From nek5000-users at lists.mcs.anl.gov Thu Feb 2 07:14:38 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 2 Feb 2017 14:14:38 +0100 Subject: [Nek5000-users] Setics subroutine in load_fld In-Reply-To: References: Message-ID: Thanks very much. Navrose. On Tuesday 31 January 2017 06:49 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Navrose, > > I do not know if there is any better method, because I would do it > probably the same way. Another way-- you can probably define another > set of routine say load_fld_pert(), with modified setics and RESTART > file, but probably it is as good as using opcopy(). > > On Tue, Jan 31, 2017 at 12:25 AM, > wrote: > > Many thanks Tanmoy. > > So each time load_fld is called it will load the base > flow variables (I am carrying out computations for incompressible N-S > equations). What if I want to load the perturbations also from a > different > file? One way that I see it is to use load_fld for the restart > file for > perturbations, copy it in the perturbation variables (vxp, vyp, > vzp, prp), > and then again use load_fld for the base flow file. Is there a > direct or > better method for this? > > Thank you. > > Best wishes, > Navrose. > > On Monday 30 January 2017 08:15 PM, > nek5000-users at lists.mcs.anl.gov > wrote: >> Hi Navrose, >> >> You are right. Two things are important in the load_fld() >> subroutine. The include file 'RESTART' and the routine setics. So >> everytime a load_fld subroutine is being called, the variable >> values read from the current file would be stored in vx(i,j,k,e), >> vy(i,j,k,e), vz(i,j,k,e), pr, t and so on... >> >> Best Regards, >> Tanmoy >> >> On Mon, Jan 30, 2017 at 6:04 AM, > > wrote: >> >> Dear Neks, >> >> I am relatively new to NEK5000. I am going through some >> the .usr files that have been used previously in my research >> group. I notice that in the /userchk/ subroutine, /load_fld >> /has been >> called a few times. Upon checking the /load_fld/ function in >> in the source code, I found that /setics /subroutine is >> called at the >> end of /load_fld/ function. >> >> Does this mean that each time /load_fld /function is called, >> the /useric/ >> subroutine in the .usr file is executed? I would like to >> mention that >> no restart file is given in the .rea file. >> >> Many thanks. >> >> Best regards, >> >> Navrose. >> >> >> >> >> _______________________________________________ >> 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 Thu Feb 9 01:34:44 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 9 Feb 2017 14:34:44 +0700 Subject: [Nek5000-users] 1d profile Message-ID: Hi, neks. I am trying to get the 1d profile. vx(y) in turbChannel, for or example. Here the code below: real myvx(ny1,nely) do e=1,nelv eg = gllel(e) call get_exyz(ex,ey,ez,eg,nelx,nely,nelz) if (ex.eq.1 .and. ez.eq.1) then do i=1,ny1 myvx(i,ey) = vx(1,i,1,e) enddo endif enddo But after this, myvx contains incorrect value, that not looks like really vx(y). What's wrong? Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Feb 9 06:56:35 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 9 Feb 2017 13:56:35 +0100 Subject: [Nek5000-users] 1d profile In-Reply-To: References: Message-ID: Hi, I guess the problem is the line eg = gllel(e) You should use eg = lglel(e) It would translate your local element number to the global one. Regards Adam On 09/02/17 08:34, nek5000-users at lists.mcs.anl.gov wrote: > Hi, neks. > I am trying to get the 1d profile. vx(y) in turbChannel, for or > example. Here the code below: > > real myvx(ny1,nely) > > do e=1,nelv > > eg = gllel(e) > call get_exyz(ex,ey,ez,eg,nelx,nely,nelz) > > if (ex.eq.1 .and. ez.eq.1) then > do i=1,ny1 > myvx(i,ey) = vx(1,i,1,e) > enddo > endif > > enddo > > But after this, myvx contains incorrect value, that not looks like > really vx(y). > What's wrong? > > Vatslav > > > _______________________________________________ > 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 9 13:17:32 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 09 Feb 2017 20:17:32 +0100 Subject: [Nek5000-users] Axisymmetric jet using genbox Message-ID: Dear Nek users, I am doing my master thesis at Technical University of Madrid and I am using Nek5000 to study an axisymmetric jet. I have generated the mesh using genbox. Then I have try to run numerical simulations: 1) 2D 2) Setting: IFAXIS T 3) Setting: IFAXIS T, IFAZIV T (and with IFHEAT T, to plot the azimuthal velocity. In all cases my simulation crashes, due to some problems in the boundary (I have tried with both ON and O BC) So, I have added artificial viscosity, but the axysimmetric simulation (case2 2 and 3) still crashes: 3.000000 p99 dealiasing:if <0 disable 0.0000000E+00 p100 reserved 1.0000000E+00 p101 No. of additional filter modes 0.0000000E+00 1.0000000E-02 p103 weight of stabilizing filter (.01) Could you give me any recommendation to follow? Thank you in advance. MViturro From nek5000-users at lists.mcs.anl.gov Fri Feb 10 11:16:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 10 Feb 2017 18:16:48 +0100 Subject: [Nek5000-users] New Git Workflow Message-ID: Hi all, we have just switched to a (hopefully) simpler Git workflow: How we do it - Anything in master is always deployable - Upcoming feature release get their own tags or branch that are branched out of master - All development happens on the master branch - To work on something new, create a short lived local branch off of master - When you need feedback or help, or your change is ready for merging, open a pull request So there is _no_ other branch than MASTER anymore. For more information, please read the README shipped with the source code. Cheers, Stefan From nek5000-users at lists.mcs.anl.gov Fri Feb 10 12:14:51 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 10 Feb 2017 19:14:51 +0100 Subject: [Nek5000-users] Problem in writing vector field in solid elements (conjugate) Message-ID: Dear All, I want to write a 3D vector field using outpost. The 3D vector field covers both solid and fluid. As suggested by Paul in an earlier post of mine, I added the following in the usr file. It works fine for 2D geometry but not 3D. I use the conjugate module, where NELV < NEL if ((mod(istep,iostep).eq.0).and.(istep.ge.iostep)) then nelf = nelv ! Save number of fluid elements nelfld(1) = nelt nelv = nelt call outpost(b1(1,1,1,1,1),b1(1,1,1,1,2),b1(1,1,1,1,3) $ ,pr,t,'mag') nelv = nelf nelfld(1) = nelf endif The vector field is being written correctly in the fluid domain (3D) and is written zero in the solid domain (3D). Can someone suggest a fix for this. Thank you in advance. Yours sincerely, Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Feb 13 07:42:50 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Feb 2017 21:42:50 +0800 (GMT+08:00) Subject: [Nek5000-users] problem about case turbChannel In-Reply-To: References: Message-ID: Hi all, When I tried to do the test "turbChannel", I found value NAN appeared in the process, and after a while the pressure solver detect rank deficiency. I tried almost all the test case, and found this problem appeared in some other cases. I want to know why and how to accomplish the turbChannel case. Should I change any values in the .usr file? Best wishes! Hu From nek5000-users at lists.mcs.anl.gov Mon Feb 13 09:46:22 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Feb 2017 16:46:22 +0100 Subject: [Nek5000-users] problem about case turbChannel In-Reply-To: References: Message-ID: Hard to say ... please post your logfile -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 13th February 2017 16:39 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] problem about case turbChannel > > Hi all, > When I tried to do the test "turbChannel", I found value NAN appeared in the process, and after a while the pressure solver detect rank deficiency. I tried almost all the > test case, and found this problem appeared in some other cases. I want to know why and how to accomplish the turbChannel case. Should I change any values in the .usr file? > > Best wishes! > Hu > > > > _______________________________________________ > 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 Mon Feb 13 10:37:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Feb 2017 09:37:48 -0700 Subject: [Nek5000-users] problem about case turbChannel In-Reply-To: References: Message-ID: Hi Hu, Please post a MWE (minimal working example), a logfile / and or a .usr file snippet which your are changing, otherwise it is hard to comment. Best Regards, Tanmoy On Mon, Feb 13, 2017 at 6:42 AM, wrote: > Hi all, > When I tried to do the test "turbChannel", I found value NAN appeared in > the process, and after a while the pressure solver detect rank deficiency. > I tried almost all the > test case, and found this problem appeared in some other cases. I want to > know why and how to accomplish the turbChannel case. Should I change any > values in the .usr file? > > Best wishes! > Hu > > > > _______________________________________________ > 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 13 15:09:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Feb 2017 21:09:30 +0000 Subject: [Nek5000-users] CFD positions available in Canada Message-ID: Master's or PhD (preferred) assistantship available for: Possibility for a Postdoctoral position also for: Research work in the development of parallel adaptive Spectral Element or Discontinuous Galerkin methods for Direct Numerical Simulation of near-turbulent or turbulent flows. Are you familiar with Nek5000, love programming and fluid flows? Please apply if you are looking for a graduate program for Fall 2017. The University of Ottawa in Ottawa, Canada, the nation's capital, is a great place to live and work. Deadlines for international (non-Canadian) applications is March 1st, 2017. Women and other members of underrepresented groups in Engineering are encouraged to apply. Please contact Prof. Catherine.Mavriplis at uottawa.ca Please use the subject line: Nek5000 Graduate Assistantship -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Feb 15 04:58:45 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 15 Feb 2017 11:58:45 +0100 Subject: [Nek5000-users] Update on axisymmetric jet problem Message-ID: Dear Nek users, Just to give some more information on the problem I mentioned some days ago (down below is the original message), here is some more data: - One of the boundary conditions is periodically oscillating velocity. - If I remove the axisymmetric conditions, that being: ? IFHEAT F ? IFAXIS F ? IFAZIV F and simply run it as a 2D example, it seems to run just fine. - Extremely high values of artificial viscosity (1.0000000E+00 p103) will make it run longer, but it ends up crashing as well. - Even when it runs for some seconds (before crashing), log file keeps giving this kind of error messages: 19565 100 **ERROR**: Failed in HMHOLTZ: PRES 6.2650E+00 8.4054E+01 1.0000E-06 Any advice will be greatly appreciated. Thank you in advance. MViturro --------Original message--------------- Dear Nek users, I am doing my master thesis at Technical University of Madrid and I am using Nek5000 to study an axisymmetric jet. I have generated the mesh using genbox. Then I have try to run numerical simulations: 1) 2D 2) Setting: IFAXIS T 3) Setting: IFAXIS T, IFAZIV T (and with IFHEAT T, to plot the azimuthal velocity. In all cases my simulation crashes, due to some problems in the boundary (I have tried with both ON and O BC) So, I have added artificial viscosity, but the axysimmetric simulation (case2 2 and 3) still crashes: 3.000000 p99 dealiasing:if <0 disable 0.0000000E+00 p100 reserved 1.0000000E+00 p101 No. of additional filter modes 0.0000000E+00 1.0000000E-02 p103 weight of stabilizing filter (.01) Could you give me any recommendation to follow? Thank you in advance. MViturro ---------------------------------------- From nek5000-users at lists.mcs.anl.gov Fri Feb 17 01:13:59 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 14:13:59 +0700 Subject: [Nek5000-users] Outflow boundary conditions Message-ID: Dear all, Is there an easy way to modify O boundary conditions. Now both non-stress and stress formulation include only pressure and viscous forces. I would like to add convection as well so that some components of full momentum flux tensor are equal zero? Is that possible? Thank you! Regards, Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Feb 17 02:37:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 16:37:52 +0800 (GMT+08:00) Subject: [Nek5000-users] problem about case turbChannel In-Reply-To: References: Message-ID: Hi, Tanmoy Thanks! Here are parts of my logfile, and please see the attachment for details. (I didn't change any data for this case) Starting time loop ... DT/DTCFL/DTFS/DTINIT 0.200E-01 0.227-314 0.227-314 0.200E-01 Step 1, t= 2.0000000E-02, DT= 2.0000000E-02, C= 0.521 0.0000E+00 0.0000E+00 filt amp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0125 0.0500 filt trn 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.9875 0.9500 Solving for fluid 1 1.00000E-05 NaN NaN NaN 1 Divergence 2 1.00000E-05 NaN NaN NaN 1 Divergence 3 1.00000E-05 NaN NaN NaN 1 Divergence Best regards! Hu -----????----- ???: nek5000-users at lists.mcs.anl.gov ????: 2017?2?14? ??? ???: nek5000-users at lists.mcs.anl.gov ??: ??: Re: [Nek5000-users] problem about case turbChannel Hi Hu, Please post a MWE (minimal working example), a logfile / and or a .usr file snippet which your are changing, otherwise it is hard to comment. Best Regards, Tanmoy On Mon, Feb 13, 2017 at 6:42 AM, wrote: Hi all, When I tried to do the test "turbChannel", I found value NAN appeared in the process, and after a while the pressure solver detect rank deficiency. I tried almost all the test case, and found this problem appeared in some other cases. I want to know why and how to accomplish the turbChannel case. Should I change any values in the .usr file? Best wishes! Hu _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbChannel.rar Type: application/octet-stream Size: 23228 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri Feb 17 05:26:45 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 12:26:45 +0100 Subject: [Nek5000-users] problem about case turbChannel In-Reply-To: References: Message-ID: What compiler are you using? Can you please download the latest master branch of Nek5000 and NekExamples on GitHub and try again. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 17th February 2017 11:34 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] problem about case turbChannel > > Hi, Tanmoy > Thanks! Here are?parts of my logfile, and please see the attachment for details. (I didn't change any data for this case) > Starting time loop ... > ???? DT/DTCFL/DTFS/DTINIT?? 0.200E-01?? 0.227-314?? 0.227-314?? 0.200E-01 > Step????? 1, t= 2.0000000E-02, DT= 2.0000000E-02, C=? 0.521 0.0000E+00 0.0000E+00 > filt amp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0125 0.0500 > filt trn 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.9875 0.9500 > ???????????? Solving for fluid > ??? 1 1.00000E-05???????? NaN???????? NaN???????? NaN?????? 1 Divergence > ??? 2 1.00000E-05???????? NaN???????? NaN???????? NaN?????? 1 Divergence > ??? 3 1.00000E-05???????? NaN???????? NaN???????? NaN?????? 1 Divergence > > Best regards! > Hu > -----????----- > ???: nek5000-users at lists.mcs.anl.gov > ????: 2017?2?14? ??? > ???: nek5000-users at lists.mcs.anl.gov > ??: > ??: Re: [Nek5000-users] problem about case turbChannel > > Hi Hu, > > Please post a MWE (minimal working example), a logfile / and or a .usr file snippet which your are changing, otherwise it is hard to comment. >
Best Regards, > Tanmoy > > On Mon, Feb 13, 2017 at 6:42 AM, > wrote: > Hi all, > When I tried to do the test "turbChannel", I found value NAN appeared in the process, and after a while the pressure solver detect rank deficiency. I tried almost all the > test case, and found this problem appeared in some other cases. I want to know why and how to accomplish the turbChannel case. Should I change any values in the .usr file? > > Best wishes! > Hu > > > > _______________________________________________ > 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 17 05:41:53 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 19:41:53 +0800 (GMT+08:00) Subject: [Nek5000-users] problem about case turbChannel In-Reply-To: References: Message-ID: Thanks a lot! I download the latest master branch of Nek5000 and NekExamples , and the problem was solved! Hu > -----????----- > ???: nek5000-users at lists.mcs.anl.gov > ????: 2017?2?17? ??? > ???: "nek5000-users at lists.mcs.anl.gov" > ??: > ??: Re: [Nek5000-users] problem about case turbChannel > > What compiler are you using? > Can you please download the latest master branch of Nek5000 and NekExamples on GitHub and try again. > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 17th February 2017 11:34 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] problem about case turbChannel > > > > Hi, Tanmoy > > Thanks! Here are?parts of my logfile, and please see the attachment for details. (I didn't change any data for this case) > > Starting time loop ... > > ???? DT/DTCFL/DTFS/DTINIT?? 0.200E-01?? 0.227-314?? 0.227-314?? 0.200E-01 > > Step????? 1, t= 2.0000000E-02, DT= 2.0000000E-02, C=? 0.521 0.0000E+00 0.0000E+00 > > filt amp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0125 0.0500 > > filt trn 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.9875 0.9500 > > ???????????? Solving for fluid > > ??? 1 1.00000E-05???????? NaN???????? NaN???????? NaN?????? 1 Divergence > > ??? 2 1.00000E-05???????? NaN???????? NaN???????? NaN?????? 1 Divergence > > ??? 3 1.00000E-05???????? NaN???????? NaN???????? NaN?????? 1 Divergence > > > > Best regards! > > Hu > > -----????----- > > ???: nek5000-users at lists.mcs.anl.gov > > ????: 2017?2?14? ??? > > ???: nek5000-users at lists.mcs.anl.gov > > ??: > > ??: Re: [Nek5000-users] problem about case turbChannel > > > > Hi Hu, > > > > Please post a MWE (minimal working example), a logfile / and or a .usr file snippet which your are changing, otherwise it is hard to comment. > >
Best Regards, > > Tanmoy > > > > On Mon, Feb 13, 2017 at 6:42 AM, > wrote: > > Hi all, > > When I tried to do the test "turbChannel", I found value NAN appeared in the process, and after a while the pressure solver detect rank deficiency. I tried almost all the > > test case, and found this problem appeared in some other cases. I want to know why and how to accomplish the turbChannel case. Should I change any values in the .usr file? > > > > Best wishes! > > Hu > > > > > > > > _______________________________________________ > > 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 Fri Feb 17 08:48:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 15:48:48 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 Message-ID: Hi all, I have recently encountered the following error during the first time step when running on an IBM/BlueGene Cluster: ... 1 Hmholtz VELZ 5 6.4574E-08 1.0000E-04 1.0000E-08 1.0000E+03 F 1 Hmholtz VELZ 6 2.6260E-09 1.0000E-04 1.0000E-08 1.0000E+03 F 1 Hmholtz VELZ 5 2.6260E-09 1.9523E-01 1.0000E-08 2017-02-10 13:50:24.545 (WARN ) [0x400011c9030] :3236143:ibm.runjob.client.Job: terminated by signal 11 2017-02-10 13:50:24.545 (WARN ) [0x400011c9030] :3236143:ibm.runjob.client.Job: abnormal termination by signal 11 from rank 0 This has happened for different user files, different parameters and resolutions, so I am not sure where to start looking. Has anyone else seen this problem? Is this likely a Nek or an IBM related problem? Best wishes, Jan From nek5000-users at lists.mcs.anl.gov Fri Feb 17 10:55:10 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 17:55:10 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: - What version of Nek5000 do you use? - Is the problem reproduceable? - Can you provide a stack trace showing where the SEG FAULT (signal 11) happens -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 17th February 2017 17:50 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Nek: abnormal termination by signal 11 > > Hi all, > I have recently encountered the following error during the first time step when running on an IBM/BlueGene Cluster: > ... > 1 Hmholtz VELZ 5 6.4574E-08 1.0000E-04 1.0000E-08 1.0000E+03 F > 1 Hmholtz VELZ 6 2.6260E-09 1.0000E-04 1.0000E-08 1.0000E+03 F > 1 Hmholtz VELZ 5 2.6260E-09 1.9523E-01 1.0000E-08 > 2017-02-10 13:50:24.545 (WARN ) [0x400011c9030] :3236143:ibm.runjob.client.Job: terminated by signal 11 > 2017-02-10 13:50:24.545 (WARN ) [0x400011c9030] :3236143:ibm.runjob.client.Job: abnormal termination by signal 11 from rank 0 > This has happened for different user files, different parameters and resolutions, so I am not sure where to start looking. Has anyone else seen this problem? Is this likely a Nek or an IBM related problem? > Best wishes, > Jan > > _______________________________________________ > 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 17 10:13:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Feb 2017 09:13:02 -0700 Subject: [Nek5000-users] Outflow boundary conditions In-Reply-To: References: Message-ID: Hi Vatslav, In bdry.f file (repo file), the 'o' boundary condition is fed through the variable pa = 0. Thats the term involving p + \nu (\grad u + \grad u^T) = 0. In the rea file you can change the 'O' boundary condition to user defined 'o' boundary condition and then in the uderbc() you can set your conditions on pa. On Fri, Feb 17, 2017 at 12:13 AM, wrote: > Dear all, > > Is there an easy way to modify O boundary conditions. Now both non-stress > and stress formulation include only pressure and viscous forces. I would > like to add convection as well so that some components of full momentum > flux tensor are equal zero? Is that possible? > > Thank you! > > Regards, > Vatslav > > _______________________________________________ > 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 Sun Feb 19 15:32:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 19 Feb 2017 22:32:02 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: Hello, the error occurs both with a current github version (16..0.0) as well as an older svn version (1.0rc1 / SVN r1115) and is reproducible on the IBM system. However, it seems that the svn version gives a longer error message: 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: terminated by signal 11 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: abnormal termination by signal 11 from rank 0 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: 1 INFO RAS event 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: most recent RAS event text: DDR Correctable Error Summary : count=36 MCFIR error status: [MEMORY_CE] This bit is set when a memory CE is detected on a non-maintenance memory read op; 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: with severity INFO Attached you find the output from the core file: +++PARALLEL TOOLS CONSORTIUM LIGHTWEIGHT COREFILE FORMAT version 1.0 +++LCB 1.0 Program : ./nek5000 Job ID : 3243396 Personality: ABCDET coordinates : 0,0,0,0,0,0 Rank : 0 Ranks per node : 16 DDR Size (MB) : 16384 +++ID Rank: 0, TGID: 1, Core: 0, HWTID:0 TID: 1 State: RUN ***FAULT Encountered unhandled signal 0x0000000b (11) (SIGSEGV) Generated by interrupt..................0x00000008 (Data TLB Miss Exception DEAR=0x00000000d716900c ESR=0x0000000000000000) While executing instruction at..........0x00000000010eba68 Dereferencing memory at.................0x00000000d716900c Fault occurred at timebase..............0x00000008296267c1 Tools attached (list of tool ids).......None Currently running on hardware thread....Y General Purpose Registers: r00=0000000000000001 r01=0000001fbfffb0c0 r02=0000000001ca4750 r03=0000000000000000 r04=00000000d7168fe8 r05=000000000000000c r06=0000000000000000 r07=0000003084023688 r08=0000000001e034a8 r09=0000000001a12ff8 r10=0000000000000008 r11=00000610c0281600 r12=00000000010eba44 r13=0000001f88007700 r14=0000000000000014 r15=0000000000000000 r16=000000000207c9a0 r17=0000000002a3eca0 r18=0000000002a1eec0 r19=00000000029f6a00 r20=0000000002a46400 r21=0000000002a47260 r22=0000000002a47118 r23=0000000000000001 r24=0000000002a41ca0 r25=0000000001884460 r26=0000000002a44ca0 r27=0000000001e0bda0 r28=00000000022dc5a0 r29=0000000001bb7ae0 r30=00000000029f8200 r31=0000000002a47340 Special Purpose Registers: lr=00000000010eba44 cr=0000000022000284 xer=0000000020000000 ctr=0000000000000000 msr=000000008002f000 dear=00000000d716900c esr=0000000000000000 fpscr=000000008a024000 sprg0=0000000000000000 sprg1=0000000000000000 sprg2=0000000000000000 sprg3=0000000000000000 sprg4=0000000000000000 sprg5=0000000000000000 sprg6=0000000000621d00 sprg7=0000000000000000 sprg8=0000000000000000 srr0=00000000010eba68 srr1=000000008002f000 csrr0=0000000000000000 csrr1=0000000000000000 mcsrr0=0000000000000000 mcsrr1=0000000000000000 dbcr0=0000000000000000 dbcr1=0000000000000000 dbcr2=0000000000000000 dbcr3=0000000000000000 dbsr=0000000000000000 Floating Point Registers: f00=4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 f01=4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 f02=3e945cb95a0164cc 3e7f94d702f1d380 3e7f94d702f1d380 3e7f94d702f1d380 f03=3e9833a753a6edba 3e6eb76fcd2c476c 3e6eb76fcd2c476c 3e6eb76fcd2c476c f04=3e9ee5beff36cb8d 3e7ac85eae3f774b 3e7ac85eae3f774b 3e7ac85eae3f774b f05=3ea3d3933ba0cb41 3e8182cef01595e9 3e8182cef01595e9 3e8182cef01595e9 f06=3ea5216efdd7d0c3 3e64ddbc2370581a 3e64ddbc2370581a 3e64ddbc2370581a f07=3eae38041864f7e0 3e922d2a351a4e3a 3e922d2a351a4e3a 3e922d2a351a4e3a f08=3eb3bf2d8e13a8e6 3e928cae0784b3d6 3e928cae0784b3d6 3e928cae0784b3d6 f09=3ebc41113831b3bc 3ea103c7543c15ab 3ea103c7543c15ab 3ea103c7543c15ab f10=3ec24a6da7c3f0cd 3ea0a7942eac5bbc 3ea0a7942eac5bbc 3ea0a7942eac5bbc f11=3ec4bd386722b714 3e939655faf6323c 3e939655faf6323c 3e939655faf6323c f12=3ec839337bca16c0 3e9bdfd8a53afd64 3e9bdfd8a53afd64 3e9bdfd8a53afd64 f13=00000008296259e2 00000008296259e2 00000008296259e2 00000008296259e2 f14=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f15=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f16=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f17=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f18=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f19=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f20=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f21=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f22=3ff0000000000000 3ff0000000000000 3ff0000000000000 3ff0000000000000 f23=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f24=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f25=4035e8a442afd2ec 4035e8a442afd2ec 4035e8a442afd2ec 4035e8a442afd2ec f26=3f95421081dc359d 3f95421081dc359d 3f95421081dc359d 3f95421081dc359d f27=4035e8a5e0d51774 3fd2ba35bb6fe313 3fd2ba35bb6fe313 3fd2ba35bb6fe313 f28=3eb0c6f7a0b5ed8d 3eb0c6f7a0b5ed8d 3eb0c6f7a0b5ed8d 3eb0c6f7a0b5ed8d f29=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f30=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f31=4035e89e6a4644de 4035e89e6a4644de 4035e89e6a4644de 4035e89e6a4644de Memory: Shared memory: 0x0000003084000000 - 0x0000003087ffffff Heap: 0x0000001f88000000 - 0x0000001f881fffff (brk at 0x0000001f881f1000) MMap: 0x0000001f88200000 - 0x0000001fbfb00000 Chunk Status Address Size [ 0]: Busy 0x0000001f88200000 9506816 [ 1]: Free 0x0000001f88b11000 922677248 Stack Guard disabled Stack pointer: 0x0000001fbfffb0c0 (bottom at 0x0000001fbfffff80 with 20160 bytes in use) SSSUUU GAI TLB V EA Range RA Range Size ThID WIMGE RWXRWX XSSP TID TL ----- - ---------------- ---------------- ---------------- ---------------- ----- ---- ----- ------ ---- ---- -- 0:3 V 0000000000001000-00000000000FFFFF 0000000000001000-00000000000FFFFF 1MB 1111 --M-- R-X--- X--- 0000 00 1:3 V 0000000000100000-00000000001FFFFF 0000000000100000-00000000001FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 2:2 V 0000010002000000-0000010002FFFFFF 0000010002000000-0000010002FFFFFF 16MB 1111 -IM-- RW---- ---- 0000 00 2:3 V 0000000000200000-00000000002FFFFF 0000000000200000-00000000002FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 3:3 V 0000000000300000-00000000003FFFFF 0000000000300000-00000000003FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 4:3 V 0000000000400000-00000000004FFFFF 0000000000400000-00000000004FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 5:3 V 0000000000500000-00000000005FFFFF 0000000000500000-00000000005FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 6:3 V 0000000000600000-00000000006FFFFF 0000000000600000-00000000006FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 7:3 V 0000000000700000-00000000007FFFFF 0000000000700000-00000000007FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 8:3 V 0000000000800000-00000000008FFFFF 0000000000800000-00000000008FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 9:3 V 0000000000900000-00000000009FFFFF 0000000000900000-00000000009FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 10:3 V 0000000000A00000-0000000000AFFFFF 0000000000A00000-0000000000AFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 11:3 V 0000000000B00000-0000000000BFFFFF 0000000000B00000-0000000000BFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 12:3 V 0000000000C00000-0000000000CFFFFF 0000000000C00000-0000000000CFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 13:3 V 0000000000D00000-0000000000DFFFFF 0000000000D00000-0000000000DFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 14:3 V 0000000000E00000-0000000000EFFFFF 0000000000E00000-0000000000EFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 16:3 V 0000000001000000-00000000010FFFFF 0000000001000000-00000000010FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 17:3 V 0000000001100000-00000000011FFFFF 0000000001100000-00000000011FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 18:2 V 0000000001200000-00000000012FFFFF 0000000001200000-00000000012FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 18:3 V 000003FDC0000000-000003FDFFFFFFFF 000003FDC0000000-000003FDFFFFFFFF 1GB 1111 -IMG- RWXrw- ---- 00E5 00 19:2 V 0000001F88000000-0000001FC7FFEFFF 0000003008000000-000000303FFFFFFF 1GB 1111 --M-- RWXrwx X--- 03ED 00 19:3 V 0000000001300000-00000000013FFFFF 0000000001300000-00000000013FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 20:3 V 0000000001400000-00000000014FFFFF 0000000001400000-00000000014FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 21:2 V 0000000001500000-00000000015FFFFF 0000000001500000-00000000015FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 21:3 V 0005000001500000-00050000015FFFFF 000003FDE8000000-000003FDE80FFFFF 1MB 1111 -IM-- RW-rw- ---- 0000 00 22:2 V 0000000001600000-00000000016FFFFF 0000000001600000-00000000016FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 22:3 V 0005000001600000-00050000016FFFFF 000003FDFE200000-000003FDFE2FFFFF 1MB 1111 -IM-- RW-rw- ---- 0000 00 23:3 V 0000000001700000-00000000017FFFFF 0000000001700000-00000000017FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 24:3 V 0000000001800000-00000000018FFFFF 0000000001800000-00000000018FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 25:3 V 0000000001900000-00000000019FFFFF 0000000001900000-00000000019FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 26:3 V 0000000001A00000-0000000001AFFFFF 0000000001A00000-0000000001AFFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 27:3 V 0000001F88000000-0000001FC7FFEFFF 0000000008000000-000000003FFFFFFF 1GB 1111 --M-- RWXrwx X--- 00E5 00 33:3 V 000403F100000000-000403F13FFFFFFF 0000010100000000-000001013FFFFFFF 1GB 1111 -IM-- RWXrw- ---- 00E5 00 34:3 V 0000000002000000-0000000002FFFFFF 0000001002000000-0000001002FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 35:3 V 0000000003000000-0000000003FFFFFF 0000001003000000-0000001003FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 36:3 V 0000003084000000-0000003084FFFFFF 0000002004000000-0000002004FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 37:3 V 0000003085000000-0000003085FFFFFF 0000002005000000-0000002005FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 38:2 V 0000003086000000-0000003086FFFFFF 0000002006000000-0000002006FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 38:3 V 00040610C0000000-00040610FFFFFFFF 00000100C0000000-00000100FFFFFFFF 1GB 1111 -IM-- RWXrw- ---- 00E5 00 39:3 V 0000003087000000-0000003087FFFFFF 0000002007000000-0000002007FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 40:3 V 0000001F88000000-0000001FC7FFEFFF 0000004008000000-000000403FFFFFFF 1GB 1111 --M-- RWXrwx X--- 0456 00 42:3 V 0000000002000000-0000000002FFFFFF 0000002002000000-0000002002FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 43:3 V 0000000003000000-0000000003FFFFFF 0000002003000000-0000002003FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 44:3 V 0000003084000000-0000003084FFFFFF 0000001004000000-0000001004FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 45:3 V 0000003085000000-0000003085FFFFFF 0000001005000000-0000001005FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 46:3 V 0000003086000000-0000003086FFFFFF 0000001006000000-0000001006FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 47:3 V 0000003087000000-0000003087FFFFFF 0000001007000000-0000001007FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 51:3 V 0000000001B00000-0000000001BFFFFF 0000002001B00000-0000002001BFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 52:3 V 0000000001C00000-0000000001CFFFFF 0000002001C00000-0000002001CFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 53:3 V 0000000001D00000-0000000001DFFFFF 0000002001D00000-0000002001DFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 54:3 V 0000000001E00000-0000000001EFFFFF 0000002001E00000-0000002001EFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 55:3 V 0000000001F00000-0000000001FFFFFF 0000002001F00000-0000002001FFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 59:3 V 0000000001B00000-0000000001BFFFFF 0000001001B00000-0000001001BFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 60:3 V 0000000001C00000-0000000001CFFFFF 0000001001C00000-0000001001CFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 61:3 V 0000000001D00000-0000000001DFFFFF 0000001001D00000-0000001001DFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 62:3 V 0000000001E00000-0000000001EFFFFF 0000001001E00000-0000001001EFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 63:3 V 0000000001F00000-0000000001FFFFFF 0000001001F00000-0000001001FFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 64:3 V 0000007001000000-0000007040FFEFFF 0000000001000000-000000003FFFFFFF 1GB 1111 --M-- RWXr-- X--- 0000 00 65:3 V 0000007040000000-000000707FFFFFFF 0000000040000000-000000007FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 66:3 V 0000007080000000-00000070BFFFFFFF 0000000080000000-00000000BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 67:3 V 00000070C0000000-00000070FFFFFFFF 00000000C0000000-00000000FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 68:3 V 0000007100000000-000000713FFFFFFF 0000000100000000-000000013FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 69:3 V 0000007140000000-000000717FFFFFFF 0000000140000000-000000017FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 70:3 V 0000007180000000-00000071BFFFFFFF 0000000180000000-00000001BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 71:3 V 00000071C0000000-00000071FFFFFFFF 00000001C0000000-00000001FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 72:2 V 0000000001E00000-0000000001EFFFFF 0000004001E00000-0000004001EFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 72:3 V 0000007200000000-000000723FFFFFFF 0000000200000000-000000023FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 73:2 V 0000000001F00000-0000000001FFFFFF 0000004001F00000-0000004001FFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 73:3 V 0000007240000000-000000727FFFFFFF 0000000240000000-000000027FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 74:2 V 0000000001C00000-0000000001CFFFFF 0000004001C00000-0000004001CFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 74:3 V 0000007280000000-00000072BFFFFFFF 0000000280000000-00000002BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 75:2 V 0000000001D00000-0000000001DFFFFF 0000004001D00000-0000004001DFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 75:3 V 00000072C0000000-00000072FFFFFFFF 00000002C0000000-00000002FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 76:3 V 0000007300000000-000000733FFFFFFF 0000000300000000-000000033FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 77:2 V 0000000001B00000-0000000001BFFFFF 0000004001B00000-0000004001BFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 77:3 V 0000007340000000-000000737FFFFFFF 0000000340000000-000000037FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 78:3 V 0000007380000000-00000073BFFFFFFF 0000000380000000-00000003BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 79:3 V 00000073C0000000-00000073FFFFFFFF 00000003C0000000-00000003FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 84:3 V 0000000002000000-0000000002FFFFFF 0000004002000000-0000004002FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 85:3 V 0000000003000000-0000000003FFFFFF 0000004003000000-0000004003FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 86:3 V 0000001F88000000-0000001FC7FFEFFF 0000002008000000-000000203FFFFFFF 1GB 1111 --M-- RWXrwx X--- 0328 00 88:3 V 0000003086000000-0000003086FFFFFF 0000004006000000-0000004006FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 89:3 V 0000003087000000-0000003087FFFFFF 0000004007000000-0000004007FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 90:3 V 0000003084000000-0000003084FFFFFF 0000004004000000-0000004004FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 91:3 V 0000003085000000-0000003085FFFFFF 0000004005000000-0000004005FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 94:3 V 0000001F88000000-0000001FC7FFEFFF 0000001008000000-000000103FFFFFFF 1GB 1111 --M-- RWXrwx X--- 02A0 00 96:3 V 0000003085000000-0000003085FFFFFF 0000003005000000-0000003005FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 97:3 V 0000003084000000-0000003084FFFFFF 0000003004000000-0000003004FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 98:3 V 0000003087000000-0000003087FFFFFF 0000003007000000-0000003007FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 99:3 V 0000003086000000-0000003086FFFFFF 0000003006000000-0000003006FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 102:3 V 0000000003000000-0000000003FFFFFF 0000000003000000-0000000003FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 103:3 V 0000000002000000-0000000002FFFFFF 0000000002000000-0000000002FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 104:3 V 0000003085000000-0000003085FFFFFF 0000000005000000-0000000005FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 105:3 V 0000003084000000-0000003084FFFFFF 0000000004000000-0000000004FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 106:3 V 0000003087000000-0000003087FFFFFF 0000000007000000-0000000007FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 107:3 V 0000003086000000-0000003086FFFFFF 0000000006000000-0000000006FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 110:3 V 0000000003000000-0000000003FFFFFF 0000003003000000-0000003003FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 111:3 V 0000000002000000-0000000002FFFFFF 0000003002000000-0000003002FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 112:3 V 0000000001D00000-0000000001DFFFFF 0000003001D00000-0000003001DFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 113:3 V 0000000001C00000-0000000001CFFFFF 0000003001C00000-0000003001CFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 114:3 V 0000000001F00000-0000000001FFFFFF 0000003001F00000-0000003001FFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 115:3 V 0000000001E00000-0000000001EFFFFF 0000003001E00000-0000003001EFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 118:3 V 0000000001B00000-0000000001BFFFFF 0000003001B00000-0000003001BFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 120:3 V 0000000001D00000-0000000001DFFFFF 0000000001D00000-0000000001DFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 121:3 V 0000000001C00000-0000000001CFFFFF 0000000001C00000-0000000001CFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 122:3 V 0000000001F00000-0000000001FFFFFF 0000000001F00000-0000000001FFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 123:3 V 0000000001E00000-0000000001EFFFFF 0000000001E00000-0000000001EFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 126:3 V 0000000001B00000-0000000001BFFFFF 0000000001B00000-0000000001BFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 127:3 V 000003FFC0000000-000003FFFFFFFFFF 000003FFC0000000-000003FFFFFFFFFF 1GB 1111 -IMG- RWX--- ---1 0000 00 +++STACK Frame Address Saved Link Reg 0000001fbfffb0c0 00000000010eba44 0000001fbfffb220 00000000010dda3c 0000001fbfffb400 0000000001061894 0000001fbfffb4e0 00000000010fb01c 0000001fbfffb600 0000000001094f0c 0000001fbfffb6e0 000000000100a4d0 0000001fbfffb7c0 0000000001007cc0 0000001fbfffb8a0 0000000001007e50 0000001fbfffb940 00000000010074f0 0000001fbfffba20 00000000010067fc 0000001fbfffbaa0 00000000017d7418 0000001fbfffbd80 00000000017d7714 0000001fbfffbe40 0000000000000000 ---STACK Interrupt Summary: System Calls 7673 External Input Interrupts 2 Data TLB Interrupts 1 ---ID ---LCB From nek5000-users at lists.mcs.anl.gov Sun Feb 19 17:37:32 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 20 Feb 2017 00:37:32 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: How can I reproduce the problem? Please provide a step-by-step instruction. The core file (w/o debugging symbols) is pretty useless. Can you recompile with "-g" and try again. You may need use "addr2line" to get a human readable STACK. Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 20th February 2017 0:33 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Nek: abnormal termination by signal 11 > > Hello, > the error occurs both with a current github version (16..0.0) as well as an older svn version (1.0rc1 / SVN r1115) and is reproducible on the IBM system. However, it seems that the svn version gives a longer error message: > > 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: terminated by signal 11 > 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: abnormal termination by signal 11 from rank 0 > 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: 1 INFO RAS event > 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: most recent RAS event text: DDR Correctable Error Summary : count=36 MCFIR error status: [MEMORY_CE] This bit is set when a memory CE is detected on a non-maintenance memory read op; > 2017-02-19 22:05:06.740 (WARN ) [0x40000e19030] :3243396:ibm.runjob.client.Job: with severity INFO > > Attached you find the output from the core file: > +++PARALLEL TOOLS CONSORTIUM LIGHTWEIGHT COREFILE FORMAT version 1.0 > +++LCB 1.0 > Program : ./nek5000 > Job ID : 3243396 > Personality: > ABCDET coordinates : 0,0,0,0,0,0 > Rank : 0 > Ranks per node : 16 > DDR Size (MB) : 16384 > +++ID Rank: 0, TGID: 1, Core: 0, HWTID:0 TID: 1 State: RUN > ***FAULT Encountered unhandled signal 0x0000000b (11) (SIGSEGV) > Generated by interrupt..................0x00000008 (Data TLB Miss Exception DEAR=0x00000000d716900c ESR=0x0000000000000000) > While executing instruction at..........0x00000000010eba68 > Dereferencing memory at.................0x00000000d716900c > Fault occurred at timebase..............0x00000008296267c1 > Tools attached (list of tool ids).......None > Currently running on hardware thread....Y > General Purpose Registers: > r00=0000000000000001 r01=0000001fbfffb0c0 r02=0000000001ca4750 r03=0000000000000000 r04=00000000d7168fe8 r05=000000000000000c r06=0000000000000000 r07=0000003084023688 > r08=0000000001e034a8 r09=0000000001a12ff8 r10=0000000000000008 r11=00000610c0281600 r12=00000000010eba44 r13=0000001f88007700 r14=0000000000000014 r15=0000000000000000 > r16=000000000207c9a0 r17=0000000002a3eca0 r18=0000000002a1eec0 r19=00000000029f6a00 r20=0000000002a46400 r21=0000000002a47260 r22=0000000002a47118 r23=0000000000000001 > r24=0000000002a41ca0 r25=0000000001884460 r26=0000000002a44ca0 r27=0000000001e0bda0 r28=00000000022dc5a0 r29=0000000001bb7ae0 r30=00000000029f8200 r31=0000000002a47340 > Special Purpose Registers: > lr=00000000010eba44 cr=0000000022000284 xer=0000000020000000 ctr=0000000000000000 > msr=000000008002f000 dear=00000000d716900c esr=0000000000000000 fpscr=000000008a024000 > sprg0=0000000000000000 sprg1=0000000000000000 sprg2=0000000000000000 sprg3=0000000000000000 sprg4=0000000000000000 > sprg5=0000000000000000 sprg6=0000000000621d00 sprg7=0000000000000000 sprg8=0000000000000000 > srr0=00000000010eba68 srr1=000000008002f000 csrr0=0000000000000000 csrr1=0000000000000000 mcsrr0=0000000000000000 mcsrr1=0000000000000000 > dbcr0=0000000000000000 dbcr1=0000000000000000 dbcr2=0000000000000000 dbcr3=0000000000000000 dbsr=0000000000000000 > Floating Point Registers: > f00=4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 f01=4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 4035e8a5e0d51774 > f02=3e945cb95a0164cc 3e7f94d702f1d380 3e7f94d702f1d380 3e7f94d702f1d380 f03=3e9833a753a6edba 3e6eb76fcd2c476c 3e6eb76fcd2c476c 3e6eb76fcd2c476c > f04=3e9ee5beff36cb8d 3e7ac85eae3f774b 3e7ac85eae3f774b 3e7ac85eae3f774b f05=3ea3d3933ba0cb41 3e8182cef01595e9 3e8182cef01595e9 3e8182cef01595e9 > f06=3ea5216efdd7d0c3 3e64ddbc2370581a 3e64ddbc2370581a 3e64ddbc2370581a f07=3eae38041864f7e0 3e922d2a351a4e3a 3e922d2a351a4e3a 3e922d2a351a4e3a > f08=3eb3bf2d8e13a8e6 3e928cae0784b3d6 3e928cae0784b3d6 3e928cae0784b3d6 f09=3ebc41113831b3bc 3ea103c7543c15ab 3ea103c7543c15ab 3ea103c7543c15ab > f10=3ec24a6da7c3f0cd 3ea0a7942eac5bbc 3ea0a7942eac5bbc 3ea0a7942eac5bbc f11=3ec4bd386722b714 3e939655faf6323c 3e939655faf6323c 3e939655faf6323c > f12=3ec839337bca16c0 3e9bdfd8a53afd64 3e9bdfd8a53afd64 3e9bdfd8a53afd64 f13=00000008296259e2 00000008296259e2 00000008296259e2 00000008296259e2 > f14=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f15=0000000000000000 0000000000000000 0000000000000000 0000000000000000 > f16=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f17=0000000000000000 0000000000000000 0000000000000000 0000000000000000 > f18=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f19=0000000000000000 0000000000000000 0000000000000000 0000000000000000 > f20=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f21=0000000000000000 0000000000000000 0000000000000000 0000000000000000 > f22=3ff0000000000000 3ff0000000000000 3ff0000000000000 3ff0000000000000 f23=0000000000000000 0000000000000000 0000000000000000 0000000000000000 > f24=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f25=4035e8a442afd2ec 4035e8a442afd2ec 4035e8a442afd2ec 4035e8a442afd2ec > f26=3f95421081dc359d 3f95421081dc359d 3f95421081dc359d 3f95421081dc359d f27=4035e8a5e0d51774 3fd2ba35bb6fe313 3fd2ba35bb6fe313 3fd2ba35bb6fe313 > f28=3eb0c6f7a0b5ed8d 3eb0c6f7a0b5ed8d 3eb0c6f7a0b5ed8d 3eb0c6f7a0b5ed8d f29=0000000000000000 0000000000000000 0000000000000000 0000000000000000 > f30=0000000000000000 0000000000000000 0000000000000000 0000000000000000 f31=4035e89e6a4644de 4035e89e6a4644de 4035e89e6a4644de 4035e89e6a4644de > Memory: > Shared memory: 0x0000003084000000 - 0x0000003087ffffff > Heap: 0x0000001f88000000 - 0x0000001f881fffff (brk at 0x0000001f881f1000) > MMap: 0x0000001f88200000 - 0x0000001fbfb00000 > Chunk Status Address Size > [ 0]: Busy 0x0000001f88200000 9506816 > [ 1]: Free 0x0000001f88b11000 922677248 > Stack Guard disabled > Stack pointer: 0x0000001fbfffb0c0 (bottom at 0x0000001fbfffff80 with 20160 bytes in use) > SSSUUU GAI > TLB V EA Range RA Range Size ThID WIMGE RWXRWX XSSP TID TL > ----- - ---------------- ---------------- ---------------- ---------------- ----- ---- ----- ------ ---- ---- -- > 0:3 V 0000000000001000-00000000000FFFFF 0000000000001000-00000000000FFFFF 1MB 1111 --M-- R-X--- X--- 0000 00 > 1:3 V 0000000000100000-00000000001FFFFF 0000000000100000-00000000001FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 2:2 V 0000010002000000-0000010002FFFFFF 0000010002000000-0000010002FFFFFF 16MB 1111 -IM-- RW---- ---- 0000 00 > 2:3 V 0000000000200000-00000000002FFFFF 0000000000200000-00000000002FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 3:3 V 0000000000300000-00000000003FFFFF 0000000000300000-00000000003FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 4:3 V 0000000000400000-00000000004FFFFF 0000000000400000-00000000004FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 5:3 V 0000000000500000-00000000005FFFFF 0000000000500000-00000000005FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 6:3 V 0000000000600000-00000000006FFFFF 0000000000600000-00000000006FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 7:3 V 0000000000700000-00000000007FFFFF 0000000000700000-00000000007FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 8:3 V 0000000000800000-00000000008FFFFF 0000000000800000-00000000008FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 9:3 V 0000000000900000-00000000009FFFFF 0000000000900000-00000000009FFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 10:3 V 0000000000A00000-0000000000AFFFFF 0000000000A00000-0000000000AFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 11:3 V 0000000000B00000-0000000000BFFFFF 0000000000B00000-0000000000BFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 12:3 V 0000000000C00000-0000000000CFFFFF 0000000000C00000-0000000000CFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 13:3 V 0000000000D00000-0000000000DFFFFF 0000000000D00000-0000000000DFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 14:3 V 0000000000E00000-0000000000EFFFFF 0000000000E00000-0000000000EFFFFF 1MB 1111 --M-- RWX--- ---- 0000 00 > 16:3 V 0000000001000000-00000000010FFFFF 0000000001000000-00000000010FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 17:3 V 0000000001100000-00000000011FFFFF 0000000001100000-00000000011FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 18:2 V 0000000001200000-00000000012FFFFF 0000000001200000-00000000012FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 18:3 V 000003FDC0000000-000003FDFFFFFFFF 000003FDC0000000-000003FDFFFFFFFF 1GB 1111 -IMG- RWXrw- ---- 00E5 00 > 19:2 V 0000001F88000000-0000001FC7FFEFFF 0000003008000000-000000303FFFFFFF 1GB 1111 --M-- RWXrwx X--- 03ED 00 > 19:3 V 0000000001300000-00000000013FFFFF 0000000001300000-00000000013FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 20:3 V 0000000001400000-00000000014FFFFF 0000000001400000-00000000014FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 21:2 V 0000000001500000-00000000015FFFFF 0000000001500000-00000000015FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 21:3 V 0005000001500000-00050000015FFFFF 000003FDE8000000-000003FDE80FFFFF 1MB 1111 -IM-- RW-rw- ---- 0000 00 > 22:2 V 0000000001600000-00000000016FFFFF 0000000001600000-00000000016FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 22:3 V 0005000001600000-00050000016FFFFF 000003FDFE200000-000003FDFE2FFFFF 1MB 1111 -IM-- RW-rw- ---- 0000 00 > 23:3 V 0000000001700000-00000000017FFFFF 0000000001700000-00000000017FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 24:3 V 0000000001800000-00000000018FFFFF 0000000001800000-00000000018FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 25:3 V 0000000001900000-00000000019FFFFF 0000000001900000-00000000019FFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 26:3 V 0000000001A00000-0000000001AFFFFF 0000000001A00000-0000000001AFFFFF 1MB 1111 --M-- RWXr-x ---- 0000 00 > 27:3 V 0000001F88000000-0000001FC7FFEFFF 0000000008000000-000000003FFFFFFF 1GB 1111 --M-- RWXrwx X--- 00E5 00 > 33:3 V 000403F100000000-000403F13FFFFFFF 0000010100000000-000001013FFFFFFF 1GB 1111 -IM-- RWXrw- ---- 00E5 00 > 34:3 V 0000000002000000-0000000002FFFFFF 0000001002000000-0000001002FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 > 35:3 V 0000000003000000-0000000003FFFFFF 0000001003000000-0000001003FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 > 36:3 V 0000003084000000-0000003084FFFFFF 0000002004000000-0000002004FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 > 37:3 V 0000003085000000-0000003085FFFFFF 0000002005000000-0000002005FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 > 38:2 V 0000003086000000-0000003086FFFFFF 0000002006000000-0000002006FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 > 38:3 V 00040610C0000000-00040610FFFFFFFF 00000100C0000000-00000100FFFFFFFF 1GB 1111 -IM-- RWXrw- ---- 00E5 00 > 39:3 V 0000003087000000-0000003087FFFFFF 0000002007000000-0000002007FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 > 40:3 V 0000001F88000000-0000001FC7FFEFFF 0000004008000000-000000403FFFFFFF 1GB 1111 --M-- RWXrwx X--- 0456 00 > 42:3 V 0000000002000000-0000000002FFFFFF 0000002002000000-0000002002FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 > 43:3 V 0000000003000000-0000000003FFFFFF 0000002003000000-0000002003FFFFFF 16MB 1111 --M-- RWXrwx ---- 0328 00 > 44:3 V 0000003084000000-0000003084FFFFFF 0000001004000000-0000001004FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 > 45:3 V 0000003085000000-0000003085FFFFFF 0000001005000000-0000001005FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 > 46:3 V 0000003086000000-0000003086FFFFFF 0000001006000000-0000001006FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 > 47:3 V 0000003087000000-0000003087FFFFFF 0000001007000000-0000001007FFFFFF 16MB 1111 --M-- RWXrwx ---- 02A0 00 > 51:3 V 0000000001B00000-0000000001BFFFFF 0000002001B00000-0000002001BFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 > 52:3 V 0000000001C00000-0000000001CFFFFF 0000002001C00000-0000002001CFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 > 53:3 V 0000000001D00000-0000000001DFFFFF 0000002001D00000-0000002001DFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 > 54:3 V 0000000001E00000-0000000001EFFFFF 0000002001E00000-0000002001EFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 > 55:3 V 0000000001F00000-0000000001FFFFFF 0000002001F00000-0000002001FFFFFF 1MB 1111 --M-- RWXrwx ---- 0328 00 > 59:3 V 0000000001B00000-0000000001BFFFFF 0000001001B00000-0000001001BFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 > 60:3 V 0000000001C00000-0000000001CFFFFF 0000001001C00000-0000001001CFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 > 61:3 V 0000000001D00000-0000000001DFFFFF 0000001001D00000-0000001001DFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 > 62:3 V 0000000001E00000-0000000001EFFFFF 0000001001E00000-0000001001EFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 > 63:3 V 0000000001F00000-0000000001FFFFFF 0000001001F00000-0000001001FFFFFF 1MB 1111 --M-- RWXrwx ---- 02A0 00 > 64:3 V 0000007001000000-0000007040FFEFFF 0000000001000000-000000003FFFFFFF 1GB 1111 --M-- RWXr-- X--- 0000 00 > 65:3 V 0000007040000000-000000707FFFFFFF 0000000040000000-000000007FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 66:3 V 0000007080000000-00000070BFFFFFFF 0000000080000000-00000000BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 67:3 V 00000070C0000000-00000070FFFFFFFF 00000000C0000000-00000000FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 68:3 V 0000007100000000-000000713FFFFFFF 0000000100000000-000000013FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 69:3 V 0000007140000000-000000717FFFFFFF 0000000140000000-000000017FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 70:3 V 0000007180000000-00000071BFFFFFFF 0000000180000000-00000001BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 71:3 V 00000071C0000000-00000071FFFFFFFF 00000001C0000000-00000001FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 72:2 V 0000000001E00000-0000000001EFFFFF 0000004001E00000-0000004001EFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 > 72:3 V 0000007200000000-000000723FFFFFFF 0000000200000000-000000023FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 73:2 V 0000000001F00000-0000000001FFFFFF 0000004001F00000-0000004001FFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 > 73:3 V 0000007240000000-000000727FFFFFFF 0000000240000000-000000027FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 74:2 V 0000000001C00000-0000000001CFFFFF 0000004001C00000-0000004001CFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 > 74:3 V 0000007280000000-00000072BFFFFFFF 0000000280000000-00000002BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 75:2 V 0000000001D00000-0000000001DFFFFF 0000004001D00000-0000004001DFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 > 75:3 V 00000072C0000000-00000072FFFFFFFF 00000002C0000000-00000002FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 76:3 V 0000007300000000-000000733FFFFFFF 0000000300000000-000000033FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 77:2 V 0000000001B00000-0000000001BFFFFF 0000004001B00000-0000004001BFFFFF 1MB 1111 --M-- RWXrwx ---- 0456 00 > 77:3 V 0000007340000000-000000737FFFFFFF 0000000340000000-000000037FFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 78:3 V 0000007380000000-00000073BFFFFFFF 0000000380000000-00000003BFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 79:3 V 00000073C0000000-00000073FFFFFFFF 00000003C0000000-00000003FFFFFFFF 1GB 1111 --M-- RWXr-- ---- 0000 00 > 84:3 V 0000000002000000-0000000002FFFFFF 0000004002000000-0000004002FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 > 85:3 V 0000000003000000-0000000003FFFFFF 0000004003000000-0000004003FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 > 86:3 V 0000001F88000000-0000001FC7FFEFFF 0000002008000000-000000203FFFFFFF 1GB 1111 --M-- RWXrwx X--- 0328 00 > 88:3 V 0000003086000000-0000003086FFFFFF 0000004006000000-0000004006FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 > 89:3 V 0000003087000000-0000003087FFFFFF 0000004007000000-0000004007FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 > 90:3 V 0000003084000000-0000003084FFFFFF 0000004004000000-0000004004FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 > 91:3 V 0000003085000000-0000003085FFFFFF 0000004005000000-0000004005FFFFFF 16MB 1111 --M-- RWXrwx ---- 0456 00 > 94:3 V 0000001F88000000-0000001FC7FFEFFF 0000001008000000-000000103FFFFFFF 1GB 1111 --M-- RWXrwx X--- 02A0 00 > 96:3 V 0000003085000000-0000003085FFFFFF 0000003005000000-0000003005FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 > 97:3 V 0000003084000000-0000003084FFFFFF 0000003004000000-0000003004FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 > 98:3 V 0000003087000000-0000003087FFFFFF 0000003007000000-0000003007FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 > 99:3 V 0000003086000000-0000003086FFFFFF 0000003006000000-0000003006FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 > 102:3 V 0000000003000000-0000000003FFFFFF 0000000003000000-0000000003FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 > 103:3 V 0000000002000000-0000000002FFFFFF 0000000002000000-0000000002FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 > 104:3 V 0000003085000000-0000003085FFFFFF 0000000005000000-0000000005FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 > 105:3 V 0000003084000000-0000003084FFFFFF 0000000004000000-0000000004FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 > 106:3 V 0000003087000000-0000003087FFFFFF 0000000007000000-0000000007FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 > 107:3 V 0000003086000000-0000003086FFFFFF 0000000006000000-0000000006FFFFFF 16MB 1111 --M-- RWXrwx ---- 00E5 00 > 110:3 V 0000000003000000-0000000003FFFFFF 0000003003000000-0000003003FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 > 111:3 V 0000000002000000-0000000002FFFFFF 0000003002000000-0000003002FFFFFF 16MB 1111 --M-- RWXrwx ---- 03ED 00 > 112:3 V 0000000001D00000-0000000001DFFFFF 0000003001D00000-0000003001DFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 > 113:3 V 0000000001C00000-0000000001CFFFFF 0000003001C00000-0000003001CFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 > 114:3 V 0000000001F00000-0000000001FFFFFF 0000003001F00000-0000003001FFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 > 115:3 V 0000000001E00000-0000000001EFFFFF 0000003001E00000-0000003001EFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 > 118:3 V 0000000001B00000-0000000001BFFFFF 0000003001B00000-0000003001BFFFFF 1MB 1111 --M-- RWXrwx ---- 03ED 00 > 120:3 V 0000000001D00000-0000000001DFFFFF 0000000001D00000-0000000001DFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 > 121:3 V 0000000001C00000-0000000001CFFFFF 0000000001C00000-0000000001CFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 > 122:3 V 0000000001F00000-0000000001FFFFFF 0000000001F00000-0000000001FFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 > 123:3 V 0000000001E00000-0000000001EFFFFF 0000000001E00000-0000000001EFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 > 126:3 V 0000000001B00000-0000000001BFFFFF 0000000001B00000-0000000001BFFFFF 1MB 1111 --M-- RWXrwx ---- 00E5 00 > 127:3 V 000003FFC0000000-000003FFFFFFFFFF 000003FFC0000000-000003FFFFFFFFFF 1GB 1111 -IMG- RWX--- ---1 0000 00 > +++STACK > Frame Address Saved Link Reg > 0000001fbfffb0c0 00000000010eba44 > 0000001fbfffb220 00000000010dda3c > 0000001fbfffb400 0000000001061894 > 0000001fbfffb4e0 00000000010fb01c > 0000001fbfffb600 0000000001094f0c > 0000001fbfffb6e0 000000000100a4d0 > 0000001fbfffb7c0 0000000001007cc0 > 0000001fbfffb8a0 0000000001007e50 > 0000001fbfffb940 00000000010074f0 > 0000001fbfffba20 00000000010067fc > 0000001fbfffbaa0 00000000017d7418 > 0000001fbfffbd80 00000000017d7714 > 0000001fbfffbe40 0000000000000000 > ---STACK > Interrupt Summary: > System Calls 7673 > External Input Interrupts 2 > Data TLB Interrupts 1 > ---ID > ---LCB > > > _______________________________________________ > 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 19 01:15:08 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 19 Feb 2017 07:15:08 +0000 Subject: [Nek5000-users] EXIT: Cannot open .rea file! Message-ID: Hi, I'm new for Nek5000. I have a problem running it for eddy_nv After I compile it. I use following command to run: ./nek5000 eddy_uv But I get an error like below: Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 9.54E-08 No file SESSION.NAME; using defaults of PATH=. and SESSION=NEK. Reading ./NEK.rea EXIT: Cannot open .rea file! 1 call exitt: dying ... backtrace(): obtained 8 stack frames. ./nek5000() [0x4ea448] ./nek5000() [0x5b9869] ./nek5000() [0x5bc90a] ./nek5000() [0x43396a] ./nek5000() [0x40460d] ./nek5000() [0x404024] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f66a08c1f45] ./nek5000() [0x403319] total elapsed time : 7.25794E-03 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec How can I fix it? Thanks. Best, Kai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Feb 20 11:22:25 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 20 Feb 2017 18:22:25 +0100 Subject: [Nek5000-users] EXIT: Cannot open .rea file! In-Reply-To: References: Message-ID: Please use one of launchers in /bin e.g. nek or nekmpi to run Nek5000. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 20th February 2017 17:35 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] EXIT: Cannot open .rea file! > > Hi, > > I'm new for Nek5000. I have a problem running it for eddy_nv > After I compile it. I use following command to run: > ./nek5000 eddy_uv > > But I get an error like below: > > ?Number of processors: ? ? ? ? ? 1 > ?REAL ? ?wdsize ? ? ?: ? ? ? ? ? 8 > ?INTEGER wdsize ? ? ?: ? ? ? ? ? 4 > ?Timer accuracy ? ? ?: 9.54E-08 > ?No file SESSION.NAME; using defaults of? > ?PATH=. and SESSION=NEK. > ?Reading ./NEK.rea ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? > EXIT: Cannot open .rea file! ? ? ? ? ?1 > call exitt: dying ... > backtrace(): obtained 8 stack frames. > ./nek5000() [0x4ea448] > ./nek5000() [0x5b9869] > ./nek5000() [0x5bc90a] > ./nek5000() [0x43396a] > ./nek5000() [0x40460d] > ./nek5000() [0x404024] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main0xf5) [0x7f66a08c1f45] > ./nek5000() [0x403319] > total elapsed time ? ? ? ? ? ? : ? 7.25794E-03 sec > total solver time incl. I/O ? ?: ? 0.00000E00 sec > time/timestep ? ? ? ? ? ? ? ? ?: ? 0.00000E00 sec > CPU seconds/timestep/gridpt ? ?: ? 0.00000E00 sec > > How can I fix it? Thanks. > > Best, > Kai > _______________________________________________ > 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 Mon Feb 20 23:46:21 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 21 Feb 2017 05:46:21 +0000 Subject: [Nek5000-users] Increase nek5000 problem size Message-ID: Hi, I'm new to use nek5000, I have a problem about checkpoint file size. I did test for eddy and set like 1x1=12, 1xd=18, lelt=3000, checkpoint file size is 0.7 MB, it seems very small, If I continue increase memory size, I cannot compile nek5000 correctly, I will get an error like bellow: obj/bdry.o: In function `trstax_': bdry.f:(.text+0x10f6): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o bdry.f:(.text+0x14f4): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in obj/navier5.o bdry.f:(.text+0x15c7): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in obj/navier5.o bdry.f:(.text+0x1793): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o obj/bdry.o: In function `nekasgn_': bdry.f:(.text+0x20d7): relocation truncated to fit: R_X86_64_32S against symbol `screv_' defined in COMMON section in obj/postpro.o bdry.f:(.text+0x20e8): relocation truncated to fit: R_X86_64_32S against symbol `screv_' defined in COMMON section in obj/postpro.o obj/coef.o: In function `area3_': coef.f:(.text+0x417): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x46f): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x477): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x682): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x6ef): additional relocation overflows omitted from the output I already set # enable BIG MEMORY suuport BIGMEM="true" So, if there any other way to to increase problem size? Thanks. Best, Kai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Feb 21 09:09:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 21 Feb 2017 16:09:02 +0100 Subject: [Nek5000-users] Increase nek5000 problem size Message-ID: Your compiler needs to support large common blocks (>2GB). For e.g. Intel please compile with "-mcmodel=medium". Do you really need such a large LELT? Typically LELT = total_number_of_elements / number_of_MPI_ranks. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Tuesday 21st February 2017 15:59 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Increase nek5000 problem size > > Hi, > > I'm new to use nek5000, I have a problem about checkpoint file size. I did test for eddy?and set like?1x1=12, 1xd=18, lelt=3000, checkpoint file size is 0.7 MB, it seems very small, If I continue increase memory size, I cannot > compile nek5000 correctly, I will get an error like bellow: > > obj/bdry.o: In function `trstax_': > bdry.f:(.text0x10f6): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > bdry.f:(.text0x14f4): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > bdry.f:(.text0x15c7): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > bdry.f:(.text0x1793): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > obj/bdry.o: In function `nekasgn_': > bdry.f:(.text0x20d7): relocation truncated to fit: R_X86_64_32S against symbol `screv_' defined in COMMON section in obj/postpro.o > bdry.f:(.text0x20e8): relocation truncated to fit: R_X86_64_32S against symbol `screv_' defined in COMMON section in obj/postpro.o > obj/coef.o: In function `area3_': > coef.f:(.text0x417): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > coef.f:(.text0x46f): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > coef.f:(.text0x477): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > coef.f:(.text0x682): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o > coef.f:(.text0x6ef): additional relocation overflows omitted from the output > I already set? > # enable BIG MEMORY suuport ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > BIGMEM="true" > > So, if there any other way to to increase problem size? Thanks. > > Best, > Kai > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Feb 21 08:34:40 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 21 Feb 2017 14:34:40 +0000 Subject: [Nek5000-users] Increase nek5000 problem size In-Reply-To: References: Message-ID: Note that the checkpoint file size will scale as the number of elements in your problem (i.e., the number of elements in the .rea file: grep -i nel eddy_uv.rea to see this). The checkpoint file will not scale as lelt in the SIZE file. The requirement for lelt is that: P*lelt > nel where P is the number of processors used in the simulation. You also need the global number of elements, lelgt > nel. ________________________________ 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 20, 2017 11:46 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Increase nek5000 problem size Hi, I'm new to use nek5000, I have a problem about checkpoint file size. I did test for eddy and set like 1x1=12, 1xd=18, lelt=3000, checkpoint file size is 0.7 MB, it seems very small, If I continue increase memory size, I cannot compile nek5000 correctly, I will get an error like bellow: obj/bdry.o: In function `trstax_': bdry.f:(.text+0x10f6): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o bdry.f:(.text+0x14f4): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in obj/navier5.o bdry.f:(.text+0x15c7): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in obj/navier5.o bdry.f:(.text+0x1793): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o obj/bdry.o: In function `nekasgn_': bdry.f:(.text+0x20d7): relocation truncated to fit: R_X86_64_32S against symbol `screv_' defined in COMMON section in obj/postpro.o bdry.f:(.text+0x20e8): relocation truncated to fit: R_X86_64_32S against symbol `screv_' defined in COMMON section in obj/postpro.o obj/coef.o: In function `area3_': coef.f:(.text+0x417): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x46f): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x477): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x682): relocation truncated to fit: R_X86_64_32S against symbol `ctmp0_' defined in COMMON section in obj/navier5.o coef.f:(.text+0x6ef): additional relocation overflows omitted from the output I already set # enable BIG MEMORY suuport BIGMEM="true" So, if there any other way to to increase problem size? Thanks. Best, Kai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Feb 23 05:50:37 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 Feb 2017 12:50:37 +0100 Subject: [Nek5000-users] **ERROR**: Failed in HMHOLTZ (axisymmetric) Message-ID: Dear Neks, I have run into this convergence error in PRES while testing an axisymmetric case (**ERROR**: Failed in HMHOLTZ...). See below: ============================================================================================= Step 51118, t= 5.1118000E+01, DT= 1.0000000E-03, C= 0.081 4.9673E+02 5.6732E-03 Solving for heat Solving for fluid T T T 51118 Hmholtz TEMP: 1 3.1921E-17 2.8762E-14 5.0000E+00 51118 5.1118E+01 2.6393E-04 Heat done 51118 7.62673E-01 2.44737E-03 3.11629E+02 8 PRES PROJECT 51118 100 **ERROR**: Failed in HMHOLTZ: PRES 1.0006E-04 3.9093E-04 1.0000E-04 51118 Hmholtz VELX: 3 8.2217E-09 4.2588E-02 1.0000E-06 51118 Hmholtz VELY: 3 1.0309E-08 3.8505E-02 1.0000E-06 L1/L2 DIV(V) : -1.5406E-09 2.6956E-03 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: -1.5406E-09 2.6956E-03 51118 5.1118E+01 8.4209E-03 Fluid done 51118 5.1118E+01 4.0915E-03 5.2924E+00 ubar dump history points done :: dump history points ============================================================================================= Time step is so small due to the domain's substantial changes in size, which make the CFL go over 1 and crash otherwise. Velocity is oscillating periodically so CFL will take very low values (such as the one above) and then reach higher values overtime (0.4 or 0.5). Even raising tolerances past a reasonable extreme will not make it converge. Any hints? Best regards, MViturro -- MAURO VITURRO BALUFO Universidad Politecnica de Madrid From nek5000-users at lists.mcs.anl.gov Thu Feb 23 09:51:51 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 Feb 2017 16:51:51 +0100 Subject: [Nek5000-users] **ERROR**: Failed in HMHOLTZ (axisymmetric) In-Reply-To: References: Message-ID: Not sure if your convergence problem is related to a stability issue. What's the maximum CFL in this run? To be stable you need a max{CFL}<0.5-0.6 (assuming TORDER=3) otherwise you have to reduce DT or turn on IFCHAR (OIFS). -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 23rd February 2017 14:51 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] **ERROR**: Failed in HMHOLTZ (axisymmetric) > > Dear Neks, > > I have run into this convergence error in PRES while testing an > axisymmetric case (**ERROR**: Failed in HMHOLTZ...). See below: > > ============================================================================================= > Step 51118, t= 5.1118000E+01, DT= 1.0000000E-03, C= 0.081 4.9673E+02 > 5.6732E-03 > Solving for heat > Solving for fluid T T T > 51118 Hmholtz TEMP: 1 3.1921E-17 2.8762E-14 > 5.0000E+00 > 51118 5.1118E+01 2.6393E-04 Heat done > 51118 7.62673E-01 2.44737E-03 3.11629E+02 8 PRES PROJECT > 51118 100 **ERROR**: Failed in HMHOLTZ: PRES 1.0006E-04 > 3.9093E-04 1.0000E-04 > 51118 Hmholtz VELX: 3 8.2217E-09 4.2588E-02 > 1.0000E-06 > 51118 Hmholtz VELY: 3 1.0309E-08 3.8505E-02 > 1.0000E-06 > L1/L2 DIV(V) : -1.5406E-09 2.6956E-03 > L1/L2 QTL : 0.0000E+00 0.0000E+00 > L1/L2 DIV(V)-QTL: -1.5406E-09 2.6956E-03 > 51118 5.1118E+01 8.4209E-03 Fluid done > 51118 5.1118E+01 4.0915E-03 5.2924E+00 ubar > dump history points > done :: dump history points > ============================================================================================= > > Time step is so small due to the domain's substantial changes in size, > which make the CFL go over 1 and crash otherwise. Velocity is > oscillating > periodically so CFL will take very low values (such as the one above) > and then reach higher values overtime (0.4 or 0.5). Even raising > tolerances > past a reasonable extreme will not make it converge. Any hints? > > Best regards, > > MViturro > > > > > > > -- > MAURO VITURRO BALUFO > Universidad Politecnica de Madrid > > _______________________________________________ > 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 Thu Feb 23 08:01:13 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 Feb 2017 15:01:13 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: Sorry Stefan, i misinterpreted your question. I have tested some of the example cases and they run fine. I have uploaded a case that produces the error here: https://uni-muenster.sciebo.de/index.php/s/8WgujGKLQNLzk3k I am not sure whether you really need the large restart file. Either way, this case runs fine on an Intel system but crashes on the first time step on IBM. I think my core file came from a case compiled with "-g?. The cluster is pretty busy at the moment so I can?t really test that much. Best wishes, Jan > Am 20.02.2017 um 00:37 schrieb nek5000-users at lists.mcs.anl.gov: > > How can I reproduce the problem? Please provide a step-by-step instruction. > The core file (w/o debugging symbols) is pretty useless. Can you recompile with "-g" and try again. You may need use "addr2line" to get a human readable STACK. > > Cheers, > Stefan > > > 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 23 10:06:34 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 Feb 2017 17:06:34 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 Message-ID: Please use addr2line to translate the STACK section in your code file. This will tell us where the SEGFAULT happens. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 23rd February 2017 17:01 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Nek: abnormal termination by signal 11 > > Sorry Stefan, i misinterpreted your question. I have tested some of the example cases and they run fine. I have uploaded a case that produces the error here: > https://uni-muenster.sciebo.de/index.php/s/8WgujGKLQNLzk3k I am not sure whether you really need the large restart file. Either way, this case runs fine on an Intel system but crashes on the first time step on IBM. > I think my core file came from a case compiled with "-g?. The cluster is pretty busy at the moment so I can?t really test that much. > Best wishes, > Jan
Am 20.02.2017 um 00:37 schrieb nek5000-users at lists.mcs.anl.gov : >
How can I reproduce the problem? Please provide a step-by-step instruction.
The core file (w/o debugging symbols) is pretty useless. Can you recompile with "-g" and try again. You may need use "addr2line" to get a human readable STACK.

Cheers,
Stefan


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 Thu Feb 23 14:57:57 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 Feb 2017 21:57:57 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: addr2line tells me the error happens in ~/Nek5000/core/hsmg.f:1466 which is nt = mg_nh(l)*mg_nh(l)*mg_nhz(l)*nelv in the subroutine hsmg_solve This is from the line While executing instruction at???.0x0000000001110414, other adresses only return ??:0. > Am 23.02.2017 um 17:06 schrieb nek5000-users at lists.mcs.anl.gov: > > Please use addr2line to translate the STACK section in your code file. This will tell us where the SEGFAULT happens. > > _______________________________________________ > 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 Thu Feb 23 17:43:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 23 Feb 2017 23:43:52 +0000 Subject: [Nek5000-users] Increase the number of elements in .rea file Message-ID: Hi all, If want to increase the number of elements in .rea file, how can I edit .rea file? Can I simply copy original data? Thanks. Best, Kai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Feb 24 07:33:33 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Feb 2017 14:33:33 +0100 Subject: [Nek5000-users] Output format of Nek5000 file Message-ID: Hello everyone, I have recently started to work with Nek5000, I have few question about the output format: -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? Thank you, From nek5000-users at lists.mcs.anl.gov Fri Feb 24 10:45:01 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Feb 2017 17:45:01 +0100 Subject: [Nek5000-users] Output format of Nek5000 file Message-ID: * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX. * Is there any special reason why you want to load the data into MATLAB? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 24th February 2017 16:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Output format of Nek5000 file > > Hello everyone, > > I have recently started to work with Nek5000, I have few question about the output format: > > -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? > > -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields > So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? > > -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? > > > Thank you, > > > _______________________________________________ > 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 24 09:15:35 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Feb 2017 16:15:35 +0100 Subject: [Nek5000-users] =?utf-8?b?Pz09P3V0Zi04P3E/ICBPdXRwdXQgZm9ybWF0?= =?utf-8?q?_of_Nek5000_file?= In-Reply-To: Message-ID: Thank you for your quick response. I just feel more comfortable working interactively with data. The reading tool of data and mesh with Matlab are already there, I just need a way to map the coordinate of those data with the mesh information. More specific reason is I read the data with Visit, and when I take slides, it appear a strange white band in my fields, and I don't know the reason so I need an alternative way to visualize my fields. On Friday, February 24, 2017 17:45 CET, nek5000-users at lists.mcs.anl.gov wrote: > * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX. > * Is there any special reason why you want to load the data into MATLAB? > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 24th February 2017 16:46 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output format of Nek5000 file > > > > Hello everyone, > > > > I have recently started to work with Nek5000, I have few question about the output format: > > > > -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? > > > > -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields > > So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? > > > > -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? > > > > > > Thank you, > > > > > > _______________________________________________ > > 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 24 11:33:13 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Feb 2017 17:33:13 +0000 Subject: [Nek5000-users] ?==?utf-8?q? Output format of Nek5000 file In-Reply-To: References: , Message-ID: Sometimes visit will have dropouts if your slice corresponds precisely to the location of an element interface. Offsetting the slice by, say, .00001, will often correct that issue... 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 24, 2017 9:15 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] ?==?utf-8?q? Output format of Nek5000 file Thank you for your quick response. I just feel more comfortable working interactively with data. The reading tool of data and mesh with Matlab are already there, I just need a way to map the coordinate of those data with the mesh information. More specific reason is I read the data with Visit, and when I take slides, it appear a strange white band in my fields, and I don't know the reason so I need an alternative way to visualize my fields. On Friday, February 24, 2017 17:45 CET, nek5000-users at lists.mcs.anl.gov wrote: > * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX. > * Is there any special reason why you want to load the data into MATLAB? > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 24th February 2017 16:46 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output format of Nek5000 file > > > > Hello everyone, > > > > I have recently started to work with Nek5000, I have few question about the output format: > > > > -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? > > > > -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields > > So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? > > > > -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? > > > > > > Thank you, > > > > > > _______________________________________________ > > 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 Fri Feb 24 12:06:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Feb 2017 18:06:29 +0000 Subject: [Nek5000-users] Increase the number of elements in .rea file Message-ID: Hi Kai, Could you please elaborate more on what you mean by increasing the number of elements in the rea file? If you have a mesh and you are trying to increase the element count in order to increase the resolution, you will have to go back to the step where you generate the mesh to do that and output a new rea. Technically you could add lines to the rea file to add more elements but that would require very careful modifications to be consistent in changing the XYZ data, curve side information and boundary condition information. Ketan From nek5000-users at lists.mcs.anl.gov Sun Feb 26 22:45:42 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Feb 2017 04:45:42 +0000 Subject: [Nek5000-users] input problem that easily increase input problem size and checkpoint size Message-ID: Hi all, For Nek5000, how can we increase checkpoint size? Also, If there is any input problem that allows us to easily increase input problem size and checkpoint size? Best, Kai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Feb 27 02:26:18 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Feb 2017 09:26:18 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: Hello, some further tests showed that the error apparently only occurs if a) a restart file is used b) the geometry gets deformed in usrdat2 I have run such cases without problems on IBM systems before, and they still run fine on Intel. Creating new restart files did not help. > Am 23.02.2017 um 21:57 schrieb nek5000-users at lists.mcs.anl.gov: > > addr2line tells me the error happens in > ~/Nek5000/core/hsmg.f:1466 > which is > nt = mg_nh(l)*mg_nh(l)*mg_nhz(l)*nelv > in the subroutine hsmg_solve > This is from the line > While executing instruction at???.0x0000000001110414, > other adresses only return ??:0. > >> > > _______________________________________________ > 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 Mon Feb 27 04:31:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Feb 2017 11:31:29 +0100 Subject: [Nek5000-users] Nek: abnormal termination by signal 11 In-Reply-To: References: Message-ID: I think this is somehow related to your case. Can you reproduce the SEGFAULT with say the pipe/stenosis example doing a restart? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 27th February 2017 11:27 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Nek: abnormal termination by signal 11 > > Hello, > some further tests showed that the error apparently only occurs if > a) a restart file is used > b) the geometry gets deformed in usrdat2 > I have run such cases without problems on IBM systems before, and they still run fine on Intel. Creating new restart files did not help. > > > Am 23.02.2017 um 21:57 schrieb nek5000-users at lists.mcs.anl.gov: > > > > addr2line tells me the error happens in > > ~/Nek5000/core/hsmg.f:1466 > > which is > > nt = mg_nh(l)*mg_nh(l)*mg_nhz(l)*nelv > > in the subroutine hsmg_solve > > This is from the line > > While executing instruction at???.0x0000000001110414, > > other adresses only return ??:0. > > > >> > > > > _______________________________________________ > > 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 Mon Feb 27 04:34:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Feb 2017 11:34:49 +0100 Subject: [Nek5000-users] input problem that easily increase input problem size and checkpoint size Message-ID: Not sure what you are after? The checkpoint size will depend on things like - polynomial order (lx1, ... in SIZE) - number of elements of your mesh - number of MPI ranks - number of output variables - output precision (SP or DP) -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 27th February 2017 7:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] input problem that easily increase input problem size and checkpoint size > > Hi all, > > For Nek5000, how can we increase checkpoint size? Also,?If there is > any ?input problem that allows us to easily increase input problem size and checkpoint size? > > Best, > Kai > _______________________________________________ > 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 Mon Feb 27 04:10:31 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Feb 2017 11:10:31 +0100 Subject: [Nek5000-users] =?utf-8?b?Pz09P3V0Zi04P3E/ID89PT91dGYtOD9xPyA/?= =?utf-8?q?=3D_Output_format_of_Nek5000_fil?= In-Reply-To: Message-ID: Hello, Thank you Paul, I tried your method and it worked. But offsetting the slide trouble me, and I would like to really handle the data freely. I got almost all the ingredient I needed, I just need a function that when I feed it the cell information, it give me the coordinates of points. It must be somewhere in the source code, or may be on Internet, is anyone know about it? Thank you very much. On Friday, February 24, 2017 18:33 CET, nek5000-users at lists.mcs.anl.gov wrote: > > Sometimes visit will have dropouts if your slice corresponds precisely to the location of an element > interface. > > Offsetting the slice by, say, .00001, will often correct that issue... > > 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 24, 2017 9:15 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] ?==?utf-8?q? Output format of Nek5000 file > > Thank you for your quick response. I just feel more comfortable working interactively with data. The reading tool of data and mesh with Matlab are already there, I just need a way to map the coordinate of those data with the mesh information. > > More specific reason is I read the data with Visit, and when I take slides, it appear a strange white band in my fields, and I don't know the reason so I need an alternative way to visualize my fields. > > > > > On Friday, February 24, 2017 17:45 CET, nek5000-users at lists.mcs.anl.gov wrote: > > > * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX. > > * Is there any special reason why you want to load the data into MATLAB? > > > > > > -----Original message----- > > > From:nek5000-users at lists.mcs.anl.gov > > > Sent: Friday 24th February 2017 16:46 > > > To: nek5000-users at lists.mcs.anl.gov > > > Subject: [Nek5000-users] Output format of Nek5000 file > > > > > > Hello everyone, > > > > > > I have recently started to work with Nek5000, I have few question about the output format: > > > > > > -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? > > > > > > -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields > > > So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? > > > > > > -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? > > > > > > > > > Thank you, > > > > > > > > > _______________________________________________ > > > 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 From nek5000-users at lists.mcs.anl.gov Tue Feb 28 03:02:07 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 28 Feb 2017 10:02:07 +0100 Subject: [Nek5000-users] ?= Output format of Nek5000 fil In-Reply-To: References: Message-ID: Hi, About format of ###.f files.f As it was written it is binary format supporting both single- and multi-file output. That is why you have single (or more) digit before the dot in the file number. If you specify multiple file output this first digit numbers files in a single snapshot and the last five digits give snapshot number. When it comes to file interior. First you have 132 character long header that is ascii and can be read directly. It contains: - wdsizo - number of words per real field (to distinguish between single and double precision output - nxo,nyo,nzo - number of grid points in the element in each direction - nelo - number of elements in given file (important for multi-file output) - nelgt - global number of elements (in all files; the same as nelo for single file output) - time - real number for simulation time - istep - time step - fid0 - current file number (for multi-file output, 0 for single file output) - nfileoo - number of files in the snapshot - few characters specifying what fields are saved; e.g. XUP - means coordinates, velocity, pressure. Notice the coordinates do not have to be saved in a file, but they can!!! - p0th - this is only in new format and gives averaged pressure (not all simulations specify this number) The header is followed by single real (4 bytes) test pattern to distinguish between big and little endian. Next come nelo integers with local-to-global element mapping, which assigns every element in the file its global identity that was used by nek5000 during simulation. After that you have fields you've specified for writing - X - physical coordinate - vector - U - velocity -vector - P - pressure - scalar - T - temperature - scalar - S - passive scalar -scalar; here you can have digits specifying number of passive scalars All variables are specified per element, however in the case of scalars you have nelo sections with nxo*nyo*nzo reals, but for vectors you get ndim*nelo sections with nxo*nyo*nzo reals, as vector component are saved per element, to per array. It means you have vx, vy, vz for first element, next vx, vy, vz for second element and so on. Concluding. If you want to know exact physical position of your grid points you have to save coordinates in the file. You do it in ###.rea file by specifying at the end of the file: 6 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE F TEMPERATURE F TEMPERATURE GRADIENT or in ###.par file be setting [MESH] writeToFieldFile = yes When you have them in the file you can easily read coordinates and use them in any way. I hope this was not too long and detailed. Regards Adam On 27/02/17 11:10, nek5000-users at lists.mcs.anl.gov wrote: > Hello, > > Thank you Paul, I tried your method and it worked. But offsetting the slide trouble me, and I would like to really handle the data freely. I got almost all the ingredient I needed, I just need a function that when I feed it the cell information, it give me the coordinates of points. It must be somewhere in the source code, or may be on Internet, is anyone know about it? > > Thank you very much. > > > > > > On Friday, February 24, 2017 18:33 CET, nek5000-users at lists.mcs.anl.gov wrote: > >> Sometimes visit will have dropouts if your slice corresponds precisely to the location of an element >> interface. >> >> Offsetting the slice by, say, .00001, will often correct that issue... >> >> 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 24, 2017 9:15 AM >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] ?==?utf-8?q? Output format of Nek5000 file >> >> Thank you for your quick response. I just feel more comfortable working interactively with data. The reading tool of data and mesh with Matlab are already there, I just need a way to map the coordinate of those data with the mesh information. >> >> More specific reason is I read the data with Visit, and when I take slides, it appear a strange white band in my fields, and I don't know the reason so I need an alternative way to visualize my fields. >> >> >> >> >> On Friday, February 24, 2017 17:45 CET, nek5000-users at lists.mcs.anl.gov wrote: >> >>> * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX. >>> * Is there any special reason why you want to load the data into MATLAB? >>> >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Friday 24th February 2017 16:46 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: [Nek5000-users] Output format of Nek5000 file >>>> >>>> Hello everyone, >>>> >>>> I have recently started to work with Nek5000, I have few question about the output format: >>>> >>>> -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? >>>> >>>> -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields >>>> So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? >>>> >>>> -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? >>>> >>>> >>>> Thank you, >>>> >>>> >>>> _______________________________________________ >>>> 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 > > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Feb 28 09:04:18 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 28 Feb 2017 16:04:18 +0100 Subject: [Nek5000-users] =?utf-8?b?Pz09P3V0Zi04P3E/ID89PT91dGYtOD9xPyA/?= =?utf-8?q?=3D_Output_format_of_Nek5000_fil?= In-Reply-To: Message-ID: Thank you very much Adam, this is exactly what I wanted. Best regards On Tuesday, February 28, 2017 10:02 CET, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > About format of ###.f files.f As it was written it is binary format > supporting both single- and multi-file output. That is why you have > single (or more) digit before the dot in the file number. If you specify > multiple file output this first digit numbers files in a single snapshot > and the last five digits give snapshot number. When it comes to file > interior. First you have 132 character long header that is ascii and can > be read directly. It contains: > - wdsizo - number of words per real field (to distinguish between > single and double precision output > - nxo,nyo,nzo - number of grid points in the element in each direction > - nelo - number of elements in given file (important for multi-file output) > - nelgt - global number of elements (in all files; the same as nelo for > single file output) > - time - real number for simulation time > - istep - time step > - fid0 - current file number (for multi-file output, 0 for single file > output) > - nfileoo - number of files in the snapshot > - few characters specifying what fields are saved; e.g. XUP - means > coordinates, velocity, pressure. Notice the coordinates do not have to > be saved in a file, but they can!!! > - p0th - this is only in new format and gives averaged pressure (not > all simulations specify this number) > > The header is followed by single real (4 bytes) test pattern to > distinguish between big and little endian. Next come nelo integers with > local-to-global element mapping, which assigns every element in the file > its global identity that was used by nek5000 during simulation. After > that you have fields you've specified for writing > - X - physical coordinate - vector > - U - velocity -vector > - P - pressure - scalar > - T - temperature - scalar > - S - passive scalar -scalar; here you can have digits specifying number > of passive scalars > All variables are specified per element, however in the case of scalars > you have nelo sections with nxo*nyo*nzo reals, but for vectors you get > ndim*nelo sections with nxo*nyo*nzo reals, as vector component are saved > per element, to per array. It means you have vx, vy, vz for first > element, next vx, vy, vz for second element and so on. > Concluding. If you want to know exact physical position of your grid > points you have to save coordinates in the file. You do it in ###.rea > file by specifying at the end of the file: > 6 SPECIFICATIONS FOLLOW > T COORDINATES > T VELOCITY > T PRESSURE > F TEMPERATURE > F TEMPERATURE GRADIENT > or in ###.par file be setting > [MESH] > writeToFieldFile = yes > > When you have them in the file you can easily read coordinates and use > them in any way. > I hope this was not too long and detailed. > Regards > Adam > > On 27/02/17 11:10, nek5000-users at lists.mcs.anl.gov wrote: > > Hello, > > > > Thank you Paul, I tried your method and it worked. But offsetting the slide trouble me, and I would like to really handle the data freely. I got almost all the ingredient I needed, I just need a function that when I feed it the cell information, it give me the coordinates of points. It must be somewhere in the source code, or may be on Internet, is anyone know about it? > > > > Thank you very much. > > > > > > > > > > > > On Friday, February 24, 2017 18:33 CET, nek5000-users at lists.mcs.anl.gov wrote: > > > >> Sometimes visit will have dropouts if your slice corresponds precisely to the location of an element > >> interface. > >> > >> Offsetting the slice by, say, .00001, will often correct that issue... > >> > >> 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 24, 2017 9:15 AM > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] ?==?utf-8?q? Output format of Nek5000 file > >> > >> Thank you for your quick response. I just feel more comfortable working interactively with data. The reading tool of data and mesh with Matlab are already there, I just need a way to map the coordinate of those data with the mesh information. > >> > >> More specific reason is I read the data with Visit, and when I take slides, it appear a strange white band in my fields, and I don't know the reason so I need an alternative way to visualize my fields. > >> > >> > >> > >> > >> On Friday, February 24, 2017 17:45 CET, nek5000-users at lists.mcs.anl.gov wrote: > >> > >>> * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX. > >>> * Is there any special reason why you want to load the data into MATLAB? > >>> > >>> > >>> -----Original message----- > >>>> From:nek5000-users at lists.mcs.anl.gov > >>>> Sent: Friday 24th February 2017 16:46 > >>>> To: nek5000-users at lists.mcs.anl.gov > >>>> Subject: [Nek5000-users] Output format of Nek5000 file > >>>> > >>>> Hello everyone, > >>>> > >>>> I have recently started to work with Nek5000, I have few question about the output format: > >>>> > >>>> -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same? > >>>> > >>>> -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel . N^3 . fields > >>>> So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced? > >>>> > >>>> -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature? > >>>> > >>>> > >>>> Thank you, > >>>> > >>>> > >>>> _______________________________________________ > >>>> 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 > > > > > > > > > > > > > > _______________________________________________ > > 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