January 2015 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > Send Nek5000-users mailing list submissions to > nek5000-users(a)lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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Error when creating own mesh
by nek5000-users＠lists.mcs.anl.gov 01 Mar '16

01 Mar '16

Dear Neks, I am have attempted to use nek5000, firstly by following some of the examples etc. Now I am trying to create my own simulation, which is based upon the ocyl examples. My efforts simply include creating my own grid points in the .rea file to create a slightly different dimension... I believe I have understood how to define the problem however I continually receive errors when creating the genmap it reads as follows.... Input (.rea) file name: ocyl Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.2 reading .rea file data ... ERROR: error reading 1 11 24 aborting 510 in routine rdbdry. 1 quit All I have done again is change the dimensions of the elements in the .rea file so I do not see why it would now not work? Thank you for any help in advance, Friedrich.

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VisIt error: The first time step in a Nek file must contain a mesh
by nek5000-users＠lists.mcs.anl.gov 01 Apr '15

01 Apr '15

Hi all, I get error of mesh need to contain the first time step in Nek file everytime I run .nek5000 file from results of some example (turbchannel, blasius and expansion). However for the 3dbox example, I got no error to open it. I've checked the first line in the first time step file (.f00001) and have the geometry (X) in them. I also changed the logic for coordinate output to (T COORDINATES) and different param66, but still getting the same error. Perhaps even if I put the mesh output for each timestep not just in first timestep, I still getting the same error. Note that I've already set the right plugin and type file during open the .Nek5000 file. In addition, I've checked the same parameters for 3dbox example which is same with the other example rea file, plus 3dbox still gives me no error even if i not switch the coordinate output to true (F COORDINATES) I really hope that anyone who has encountered the same problem and has solved it to assist me. That would be really helpful. Regards, -- Muhsin Mohd Amin Graduate Student Department of Mechanical Engineering The University of Sheffield

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Parallel on several nodes
by nek5000-users＠lists.mcs.anl.gov 12 Feb '15

12 Feb '15

Hi guys, I have a naive questions but I couldn't find my answer in existing posts. Is it possible to run Nek on several nodes, say, on a cluster? If so, which script should be used? A command like /nekmpi eddy_uv 4/ does not help becaue on each node I have 8 CPUs but I'd like to have my 16 nodes (each have 12 CPUs) run together. Any help is appreciated. Saleh

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Re: [Nek5000-users] Error in Hmholtz solving
by nek5000-users＠lists.mcs.anl.gov 30 Jan '15

30 Jan '15

Hi Paul, I've got it now. Thank you very much for the information. Best regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 30 January 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 71, Issue 17 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Re: Error in Hmholtz solving (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Error in Hmholtz solving (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Jan 2015 19:44:28 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] Error in Hmholtz solving Message-ID: <mailman.14280.1422560694.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Hi Paul, Many thanks for your help. Yes, my simulation is scaled in convective time units. As you pointed out, the solutions are well converged. I just have a question about the projection and dealiasing. I'm still not sure when I need to use them in my simulations. Say I'm doing simulations without any models, do I need to turn on projection and dealiasing? I actually don't know how they will affect the solutions, would projection or dealiasing (off, old or new?) change the solutions? It would be great if you could briefly explain this bit to me. Thank you very much. Best regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 29 January 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 71, Issue 16 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Error in Hmholtz solving (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Error in Hmholtz solving (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Jan 2015 15:50:43 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Error in Hmholtz solving Message-ID: <mailman.14256.1422546648.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I'm getting the error message of '**ERROR**: Failed in HMHOLTZ: ' when running my simulation. I've checked the subroutine 'cggo' in hmholtz.f where the error message is printed. I understand that when the tolerance is not satisfied, the code would output this error message. But what I'm wondering is why the maximum iteration number is only 100. In the subroutine 'cggo', niter is equal to min(maxit,maxcg) where maxit=200 and maxcg=900. I can't see other places where maxit is restricted to only 100. So why the maximum iteration number is 100 when solving the Hmholtz equation? Also, is it right that if I increase the maximum number of iterations to certain point where the tolerance is satisfied, I won't get the error message? Hope anyone can help me on this. Thank you very much in advance. Best regards, Tony Example of the error message: Step 52, t= 2.5600000E+01, DT= 5.0000000E-02, C= 2.689 5.6747E+02 1.0237E+01 Solving for fluid T T T 52 PRES gmres: 29 9.7057E-07 1.0000E-06 1.5219E-03 1.0926E+00 2.1480E+00 F 52 Hmholtz VELX: 99 8.5954E-10 6.0898E-03 1.0000E-09 52 100 **ERROR**: Failed in HMHOLTZ: VELY 1.7088E-09 2.5049E-02 1.0000E-09 52 100 **ERROR**: Failed in HMHOLTZ: VELZ 1.4665E-09 2.5165E-02 1.0000E-09 L1/L2 DIV(V) : 2.7573E-18 9.1661E-04 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 2.7573E-18 9.1661E-04 52 2.5600E+01 1.0094E+01 Fluid done Step 53, t= 2.5650000E+01, DT= 5.0000000E-02, C= 2.697 5.7766E+02 1.0186E+01 Solving for fluid T T T 53 PRES gmres: 28 9.6076E-07 1.0000E-06 1.1322E-03 1.0558E+00 2.0542E+00 F 53 Hmholtz VELX: 98 9.4891E-10 5.8783E-03 1.0000E-09 53 100 **ERROR**: Failed in HMHOLTZ: VELY 1.6450E-09 2.4941E-02 1.0000E-09 53 100 **ERROR**: Failed in HMHOLTZ: VELZ 1.4160E-09 2.5049E-02 1.0000E-09 L1/L2 DIV(V) : 2.4695E-18 1.0845E-03 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 2.4695E-18 1.0845E-03 53 2.5650E+01 9.9794E+00 Fluid done

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Re: [Nek5000-users] Error in Hmholtz solving
by nek5000-users＠lists.mcs.anl.gov 29 Jan '15

29 Jan '15

Hi Paul, Many thanks for your help. Yes, my simulation is scaled in convective time units. As you pointed out, the solutions are well converged. I just have a question about the projection and dealiasing. I'm still not sure when I need to use them in my simulations. Say I'm doing simulations without any models, do I need to turn on projection and dealiasing? I actually don't know how they will affect the solutions, would projection or dealiasing (off, old or new?) change the solutions? It would be great if you could briefly explain this bit to me. Thank you very much. Best regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 29 January 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 71, Issue 16 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Error in Hmholtz solving (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Error in Hmholtz solving (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Jan 2015 15:50:43 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Error in Hmholtz solving Message-ID: <mailman.14256.1422546648.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I'm getting the error message of '**ERROR**: Failed in HMHOLTZ: ' when running my simulation. I've checked the subroutine 'cggo' in hmholtz.f where the error message is printed. I understand that when the tolerance is not satisfied, the code would output this error message. But what I'm wondering is why the maximum iteration number is only 100. In the subroutine 'cggo', niter is equal to min(maxit,maxcg) where maxit=200 and maxcg=900. I can't see other places where maxit is restricted to only 100. So why the maximum iteration number is 100 when solving the Hmholtz equation? Also, is it right that if I increase the maximum number of iterations to certain point where the tolerance is satisfied, I won't get the error message? Hope anyone can help me on this. Thank you very much in advance. Best regards, Tony Example of the error message: Step 52, t= 2.5600000E+01, DT= 5.0000000E-02, C= 2.689 5.6747E+02 1.0237E+01 Solving for fluid T T T 52 PRES gmres: 29 9.7057E-07 1.0000E-06 1.5219E-03 1.0926E+00 2.1480E+00 F 52 Hmholtz VELX: 99 8.5954E-10 6.0898E-03 1.0000E-09 52 100 **ERROR**: Failed in HMHOLTZ: VELY 1.7088E-09 2.5049E-02 1.0000E-09 52 100 **ERROR**: Failed in HMHOLTZ: VELZ 1.4665E-09 2.5165E-02 1.0000E-09 L1/L2 DIV(V) : 2.7573E-18 9.1661E-04 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 2.7573E-18 9.1661E-04 52 2.5600E+01 1.0094E+01 Fluid done Step 53, t= 2.5650000E+01, DT= 5.0000000E-02, C= 2.697 5.7766E+02 1.0186E+01 Solving for fluid T T T 53 PRES gmres: 28 9.6076E-07 1.0000E-06 1.1322E-03 1.0558E+00 2.0542E+00 F 53 Hmholtz VELX: 98 9.4891E-10 5.8783E-03 1.0000E-09 53 100 **ERROR**: Failed in HMHOLTZ: VELY 1.6450E-09 2.4941E-02 1.0000E-09 53 100 **ERROR**: Failed in HMHOLTZ: VELZ 1.4160E-09 2.5049E-02 1.0000E-09 L1/L2 DIV(V) : 2.4695E-18 1.0845E-03 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 2.4695E-18 1.0845E-03 53 2.5650E+01 9.9794E+00 Fluid done

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Error in Hmholtz solving
by nek5000-users＠lists.mcs.anl.gov 29 Jan '15

29 Jan '15

Dear Neks, I'm getting the error message of '**ERROR**: Failed in HMHOLTZ: ' when running my simulation. I've checked the subroutine 'cggo' in hmholtz.f where the error message is printed. I understand that when the tolerance is not satisfied, the code would output this error message. But what I'm wondering is why the maximum iteration number is only 100. In the subroutine 'cggo', niter is equal to min(maxit,maxcg) where maxit=200 and maxcg=900. I can't see other places where maxit is restricted to only 100. So why the maximum iteration number is 100 when solving the Hmholtz equation? Also, is it right that if I increase the maximum number of iterations to certain point where the tolerance is satisfied, I won't get the error message? Hope anyone can help me on this. Thank you very much in advance. Best regards, Tony Example of the error message: Step 52, t= 2.5600000E+01, DT= 5.0000000E-02, C= 2.689 5.6747E+02 1.0237E+01 Solving for fluid T T T 52 PRES gmres: 29 9.7057E-07 1.0000E-06 1.5219E-03 1.0926E+00 2.1480E+00 F 52 Hmholtz VELX: 99 8.5954E-10 6.0898E-03 1.0000E-09 52 100 **ERROR**: Failed in HMHOLTZ: VELY 1.7088E-09 2.5049E-02 1.0000E-09 52 100 **ERROR**: Failed in HMHOLTZ: VELZ 1.4665E-09 2.5165E-02 1.0000E-09 L1/L2 DIV(V) : 2.7573E-18 9.1661E-04 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 2.7573E-18 9.1661E-04 52 2.5600E+01 1.0094E+01 Fluid done Step 53, t= 2.5650000E+01, DT= 5.0000000E-02, C= 2.697 5.7766E+02 1.0186E+01 Solving for fluid T T T 53 PRES gmres: 28 9.6076E-07 1.0000E-06 1.1322E-03 1.0558E+00 2.0542E+00 F 53 Hmholtz VELX: 98 9.4891E-10 5.8783E-03 1.0000E-09 53 100 **ERROR**: Failed in HMHOLTZ: VELY 1.6450E-09 2.4941E-02 1.0000E-09 53 100 **ERROR**: Failed in HMHOLTZ: VELZ 1.4160E-09 2.5049E-02 1.0000E-09 L1/L2 DIV(V) : 2.4695E-18 1.0845E-03 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 2.4695E-18 1.0845E-03 53 2.5650E+01 9.9794E+00 Fluid done

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Re: [Nek5000-users] uniform interpolation
by nek5000-users＠lists.mcs.anl.gov 26 Jan '15

26 Jan '15

Hi Tanmoy, thanks for the answer int_tp is working perfectly for me now, the only issue is that it works only for ASCII input files. For my 3D simulation each text file occupies 100mb and I need more than 1000 time slices for analysis, so it becomes a real issue. 1. I have not understood the purpose of you script, to make file.list I just execute a command like ls -1 *0.f* > file.list What was annoying for me is the manual confirmations after each file in list. I got rid of that by moving the part of int_tp.f file: --- write(6,*) 'Input File Format: 0 - ASCII, 1 - binary(fld), --- $ 2 - binary(0.f0000?) ? ' --- read (5,*) ib --- ifbyte=.false. --- iffbin=.false. --- if(ib.ne.0) ifbyte = .true. --- if(ib.eq.2) iffbin = .true. out of the cycle. But what I can't figure out is how to make it working properly with binary input format 2. If I am correct ifreguo = .true. allows you write on a uniform mesh inside each element instead of GLL points. But I have a nonuniform mesh in terms of elements -- the density of elements is greater near the boundaries. So uniform mesh inside elements will not give me global uniform mesh. 3. For Fourier analysis I use either fftw (www.fftw.org) or routines from matlab, which are based on fftw. Really i need to filter spacial waves on different time frequency, and for that I need both time and space analysis (Hilbert transform), which can be also done with direct and inverse fft. >From results of int_tp I can construct a vector or square matrix (in 2D case) in matlab and apply fft to it. Best regards, Ilias Hi Ilias to circumvent, writing too mainy files in the "file.list" > > > *--------------------------------------------------------------------------------* > program lst1 > implicit none > > integer, parameter :: N = 140 > character*80,dimension(N) :: filename > integer :: i,j,k > > > open(unit = 10,file='file.list',action='write') > write(10,"(I3)") N > do i = 1,N > > if(i .lt. 100)then > write(filename(i),'(A,I5.5)') 'turbChannel0.f',i > else > write(filename(i),'(A,I5.5)') 'turbChannel0.f',i > endif > enddo > > do i = 1,N > write(10,*) trim(filename(i)) > enddo > > > close(10) > stop > end program lst1 > > *--------------------------------------------------------------------------------* > > For various post-processing format I use this script to write multiple > files in file-list. > > > I was previously using ifreguo = .true. in post-processing format of nek > for uniform interpolation. But, how are you performing FFT after > interpolating to uniform mesh. Are you using a library, could you > elucidate/ describe a little more on the process, on how you do that? I was > trying to do that as well. > > Sincerely, > Tanmoy > > Best Regards, > Tanmoy > > On Sat, Jan 24, 2015 at 11:08 AM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > >> >> For time-space Fourier analysis I need data on a uniform mesh. >> So I have used int_tp. >> >> When I applied int_tp to binary *0.f* files (param(66) = 6) I have got a >> strange pictures which reflect the solution, but as if some elements were >> switched before interpolation. >> >> So I tried to make uniform interpolation to the most simple tutorial >> examples, namely Rayleigh-Bendard ray_nn case. >> >> Again if I apply int_tp to binary *0.f* of *fld*, then the result is as >> if the some space patches where switched, >> but if int_tp is applied ot ASCII fld files (param(66) = 6) then int_tp >> works and saves the result correctly to both text and binary format. >> >> Is it a common problem, or I miss something? (input files in text format >> work for me but occupie too much space.) >> >> Also, for each file in file.list int_tp asks for input file format. >> But to make time-space analysis I need more that 1000 files in file.list, >> and >> it is tiresome to type an answer that number of times. >> It could be better to choose input file format just once at the beginning? >> >> Thank you in advance, Ilias >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >

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nek5000 compilation error of on NERSC edison/hopper
by nek5000-users＠lists.mcs.anl.gov 24 Jan '15

24 Jan '15

Dear NEK users, I am trying to compile nek model on NERSC machines edison/hopper, encountering an error. Tail of the compilation message is as below: _____________________________________________________________________ /global/homes/r/rtumkur/nek5_svn/trunk/nek/prepost.f(2482): warning #5117: Bad # preprocessor line #ifdef MPIIO -^ /global/homes/r/rtumkur/nek5_svn/trunk/nek/prepost.f(2484): warning #5117: Bad # preprocessor line #else -^ /global/homes/r/rtumkur/nek5_svn/trunk/nek/prepost.f(2486): warning #5117: Bad # preprocessor line #endif -^ compilation aborted for /global/homes/r/rtumkur/nek5_svn/trunk/nek/prepost.f (code 1) make: *** [obj/prepost.o] Error 1 make: *** Waiting for unfinished jobs.... ifort: command line warning #10006: ignoring unknown option '-Mpreprocess' ____________________________________________________________________ Here are the steps I have taken leading up the error. I downloaded the 1. Downloaded and build the nek svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn cd nek5_svn/trunk/tools/ ./maketools all 2. Updated the makenek file as per the instructions provide at the link https://www.nersc.gov/users/computational-systems/hopper/programming/compil… Accordingly, I have loaded Intel compiler module and specified the wrapper in makenek: # Fortran compiler F77="ftn" # C compiler CC="cc" Also included OpenMP Compilation in the general compiler flag: # generic compiler flags G="-g -openmp" 3. Compiled the code makenek sprcyl Any help in resolving this error is much appreciated. I have inserted the SIZE file and makenek file for your reference. ____________________SIZE___________________________ C Dimension file to be included C C HCUBE array dimensions C parameter (ldim=2) parameter (lx1=6,ly1=lx1,lz1=1,lelt=1500,lelv=lelt) parameter (lxd=9,lyd=lxd,lzd=1) parameter (lelx=1,lely=1,lelz=1) parameter (lp = 32768) parameter (lelg = 50000) parameter (lzl=3 + 2*(ldim-3)) c parameter (lx2=lx1-2) parameter (ly2=ly1-2) parameter (lz2=lz1 ) 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= 1) ! 3 passive scalars + T parameter (ldimt1=ldimt+1) parameter (ldimt3=ldimt+3) 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=100) 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 = 20) 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 $,NXD,NYD,NZD c automatically added by makenek parameter(lxo = lx1) ! max output grid size (lxo>=lx1) c automatically added by makenek parameter(lpart = 1 ) ! max number of particles c automatically added by makenek integer ax1,ay1,az1,ax2,ay2,az2 parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! running averages c automatically added by makenek parameter (lxs=1,lys=lxs,lzs=(lxs-1)*(ldim-2)+1) !New Pressure Preconditioner c automatically added by makenek parameter (lfdm=0) ! == 1 for fast diagonalization method c automatically added by makenek common/IOFLAG/nio ! for logfile verbosity control _____________________makenek (initial part)__________________ !/bin/bash # Nek5000 build config file # (c) 2008,2009,2010 UCHICAGO ARGONNE, LLC # source path SOURCE_ROOT="$HOME/nek5_svn/trunk/nek" # Fortran compiler F77="ftn" # C compiler CC="cc" # pre-processor symbol list # (set PPLIST=? to get a list of available symbols) #PPLIST="-openmp" # plug-in list PLUGIN_LIST="" # OPTIONAL SETTINGS # ----------------- # enable MPI (default true) #IFMPI="false" # auxilliary files to compile # NOTE: source files have to located in the same directory as makenek # a makefile_usr.inc has to be provided containing the build rules #USR="foo.o" # linking flags #USR_LFLAGS="-L/usr/lib -lfoo" # generic compiler flags G="-g -openmp" # optimization flags #OPT_FLAGS_STD="" #OPT_FLAGS_MAG="" # enable AMG coarse grid solver (default XXT) #IFAMG="true" #IFAMG_DUMP="true" # CVODE path #CVODE_DIR=$HOME/cvode/lib # MOAB/iMESH path #MOAB_DIR="$HOME/moab" # For linking to MOAB, the following might be needed: # NOTE: compiler specific, use the appropriate one depending on your compiler #GNU="-fopenmp" -- Ravi Kumar R. Tumkur, PhD. Phone: 217 778 7538

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uniform interpolation
by nek5000-users＠lists.mcs.anl.gov 24 Jan '15

24 Jan '15

For time-space Fourier analysis I need data on a uniform mesh. So I have used int_tp. When I applied int_tp to binary *0.f* files (param(66) = 6) I have got a strange pictures which reflect the solution, but as if some elements were switched before interpolation. So I tried to make uniform interpolation to the most simple tutorial examples, namely Rayleigh-Bendard ray_nn case. Again if I apply int_tp to binary *0.f* of *fld*, then the result is as if the some space patches where switched, but if int_tp is applied ot ASCII fld files (param(66) = 6) then int_tp works and saves the result correctly to both text and binary format. Is it a common problem, or I miss something? (input files in text format work for me but occupie too much space.) Also, for each file in file.list int_tp asks for input file format. But to make time-space analysis I need more that 1000 files in file.list, and it is tiresome to type an answer that number of times. It could be better to choose input file format just once at the beginning? Thank you in advance, Ilias

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