything looks consistent from what I had before, > could it still be corrupted even then? > > > > I have 5???? *.f?? files in increments of 4 seconds. I terminated the run > to change something with 'echo -2 >ioinfo'.?? > > Fld??files 3-5 give the problem, while number 2 worked. > > > > > > -Michael > > > ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: > "Nekton User List" Sent: Tuesday, November > 30, 2010 7:21:09 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] > A Restart Issue with NaNs > > Hi Micheal, How did this computation finish on the prior run? Is the data > corrupted? (i.e., are there nans in the file?) You might try setting nsteps > to zero and then checking via glmin/glmax or something to see if the restart > file is corrupted. Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov > wrote: > > > Hi, > > > > I am having an issue with a simulation in which I > restart using the restart options in the Rea file. At the very first time > step > > I get NaN's in the Helmholtz VelZ .?? I have done several restarts > of the same simulation at earlier points to arrive at where I am at > > now, > however I get this upon trying to continue the simulation further.?? > > > > > Any ideas on why this could be, or how to troubleshoot it??? I'm not sure > what I could do since this is showing up on the very > > first time step. > > > > > Thanks a lot, > > Michael > > > > _______________________________________________ Nek5000-users mailing > > > list Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Nov 30 20:51:55 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 Nov 2010 20:51:55 -0600 (CST) Subject: [Nek5000-users] A Restart Issue with NaNs In-Reply-To: Message-ID: <14959631.11890451291171915349.JavaMail.root@neo-mail-3> I will try adjusting the dt to a smaller value. Sorry for the confusion, let me try to clarify: By restart without difficulty, I mean that I had been running the simulation to obtain data, stopping it, then starting again from where I left off. So it hadn't been a problem. Now?the issue. After a successfull restart to continue the simulation, I now have 5 new fld files progressing in 4 second intervals. These files are where I am having the issue. I only noticed it by trying to use the most recent file again for a restart. When it didn't work I tried the most recent after that and so on until only the "2nd fld file" worked. So somewhere during that time this happened and I'm not sure why.? Let me try?the dt?and I'll post my result again. - Michael ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, November 30, 2010 8:43:53 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] A Restart Issue with NaNs Hi Michael, One of my favorite tests at this point is to reduce dt to a ridiculously low value, e.g., 1.e-6 or so... At that point, inertia should conquer all and the solution should change very little... >From your earlier email, I had the impression that you had made several runs (for this case?) with restart w/o difficulty, but now it looks like you're indicating you get the problem for any of the restart files? Has something changed in the .usr file or .rea file? Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > I don't believe it is corrupted. I?min/max values given after the restart > files load looks good, and I also > > just confirmed it using glmax/glmin. > > > > Also,?I have several restart files that I have tried, all resulting in the > same problem. I have also looked > > at them in visit and everything looks consistent from what I had before, > could it still be corrupted even then? > > > > I have 5?? *.f? files in increments of 4 seconds. I terminated the run > to change something with 'echo -2 >ioinfo'.? > > Fld?files 3-5 give the problem, while number 2 worked. > > > > > > -Michael > > > ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: > "Nekton User List" Sent: Tuesday, November > 30, 2010 7:21:09 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] > A Restart Issue with NaNs > > Hi Micheal, How did this computation finish on the prior run? Is the data > corrupted? (i.e., are there nans in the file?) You might try setting nsteps > to zero and then checking via glmin/glmax or something to see if the restart > file is corrupted. Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov > wrote: > > > Hi, > > > > I am having an issue with a simulation in which I > restart using the restart options in the Rea file. At the very first time > step > > I get NaN's in the Helmholtz VelZ .? I have done several restarts > of the same simulation at earlier points to arrive at where I am at > > now, > however I get this upon trying to continue the simulation further.? > > > > > Any ideas on why this could be, or how to troubleshoot it?? I'm not sure > what I could do since this is showing up on the very > > first time step. > > > > > Thanks a lot, > > Michael > > > > _______________________________________________ Nek5000-users mailing > > > list Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 30 22:17:48 2010 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 Nov 2010 22:17:48 -0600 (CST) Subject: [Nek5000-users] A Restart Issue with NaNs In-Reply-To: <14959631.11890451291171915349.JavaMail.root@neo-mail-3> Message-ID: <1619709631.11916721291177068390.JavaMail.root@neo-mail-3> Hi Paul, I've tried dt = e-6, -8 and -10...same result. ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, November 30, 2010 8:51:55 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] A Restart Issue with NaNs I will try adjusting the dt to a smaller value. Sorry for the confusion, let me try to clarify: By restart without difficulty, I mean that I had been running the simulation to obtain data, stopping it, then starting again from where I left off. So it hadn't been a problem. Now?the issue. After a successfull restart to continue the simulation, I now have 5 new fld files progressing in 4 second intervals. These files are where I am having the issue. I only noticed it by trying to use the most recent file again for a restart. When it didn't work I tried the most recent after that and so on until only the "2nd fld file" worked. So somewhere during that time this happened and I'm not sure why.? Let me try?the dt?and I'll post my result again. - Michael ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, November 30, 2010 8:43:53 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] A Restart Issue with NaNs Hi Michael, One of my favorite tests at this point is to reduce dt to a ridiculously low value, e.g., 1.e-6 or so... At that point, inertia should conquer all and the solution should change very little... >From your earlier email, I had the impression that you had made several runs (for this case?) with restart w/o difficulty, but now it looks like you're indicating you get the problem for any of the restart files? Has something changed in the .usr file or .rea file? Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > I don't believe it is corrupted. I?min/max values given after the restart > files load looks good, and I also > > just confirmed it using glmax/glmin. > > > > Also,?I have several restart files that I have tried, all resulting in the > same problem. I have also looked > > at them in visit and everything looks consistent from what I had before, > could it still be corrupted even then? > > > > I have 5?? *.f? files in increments of 4 seconds. I terminated the run > to change something with 'echo -2 >ioinfo'.? > > Fld?files 3-5 give the problem, while number 2 worked. > > > > > > -Michael > > > ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: > "Nekton User List" Sent: Tuesday, November > 30, 2010 7:21:09 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] > A Restart Issue with NaNs > > Hi Micheal, How did this computation finish on the prior run? Is the data > corrupted? (i.e., are there nans in the file?) You might try setting nsteps > to zero and then checking via glmin/glmax or something to see if the restart > file is corrupted. Paul On Tue, 30 Nov 2010, nek5000-users at lists.mcs.anl.gov > wrote: > > > Hi, > > > > I am having an issue with a simulation in which I > restart using the restart options in the Rea file. At the very first time > step > > I get NaN's in the Helmholtz VelZ .? I have done several restarts > of the same simulation at earlier points to arrive at where I am at > > now, > however I get this upon trying to continue the simulation further.? > > > > > Any ideas on why this could be, or how to troubleshoot it?? I'm not sure > what I could do since this is showing up on the very > > first time step. > > > > > Thanks a lot, > > Michael > > > > _______________________________________________ Nek5000-users mailing > > > list Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: