From nek5000-users at lists.mcs.anl.gov Mon Feb 2 11:51:55 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Feb 2015 18:51:55 +0100 Subject: [Nek5000-users] Compute Pressure from a given velocity field Message-ID: Howdy Nek's, I was wondering if anyone could explain to me how to compute the pressure from a given velocity field? Say I have a blah0.f00001 field containing only vx,vy, and vz. Once I have loaded it in userchk in postprocess mode, is there anyway I can compute the corresponding pressure field? Best regards, JC -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Feb 2 12:12:09 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Feb 2015 18:12:09 +0000 Subject: [Nek5000-users] Compute Pressure from a given velocity field In-Reply-To: References: Message-ID: Dear JC, I would take about 10 very small timesteps. The inertia should keep the flow from changing; going to step 10 will get you past peculiarities of Nek's start-up process for the BDFk/EXTk start-up procedure. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, February 02, 2015 11:51 AM To: Nek 5000 Subject: [Nek5000-users] Compute Pressure from a given velocity field Howdy Nek's, I was wondering if anyone could explain to me how to compute the pressure from a given velocity field? Say I have a blah0.f00001 field containing only vx,vy, and vz. Once I have loaded it in userchk in postprocess mode, is there anyway I can compute the corresponding pressure field? Best regards, JC -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 4 13:09:37 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 14:09:37 -0500 Subject: [Nek5000-users] question about efficient running nek5000 Message-ID: Hi, I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per node, however in second case I got lower efficiency, simulation goes slower about 5~8 percent!! I ran both cases on the same cluster!! Does anyone have any idea why I do not get higher efficiency with the higher number of CPUs but less nodes involved!? Could memory be a limitation here or since numbers in first case are power of 2, it is more efficient!? Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 4 13:17:16 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 19:17:16 +0000 Subject: [Nek5000-users] question about efficient running nek5000 In-Reply-To: References: Message-ID: Hi Ami, How many nodes were in your simulation? Nek scales well if your number of gridpoints per core is large enough, e.g., greater than 20K or so in my experience. It's not clear to me if the power-of-two issue would be the cause here; perhaps Paul could comment. Mike On Feb 4, 2015, at 12:09 PM, wrote: > Hi, > > I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per node, however in second case I got lower efficiency, simulation goes slower about 5~8 percent!! I ran both cases on the same cluster!! Does anyone have any idea why I do not get higher efficiency with the higher number of CPUs but less nodes involved!? Could memory be a limitation here or since numbers in first case are power of 2, it is more efficient!? > > Thanks, > Ami > _______________________________________________ > 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 Feb 4 13:26:14 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 14:26:14 -0500 Subject: [Nek5000-users] question about efficient running nek5000 In-Reply-To: References: Message-ID: Mike, Thanks for your answer!, Total grid points is 32499936, which I believe it is greater than 20k for both cases! Ami On Wed, Feb 4, 2015 at 2:17 PM, wrote: > Hi Ami, > > How many nodes were in your simulation? Nek scales well if your number of > gridpoints per core is large enough, e.g., greater than 20K or so in my > experience. > > It's not clear to me if the power-of-two issue would be the cause here; > perhaps Paul could comment. > > Mike > > On Feb 4, 2015, at 12:09 PM, > wrote: > > > Hi, > > > > I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per > node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per > node, however in second case I got lower efficiency, simulation goes slower > about 5~8 percent!! I ran both cases on the same cluster!! Does anyone have > any idea why I do not get higher efficiency with the higher number of CPUs > but less nodes involved!? Could memory be a limitation here or since > numbers in first case are power of 2, it is more efficient!? > > > > Thanks, > > Ami > > _______________________________________________ > > 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 Wed Feb 4 13:30:25 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 13:30:25 -0600 (CST) Subject: [Nek5000-users] question about efficient running nek5000 In-Reply-To: References: Message-ID: Hi Ami, Could you try your 12 core-per-node case running with only 11 cores per node (and increasing the total number of nodes to keep the number of CPU fixed)? Aleks On Wed, 4 Feb 2015, nek5000-users at lists.mcs.anl.gov wrote: > Mike, > > Thanks for your answer!, Total grid points is 32499936, which I believe it > is greater than 20k for both cases! > > Ami > > On Wed, Feb 4, 2015 at 2:17 PM, wrote: > >> Hi Ami, >> >> How many nodes were in your simulation? Nek scales well if your number of >> gridpoints per core is large enough, e.g., greater than 20K or so in my >> experience. >> >> It's not clear to me if the power-of-two issue would be the cause here; >> perhaps Paul could comment. >> >> Mike >> >> On Feb 4, 2015, at 12:09 PM, >> wrote: >> >>> Hi, >>> >>> I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per >> node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per >> node, however in second case I got lower efficiency, simulation goes slower >> about 5~8 percent!! I ran both cases on the same cluster!! Does anyone have >> any idea why I do not get higher efficiency with the higher number of CPUs >> but less nodes involved!? Could memory be a limitation here or since >> numbers in first case are power of 2, it is more efficient!? >>> >>> Thanks, >>> Ami >>> _______________________________________________ >>> 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 Wed Feb 4 13:33:21 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 19:33:21 +0000 Subject: [Nek5000-users] question about efficient running nek5000 In-Reply-To: References: Message-ID: Ok, that gives 31k and 27k. Those numbers are in a questionable region; you can see some scaling results for channel flow here: http://www.mcs.anl.gov/~fischer/nek5000/sprague_nek5000_dec2010.pdf We found great scaling for 50k or greater gridpoints per core. I would be interested to know if the power-of-two issue is at fault here. Mike On Feb 4, 2015, at 12:26 PM, > > wrote: Mike, Thanks for your answer!, Total grid points is 32499936, which I believe it is greater than 20k for both cases! Ami On Wed, Feb 4, 2015 at 2:17 PM, > wrote: Hi Ami, How many nodes were in your simulation? Nek scales well if your number of gridpoints per core is large enough, e.g., greater than 20K or so in my experience. It's not clear to me if the power-of-two issue would be the cause here; perhaps Paul could comment. Mike On Feb 4, 2015, at 12:09 PM, > wrote: > Hi, > > I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per node, however in second case I got lower efficiency, simulation goes slower about 5~8 percent!! I ran both cases on the same cluster!! Does anyone have any idea why I do not get higher efficiency with the higher number of CPUs but less nodes involved!? Could memory be a limitation here or since numbers in first case are power of 2, it is more efficient!? > > Thanks, > Ami > _______________________________________________ > 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 From nek5000-users at lists.mcs.anl.gov Wed Feb 4 13:35:26 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 14:35:26 -0500 Subject: [Nek5000-users] question about efficient running nek5000 In-Reply-To: References: Message-ID: Hi Aleks, Approximately I can do that! Ami On Wed, Feb 4, 2015 at 2:30 PM, wrote: > Hi Ami, > > Could you try your 12 core-per-node case running with only 11 cores per > node (and increasing the total number of nodes to keep the number of CPU > fixed)? > > Aleks > > > On Wed, 4 Feb 2015, nek5000-users at lists.mcs.anl.gov wrote: > > Mike, >> >> Thanks for your answer!, Total grid points is 32499936, which I believe it >> is greater than 20k for both cases! >> >> Ami >> >> On Wed, Feb 4, 2015 at 2:17 PM, wrote: >> >> Hi Ami, >>> >>> How many nodes were in your simulation? Nek scales well if your number of >>> gridpoints per core is large enough, e.g., greater than 20K or so in my >>> experience. >>> >>> It's not clear to me if the power-of-two issue would be the cause here; >>> perhaps Paul could comment. >>> >>> Mike >>> >>> On Feb 4, 2015, at 12:09 PM, >>> wrote: >>> >>> Hi, >>>> >>>> I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per >>>> >>> node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per >>> node, however in second case I got lower efficiency, simulation goes >>> slower >>> about 5~8 percent!! I ran both cases on the same cluster!! Does anyone >>> have >>> any idea why I do not get higher efficiency with the higher number of >>> CPUs >>> but less nodes involved!? Could memory be a limitation here or since >>> numbers in first case are power of 2, it is more efficient!? >>> >>>> >>>> Thanks, >>>> Ami >>>> _______________________________________________ >>>> 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: From nek5000-users at lists.mcs.anl.gov Wed Feb 4 17:55:25 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Feb 2015 23:55:25 +0000 Subject: [Nek5000-users] Changed mesh coordinates In-Reply-To: References: Message-ID: Dear Neks, Sorry for bringing this up again. Just want to know has anyone seen this before? Why are the coordinates for some points at 0.0e0 changed? Thank you very much. Kind regards, Tony ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: 01 February 2015 18:00 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 72, Issue 1 Send Nek5000-users mailing list submissions to nek5000-users at 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 at lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner at 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. Changed mesh coordinates (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Sun, 1 Feb 2015 05:05:07 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: [Nek5000-users] Changed mesh coordinates Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I'm doing some data processing for my simulations in nek5000. I found for some elements, however, the coordinates are not exactly as specified. For example, I have an element whose vertices are as follows. ELEMENT 195 [ 1m] GROUP 0 0.000000E+00 -0.130526E+00 -0.129129E+00 0.000000E+00 0.100000E+01 0.991445E+00 0.979179E+00 0.987876E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -0.130526E+00 -0.129129E+00 0.000000E+00 0.100000E+01 0.991445E+00 0.979179E+00 0.987876E+00 0.263158E+00 0.263158E+00 0.263158E+00 0.263158E+00 When I used the following code to print the coordinates for this element, I got the values below. do e=1,nelv eg = lglel(e) if(eg .eq. 195) then write(*,*) xm1(1,1,1,e),ym1(1,1,1,e),zm1(1,1,1,e) write(*,*) cbc(1:6,e,1) end if end do 7.500381456730263E-017 1.00000000000000 0.000000000000000E+000 0.000000000000000E+000 W E E E P E Is there any reason why the x coordinate for the first element vertex is not exactly 0.0e0? Hope someone can help. Thank you very much. Best regards, Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users End of Nek5000-users Digest, Vol 72, Issue 1 ******************************************** From nek5000-users at lists.mcs.anl.gov Thu Feb 5 09:28:59 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Feb 2015 15:28:59 +0000 Subject: [Nek5000-users] Postdoc position available In-Reply-To: Message-ID: Prof. Mavriplis and the University of Ottawa are currently looking for a postdoctoral researcher interested in pursuing research in the field of Computational Fluid Dynamics (CFD). The main topic of research will be adaptive discontinuous Galerkin or spectral element methods for direct simulation (incompressible Navier-Stokes equations), and other projects may include control of separated flows, transition, aerodynamics and CFD for blood flow. A PhD degree in CFD or Fluid Dynamics including code development and high performance computing is necessary. The candidate must have already published journal articles. Experience with spectral methods, Nek5000, and VISIT is a plus. The ideal candidate will have excellent computer programming skills, communication skills (written, oral, graphical and with others in the research group), self-motivation and an open mind. The position also requires some training of graduate students. Ideally this would be for the spring timeframe. The position is at University of Ottawa in Ottawa, Canada. Please send a short email with cv attached by email with 'Nek5000 PhD application' in the subject line. Catherine Mavriplis http://www.engineering.uottawa.ca/en/directory/view/mavriplis_catherine -- Prof. Catherine Mavriplis Dept. of Mechanical Engineering / G?nie m?canique University of Ottawa / Universit? d'Ottawa 161 Louis Pasteur Room A331 Ottawa, Ontario CANADA K1N 6N5 Catherine.Mavriplis at uottawa.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Feb 10 05:32:28 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Feb 2015 11:32:28 +0000 Subject: [Nek5000-users] Dump on both regular and SEM grids Message-ID: Dear All, Is there a possibility to dump result files during run time on both an SEM grid and another regular grid (as done if ifreguo = .true. ). Therefore avoiding the need to run a separate conversion in post-processing (as explained in https://nek5000.mcs.anl.gov/index.php/Data_processing_example ). Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Feb 10 06:49:10 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Feb 2015 12:49:10 +0000 Subject: [Nek5000-users] Dump on both regular and SEM grids In-Reply-To: References: Message-ID: Hi JP, You could dump another sequence of files with the fields interpolated to a mesh of equally spaced points instead of the defualt GLL points with something like the following in your userchk() ifreguo = .true. !uniform mesh output nrg = 8 !lxo = 8 - fine grid irstep = iostep/5 !dump more often if(mod(istep,irstep).eq.0) call outpost(vx,vy,vz,pr,t,' ') ifreguo = .false. !unset uniform mesh output Note that the mesh spacing will vary from element to element unless the elements are of equal dimensions. Aleks ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, February 10, 2015 5:32 AM To: nek5000-users Subject: [Nek5000-users] Dump on both regular and SEM grids Dear All, Is there a possibility to dump result files during run time on both an SEM grid and another regular grid (as done if ifreguo = .true. ). Therefore avoiding the need to run a separate conversion in post-processing (as explained in https://nek5000.mcs.anl.gov/index.php/Data_processing_example ). Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Feb 10 19:56:55 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Feb 2015 20:56:55 -0500 Subject: [Nek5000-users] question about efficient running nek5000 In-Reply-To: References: Message-ID: Hi, I have tried running on 11 cores per node and increased the number of cores and it went faster ~2-3 percent than the one that I used 12 cores per node with the same total cores, however it is still slower than the one that I used 8 cores per nodes and less number of nodes!! So it seems with increasing number of nodes, I get the better efficiency, not much matter of how many cores per node I use!! Is this an issue of memory allocation?!! Thanks, Ami On Wed, Feb 4, 2015 at 2:35 PM, wrote: > Hi Aleks, > > Approximately I can do that! > > Ami > > On Wed, Feb 4, 2015 at 2:30 PM, wrote: > >> Hi Ami, >> >> Could you try your 12 core-per-node case running with only 11 cores per >> node (and increasing the total number of nodes to keep the number of CPU >> fixed)? >> >> Aleks >> >> >> On Wed, 4 Feb 2015, nek5000-users at lists.mcs.anl.gov wrote: >> >> Mike, >>> >>> Thanks for your answer!, Total grid points is 32499936, which I believe >>> it >>> is greater than 20k for both cases! >>> >>> Ami >>> >>> On Wed, Feb 4, 2015 at 2:17 PM, wrote: >>> >>> Hi Ami, >>>> >>>> How many nodes were in your simulation? Nek scales well if your number >>>> of >>>> gridpoints per core is large enough, e.g., greater than 20K or so in my >>>> experience. >>>> >>>> It's not clear to me if the power-of-two issue would be the cause here; >>>> perhaps Paul could comment. >>>> >>>> Mike >>>> >>>> On Feb 4, 2015, at 12:09 PM, >>>> wrote: >>>> >>>> Hi, >>>>> >>>>> I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores >>>>> per >>>>> >>>> node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per >>>> node, however in second case I got lower efficiency, simulation goes >>>> slower >>>> about 5~8 percent!! I ran both cases on the same cluster!! Does anyone >>>> have >>>> any idea why I do not get higher efficiency with the higher number of >>>> CPUs >>>> but less nodes involved!? Could memory be a limitation here or since >>>> numbers in first case are power of 2, it is more efficient!? >>>> >>>>> >>>>> Thanks, >>>>> Ami >>>>> _______________________________________________ >>>>> 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 >> > > > _______________________________________________ > 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 Wed Feb 11 04:12:57 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Feb 2015 10:12:57 +0000 Subject: [Nek5000-users] Dump on both regular and SEM grids Message-ID: Dear Aleks, Thank you. It is exactly what I was looking for. Regards, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 11 05:00:14 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Feb 2015 11:00:14 +0000 Subject: [Nek5000-users] Dump on both regular and SEM grids Message-ID: Dear Aleks, Sorry to bother you again, a quick question, what if I were to output at a specific time interval, i.e. using IOTIME.. how should I refer to the correct variables / go about it? Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 11 06:41:39 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Feb 2015 12:41:39 +0000 Subject: [Nek5000-users] Dump on both regular and SEM grids In-Reply-To: References: Message-ID: Hi JP, I prefer to use iostep but I suppose you could copy a part of prepost.f: timdump=0 if(timeio.ne.0.0)then if(time .ge. (ntdump + 1) * timeio) then timdump=1. ntdump=ntdump+1 call outpost..... endif endif Aleks ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Wednesday, February 11, 2015 5:00 AM To: nek5000-users Subject: Re: [Nek5000-users] Dump on both regular and SEM grids Dear Aleks, Sorry to bother you again, a quick question, what if I were to output at a specific time interval, i.e. using IOTIME.. how should I refer to the correct variables / go about it? Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 11 10:38:13 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Feb 2015 17:38:13 +0100 Subject: [Nek5000-users] Dump on both regular and SEM grids In-Reply-To: References: Message-ID: Hi Aleks, Does Nek automatically creates this equally spaced regular grid or should we create it ? At present I am using 'Hpts()' to dump data, but it is lot of time and memory consuming I can create a regular mesh using a small routine but how do I make NEK to dump data to that particular mesh ? What is ' nrg ' ? Thanks, KS On 10/02/2015 13:49, nek5000-users at lists.mcs.anl.gov wrote: > Hi JP, > > You could dump another sequence of files with the fields interpolated > to a mesh of equally spaced points instead of the defualt GLL points > with something like the following in your userchk() > > > ifreguo = .true. !uniform mesh output > nrg = 8 !lxo = 8 - fine grid > irstep = iostep/5 !dump more often > if(mod(istep,irstep).eq.0) call outpost(vx,vy,vz,pr,t,' ') > ifreguo = .false. !unset uniform mesh output > > Note that the mesh spacing will vary from element to element unless > the elements are of equal dimensions. > > Aleks > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Tuesday, February 10, 2015 5:32 AM > *To:* nek5000-users > *Subject:* [Nek5000-users] Dump on both regular and SEM grids > > Dear All, > > Is there a possibility to dump result files during run time on both an > SEM grid and another regular grid (as done if ifreguo = .true. ). > Therefore avoiding the need to run a separate conversion in > post-processing (as explained in > https://nek5000.mcs.anl.gov/index.php/Data_processing_example ). > > Thank you, > JP > > > _______________________________________________ > 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 Thu Feb 12 17:43:55 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Feb 2015 18:43:55 -0500 Subject: [Nek5000-users] Parallel on several nodes In-Reply-To: References: Message-ID: Hi Tanmoy I still get errors using the shell script. Here is what happens: On our cluster, we have 12 processors for each node; if I set the number of processors up to 12 there are results generated and the total simulation time decreases. Everything works fine and below is the script: #!/bin/bash #PBS -l nodes=2:ppn=12 #PBS -l mem=16gb #PBS -l walltime=1:00:00 cd /data/User/Nek5000/nek5_svn/examples/eddy echo eddy_uv > SESSION.NAME echo `pwd`'/' >> SESSION.NAME rm -f eddy_uv.his1 rm -f eddy_uv.sch1 rm -f eddy_uv.log1 mv eddy_uv.log eddy_uv.log1 mv eddy_uv.his eddy_uv.his1 mv eddy_uv.sch eddy_uv.sch1 rm -f logfile rm -f ioinfo sleep 5 mpiexec -n 12 -machinefile $PBS_NODEFILE nek5000 > eddy_uv.log sleep 5 ln eddy_uv.log logfile exit 0; However, when I set the number of CPUs to 16 there is no outcome. Here is the script: #!/bin/bash #PBS -l nodes=4:ppn=4 #PBS -l mem=16gb #PBS -l walltime=1:00:00 cd /data/User/Nek5000/nek5_svn/examples/eddy echo eddy_uv > SESSION.NAME echo `pwd`'/' >> SESSION.NAME rm -f eddy_uv.his1 rm -f eddy_uv.sch1 rm -f eddy_uv.log1 mv eddy_uv.log eddy_uv.log1 mv eddy_uv.his eddy_uv.his1 mv eddy_uv.sch eddy_uv.sch1 rm -f logfile rm -f ioinfo sleep 5 mpiexec -n 16 -machinefile $PBS_NODEFILE nek5000 > eddy_uv.log sleep 5 ln eddy_uv.log logfile exit 0; I'm not sure what I'm missing here? (in short I'm not able to increase the number of CPUs more than 12, which is the maximum number of processors per node.) On 1/14/2015 11:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > #PBS -j oe > #PBS -o sparkyLog From nek5000-users at lists.mcs.anl.gov Thu Feb 12 18:19:38 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Feb 2015 17:19:38 -0700 Subject: [Nek5000-users] Parallel on several nodes In-Reply-To: References: Message-ID: Hi Saleh, CPU's would refer to the number of processors in each core, that sits on a node..You may have multiple cores on a node. So, theoretically, you can have CPU's = 12X2, set in your PBS script, but that will not speed up your code, since it will turn on the 2 hyperthreads/ processor in the core. I see in the 2nd PBS script, you have total 16 processors, and 4 processors per node. Even though it is a very inefficient way of running your script, I would say it would still work. like 4 nodes and 4 nodes/ processor. However, I don?t have the expertise to comment further without knowing the architecture of your nodes. However, I can say, it is a good practise to keep ppn = (12 in your case always) and change nodes = x, where x = 1,2,3,4 or whatever. That is a lot more efficient, and scaling analysis is also very elegant that way. Best Regards, Tanmoy On Thu, Feb 12, 2015 at 4:43 PM, wrote: > Hi Tanmoy > > I still get errors using the shell script. Here is what happens: > On our cluster, we have 12 processors for each node; if I set the number > of processors up to 12 there are results generated and the total simulation > time decreases. Everything works fine and below is the script: > > #!/bin/bash > #PBS -l nodes=2:ppn=12 > #PBS -l mem=16gb > #PBS -l walltime=1:00:00 > cd /data/User/Nek5000/nek5_svn/examples/eddy > echo eddy_uv > SESSION.NAME > echo `pwd`'/' >> SESSION.NAME > rm -f eddy_uv.his1 > rm -f eddy_uv.sch1 > rm -f eddy_uv.log1 > mv eddy_uv.log eddy_uv.log1 > mv eddy_uv.his eddy_uv.his1 > mv eddy_uv.sch eddy_uv.sch1 > rm -f logfile > rm -f ioinfo > sleep 5 > mpiexec -n 12 -machinefile $PBS_NODEFILE nek5000 > eddy_uv.log > sleep 5 > ln eddy_uv.log logfile > exit 0; > > However, when I set the number of CPUs to 16 there is no outcome. Here is > the script: > > #!/bin/bash > #PBS -l nodes=4:ppn=4 > #PBS -l mem=16gb > #PBS -l walltime=1:00:00 > cd /data/User/Nek5000/nek5_svn/examples/eddy > echo eddy_uv > SESSION.NAME > echo `pwd`'/' >> SESSION.NAME > rm -f eddy_uv.his1 > rm -f eddy_uv.sch1 > rm -f eddy_uv.log1 > mv eddy_uv.log eddy_uv.log1 > mv eddy_uv.his eddy_uv.his1 > mv eddy_uv.sch eddy_uv.sch1 > rm -f logfile > rm -f ioinfo > sleep 5 > mpiexec -n 16 -machinefile $PBS_NODEFILE nek5000 > eddy_uv.log > sleep 5 > ln eddy_uv.log logfile > exit 0; > > > I'm not sure what I'm missing here? (in short I'm not able to increase the > number of CPUs more than 12, which is the maximum number of processors per > node.) > > > > On 1/14/2015 11:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > >> #PBS -j oe >> #PBS -o sparkyLog >> > > > _______________________________________________ > 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 Mon Feb 16 11:44:59 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Feb 2015 17:44:59 +0000 Subject: [Nek5000-users] Spatial average of velocity and pressure Message-ID: Dear Neks, I've been looking at the subroutines for spatial average of variables in nek5000. I'm using PnPn-2 method and my domain is periodic in both X and Z directions. I noticed that the weights for Gauss-Lobatto Legendre points are WXM1, WYM1, WZM1 and the weights for Gauss Legendre points are WXM2, WYM2, WZM2. I'm using the first set of weights for spatial average of my velocity field and the second set of weights for my pressure field, but I'm not sure if that's the correct way to take the spatial average of variables in certain directions?? When I looked at the subroutine planar_average_s in turbChannel example, aa = zz*area(i,k,1,e) + (1-zz)*area(i,k,3,e) (where zz = (1.-zgm1(j,2))/2.) is used for spatial average on r-t plane. I'm wondering which type of weights I should use for spatial average of velocity and pressure in my case. Can I use WXM1 (or WXM2) to average the variables in X direction first and then use WZM1 (or WZM2) to average the variables in Z direction? Hope anyone can help me on this. Thank you very much in advance. Best regards, Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Feb 17 12:54:18 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Feb 2015 19:54:18 +0100 Subject: [Nek5000-users] Mesh morphing Message-ID: Dear Neks, I thought this question might be of interest for someone else as well, so posting it here: I have been looking at the oscillating cylinder example. I would like to do something similar, but instead of a prescribed boundary velocity, would like to prescribe a given displacement of one boundary, and morph my mesh smoothly everywhere to match this displacement. For example, if one were to describe a deformation of the cylinder rather than a velocity (but without altering the other boundaries and without scaling the mesh). This just needs to be done once, not at every time step. Is there an easy way to do this? Can I arrive there somehow by minor modifications of the elasticity solver? What equation exactly is the elasticity solver solving at every time step? (When I outputted the files after every time step for the oscillating cylinder, the mesh deformation seemed to match the prescribed one only after 2 time steps. Is there a reason for this, or did I do something wrong?) Best regards, Outi From nek5000-users at lists.mcs.anl.gov Wed Feb 18 00:23:53 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Feb 2015 06:23:53 +0000 Subject: [Nek5000-users] Error trying to visualize results in VisIt for Eddy_UV example Message-ID: Hi, I am a new user and I am just getting started with the examples in the Nek guide. I tried using VisIt to visualize results for Eddy_UV example but I get this error: VisIt could not read from the file "/Users/K10/eddy/vis.nek3d". The generated error message was: There was an error opening /Users/K10/eddy/vis.nek3d. It may be an invalid file. VisIt tried using the following file format readers to open the file: Nek5000, Silo The following error(s) may be helpful in identifying the problem: There was an error opening the file: When attempting to use "Nek", the file matched the general format expected by the reader but eventually encountered this error: "The first time step in a Nek file must contain a mesh". Could you please tell me why this might be happening? Ketan Mittal -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 18 00:44:38 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Feb 2015 23:44:38 -0700 Subject: [Nek5000-users] Error trying to visualize results in VisIt for Eddy_UV example In-Reply-To: References: Message-ID: Hi Ketan, Why dont you try visnek . Visit will generate a .nek5000 metadata file. You can read that in visit. Also, you need to make sure, that at least first fld file should have mesh information, otherwise visit will fail to read the data. So make sure when the .fld01 file is generated ifxyo = .true., it can be false or true every where. Best Regards, Tanmoy On Tue, Feb 17, 2015 at 11:23 PM, wrote: > Hi, > > I am a new user and I am just getting started with the examples in the > Nek guide. I tried using VisIt to visualize results for Eddy_UV example but > I get this error: > > VisIt could not read from the file "/Users/K10/eddy/vis.nek3d". > > > The generated error message was: > > > There was an error opening /Users/K10/eddy/vis.nek3d. It may be an > invalid file. VisIt tried using the following file format readers to open > the file: Nek5000, Silo > > > The following error(s) may be helpful in identifying the problem: > > There was an error opening the file: When attempting to use "Nek", the > file matched the general format expected by the reader but eventually > encountered this error: "The first time step in a Nek file must contain a > mesh". > > > > Could you please tell me why this might be happening? > > Ketan Mittal > > _______________________________________________ > 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 Wed Feb 18 03:40:36 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Feb 2015 10:40:36 +0100 Subject: [Nek5000-users] ALE formulation Message-ID: Hello NEK's I am just getting started to work with ALE formulation and I have a couple of questions regarding it. I try to do the simulation of flow in the channel with the elastic wall. 1. How can I impose the external pressure as boundary conditions for the part on the channel where the wall is elastic? 2. How can I collect the coordinates of the deforming mesh and the ALE velocities of mesh in the each step of time? Thanks a lot. Best regards, Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Feb 19 10:35:39 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Feb 2015 16:35:39 +0000 Subject: [Nek5000-users] Error trying to visualize results in VisIt for Eddy_UV example Message-ID: Based on the NEK5000 documentation that I have read so far, I am supposed to find "ifxyo" option in the .rea file, but I don?t see it there. Is it supposed to be a different option or is it in a different file? Ketan From nek5000-users at lists.mcs.anl.gov Thu Feb 19 10:50:21 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Feb 2015 09:50:21 -0700 Subject: [Nek5000-users] Error trying to visualize results in VisIt for Eddy_UV example In-Reply-To: References: Message-ID: Hi Ketan, You have to insert ifxyo = .true. in the usrchk routine of .usr file, or you can add IFXYO T, below the list of logicals in rea file by yourself. Best Regards, Tanmoy On Thu, Feb 19, 2015 at 9:35 AM, wrote: > Based on the NEK5000 documentation that I have read so far, I am supposed > to find "ifxyo" option in the .rea file, but I don?t see it there. Is it > supposed to be a different option or is it in a different file? > > Ketan > _______________________________________________ > 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 Feb 20 11:39:17 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Feb 2015 18:39:17 +0100 Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) In-Reply-To: <20150217195418.Horde.kBfYvzXQjnLW9MGGXpBSXg6@www.mech.kth.se> References: <20150217195418.Horde.kBfYvzXQjnLW9MGGXpBSXg6@www.mech.kth.se> Message-ID: Dear Neks, What I actually would like to accomplish is to solve the Laplace equation for the mesh (with the boundary deformation as a BC). I saw that this has been done already at least by Paul (a thread 2009) and Matt (for smoothing of a wing mesh, with zero deformation). Could any of you please give me a hint on how to solve the Laplace equation for the mesh like this? Matt? Paul? I would be very grateful. Best regards, Outi Quoting Outi Tammisola : > Dear Neks, > > I thought this question might be of interest for someone else as > well, so posting it here: > > I have been looking at the oscillating cylinder example. I would > like to do something similar, but instead of a prescribed boundary > velocity, would like to prescribe a given displacement of one > boundary, and morph my mesh smoothly everywhere to match this > displacement. For example, if one were to describe a deformation of > the cylinder rather than a velocity (but without altering the other > boundaries and without scaling the mesh). This just needs to be done > once, not at every time step. > > Is there an easy way to do this? Can I arrive there somehow by minor > modifications of the elasticity solver? What equation exactly is the > elasticity solver solving at every time step? > (When I outputted the files after every time step for the > oscillating cylinder, the mesh deformation seemed to match the > prescribed one only after 2 time steps. Is there a reason for this, > or did I do something wrong?) > > Best regards, > Outi From nek5000-users at lists.mcs.anl.gov Fri Feb 20 13:58:50 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Feb 2015 19:58:50 +0000 Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) In-Reply-To: References: <20150217195418.Horde.kBfYvzXQjnLW9MGGXpBSXg6@www.mech.kth.se>, Message-ID: Dear Outi, I have just added "ocyl2" to the ocyl example directory. I think it addresses the question you raise. Please advise and let us know if you have any difficulties. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, February 20, 2015 11:39 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) Dear Neks, What I actually would like to accomplish is to solve the Laplace equation for the mesh (with the boundary deformation as a BC). I saw that this has been done already at least by Paul (a thread 2009) and Matt (for smoothing of a wing mesh, with zero deformation). Could any of you please give me a hint on how to solve the Laplace equation for the mesh like this? Matt? Paul? I would be very grateful. Best regards, Outi Quoting Outi Tammisola : > Dear Neks, > > I thought this question might be of interest for someone else as > well, so posting it here: > > I have been looking at the oscillating cylinder example. I would > like to do something similar, but instead of a prescribed boundary > velocity, would like to prescribe a given displacement of one > boundary, and morph my mesh smoothly everywhere to match this > displacement. For example, if one were to describe a deformation of > the cylinder rather than a velocity (but without altering the other > boundaries and without scaling the mesh). This just needs to be done > once, not at every time step. > > Is there an easy way to do this? Can I arrive there somehow by minor > modifications of the elasticity solver? What equation exactly is the > elasticity solver solving at every time step? > (When I outputted the files after every time step for the > oscillating cylinder, the mesh deformation seemed to match the > prescribed one only after 2 time steps. Is there a reason for this, > or did I do something wrong?) > > Best regards, > Outi _______________________________________________ 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 Feb 20 17:11:53 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 21 Feb 2015 00:11:53 +0100 Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) In-Reply-To: References: <20150217195418.Horde.kBfYvzXQjnLW9MGGXpBSXg6@www.mech.kth.se> Message-ID: Dear Paul, Thank you very much, the idea seems exactly like what I would like to do. However, there is an error appearing in the Helmholtz solver. From logfile: call userchk 1.000000000000000E-006 p22 0 1 0 200 **ERROR**: Failed in HMHOLTZ: mshv 1.3206E-02 2.7147E+03 1.0000E-06 done :: userchk Best regards, Outi Quoting nek5000-users at lists.mcs.anl.gov: > Dear Outi, > > I have just added "ocyl2" to the ocyl example directory. > > I think it addresses the question you raise. Please advise and let > us know if you have any difficulties. > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Friday, February 20, 2015 11:39 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) > > Dear Neks, > > What I actually would like to accomplish is to solve the Laplace > equation for the mesh (with the boundary deformation as a BC). I saw > that this has been done already at least by Paul (a thread 2009) and > Matt (for smoothing of a wing mesh, with zero deformation). > Could any of you please give me a hint on how to solve the Laplace > equation for the mesh like this? Matt? Paul? > I would be very grateful. > > Best regards, > Outi > > Quoting Outi Tammisola : > >> Dear Neks, >> >> I thought this question might be of interest for someone else as >> well, so posting it here: >> >> I have been looking at the oscillating cylinder example. I would >> like to do something similar, but instead of a prescribed boundary >> velocity, would like to prescribe a given displacement of one >> boundary, and morph my mesh smoothly everywhere to match this >> displacement. For example, if one were to describe a deformation of >> the cylinder rather than a velocity (but without altering the other >> boundaries and without scaling the mesh). This just needs to be done >> once, not at every time step. >> >> Is there an easy way to do this? Can I arrive there somehow by minor >> modifications of the elasticity solver? What equation exactly is the >> elasticity solver solving at every time step? >> (When I outputted the files after every time step for the >> oscillating cylinder, the mesh deformation seemed to match the >> prescribed one only after 2 time steps. Is there a reason for this, >> or did I do something wrong?) >> >> Best regards, >> Outi > > > _______________________________________________ > 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 Feb 20 18:34:37 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 21 Feb 2015 00:34:37 +0000 Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) In-Reply-To: References: <20150217195418.Horde.kBfYvzXQjnLW9MGGXpBSXg6@www.mech.kth.se> , Message-ID: Hi Outi, It's ok... it just means that the solver did not converge all the way... but the resulting field is nonetheless sufficiently smooth. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, February 20, 2015 5:11 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) Dear Paul, Thank you very much, the idea seems exactly like what I would like to do. However, there is an error appearing in the Helmholtz solver. From logfile: call userchk 1.000000000000000E-006 p22 0 1 0 200 **ERROR**: Failed in HMHOLTZ: mshv 1.3206E-02 2.7147E+03 1.0000E-06 done :: userchk Best regards, Outi Quoting nek5000-users at lists.mcs.anl.gov: > Dear Outi, > > I have just added "ocyl2" to the ocyl example directory. > > I think it addresses the question you raise. Please advise and let > us know if you have any difficulties. > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Friday, February 20, 2015 11:39 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Solving mesh Laplace equation (Re: Mesh morphing) > > Dear Neks, > > What I actually would like to accomplish is to solve the Laplace > equation for the mesh (with the boundary deformation as a BC). I saw > that this has been done already at least by Paul (a thread 2009) and > Matt (for smoothing of a wing mesh, with zero deformation). > Could any of you please give me a hint on how to solve the Laplace > equation for the mesh like this? Matt? Paul? > I would be very grateful. > > Best regards, > Outi > > Quoting Outi Tammisola : > >> Dear Neks, >> >> I thought this question might be of interest for someone else as >> well, so posting it here: >> >> I have been looking at the oscillating cylinder example. I would >> like to do something similar, but instead of a prescribed boundary >> velocity, would like to prescribe a given displacement of one >> boundary, and morph my mesh smoothly everywhere to match this >> displacement. For example, if one were to describe a deformation of >> the cylinder rather than a velocity (but without altering the other >> boundaries and without scaling the mesh). This just needs to be done >> once, not at every time step. >> >> Is there an easy way to do this? Can I arrive there somehow by minor >> modifications of the elasticity solver? What equation exactly is the >> elasticity solver solving at every time step? >> (When I outputted the files after every time step for the >> oscillating cylinder, the mesh deformation seemed to match the >> prescribed one only after 2 time steps. Is there a reason for this, >> or did I do something wrong?) >> >> Best regards, >> Outi > > > _______________________________________________ > 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 From nek5000-users at lists.mcs.anl.gov Sun Feb 22 04:21:59 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Feb 2015 04:21:59 -0600 Subject: [Nek5000-users] Installation failed - maketools all Message-ID: Dear nek5000 users, Hello everyone, I am a new user. I got stuck when I follow the Quick Start page . I follow up till the command - "maketools all" Trouble happens. The error occurs : genbox.f:(.text+0x174cc): undefined reference to `_gfortran_transfer_real_write' And a number of similar errors. Does anyone know how to correct that? Thank you. Regards, Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Feb 22 11:06:16 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Feb 2015 10:06:16 -0700 Subject: [Nek5000-users] Installation failed - maketools all In-Reply-To: References: Message-ID: Hi Simon, it seems like you do not have gfortran installed correctly, or a bugged one install, and some how, gcc or g++ (which are default in linux systems) is trying to link up your fortran codes in genbox.f generating those errors. In order to upgrade all the utilities and compilers, link files, make sure you install all this utility files and compilers before you install nek5000. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mesa-utils, tcsh, subversion, libx11-*, libxt-dev , xfonts-100dpi, xfonts-100dpi-transcoded xfonts-75dpi, xfonts-75dpi-transcoded, gfortran, gcc, g++, mpich2, vim ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Hope this would work for you Sincerely, Tanmoy Best Regards, Tanmoy On Sun, Feb 22, 2015 at 3:21 AM, wrote: > Dear nek5000 users, > > Hello everyone, I am a new user. I got stuck when I follow the Quick > Start page . I follow > up till the command - "maketools all" Trouble happens. > > The error occurs : > genbox.f:(.text+0x174cc): undefined reference to > `_gfortran_transfer_real_write' > > And a number of similar errors. Does anyone know how to correct that? > Thank you. > > Regards, > Simon > > _______________________________________________ > 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 Sat Feb 28 08:49:39 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 28 Feb 2015 15:49:39 +0100 Subject: [Nek5000-users] Dump on both regular and SEM grids Message-ID: Hi Aleks (and anyone interested), Just to share an extra solution, I make Nek dump both to uniform and GLL grids simultaneously, when using IOTIME, by adding the following at approximately line 136 of prepost.f : ifreguo = .true. if (ifdoit) call outfld(prefix) ifreguo = .false. Otherwise, when using NSTEPS, the solution you gave me works just fine. Thanks again, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Feb 28 09:24:31 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 28 Feb 2015 10:24:31 -0500 Subject: [Nek5000-users] Linear Advection Equation Message-ID: Dear Users, Is there a way to solve a linear advection equation in nek5k without computing the Navier-Stokes equations? I am simply interested in advecting a profile according to the following: D(phi)/Dt = d (phi) /dt + v*.*grad(phi)= 0 where v*.*grad(phi) = u.d(phi)/dx + v.d(phi)/dy + w.d(phi)/dz and v is a prescribed velocity (for example v = (1,1) in 2D) Best, Saumil -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Feb 28 09:31:49 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 28 Feb 2015 15:31:49 +0000 Subject: [Nek5000-users] Linear Advection Equation In-Reply-To: References: Message-ID: Set ifflow to false and ifheat to T and ifadvc = F T F F F F... in the .rea file. Then, supply your velocity field in useric (ux, uy, uz), or, if you want time-varying velocity, do so in usrchk by over-writing the velocity field arrays, vx(), vy(), and vz() at each step. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Saturday, February 28, 2015 9:24 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Linear Advection Equation Dear Users, Is there a way to solve a linear advection equation in nek5k without computing the Navier-Stokes equations? I am simply interested in advecting a profile according to the following: D(phi)/Dt = d (phi) /dt + v.grad(phi)= 0 where v.grad(phi) = u.d(phi)/dx + v.d(phi)/dy + w.d(phi)/dz and v is a prescribed velocity (for example v = (1,1) in 2D) Best, Saumil -------------- next part -------------- An HTML attachment was scrubbed... URL: