November 2014 - 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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IO problem
by nek5000-users＠lists.mcs.anl.gov 24 Nov '14

24 Nov '14

Hello all, I have sometimes experienced an IO issue, when running on a relatively large number of machines on our bgq cluster with MPIIO enabled and p65=0. The issue is that while the status of the job shows normal running, no output files and even .log file are written on the file system. What is strange is that the issue happens occasionally and for jobs with more than 512 nodes, as I haven't seen this for smaller scale problems and resources. Usually, cancelling and resubmitting the job will solve the issue. I contacted the technical staff of our cluster and they performed several tests but they have not yet been able to reproduce the problem on small scales. It is more likely that the this problem is caused by a hardware issue rather than a code issue since it is not happened all the time. However, I wanted to contact you and wondered if anyone has any comments or similar experience. Thanks Mohsen

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Recycling BC
by nek5000-users＠lists.mcs.anl.gov 13 Nov '14

13 Nov '14

Dear Neks, I am using the turbJet example to set up my own recycling boundary case. As far as I understand the velocity that is passing through stack 8 (element 8) in the turbJet example should then be recycled back to the inlet. However when I plot the instantaneous velocity profiles for these two points they are non-identical. Is this deliberately so, I presume it should behave like a periodic boundary condition, or have I missed the point? Thank you for your time, Friedrich.

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Nekton (pre/post-processing)
by nek5000-users＠lists.mcs.anl.gov 11 Nov '14

11 Nov '14

Hello, I am wondering if there's any manual for the nekton 2.6 out there. I have problem to work on with the pre-processing as menu feature provided by the existing manual is different with the one use in the version 2.6. Especially right at the beginning in the build menu (there's no ADD ELEMENT). Or perhaps is there any suggestion on other option of pre-processing. Thanks Best, Muhsin

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Re: [Nek5000-users] problem with running nek5000 on supercomputers
by nek5000-users＠lists.mcs.anl.gov 11 Nov '14

11 Nov '14

It seems that for each time I had to clean compiled files before changing the processor count and run it again! It works now! Thanks, Ami On Mon, Nov 10, 2014 at 4:29 PM, Amirreza Hashemi <amirezahashemi(a)gmail.com> wrote: > Dr. Fishcer, > > Thanks for your answer, for sure, I change the lelt and lelg and keep them > as lowest even number that I can pick when I increase the number of CPUs. I > picked also lp=32768, but I still get this "allocation failed" error. Is > there any thing else that effect on the allocation which I have to change > it?! > > Thanks, > Ami > > On Mon, Nov 10, 2014 at 8:55 AM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > >> >> Hi Ami, >> >> When you increase the processor count, you can recompile with a smaller >> lelt. >> >> Suppose you have lelt=1000 and you go from P=64 to P=128. Then set >> lelt=500 and >> recompile. >> >> Make certain lelg >= 500*P and lp >= 128. >> >> I would suggest lelg="big enough" (and an even number) and lp=32768. >> >> Paul >> >> ------------------------------ >> *From:* nek5000-users-bounces(a)lists.mcs.anl.gov [ >> nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of >> nek5000-users(a)lists.mcs.anl.gov [nek5000-users(a)lists.mcs.anl.gov] >> *Sent:* Monday, November 10, 2014 5:05 AM >> *To:* nek5000-users(a)lists.mcs.anl.gov >> *Subject:* [Nek5000-users] problem with running nek5000 on supercomputers >> >> Hi Neks, >> >> I am trying to run my simulation with nek5000 on supercomputers, the >> size of the problem is something like: >> >> text data bss dec hex filename >> 2233955 187412 2554984280 2557405647 986ee9cf nek5000 >> >> I don't have any problem when I use 32~64 CPUs to run parallel on >> supercomputers, but once I go for more than 64 CPUs, I always get >> "allocation failed" error. I have tried to run on different supercomputer >> like as Gordon SDSC, OSC, TACC, but I got the same type of error each time. >> I have checked the active memories, it seems for each of them memories have >> large unused portion. Does any one have any idea why when I increase the >> number of CPUs I get this allocation error?! >> >> Thank you, >> Ami >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >

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Re: [Nek5000-users] problem with running nek5000 on supercomputers
by nek5000-users＠lists.mcs.anl.gov 10 Nov '14

10 Nov '14

Dr. Fishcer, Thanks for your answer, for sure, I change the lelt and lelg and keep them as lowest even number that I can pick when I increase the number of CPUs. I picked also lp=32768, but I still get this "allocation failed" error. Is there any thing else that effect on the allocation which I have to change it?! Thanks, Ami On Mon, Nov 10, 2014 at 8:55 AM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > > Hi Ami, > > When you increase the processor count, you can recompile with a smaller > lelt. > > Suppose you have lelt=1000 and you go from P=64 to P=128. Then set > lelt=500 and > recompile. > > Make certain lelg >= 500*P and lp >= 128. > > I would suggest lelg="big enough" (and an even number) and lp=32768. > > Paul > > ------------------------------ > *From:* nek5000-users-bounces(a)lists.mcs.anl.gov [ > nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of > nek5000-users(a)lists.mcs.anl.gov [nek5000-users(a)lists.mcs.anl.gov] > *Sent:* Monday, November 10, 2014 5:05 AM > *To:* nek5000-users(a)lists.mcs.anl.gov > *Subject:* [Nek5000-users] problem with running nek5000 on supercomputers > > Hi Neks, > > I am trying to run my simulation with nek5000 on supercomputers, the size > of the problem is something like: > > text data bss dec hex filename > 2233955 187412 2554984280 2557405647 986ee9cf nek5000 > > I don't have any problem when I use 32~64 CPUs to run parallel on > supercomputers, but once I go for more than 64 CPUs, I always get > "allocation failed" error. I have tried to run on different supercomputer > like as Gordon SDSC, OSC, TACC, but I got the same type of error each time. > I have checked the active memories, it seems for each of them memories have > large unused portion. Does any one have any idea why when I increase the > number of CPUs I get this allocation error?! > > Thank you, > Ami > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >

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problem with running nek5000 on supercomputers
by nek5000-users＠lists.mcs.anl.gov 10 Nov '14

10 Nov '14

Hi Neks, I am trying to run my simulation with nek5000 on supercomputers, the size of the problem is something like: text data bss dec hex filename 2233955 187412 2554984280 2557405647 986ee9cf nek5000 I don't have any problem when I use 32~64 CPUs to run parallel on supercomputers, but once I go for more than 64 CPUs, I always get "allocation failed" error. I have tried to run on different supercomputer like as Gordon SDSC, OSC, TACC, but I got the same type of error each time. I have checked the active memories, it seems for each of them memories have large unused portion. Does any one have any idea why when I increase the number of CPUs I get this allocation error?! Thank you, Ami

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Prex problem
by nek5000-users＠lists.mcs.anl.gov 06 Nov '14

06 Nov '14

Hello, I have been struggling with this for a few days. I am just getting used to using nek5000. I am able to compile and run the examples on a multi-thread linux machine. However prex etc which includes a GUI opens up but I cannot see any text in the GUI window. They all appear as colored boxes. It actually took me a while to figure out what those colored boxes are. I have a feeling it's a compatibility issue. Any help would be appreciated. Thank you, -Eb

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**ERROR**: Failed in HMHOLTZ
by nek5000-users＠lists.mcs.anl.gov 06 Nov '14

06 Nov '14

Hi Neks when I setup a profile 2D flow, there are informations like this, but the simulation is not crash, Step 800, t= 8.0000000E-02, DT= 1.0000000E-04, C= 0.431 9.2444E+03 1.0117E+01 Solving for fluid F T T 800 100 **ERROR**: Failed in HMHOLTZ: VELX 3.7727E-16 5.3129E-02 1.0000E-16 800 100 **ERROR**: Failed in HMHOLTZ: VELY 2.4683E-16 3.5181E-02 1.0000E-16 800 U-PRES gmres: 23 5.6827E-15 1.0000E-14 9.6473E-07 9.5640E-01 2.4052E+00 800 8.0000E-02 1.0044E+01 Fluid done 800 8.00000000000E-02 6.70022578679E-01 1.99103625323E-01 4.70918953356E-01 1dragx 800 8.00000000000E-02 4.12612202513E-01 5.10664067531E-01 -9.80518650173E-02 1dragy dump history points done :: dump history points The CFL number is below than 0.5 already, the polynomial order is 7 in this case. when I choose a lower order p, this information will be disappeared after several iteration steps. I have checked the mesh looks fine, the parameters setting are copied from “ext_cyl” with a smaller values of p21 to p25, I don’t know what is wrong, should I ignore ? thanks, Wei

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