From nek5000-users at lists.mcs.anl.gov Wed May 3 04:37:27 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 3 May 2017 11:37:27 +0200 Subject: [Nek5000-users] Robin boundary condition on velocity Message-ID: Hi Sudhakar, thank you, I finally managed to implement it as an extension of the standar "SYM" boundary condition. Thank you very much again! Cheers Francesco -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 8 06:52:55 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 May 2017 11:52:55 +0000 Subject: [Nek5000-users] Adjacent vertices / cells Message-ID: Hi all, I'm just wondering if there's a way (given a particular velocity cell's local (i,j,k,e) co-ordinates within the domain) to access the 6 adjacent cells - even if they are located inside a different element. If so, how does this deal with cells on the boundary, where there may exist fewer than 6 adjacent cells. Many thanks, Lee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 8 07:26:13 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 May 2017 12:26:13 +0000 Subject: [Nek5000-users] Adjacent vertices / cells In-Reply-To: References: Message-ID: Hi Lee, The SEM is more function-based than cell based. My guess is that Nek might alread support the higher-level operation you are trying to implement. What is your objective? Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 6:52 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Adjacent vertices / cells Hi all, I'm just wondering if there's a way (given a particular velocity cell's local (i,j,k,e) co-ordinates within the domain) to access the 6 adjacent cells - even if they are located inside a different element. If so, how does this deal with cells on the boundary, where there may exist fewer than 6 adjacent cells. Many thanks, Lee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 8 07:38:58 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 May 2017 12:38:58 +0000 Subject: [Nek5000-users] Adjacent vertices / cells In-Reply-To: References: , Message-ID: Hi Paul, Thankyou very much for your prompt response, I'm tracking an immersed object within the fluid. I can determine whether a velocity point is within the boundary using face normals and dot-products, but I need to know whether it is connected to an outside-boundary cell. Cheers, Lee ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: 08 May 2017 13:26:13 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Lee, The SEM is more function-based than cell based. My guess is that Nek might alread support the higher-level operation you are trying to implement. What is your objective? Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 6:52 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Adjacent vertices / cells Hi all, I'm just wondering if there's a way (given a particular velocity cell's local (i,j,k,e) co-ordinates within the domain) to access the 6 adjacent cells - even if they are located inside a different element. If so, how does this deal with cells on the boundary, where there may exist fewer than 6 adjacent cells. Many thanks, Lee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 8 08:04:39 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 May 2017 13:04:39 +0000 Subject: [Nek5000-users] Adjacent vertices / cells In-Reply-To: References: , , Message-ID: Hi Lee, Just to be clear re. your original question - the (i,j,k,e) topology is point-based, not cell-based, so one doesn't have a concept of 6 neighbors unless you are in the interior of a spectral element or on the face of a spectral element. At an edge or corner, you could have more or fewer than 6 neighbors. If you instead define a cell (which would be defined, say, at the centroids of the N^3 cells within each element), you would have 6 neighbors unless you're on the boundary. I would normally find these neighbors by invoking calls to setupds and dssum(). In one exchange, you could exchange your neighbors element number. In a subsequent exchange you could exchange the cell index. If you use gs_op() directly, I believe it supports integer arguments, rather than making the unseeingly an perhaps error-prone conversion to integers, though I've never had any difficulty call dssum directly and using reals. It's important to use the gs_op (or equivalent drum) operations as that is the only viable/scalable approach in parallel. (Everything has been tested on anywhere from 1 to 6 million ranks). I've done this several times before...and can probably dig up some code to give you cell based data, assuming that's what you want. Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 7:38 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Paul, Thankyou very much for your prompt response, I'm tracking an immersed object within the fluid. I can determine whether a velocity point is within the boundary using face normals and dot-products, but I need to know whether it is connected to an outside-boundary cell. Cheers, Lee ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: 08 May 2017 13:26:13 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Lee, The SEM is more function-based than cell based. My guess is that Nek might alread support the higher-level operation you are trying to implement. What is your objective? Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 6:52 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Adjacent vertices / cells Hi all, I'm just wondering if there's a way (given a particular velocity cell's local (i,j,k,e) co-ordinates within the domain) to access the 6 adjacent cells - even if they are located inside a different element. If so, how does this deal with cells on the boundary, where there may exist fewer than 6 adjacent cells. Many thanks, Lee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 8 08:20:03 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 May 2017 13:20:03 +0000 Subject: [Nek5000-users] Adjacent vertices / cells In-Reply-To: References: , , , Message-ID: Hi Paul, Ah I see! That's very helpful, seems I was visualizing elements incorrectly. Am I right in thinking then that adjacent elements 'share' sets of points on their faces? I'm unfamiliar with these subroutines but I'll check them out. Any code that sheds more light on the way they are used would be greatly appreciated. Cheers, Lee ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: 08 May 2017 14:04:39 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Lee, Just to be clear re. your original question - the (i,j,k,e) topology is point-based, not cell-based, so one doesn't have a concept of 6 neighbors unless you are in the interior of a spectral element or on the face of a spectral element. At an edge or corner, you could have more or fewer than 6 neighbors. If you instead define a cell (which would be defined, say, at the centroids of the N^3 cells within each element), you would have 6 neighbors unless you're on the boundary. I would normally find these neighbors by invoking calls to setupds and dssum(). In one exchange, you could exchange your neighbors element number. In a subsequent exchange you could exchange the cell index. If you use gs_op() directly, I believe it supports integer arguments, rather than making the unseeingly an perhaps error-prone conversion to integers, though I've never had any difficulty call dssum directly and using reals. It's important to use the gs_op (or equivalent drum) operations as that is the only viable/scalable approach in parallel. (Everything has been tested on anywhere from 1 to 6 million ranks). I've done this several times before...and can probably dig up some code to give you cell based data, assuming that's what you want. Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 7:38 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Paul, Thankyou very much for your prompt response, I'm tracking an immersed object within the fluid. I can determine whether a velocity point is within the boundary using face normals and dot-products, but I need to know whether it is connected to an outside-boundary cell. Cheers, Lee ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: 08 May 2017 13:26:13 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Lee, The SEM is more function-based than cell based. My guess is that Nek might alread support the higher-level operation you are trying to implement. What is your objective? Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 6:52 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Adjacent vertices / cells Hi all, I'm just wondering if there's a way (given a particular velocity cell's local (i,j,k,e) co-ordinates within the domain) to access the 6 adjacent cells - even if they are located inside a different element. If so, how does this deal with cells on the boundary, where there may exist fewer than 6 adjacent cells. Many thanks, Lee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 8 08:56:34 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 8 May 2017 13:56:34 +0000 Subject: [Nek5000-users] Adjacent vertices / cells In-Reply-To: References: , , , , Message-ID: Correct. Face-based vertices are shared (and are thus stored redundantly in separate elements/processors). Same for edge and corner based vertices. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 8:20 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Paul, Ah I see! That's very helpful, seems I was visualizing elements incorrectly. Am I right in thinking then that adjacent elements 'share' sets of points on their faces? I'm unfamiliar with these subroutines but I'll check them out. Any code that sheds more light on the way they are used would be greatly appreciated. Cheers, Lee ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: 08 May 2017 14:04:39 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Lee, Just to be clear re. your original question - the (i,j,k,e) topology is point-based, not cell-based, so one doesn't have a concept of 6 neighbors unless you are in the interior of a spectral element or on the face of a spectral element. At an edge or corner, you could have more or fewer than 6 neighbors. If you instead define a cell (which would be defined, say, at the centroids of the N^3 cells within each element), you would have 6 neighbors unless you're on the boundary. I would normally find these neighbors by invoking calls to setupds and dssum(). In one exchange, you could exchange your neighbors element number. In a subsequent exchange you could exchange the cell index. If you use gs_op() directly, I believe it supports integer arguments, rather than making the unseeingly an perhaps error-prone conversion to integers, though I've never had any difficulty call dssum directly and using reals. It's important to use the gs_op (or equivalent drum) operations as that is the only viable/scalable approach in parallel. (Everything has been tested on anywhere from 1 to 6 million ranks). I've done this several times before...and can probably dig up some code to give you cell based data, assuming that's what you want. Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 7:38 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Paul, Thankyou very much for your prompt response, I'm tracking an immersed object within the fluid. I can determine whether a velocity point is within the boundary using face normals and dot-products, but I need to know whether it is connected to an outside-boundary cell. Cheers, Lee ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: 08 May 2017 13:26:13 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Adjacent vertices / cells Hi Lee, The SEM is more function-based than cell based. My guess is that Nek might alread support the higher-level operation you are trying to implement. What is your objective? Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 08, 2017 6:52 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Adjacent vertices / cells Hi all, I'm just wondering if there's a way (given a particular velocity cell's local (i,j,k,e) co-ordinates within the domain) to access the 6 adjacent cells - even if they are located inside a different element. If so, how does this deal with cells on the boundary, where there may exist fewer than 6 adjacent cells. Many thanks, Lee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 10 06:18:12 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 10 May 2017 19:18:12 +0800 (GMT+08:00) Subject: [Nek5000-users] About Reynold Averaged Navier-Stokes model in Nek5000 In-Reply-To: References: , Message-ID: Hi all, I want to accomplish a turbulent inflow generation method in boundary flow simulation by Spectral Element Method (SEM).I have already tried Recycling-Rescaling Method, but failed. And I wondered whether Reynold Averaged Navier-Stokes (RANS) model have been absorbed in Nek5000, then I can directly use RANS to get a turbulent inflow condition similarly? Or does it have any other approach for me to get a turbulent inflow condition? I tried really a lot on this, but still have no result. Sincerely hope somebody can give me an advice. Thanks a lot! Best regards! Hu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 10 09:17:54 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 10 May 2017 16:17:54 +0200 Subject: [Nek5000-users] Nek started to use AMG? Message-ID: Hi all, after the last update to the recent github version, a case I use seems to have started to demand AMG files: gs_setup: 24196 unique labels shared pairwise times (avg, min, max): 0.000191137 0.000163524 0.000223323 crystal router : 0.000267723 0.000264667 0.000273955 all reduce : 0.000187082 0.000186959 0.000187183 used all_to_all method: allreduce handle bytes (avg, min, max): 2906.93 2612 3356 buffer bytes (avg, min, max): 387136 387136 387136 AMG files not found, dumping data ... AMG writing data from proc 0 AMG writing data from proc 1 ? AMG writing data from proc 2046 AMG writing data from proc 2047 AMG dump successful call exitt: dying ? However, I never used AMG, and have also tried to explicitly deactivate IFAMG and IFAMG_DUMP in the makefile (with the same error). Is there any way AMG can get switched on by accident? Cheers, Jan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 10 09:20:43 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 10 May 2017 16:20:43 +0200 Subject: [Nek5000-users] Nek started to use AMG? In-Reply-To: References: Message-ID: Please consult the RELEASE.md shipped with the source. It looks like p40 (in your .rea file) is non-zero. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 10th May 2017 16:17 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Nek started to use AMG? > > Hi all, > after the last update to the recent github version, a case I use seems to have started to demand AMG files: >
gs_setup: 24196 unique labels shared > ?? pairwise times (avg, min, max): 0.000191137 0.000163524 0.000223323 > ?? crystal router? ? ? ? ? ? ? ? : 0.000267723 0.000264667 0.000273955 > ?? all reduce? ? ? ? ? ? ? ? ? ? : 0.000187082 0.000186959 0.000187183 > ?? used all_to_all method: allreduce > ?? handle bytes (avg, min, max): 2906.93 2612 3356 > ?? buffer bytes (avg, min, max): 387136 387136 387136 > AMG files not found, dumping data ... > AMG writing data from proc 0 > AMG writing data from proc 1 > ? > AMG writing data from proc 2046 > AMG writing data from proc 2047 > AMG dump successful > ??
call exitt: dying ? >
However, I never used AMG, and have also tried to explicitly deactivate IFAMG and IFAMG_DUMP in the makefile (with the same error). Is there any way AMG can get switched on by accident? >
Cheers, > 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 Sun May 14 10:09:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 14 May 2017 11:09:48 -0400 Subject: [Nek5000-users] Time derivative of Scalar field In-Reply-To: References: Message-ID: Hi Ketan, I have tried your .usr file and it compiles. But I think it does not write out the 'ddt' right? For my case it doesn't write it out in the 'output', or in the .fld files. I was also trying the 'vxlag' in the common block in userchk subroutine like Paul suggested but that leads to errors. Can you let me know, is there a subroutine that does that? Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Tue, Apr 25, 2017 at 2:06 PM, wrote: > Hi Saikat, > > I have attached a usr file that shows how to calculate finite difference > based first derivative of the first passive scalar t(1,1,1,1,2) using the > current time step and two previous time steps. The coefficients for the > derivative are obtained using a call to fd_weights_full, and I am using a > common block for storing the values of the scalar at two previous > time-steps. > > Ketan > > > > > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun May 14 10:21:42 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 14 May 2017 11:21:42 -0400 Subject: [Nek5000-users] Time derivative of Scalar field Message-ID: Hello Neks and Paul, I wanted to find out the time derivative of Scalar field in my Rayleigh Benard calculations. I am attaching my test case in which I have used common block in the .usr file usrchk subroutine to compute the derivative at each time step. I believe vxlag() stores the previous time step values. But this leads to error in my output. I would also like to know how to print out the values of dcdt, along with my scalars when I am writing out my .fld files. Thanks a lot, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. -------------- next part -------------- An HTML attachment was scrubbed... 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Name: box20test.map Type: application/octet-stream Size: 27988 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Sun May 14 12:26:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 14 May 2017 17:26:52 +0000 Subject: [Nek5000-users] Crash when implementing additional scalars Message-ID: Dear Neks, I get the following crash when implementing 3 scalar fields (temperature + 2 additional scalar fields): ************** Step 4, t= 4.0000000E-03, DT= 1.0000000E-03, C= 0.331 7.1728E+01 2.2114E+01 Solving for heat Solving for fluid F T T 4 2.51148E-02 6.07580E-04 4.13357E+01 1 TEMP PROJECT 4 Hmholtz TEMP: 4 3.0551E-08 8.0302E-04 1.0000E-07 4 2.51148E-02 1.60663E-08 1.56319E+06 2 PS 1 PROJECT 4 Hmholtz PS 1: 0 3.0509E-08 3.0509E-08 1.0000E-07 4 2.51148E-02 3.38605E-02 7.41712E-01 3 PS 2 PROJECT 4 100 **ERROR**: Failed in HMHOLTZ: PS 2 1.6090E+10 5.4264E-02 1.0000E-07 4proj_ortho: 3 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4proj_ortho: 2 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4proj_ortho: 1 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4 4.0000E-03 1.2605E+01 Heat done Reorthogonalize Basis: 4 2.21548E-02 2.27058E-02 9.75731E-01 1 velx PROJECT 4 Hmholtz velx: 5 7.8903E-08 4.8255E-02 1.0000E-07 Reorthogonalize Basis: 4 2.21455E-02 2.26942E-02 9.75823E-01 1 vely PROJECT 4 Hmholtz vely: 5 7.8987E-08 4.8248E-02 1.0000E-07 Reorthogonalize Basis: 4 2.54684E-01 2.57237E-01 9.90076E-01 1 velz PROJECT 4 Hmholtz velz: 6 1.7695E-08 5.4216E-01 1.0000E-07 4 U-PRES gmres: 13 9.8513E-07 1.0000E-06 3.0328E-03 1.1984E+00 4.7670E+00 4 4.0000E-03 8.4136E+00 Fluid done 4 4 qfilt: 6.2753E-08 1.4966E-07 4.9326E-10 5.7232E-14 5.7288E-14 2.1974E+09 ***************** The strange thing is that this does not happen when I run with only temperature. I develop my simulation in small steps, but at the step when I also simulate the scalars (that are treated identically as the temperature), I get this crash. I wonder if there is somthing that I missed when increasing the number of scalars? Below I describe how I set up the simulation. Best, Johan ***************************** *** Only temperature case *** I generate a mesh from six .box files using genbox. The corresponding .rea files were modified slightly, merged and extended to 3D using n2to3. The 3D .rea files were merged using nekmerge2. If I start from .box files with only temperature I get a .rea file with p023 = 0 (NPSCAL). I set the Peclet number to -233, and the field settings to T T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) end everything works excellently. *** 3 scalar case *** If modify the previously mentioned .box files by adding 2 to the number of fields, and adding the same BC:s to them. I get a .rea file with p023 = 2 (NPSCAL). I set the Peclet number for the new scalars to -233, so that they are the same as for the temperature. I change the field settings to: T T T T F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F F F T T T T T T T T IFTMSH (IF mesh for this field is T mesh) Now I get the crash described above. ***************************** *** The .usr file*** The temperature is read out in userf as: ffz = -t(ix,iy,iz,e,1)/1.32 All the scalars have the same boundary and initial conditions (they enter useric and userf only as "temp"). *** The SIZE file *** I use the maximum number of passive scalars (ldimt) = 4 for both cases. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun May 14 12:30:09 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 14 May 2017 17:30:09 +0000 Subject: [Nek5000-users] Crash when implementing additional scalars In-Reply-To: References: Message-ID: Dear Johan, Try setting param 94=0 in your .rea file. Best, 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: Sunday, May 14, 2017 12:26 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Crash when implementing additional scalars Dear Neks, I get the following crash when implementing 3 scalar fields (temperature + 2 additional scalar fields): ************** Step 4, t= 4.0000000E-03, DT= 1.0000000E-03, C= 0.331 7.1728E+01 2.2114E+01 Solving for heat Solving for fluid F T T 4 2.51148E-02 6.07580E-04 4.13357E+01 1 TEMP PROJECT 4 Hmholtz TEMP: 4 3.0551E-08 8.0302E-04 1.0000E-07 4 2.51148E-02 1.60663E-08 1.56319E+06 2 PS 1 PROJECT 4 Hmholtz PS 1: 0 3.0509E-08 3.0509E-08 1.0000E-07 4 2.51148E-02 3.38605E-02 7.41712E-01 3 PS 2 PROJECT 4 100 **ERROR**: Failed in HMHOLTZ: PS 2 1.6090E+10 5.4264E-02 1.0000E-07 4proj_ortho: 3 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4proj_ortho: 2 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4proj_ortho: 1 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4 4.0000E-03 1.2605E+01 Heat done Reorthogonalize Basis: 4 2.21548E-02 2.27058E-02 9.75731E-01 1 velx PROJECT 4 Hmholtz velx: 5 7.8903E-08 4.8255E-02 1.0000E-07 Reorthogonalize Basis: 4 2.21455E-02 2.26942E-02 9.75823E-01 1 vely PROJECT 4 Hmholtz vely: 5 7.8987E-08 4.8248E-02 1.0000E-07 Reorthogonalize Basis: 4 2.54684E-01 2.57237E-01 9.90076E-01 1 velz PROJECT 4 Hmholtz velz: 6 1.7695E-08 5.4216E-01 1.0000E-07 4 U-PRES gmres: 13 9.8513E-07 1.0000E-06 3.0328E-03 1.1984E+00 4.7670E+00 4 4.0000E-03 8.4136E+00 Fluid done 4 4 qfilt: 6.2753E-08 1.4966E-07 4.9326E-10 5.7232E-14 5.7288E-14 2.1974E+09 ***************** The strange thing is that this does not happen when I run with only temperature. I develop my simulation in small steps, but at the step when I also simulate the scalars (that are treated identically as the temperature), I get this crash. I wonder if there is somthing that I missed when increasing the number of scalars? Below I describe how I set up the simulation. Best, Johan ***************************** *** Only temperature case *** I generate a mesh from six .box files using genbox. The corresponding .rea files were modified slightly, merged and extended to 3D using n2to3. The 3D .rea files were merged using nekmerge2. If I start from .box files with only temperature I get a .rea file with p023 = 0 (NPSCAL). I set the Peclet number to -233, and the field settings to T T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) end everything works excellently. *** 3 scalar case *** If modify the previously mentioned .box files by adding 2 to the number of fields, and adding the same BC:s to them. I get a .rea file with p023 = 2 (NPSCAL). I set the Peclet number for the new scalars to -233, so that they are the same as for the temperature. I change the field settings to: T T T T F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F F F T T T T T T T T IFTMSH (IF mesh for this field is T mesh) Now I get the crash described above. ***************************** *** The .usr file*** The temperature is read out in userf as: ffz = -t(ix,iy,iz,e,1)/1.32 All the scalars have the same boundary and initial conditions (they enter useric and userf only as "temp"). *** The SIZE file *** I use the maximum number of passive scalars (ldimt) = 4 for both cases. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun May 14 21:15:55 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 15 May 2017 10:15:55 +0800 (GMT+08:00) Subject: [Nek5000-users] Two dimensional LES in case Turbchannel In-Reply-To: References: Message-ID: Hi all, I have already tried the case turbChannel for three-dimensional LES. And I want to try Two-dimensional LES. I modifed the subroutine functions such as: eddy_visc, comp_lij, comp_mij. And I comment out the warning "ERROR in tens3d1. Increase lw." in subroutine tens3d1 in postprof.f. But still have some problems! After 8 time steps, the L1/L2 DIV(V) is too large (about 1.48e6), and finally lead to a very large CFL number(1.8e6).Details can be seen in attachment. I don't know why this happened! How can I finish this 2d-LES case in turbchannel? Best regards! Hu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbchannel-2d.rar Type: application/octet-stream Size: 13235 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Too large CFL number.png Type: image/png Size: 85628 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Sun May 14 21:35:03 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 14 May 2017 20:35:03 -0600 Subject: [Nek5000-users] Time derivative of Scalar field Message-ID: Hi Saikat, No it does not. If you want to write it out, you have to say: call outpost(ddt,vy,vz,pr,t,' ') You can replace vy, vz etc with other variables of your choice. You can also specify the name of the file to be output using 3 characters of your choice instead of 3 blanks that I have used. 3 blanks leads to file being written out using the case name. So you probably want to use: call outpost(ddt,vy,vz,pr,t,'ddt') Ketan Sent from my iPhone From nek5000-users at lists.mcs.anl.gov Mon May 15 01:43:59 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 15 May 2017 14:43:59 +0800 (GMT+08:00) Subject: [Nek5000-users] Two dimensional LES in case Turbchannel In-Reply-To: References: Message-ID: I checked it again and finally solved this problem. Thanks! Hu -----Original Messages----- From: nek5000-users at lists.mcs.anl.gov Sent Time: Monday, May 15, 2017 To: nek5000-users at lists.mcs.anl.gov Cc: Subject: [Nek5000-users] Two dimensional LES in case Turbchannel Hi all, I have already tried the case turbChannel for three-dimensional LES. And I want to try Two-dimensional LES. I modifed the subroutine functions such as: eddy_visc, comp_lij, comp_mij. And I comment out the warning "ERROR in tens3d1. Increase lw." in subroutine tens3d1 in postprof.f. But still have some problems! After 8 time steps, the L1/L2 DIV(V) is too large (about 1.48e6), and finally lead to a very large CFL number(1.8e6).Details can be seen in attachment. I don't know why this happened! How can I finish this 2d-LES case in turbchannel? Best regards! Hu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 15 02:40:25 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 15 May 2017 07:40:25 +0000 Subject: [Nek5000-users] Crash when implementing additional scalars In-Reply-To: References: , Message-ID: Thank you, this solved the problem! Now all scalars behave identically as they should and no crash. How should I understand the reason for the previous crash? ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Sunday, May 14, 2017 7:30 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Crash when implementing additional scalars Dear Johan, Try setting param 94=0 in your .rea file. Best, 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: Sunday, May 14, 2017 12:26 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Crash when implementing additional scalars Dear Neks, I get the following crash when implementing 3 scalar fields (temperature + 2 additional scalar fields): ************** Step 4, t= 4.0000000E-03, DT= 1.0000000E-03, C= 0.331 7.1728E+01 2.2114E+01 Solving for heat Solving for fluid F T T 4 2.51148E-02 6.07580E-04 4.13357E+01 1 TEMP PROJECT 4 Hmholtz TEMP: 4 3.0551E-08 8.0302E-04 1.0000E-07 4 2.51148E-02 1.60663E-08 1.56319E+06 2 PS 1 PROJECT 4 Hmholtz PS 1: 0 3.0509E-08 3.0509E-08 1.0000E-07 4 2.51148E-02 3.38605E-02 7.41712E-01 3 PS 2 PROJECT 4 100 **ERROR**: Failed in HMHOLTZ: PS 2 1.6090E+10 5.4264E-02 1.0000E-07 4proj_ortho: 3 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4proj_ortho: 2 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4proj_ortho: 1 4 PS 2 Detect rank deficiency: NaN 1.0000E+00 4 4.0000E-03 1.2605E+01 Heat done Reorthogonalize Basis: 4 2.21548E-02 2.27058E-02 9.75731E-01 1 velx PROJECT 4 Hmholtz velx: 5 7.8903E-08 4.8255E-02 1.0000E-07 Reorthogonalize Basis: 4 2.21455E-02 2.26942E-02 9.75823E-01 1 vely PROJECT 4 Hmholtz vely: 5 7.8987E-08 4.8248E-02 1.0000E-07 Reorthogonalize Basis: 4 2.54684E-01 2.57237E-01 9.90076E-01 1 velz PROJECT 4 Hmholtz velz: 6 1.7695E-08 5.4216E-01 1.0000E-07 4 U-PRES gmres: 13 9.8513E-07 1.0000E-06 3.0328E-03 1.1984E+00 4.7670E+00 4 4.0000E-03 8.4136E+00 Fluid done 4 4 qfilt: 6.2753E-08 1.4966E-07 4.9326E-10 5.7232E-14 5.7288E-14 2.1974E+09 ***************** The strange thing is that this does not happen when I run with only temperature. I develop my simulation in small steps, but at the step when I also simulate the scalars (that are treated identically as the temperature), I get this crash. I wonder if there is somthing that I missed when increasing the number of scalars? Below I describe how I set up the simulation. Best, Johan ***************************** *** Only temperature case *** I generate a mesh from six .box files using genbox. The corresponding .rea files were modified slightly, merged and extended to 3D using n2to3. The 3D .rea files were merged using nekmerge2. If I start from .box files with only temperature I get a .rea file with p023 = 0 (NPSCAL). I set the Peclet number to -233, and the field settings to T T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) end everything works excellently. *** 3 scalar case *** If modify the previously mentioned .box files by adding 2 to the number of fields, and adding the same BC:s to them. I get a .rea file with p023 = 2 (NPSCAL). I set the Peclet number for the new scalars to -233, so that they are the same as for the temperature. I change the field settings to: T T T T F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F F F T T T T T T T T IFTMSH (IF mesh for this field is T mesh) Now I get the crash described above. ***************************** *** The .usr file*** The temperature is read out in userf as: ffz = -t(ix,iy,iz,e,1)/1.32 All the scalars have the same boundary and initial conditions (they enter useric and userf only as "temp"). *** The SIZE file *** I use the maximum number of passive scalars (ldimt) = 4 for both cases. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 15 04:47:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 15 May 2017 10:47:02 +0100 Subject: [Nek5000-users] velocity averaging code in .usr file for a pipe Message-ID: Hi nek, Are there any examples of averaging velocity for fluid and particles (if it is a two-phase flow) in a pipe in .usr file? Kind regards, Jian -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 16 04:58:36 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 May 2017 11:58:36 +0200 Subject: [Nek5000-users] Reading rea file on IBM Blue Gene/Q server Message-ID: Hi Neks, We are carrying out an optimization study on IBM Blue Gene/Q server of IDRIS using direct-adjoint method. The direct and adjoint equations are solved using Nek5000. We have observed that for moderate to large number of processors Nek5000 spends considerable time in reading the .rea file. When we reduce the number of processors, the .rea file is read in lesser time but the time taken for solver increases. To give an idea, a 3D case for incompressible flow with 12000 elements spends 22.132 seconds in reading .rea file if we use 400 processors. If we increase the number of processors to 1000, it takes more than 90 seconds to read the same .rea file. Can someone provide us a solution on how to make Nek read the rea file quickly? Would using .re2 file instead of .rea increase the performance considering the number of elements is not very large.? I would like to mention that we are using PPLIST="MPIIO" in the makenek file. Many thanks. From nek5000-users at lists.mcs.anl.gov Tue May 16 05:56:15 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 May 2017 12:56:15 +0200 Subject: [Nek5000-users] Reading rea file on IBM Blue Gene/Q server In-Reply-To: References: Message-ID: For performance use .re2 and the latest master available on GitHub. On 16 May 2017, at 11:57, "nek5000-users at lists.mcs.anl.gov " > wrote: Hi Neks, ? We are carrying out an optimization study on IBM Blue Gene/Q server of IDRIS using direct-adjoint method. The direct and adjoint equations are solved using Nek5000. We have observed that for moderate to large number of processors? Nek5000 spends considerable time in reading the .rea file. When we reduce the number of processors, the .rea file is read in lesser time but the time taken for solver increases. To give an idea, a 3D case for incompressible flow with 12000 elements spends 22.132 seconds in reading .rea file if we use 400 processors. If we increase the number of processors to 1000, it takes more than 90 seconds to read the same .rea file. Can someone provide us a solution on how to make Nek read the rea file quickly? Would using .re2 file instead of .rea increase the performance considering the number of elements is not very large.? I would like to mention that we are using PPLIST="MPIIO" in the makenek file. Many thanks. _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 16 10:09:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 16 May 2017 17:09:52 +0200 Subject: [Nek5000-users] Pressure BC in PN-PN Message-ID: Dear Neks, In a 3D simulation, is it possible to specify Dirichlet conditions for two components of velocity and pressure on one side of the computational domain? Is this combination physically consistent? We are doing coupled simulations using Nek-Nek, and possibility of specifying this condition will simplify many things. Thank you, Regards, Sudhakar From nek5000-users at lists.mcs.anl.gov Wed May 17 02:08:45 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 17 May 2017 09:08:45 +0200 Subject: [Nek5000-users] Reading rea file on IBM Blue Gene/Q server In-Reply-To: References: Message-ID: Thank you very much. Using .re2 instead of .rea brought down the time from 27 sec to 0.8 sec. On Tuesday 16 May 2017 12:56 PM, nek5000-users at lists.mcs.anl.gov wrote: > For performance use .re2 and the latest master available on GitHub. > > On 16 May 2017, at 11:57, "nek5000-users at lists.mcs.anl.gov > " > > wrote: > >> Hi Neks, >> >> We are carrying out an optimization study on IBM Blue Gene/Q server >> of IDRIS using direct-adjoint method. The direct and adjoint equations >> are solved using Nek5000. We have observed that for moderate to large >> number of >> processors Nek5000 spends considerable time in reading the .rea file. >> When we reduce the number of processors, the .rea file is read in lesser >> time but >> the time taken for solver increases. To give an idea, a 3D case for >> incompressible flow >> with 12000 elements spends 22.132 seconds in reading .rea file if we use >> 400 processors. If we increase the number of processors to 1000, it >> takes more than >> 90 seconds to read the same .rea file. Can someone provide us a >> solution on >> how to make Nek read the rea file quickly? Would using .re2 file instead >> of .rea increase >> the performance considering the number of elements is not very large.? >> I would like to mention that we are using PPLIST="MPIIO" in the makenek >> file. >> >> Many thanks. >> >> >> >> _______________________________________________ >> 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 May 18 09:02:06 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:02:06 +0200 Subject: [Nek5000-users] Problem in using .re2 file Message-ID: Hi Neks, I have encountered a problem while using .re2 file. When I use it, I get the following warning in the output file and the code hangs up. WARNINGb: Detected non-right-handed element. Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 .0000E+00 WARNINGb: Detected non-right-handed element. WARNINGb: Detected non-right-handed element. If, however, I use the full ASCII .rea file, the code runs fine. What could be the problem in using .re2 file? Kindly suggest a remedy. I would like to mention that first I create the full ASCII .rea file and generate the .map file from it. Then, I use the executable "reatore2" to make the .re2 file and smaller ASCII .rea file. I do not make any change in the smaller ASCII .rea file. Many thanks, NN. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 18 09:06:41 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:06:41 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: How do you generate your mesh/rea? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 18th May 2017 16:02 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Problem in using .re2 file > > Hi Neks, > ?I have encountered a problem while using .re2 file. When I use > it, > I get the following warning in the output file and the code hangs > up. > ? ? WARNINGb: Detected non-right-handed element. > ? Number?? 14621? V1-8:? -.1290E+21?? .0000E+00?? .6991E+01?? > .0000E+00 > ? WARNINGb: Detected non-right-handed element. > ? WARNINGb: Detected non-right-handed element. > If, however, I use the full ASCII? .rea file, the code runs fine. > What > could be the problem in using .re2 file? Kindly suggest a remedy. > I would like to mention that first I create the full ASCII .rea > file and generate > the .map file from it. Then, I use the executable "reatore2" to > make the > .re2 file and smaller ASCII .rea file. I do not make any change in > the smaller > ASCII .rea file. > Many thanks, > NN. > _______________________________________________ > 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 May 18 09:13:08 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:13:08 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: I have prepared the mesh using GAMBIT. Then using a converter I generated the .rea file in ASCII format. This .rea file works fine with NEK5000. However, when I convert to .re2 the problem shows up... On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > How do you generate your mesh/rea? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 18th May 2017 16:02 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] Problem in using .re2 file >> >> Hi Neks, >> I have encountered a problem while using .re2 file. When I use >> it, >> I get the following warning in the output file and the code hangs >> up. >> WARNINGb: Detected non-right-handed element. >> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 >> .0000E+00 >> WARNINGb: Detected non-right-handed element. >> WARNINGb: Detected non-right-handed element. >> If, however, I use the full ASCII .rea file, the code runs fine. >> What >> could be the problem in using .re2 file? Kindly suggest a remedy. >> I would like to mention that first I create the full ASCII .rea >> file and generate >> the .map file from it. Then, I use the executable "reatore2" to >> make the >> .re2 file and smaller ASCII .rea file. I do not make any change in >> the smaller >> ASCII .rea file. >> Many thanks, >> NN. >> _______________________________________________ >> 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 May 18 09:19:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:19:49 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Can you please post your .rea file -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 18th May 2017 16:13 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Problem in using .re2 file > > I have prepared the mesh using GAMBIT. Then using a converter I generated > the .rea file in ASCII format. This .rea file works fine with NEK5000. > However, > when I convert to .re2 the problem shows up... > > > On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > > How do you generate your mesh/rea? > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Thursday 18th May 2017 16:02 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: [Nek5000-users] Problem in using .re2 file > >> > >> Hi Neks, > >> I have encountered a problem while using .re2 file. When I use > >> it, > >> I get the following warning in the output file and the code hangs > >> up. > >> WARNINGb: Detected non-right-handed element. > >> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 > >> .0000E+00 > >> WARNINGb: Detected non-right-handed element. > >> WARNINGb: Detected non-right-handed element. > >> If, however, I use the full ASCII .rea file, the code runs fine. > >> What > >> could be the problem in using .re2 file? Kindly suggest a remedy. > >> I would like to mention that first I create the full ASCII .rea > >> file and generate > >> the .map file from it. Then, I use the executable "reatore2" to > >> make the > >> .re2 file and smaller ASCII .rea file. I do not make any change in > >> the smaller > >> ASCII .rea file. > >> Many thanks, > >> NN. > >> _______________________________________________ > >> 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 Thu May 18 09:25:18 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:25:18 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Please attached the .rea file. This is the smaller version (generated with the .re2 file). Please let me know if you want the full version as well. Thanks for your time. NN. On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: > Can you please post your .rea file > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 18th May 2017 16:13 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Problem in using .re2 file >> >> I have prepared the mesh using GAMBIT. Then using a converter I generated >> the .rea file in ASCII format. This .rea file works fine with NEK5000. >> However, >> when I convert to .re2 the problem shows up... >> >> >> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> How do you generate your mesh/rea? >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Thursday 18th May 2017 16:02 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: [Nek5000-users] Problem in using .re2 file >>>> >>>> Hi Neks, >>>> I have encountered a problem while using .re2 file. When I use >>>> it, >>>> I get the following warning in the output file and the code hangs >>>> up. >>>> WARNINGb: Detected non-right-handed element. >>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 >>>> .0000E+00 >>>> WARNINGb: Detected non-right-handed element. >>>> WARNINGb: Detected non-right-handed element. >>>> If, however, I use the full ASCII .rea file, the code runs fine. >>>> What >>>> could be the problem in using .re2 file? Kindly suggest a remedy. >>>> I would like to mention that first I create the full ASCII .rea >>>> file and generate >>>> the .map file from it. Then, I use the executable "reatore2" to >>>> make the >>>> .re2 file and smaller ASCII .rea file. I do not make any change in >>>> the smaller >>>> ASCII .rea file. >>>> Many thanks, >>>> NN. >>>> _______________________________________________ >>>> 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 -------------- ****** PARAMETERS ***** 2.610000 NEKTON VERSION 3 DIMENSIONAL RUN 103 PARAMETERS FOLLOW 1.00000 p1 DENSITY -100.00 p2 VISCOS 0. 0. 0. 0. 1.00000 p7 RHOCP 1.00000 p8 CONDUCT 0. 0. p10 FINTIME 80000.0 p11 NSTEPS -0.0015 p12 DT 0. p13 IOCOMM 0. p14 IOTIME 500.000 p15 IOSTEP 0. p16 PSSOLVER 0. 0.250000E-01 p18 GRID -1.00000 p19 INTYPE 7.0000 p20 NORDER 0.100000E-10 p21 DIVERGENCE 0.100000E-11 p22 HELMHOLTZ 0 p23 NPSCAL 0.100000E-09 p24 TOLREL 0.100000E-09 p25 TOLABS 5.00000 p26 COURANT/NTAU 2.00000 p27 TORDER 0. p28 TORDER: mesh velocity (0: p28=p27) 0. p29 magnetic visc if > 0, = -1/Rm if < 0 0. p30 > 0 ==> properties set in uservp() -1. p31 NPERT: #perturbation modes 0. p32 #BCs in re2 file, if > 0 0. 0. 0. 0. 0. 0. 0. 0. 0. p41 1-->multiplicative SEMG 0. p42 0=gmres/1=pcg 0.00000 p43 0=semg/1=schwarz 0. p44 0=E-based/1=A-based prec. 0. p45 Relaxation factor for DTFS 0. p46 reserved 0. p47 vnu: mesh matieral prop 0. 0. 0. 0. 0. p52 IOHIS 0. 0. p54 1,2,3-->fixed flow rate dir=x,y,z 0. p55 vol.flow rate (p54>0) or Ubar (p54<0) 0. 0. 0. 0. p59 !=0 --> full Jac. eval. for each el. 0. p60 !=0 --> init. velocity to small nonzero 0. 0. p62 >0 --> force byte_swap for output 0. p63 =8 --> force 8-byte output 0. p64 =1 --> perturbation restart 1. p65 #iofiles (eg, 0 or 64); <0 --> sep. dirs 4.000 p66 output : <0=ascii, else binary 4.000 p67 restart: <0=ascii, else binary 0. p68 iastep: freq for avg_all 0. 0. 0. 0. 0. 0. p74 verbose Helmholtz 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. p84 !=0 --> sets initial timestep if p12>0 0. p85 dt ratio if p84 !=0, for timesteps>0 0. p86 reserved 0. 0. 0. 0. 0. 0. 20.0000 p93 Number of previous pressure solns saved 5.00000 p94 start projecting velocity after p94 step 3.00000 p95 start projecting pressure after p95 step 0.00000 p96 u0 translational velocity (in .usr) 0.00000 p97 v0 translational velocity (in .usr) 0. 4.00000 p99 dealiasing: <0--> off/3--> old/4--> new 0. 0. p101 No. of additional filter modes 1.00000 p102 Dump out divergence at each time step .000 p103 weight of stabilizing filter (.01) 4 Lines of passive scalar data follows2 CONDUCT; 2RHOCP 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 13 LOGICAL SWITCHES FOLLOW T IFFLOW F IFHEAT T IFTRAN T F F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) F IFAXIS F IFSTRS F IFSPLIT F IFMGRID F IFMODEL F IFKEPS F IFMVBD F IFCHAR 8.00000 8.00000 -0.500000 -4.00000 XFAC,YFAC,XZERO,YZERO **MESH DATA** 6 lines are X,Y,Z;X,Y,Z. Columns corners 1-4;5-8 -21336 3 21336 NELT,NDIM,NELV 0 PRESOLVE/RESTART OPTIONS ***** 7 INITIAL CONDITIONS ***** C Default C Default C Default C Default C Default C Default C Default ***** DRIVE FORCE DATA ***** BODY FORCE, FLOW, Q 4 Lines of Drive force data follow C C C C ***** Variable Property Data ***** Overrrides Parameter data. 1 Lines follow. 0 PACKETS OF DATA FOLLOW ***** HISTORY AND INTEGRAL DATA ***** 0 POINTS. Hcode, I,J,H,IEL ***** OUTPUT FIELD SPECIFICATION ***** 6 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE F TEMPERATURE F TEMPERATURE GRADIENT 0 PASSIVE SCALARS ***** OBJECT SPECIFICATION ***** 0 Surface Objects 0 Volume Objects 0 Edge Objects 0 Point Object From nek5000-users at lists.mcs.anl.gov Thu May 18 09:31:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:31:52 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: I am looking for the ASCII file containing the mesh. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 18th May 2017 16:24 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Problem in using .re2 file > > Please attached the .rea file. This is the smaller version (generated > with the .re2 file). Please let me know if you want the full version as > well. > > Thanks for your time. > > NN. > > > On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Can you please post your .rea file > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Thursday 18th May 2017 16:13 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] Problem in using .re2 file > >> > >> I have prepared the mesh using GAMBIT. Then using a converter I generated > >> the .rea file in ASCII format. This .rea file works fine with NEK5000. > >> However, > >> when I convert to .re2 the problem shows up... > >> > >> > >> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > >>> How do you generate your mesh/rea? > >>> > >>> -----Original message----- > >>>> From:nek5000-users at lists.mcs.anl.gov > >>>> Sent: Thursday 18th May 2017 16:02 > >>>> To: nek5000-users at lists.mcs.anl.gov > >>>> Subject: [Nek5000-users] Problem in using .re2 file > >>>> > >>>> Hi Neks, > >>>> I have encountered a problem while using .re2 file. When I use > >>>> it, > >>>> I get the following warning in the output file and the code hangs > >>>> up. > >>>> WARNINGb: Detected non-right-handed element. > >>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 > >>>> .0000E+00 > >>>> WARNINGb: Detected non-right-handed element. > >>>> WARNINGb: Detected non-right-handed element. > >>>> If, however, I use the full ASCII .rea file, the code runs fine. > >>>> What > >>>> could be the problem in using .re2 file? Kindly suggest a remedy. > >>>> I would like to mention that first I create the full ASCII .rea > >>>> file and generate > >>>> the .map file from it. Then, I use the executable "reatore2" to > >>>> make the > >>>> .re2 file and smaller ASCII .rea file. I do not make any change in > >>>> the smaller > >>>> ASCII .rea file. > >>>> Many thanks, > >>>> NN. > >>>> _______________________________________________ > >>>> 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 Thu May 18 09:37:21 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 18 May 2017 16:37:21 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Please find attached a compressed folder that contains the ASCII file with mesh. NN. On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov wrote: > I am looking for the ASCII file containing the mesh. > > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 18th May 2017 16:24 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Problem in using .re2 file >> >> Please attached the .rea file. This is the smaller version (generated >> with the .re2 file). Please let me know if you want the full version as >> well. >> >> Thanks for your time. >> >> NN. >> >> >> On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> Can you please post your .rea file >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Thursday 18th May 2017 16:13 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>> >>>> I have prepared the mesh using GAMBIT. Then using a converter I generated >>>> the .rea file in ASCII format. This .rea file works fine with NEK5000. >>>> However, >>>> when I convert to .re2 the problem shows up... >>>> >>>> >>>> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>> How do you generate your mesh/rea? >>>>> >>>>> -----Original message----- >>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>> Sent: Thursday 18th May 2017 16:02 >>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>> Subject: [Nek5000-users] Problem in using .re2 file >>>>>> >>>>>> Hi Neks, >>>>>> I have encountered a problem while using .re2 file. When I use >>>>>> it, >>>>>> I get the following warning in the output file and the code hangs >>>>>> up. >>>>>> WARNINGb: Detected non-right-handed element. >>>>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 >>>>>> .0000E+00 >>>>>> WARNINGb: Detected non-right-handed element. >>>>>> WARNINGb: Detected non-right-handed element. >>>>>> If, however, I use the full ASCII .rea file, the code runs fine. >>>>>> What >>>>>> could be the problem in using .re2 file? Kindly suggest a remedy. >>>>>> I would like to mention that first I create the full ASCII .rea >>>>>> file and generate >>>>>> the .map file from it. Then, I use the executable "reatore2" to >>>>>> make the >>>>>> .re2 file and smaller ASCII .rea file. I do not make any change in >>>>>> the smaller >>>>>> ASCII .rea file. >>>>>> Many thanks, >>>>>> NN. >>>>>> _______________________________________________ >>>>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: REA.tar.gz Type: application/x-gzip Size: 1404270 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri May 19 04:50:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 11:50:29 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: I just ran reatore2 and the resulting .re2 file works for me. Are you using the latest master available on GitHub or an older version? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 18th May 2017 16:37 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Problem in using .re2 file > > Please find attached a compressed folder that contains > the ASCII file with mesh. > > NN. > > > On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov wrote: > > I am looking for the ASCII file containing the mesh. > > > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Thursday 18th May 2017 16:24 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] Problem in using .re2 file > >> > >> Please attached the .rea file. This is the smaller version (generated > >> with the .re2 file). Please let me know if you want the full version as > >> well. > >> > >> Thanks for your time. > >> > >> NN. > >> > >> > >> On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: > >>> Can you please post your .rea file > >>> > >>> -----Original message----- > >>>> From:nek5000-users at lists.mcs.anl.gov > >>>> Sent: Thursday 18th May 2017 16:13 > >>>> To: nek5000-users at lists.mcs.anl.gov > >>>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>>> > >>>> I have prepared the mesh using GAMBIT. Then using a converter I generated > >>>> the .rea file in ASCII format. This .rea file works fine with NEK5000. > >>>> However, > >>>> when I convert to .re2 the problem shows up... > >>>> > >>>> > >>>> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > >>>>> How do you generate your mesh/rea? > >>>>> > >>>>> -----Original message----- > >>>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>>> Sent: Thursday 18th May 2017 16:02 > >>>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>>> Subject: [Nek5000-users] Problem in using .re2 file > >>>>>> > >>>>>> Hi Neks, > >>>>>> I have encountered a problem while using .re2 file. When I use > >>>>>> it, > >>>>>> I get the following warning in the output file and the code hangs > >>>>>> up. > >>>>>> WARNINGb: Detected non-right-handed element. > >>>>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 > >>>>>> .0000E+00 > >>>>>> WARNINGb: Detected non-right-handed element. > >>>>>> WARNINGb: Detected non-right-handed element. > >>>>>> If, however, I use the full ASCII .rea file, the code runs fine. > >>>>>> What > >>>>>> could be the problem in using .re2 file? Kindly suggest a remedy. > >>>>>> I would like to mention that first I create the full ASCII .rea > >>>>>> file and generate > >>>>>> the .map file from it. Then, I use the executable "reatore2" to > >>>>>> make the > >>>>>> .re2 file and smaller ASCII .rea file. I do not make any change in > >>>>>> the smaller > >>>>>> ASCII .rea file. > >>>>>> Many thanks, > >>>>>> NN. > >>>>>> _______________________________________________ > >>>>>> 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 > > _______________________________________________ > 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 May 19 05:00:35 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 12:00:35 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Thanks for your time. I am using an older version of NEK5000. To switch to the new version I might have to make significant changes to some of the new core files. The changes were made by earlier members of the research group in the old version. Is it possible to use .re2 using an older version of NEK5000 by simply replacing some subroutines with new one? NN. On Friday 19 May 2017 11:50 AM, nek5000-users at lists.mcs.anl.gov wrote: > I just ran reatore2 and the resulting .re2 file works for me. Are you using the latest master available on GitHub or an older version? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 18th May 2017 16:37 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Problem in using .re2 file >> >> Please find attached a compressed folder that contains >> the ASCII file with mesh. >> >> NN. >> >> >> On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> I am looking for the ASCII file containing the mesh. >>> >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Thursday 18th May 2017 16:24 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>> >>>> Please attached the .rea file. This is the smaller version (generated >>>> with the .re2 file). Please let me know if you want the full version as >>>> well. >>>> >>>> Thanks for your time. >>>> >>>> NN. >>>> >>>> >>>> On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>> Can you please post your .rea file >>>>> >>>>> -----Original message----- >>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>> Sent: Thursday 18th May 2017 16:13 >>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>> >>>>>> I have prepared the mesh using GAMBIT. Then using a converter I generated >>>>>> the .rea file in ASCII format. This .rea file works fine with NEK5000. >>>>>> However, >>>>>> when I convert to .re2 the problem shows up... >>>>>> >>>>>> >>>>>> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>>>> How do you generate your mesh/rea? >>>>>>> >>>>>>> -----Original message----- >>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>> Sent: Thursday 18th May 2017 16:02 >>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>> Subject: [Nek5000-users] Problem in using .re2 file >>>>>>>> >>>>>>>> Hi Neks, >>>>>>>> I have encountered a problem while using .re2 file. When I use >>>>>>>> it, >>>>>>>> I get the following warning in the output file and the code hangs >>>>>>>> up. >>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 >>>>>>>> .0000E+00 >>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>> If, however, I use the full ASCII .rea file, the code runs fine. >>>>>>>> What >>>>>>>> could be the problem in using .re2 file? Kindly suggest a remedy. >>>>>>>> I would like to mention that first I create the full ASCII .rea >>>>>>>> file and generate >>>>>>>> the .map file from it. Then, I use the executable "reatore2" to >>>>>>>> make the >>>>>>>> .re2 file and smaller ASCII .rea file. I do not make any change in >>>>>>>> the smaller >>>>>>>> ASCII .rea file. >>>>>>>> Many thanks, >>>>>>>> NN. >>>>>>>> _______________________________________________ >>>>>>>> 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 >> _______________________________________________ >> 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 May 19 05:02:24 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 12:02:24 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Try to use reatore2 from the latest master and use the .re2 with the old Nek5000 version. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 19th May 2017 12:00 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Problem in using .re2 file > > Thanks for your time. I am using an older version of NEK5000. > To switch to the new version I might have to make significant > changes to some of the new core files. The changes were made by > earlier members of the research group in the old version. > > Is it possible to use .re2 using an older version of NEK5000 by > simply replacing some subroutines with new one? > > NN. > > On Friday 19 May 2017 11:50 AM, nek5000-users at lists.mcs.anl.gov wrote: > > I just ran reatore2 and the resulting .re2 file works for me. Are you using the latest master available on GitHub or an older version? > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Thursday 18th May 2017 16:37 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] Problem in using .re2 file > >> > >> Please find attached a compressed folder that contains > >> the ASCII file with mesh. > >> > >> NN. > >> > >> > >> On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov wrote: > >>> I am looking for the ASCII file containing the mesh. > >>> > >>> > >>> -----Original message----- > >>>> From:nek5000-users at lists.mcs.anl.gov > >>>> Sent: Thursday 18th May 2017 16:24 > >>>> To: nek5000-users at lists.mcs.anl.gov > >>>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>>> > >>>> Please attached the .rea file. This is the smaller version (generated > >>>> with the .re2 file). Please let me know if you want the full version as > >>>> well. > >>>> > >>>> Thanks for your time. > >>>> > >>>> NN. > >>>> > >>>> > >>>> On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: > >>>>> Can you please post your .rea file > >>>>> > >>>>> -----Original message----- > >>>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>>> Sent: Thursday 18th May 2017 16:13 > >>>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>>>>> > >>>>>> I have prepared the mesh using GAMBIT. Then using a converter I generated > >>>>>> the .rea file in ASCII format. This .rea file works fine with NEK5000. > >>>>>> However, > >>>>>> when I convert to .re2 the problem shows up... > >>>>>> > >>>>>> > >>>>>> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: > >>>>>>> How do you generate your mesh/rea? > >>>>>>> > >>>>>>> -----Original message----- > >>>>>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>>>>> Sent: Thursday 18th May 2017 16:02 > >>>>>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>>>>> Subject: [Nek5000-users] Problem in using .re2 file > >>>>>>>> > >>>>>>>> Hi Neks, > >>>>>>>> I have encountered a problem while using .re2 file. When I use > >>>>>>>> it, > >>>>>>>> I get the following warning in the output file and the code hangs > >>>>>>>> up. > >>>>>>>> WARNINGb: Detected non-right-handed element. > >>>>>>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 > >>>>>>>> .0000E+00 > >>>>>>>> WARNINGb: Detected non-right-handed element. > >>>>>>>> WARNINGb: Detected non-right-handed element. > >>>>>>>> If, however, I use the full ASCII .rea file, the code runs fine. > >>>>>>>> What > >>>>>>>> could be the problem in using .re2 file? Kindly suggest a remedy. > >>>>>>>> I would like to mention that first I create the full ASCII .rea > >>>>>>>> file and generate > >>>>>>>> the .map file from it. Then, I use the executable "reatore2" to > >>>>>>>> make the > >>>>>>>> .re2 file and smaller ASCII .rea file. I do not make any change in > >>>>>>>> the smaller > >>>>>>>> ASCII .rea file. > >>>>>>>> Many thanks, > >>>>>>>> NN. > >>>>>>>> _______________________________________________ > >>>>>>>> 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 > >> _______________________________________________ > >> 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 May 19 05:22:59 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 12:22:59 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Thanks. I will do this and get back to the list in case I run into any problem. NN. On Friday 19 May 2017 12:02 PM, nek5000-users at lists.mcs.anl.gov wrote: > Try to use reatore2 from the latest master and use the .re2 with the old Nek5000 version. > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 19th May 2017 12:00 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Problem in using .re2 file >> >> Thanks for your time. I am using an older version of NEK5000. >> To switch to the new version I might have to make significant >> changes to some of the new core files. The changes were made by >> earlier members of the research group in the old version. >> >> Is it possible to use .re2 using an older version of NEK5000 by >> simply replacing some subroutines with new one? >> >> NN. >> >> On Friday 19 May 2017 11:50 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> I just ran reatore2 and the resulting .re2 file works for me. Are you using the latest master available on GitHub or an older version? >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Thursday 18th May 2017 16:37 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>> >>>> Please find attached a compressed folder that contains >>>> the ASCII file with mesh. >>>> >>>> NN. >>>> >>>> >>>> On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>> I am looking for the ASCII file containing the mesh. >>>>> >>>>> >>>>> -----Original message----- >>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>> Sent: Thursday 18th May 2017 16:24 >>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>> >>>>>> Please attached the .rea file. This is the smaller version (generated >>>>>> with the .re2 file). Please let me know if you want the full version as >>>>>> well. >>>>>> >>>>>> Thanks for your time. >>>>>> >>>>>> NN. >>>>>> >>>>>> >>>>>> On Thursday 18 May 2017 04:19 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>>>> Can you please post your .rea file >>>>>>> >>>>>>> -----Original message----- >>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>> Sent: Thursday 18th May 2017 16:13 >>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>>>> >>>>>>>> I have prepared the mesh using GAMBIT. Then using a converter I generated >>>>>>>> the .rea file in ASCII format. This .rea file works fine with NEK5000. >>>>>>>> However, >>>>>>>> when I convert to .re2 the problem shows up... >>>>>>>> >>>>>>>> >>>>>>>> On Thursday 18 May 2017 04:06 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>>>>>> How do you generate your mesh/rea? >>>>>>>>> >>>>>>>>> -----Original message----- >>>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>>> Sent: Thursday 18th May 2017 16:02 >>>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>>> Subject: [Nek5000-users] Problem in using .re2 file >>>>>>>>>> >>>>>>>>>> Hi Neks, >>>>>>>>>> I have encountered a problem while using .re2 file. When I use >>>>>>>>>> it, >>>>>>>>>> I get the following warning in the output file and the code hangs >>>>>>>>>> up. >>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>> Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 >>>>>>>>>> .0000E+00 >>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>> If, however, I use the full ASCII .rea file, the code runs fine. >>>>>>>>>> What >>>>>>>>>> could be the problem in using .re2 file? Kindly suggest a remedy. >>>>>>>>>> I would like to mention that first I create the full ASCII .rea >>>>>>>>>> file and generate >>>>>>>>>> the .map file from it. Then, I use the executable "reatore2" to >>>>>>>>>> make the >>>>>>>>>> .re2 file and smaller ASCII .rea file. I do not make any change in >>>>>>>>>> the smaller >>>>>>>>>> ASCII .rea file. >>>>>>>>>> Many thanks, >>>>>>>>>> NN. >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>> _______________________________________________ >>>> 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 Fri May 19 05:45:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 12:45:49 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: I am getting the same problem of "non-right handed elements" even if I use reatore2 from the latest master. NN. On Friday 19 May 2017 12:22 PM, nek5000-users at lists.mcs.anl.gov wrote: > Thanks. I will do this and get back to the list in case I run into any > problem. > > NN. > > > On Friday 19 May 2017 12:02 PM, nek5000-users at lists.mcs.anl.gov wrote: >> Try to use reatore2 from the latest master and use the .re2 with the >> old Nek5000 version. >> >> -----Original message----- >>> From:nek5000-users at lists.mcs.anl.gov >>> Sent: Friday 19th May 2017 12:00 >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>> >>> Thanks for your time. I am using an older version of NEK5000. >>> To switch to the new version I might have to make significant >>> changes to some of the new core files. The changes were made by >>> earlier members of the research group in the old version. >>> >>> Is it possible to use .re2 using an older version of NEK5000 by >>> simply replacing some subroutines with new one? >>> >>> NN. >>> >>> On Friday 19 May 2017 11:50 AM, nek5000-users at lists.mcs.anl.gov wrote: >>>> I just ran reatore2 and the resulting .re2 file works for me. Are >>>> you using the latest master available on GitHub or an older version? >>>> >>>> -----Original message----- >>>>> From:nek5000-users at lists.mcs.anl.gov >>>>> >>>>> Sent: Thursday 18th May 2017 16:37 >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>> >>>>> Please find attached a compressed folder that contains >>>>> the ASCII file with mesh. >>>>> >>>>> NN. >>>>> >>>>> >>>>> On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov >>>>> wrote: >>>>>> I am looking for the ASCII file containing the mesh. >>>>>> >>>>>> -----Original message----- >>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>> >>>>>>> Sent: Thursday 18th May 2017 16:24 >>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>>> >>>>>>> Please attached the .rea file. This is the smaller version >>>>>>> (generated >>>>>>> with the .re2 file). Please let me know if you want the full >>>>>>> version as >>>>>>> well. >>>>>>> >>>>>>> Thanks for your time. >>>>>>> >>>>>>> NN. >>>>>>> >>>>>>> >>>>>>> On Thursday 18 May 2017 04:19 PM, >>>>>>> nek5000-users at lists.mcs.anl.gov wrote: >>>>>>>> Can you please post your .rea file >>>>>>>> -----Original message----- >>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>> >>>>>>>>> Sent: Thursday 18th May 2017 16:13 >>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>>>>> >>>>>>>>> I have prepared the mesh using GAMBIT. Then using a converter >>>>>>>>> I generated >>>>>>>>> the .rea file in ASCII format. This .rea file works fine with >>>>>>>>> NEK5000. >>>>>>>>> However, >>>>>>>>> when I convert to .re2 the problem shows up... >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thursday 18 May 2017 04:06 PM, >>>>>>>>> nek5000-users at lists.mcs.anl.gov wrote: >>>>>>>>>> How do you generate your mesh/rea? >>>>>>>>>> -----Original message----- >>>>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>>>> >>>>>>>>>>> Sent: Thursday 18th May 2017 16:02 >>>>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>>>> Subject: [Nek5000-users] Problem in using .re2 file >>>>>>>>>>> >>>>>>>>>>> Hi Neks, >>>>>>>>>>> I have encountered a problem while using .re2 file. >>>>>>>>>>> When I use >>>>>>>>>>> it, >>>>>>>>>>> I get the following warning in the output file >>>>>>>>>>> and the code hangs >>>>>>>>>>> up. >>>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>>> Number 14621 V1-8: -.1290E+21 >>>>>>>>>>> .0000E+00 .6991E+01 >>>>>>>>>>> .0000E+00 >>>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>>> If, however, I use the full ASCII .rea file, the code runs >>>>>>>>>>> fine. >>>>>>>>>>> What >>>>>>>>>>> could be the problem in using .re2 file? Kindly >>>>>>>>>>> suggest a remedy. >>>>>>>>>>> I would like to mention that first I create the full ASCII .rea >>>>>>>>>>> file and generate >>>>>>>>>>> the .map file from it. Then, I use the executable >>>>>>>>>>> "reatore2" to >>>>>>>>>>> make the >>>>>>>>>>> .re2 file and smaller ASCII .rea file. I do not >>>>>>>>>>> make any change in >>>>>>>>>>> the smaller >>>>>>>>>>> ASCII .rea file. >>>>>>>>>>> Many thanks, >>>>>>>>>>> NN. >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>> _______________________________________________ >>>>> 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 Fri May 19 05:48:39 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 12:48:39 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: Can you run the .re2 file with the latest master. Just to double check if this really cures your problem. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 19th May 2017 12:44 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Problem in using .re2 file > > I am getting the same problem of "non-right handed elements" even if > I use reatore2 from the latest master. > > NN. > > > On Friday 19 May 2017 12:22 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Thanks. I will do this and get back to the list in case I run into any > > problem. > > > > NN. > > > > > > On Friday 19 May 2017 12:02 PM, nek5000-users at lists.mcs.anl.gov wrote: > >> Try to use reatore2 from the latest master and use the .re2 with the > >> old Nek5000 version. > >> > >> -----Original message----- > >>> From:nek5000-users at lists.mcs.anl.gov > >>> Sent: Friday 19th May 2017 12:00 > >>> To: nek5000-users at lists.mcs.anl.gov > >>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>> > >>> Thanks for your time. I am using an older version of NEK5000. > >>> To switch to the new version I might have to make significant > >>> changes to some of the new core files. The changes were made by > >>> earlier members of the research group in the old version. > >>> > >>> Is it possible to use .re2 using an older version of NEK5000 by > >>> simply replacing some subroutines with new one? > >>> > >>> NN. > >>> > >>> On Friday 19 May 2017 11:50 AM, nek5000-users at lists.mcs.anl.gov wrote: > >>>> I just ran reatore2 and the resulting .re2 file works for me. Are > >>>> you using the latest master available on GitHub or an older version? > >>>> > >>>> -----Original message----- > >>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>> > >>>>> Sent: Thursday 18th May 2017 16:37 > >>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>>>> > >>>>> Please find attached a compressed folder that contains > >>>>> the ASCII file with mesh. > >>>>> > >>>>> NN. > >>>>> > >>>>> > >>>>> On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov > >>>>> wrote: > >>>>>> I am looking for the ASCII file containing the mesh. > >>>>>> > >>>>>> -----Original message----- > >>>>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>>>> > >>>>>>> Sent: Thursday 18th May 2017 16:24 > >>>>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>>>>>> > >>>>>>> Please attached the .rea file. This is the smaller version > >>>>>>> (generated > >>>>>>> with the .re2 file). Please let me know if you want the full > >>>>>>> version as > >>>>>>> well. > >>>>>>> > >>>>>>> Thanks for your time. > >>>>>>> > >>>>>>> NN. > >>>>>>> > >>>>>>> > >>>>>>> On Thursday 18 May 2017 04:19 PM, > >>>>>>> nek5000-users at lists.mcs.anl.gov wrote: > >>>>>>>> Can you please post your .rea file > >>>>>>>> -----Original message----- > >>>>>>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>>>>>> > >>>>>>>>> Sent: Thursday 18th May 2017 16:13 > >>>>>>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file > >>>>>>>>> > >>>>>>>>> I have prepared the mesh using GAMBIT. Then using a converter > >>>>>>>>> I generated > >>>>>>>>> the .rea file in ASCII format. This .rea file works fine with > >>>>>>>>> NEK5000. > >>>>>>>>> However, > >>>>>>>>> when I convert to .re2 the problem shows up... > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> On Thursday 18 May 2017 04:06 PM, > >>>>>>>>> nek5000-users at lists.mcs.anl.gov wrote: > >>>>>>>>>> How do you generate your mesh/rea? > >>>>>>>>>> -----Original message----- > >>>>>>>>>>> From:nek5000-users at lists.mcs.anl.gov > >>>>>>>>>>> > >>>>>>>>>>> Sent: Thursday 18th May 2017 16:02 > >>>>>>>>>>> To: nek5000-users at lists.mcs.anl.gov > >>>>>>>>>>> Subject: [Nek5000-users] Problem in using .re2 file > >>>>>>>>>>> > >>>>>>>>>>> Hi Neks, > >>>>>>>>>>> I have encountered a problem while using .re2 file. > >>>>>>>>>>> When I use > >>>>>>>>>>> it, > >>>>>>>>>>> I get the following warning in the output file > >>>>>>>>>>> and the code hangs > >>>>>>>>>>> up. > >>>>>>>>>>> WARNINGb: Detected non-right-handed element. > >>>>>>>>>>> Number 14621 V1-8: -.1290E+21 > >>>>>>>>>>> .0000E+00 .6991E+01 > >>>>>>>>>>> .0000E+00 > >>>>>>>>>>> WARNINGb: Detected non-right-handed element. > >>>>>>>>>>> WARNINGb: Detected non-right-handed element. > >>>>>>>>>>> If, however, I use the full ASCII .rea file, the code runs > >>>>>>>>>>> fine. > >>>>>>>>>>> What > >>>>>>>>>>> could be the problem in using .re2 file? Kindly > >>>>>>>>>>> suggest a remedy. > >>>>>>>>>>> I would like to mention that first I create the full ASCII .rea > >>>>>>>>>>> file and generate > >>>>>>>>>>> the .map file from it. Then, I use the executable > >>>>>>>>>>> "reatore2" to > >>>>>>>>>>> make the > >>>>>>>>>>> .re2 file and smaller ASCII .rea file. I do not > >>>>>>>>>>> make any change in > >>>>>>>>>>> the smaller > >>>>>>>>>>> ASCII .rea file. > >>>>>>>>>>> Many thanks, > >>>>>>>>>>> NN. > >>>>>>>>>>> _______________________________________________ > >>>>>>>>>>> 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 > >>>>> _______________________________________________ > >>>>> 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 > From nek5000-users at lists.mcs.anl.gov Fri May 19 07:33:17 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 14:33:17 +0200 Subject: [Nek5000-users] Resolution problems at computation of the energy spectrum Message-ID: Hi Neks, I am currently performing DNS of a 3d periodic box. It seems I might have encountered a resolution problem while working on the spectral analysis of the velocity field. In short: The high wavenumber modes appear to be insufficiently resolved by the GLL points / polynomials causing effects similar to aliasing and therefore a significant distortion of the energy spectrum, which can also be observed away from the high wavenumber end. The comparison of my energy spectra with literature values revealed that the energy in the high wavenumber end is significantly underestimated. In order to make sure that this deviation is not caused by a bug in my post processing, I bypassed the routine by analyzing the NEK output of a simple test case in MATLAB. In this simple 3d 2pi box the velocity is initialized as vx=sin(30*x), vy=vz=0.0 on a grid with N=65 (nelx=8,lx1=9). The regular grid output (ifreguo=.true.) of this initial time step (zeroth time step - no equations were solved) was compared to sin(30*x). Here is a plot of this comparison http://imgur.com/a/2c1q5. The deviations lead to a redistribution of the energy among several modes. Currently I am wondering if there is any solution which allows for a computation of a less distorted energy spectrum without increasing the number of elements or polynomial order, and to subsequently cutting off the high modes. I already increased the number of equidistant grid points by increasing lxo to 1.5*lx1, however the quality of the energy spectrum is not improved as the interpolation deviates nonetheless. I am looking forward to helpful suggestions or an interesting discussion, Daniel From nek5000-users at lists.mcs.anl.gov Fri May 19 08:54:43 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 15:54:43 +0200 Subject: [Nek5000-users] Problem in using .re2 file In-Reply-To: References: Message-ID: I tried .re2 file with the latest master and it runs fine. So I guess the problem is with the older version of NEK5000. Now I have to track the modifications made by earlier members of my research group and implement them in new version. Thanks very much for your inputs. NN. On Friday 19 May 2017 12:48 PM, nek5000-users at lists.mcs.anl.gov wrote: > Can you run the .re2 file with the latest master. Just to double check if this really cures your problem. > > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 19th May 2017 12:44 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Problem in using .re2 file >> >> I am getting the same problem of "non-right handed elements" even if >> I use reatore2 from the latest master. >> >> NN. >> >> >> On Friday 19 May 2017 12:22 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> Thanks. I will do this and get back to the list in case I run into any >>> problem. >>> >>> NN. >>> >>> >>> On Friday 19 May 2017 12:02 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>> Try to use reatore2 from the latest master and use the .re2 with the >>>> old Nek5000 version. >>>> >>>> -----Original message----- >>>>> From:nek5000-users at lists.mcs.anl.gov >>>>> Sent: Friday 19th May 2017 12:00 >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>> >>>>> Thanks for your time. I am using an older version of NEK5000. >>>>> To switch to the new version I might have to make significant >>>>> changes to some of the new core files. The changes were made by >>>>> earlier members of the research group in the old version. >>>>> >>>>> Is it possible to use .re2 using an older version of NEK5000 by >>>>> simply replacing some subroutines with new one? >>>>> >>>>> NN. >>>>> >>>>> On Friday 19 May 2017 11:50 AM, nek5000-users at lists.mcs.anl.gov wrote: >>>>>> I just ran reatore2 and the resulting .re2 file works for me. Are >>>>>> you using the latest master available on GitHub or an older version? >>>>>> >>>>>> -----Original message----- >>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>> >>>>>>> Sent: Thursday 18th May 2017 16:37 >>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>>> >>>>>>> Please find attached a compressed folder that contains >>>>>>> the ASCII file with mesh. >>>>>>> >>>>>>> NN. >>>>>>> >>>>>>> >>>>>>> On Thursday 18 May 2017 04:31 PM, nek5000-users at lists.mcs.anl.gov >>>>>>> wrote: >>>>>>>> I am looking for the ASCII file containing the mesh. >>>>>>>> >>>>>>>> -----Original message----- >>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>> >>>>>>>>> Sent: Thursday 18th May 2017 16:24 >>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>>>>> >>>>>>>>> Please attached the .rea file. This is the smaller version >>>>>>>>> (generated >>>>>>>>> with the .re2 file). Please let me know if you want the full >>>>>>>>> version as >>>>>>>>> well. >>>>>>>>> >>>>>>>>> Thanks for your time. >>>>>>>>> >>>>>>>>> NN. >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thursday 18 May 2017 04:19 PM, >>>>>>>>> nek5000-users at lists.mcs.anl.gov wrote: >>>>>>>>>> Can you please post your .rea file >>>>>>>>>> -----Original message----- >>>>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>>>> >>>>>>>>>>> Sent: Thursday 18th May 2017 16:13 >>>>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>>>> Subject: Re: [Nek5000-users] Problem in using .re2 file >>>>>>>>>>> >>>>>>>>>>> I have prepared the mesh using GAMBIT. Then using a converter >>>>>>>>>>> I generated >>>>>>>>>>> the .rea file in ASCII format. This .rea file works fine with >>>>>>>>>>> NEK5000. >>>>>>>>>>> However, >>>>>>>>>>> when I convert to .re2 the problem shows up... >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thursday 18 May 2017 04:06 PM, >>>>>>>>>>> nek5000-users at lists.mcs.anl.gov wrote: >>>>>>>>>>>> How do you generate your mesh/rea? >>>>>>>>>>>> -----Original message----- >>>>>>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>>>>>> >>>>>>>>>>>>> Sent: Thursday 18th May 2017 16:02 >>>>>>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>>>>>> Subject: [Nek5000-users] Problem in using .re2 file >>>>>>>>>>>>> >>>>>>>>>>>>> Hi Neks, >>>>>>>>>>>>> I have encountered a problem while using .re2 file. >>>>>>>>>>>>> When I use >>>>>>>>>>>>> it, >>>>>>>>>>>>> I get the following warning in the output file >>>>>>>>>>>>> and the code hangs >>>>>>>>>>>>> up. >>>>>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>>>>> Number 14621 V1-8: -.1290E+21 >>>>>>>>>>>>> .0000E+00 .6991E+01 >>>>>>>>>>>>> .0000E+00 >>>>>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>>>>> WARNINGb: Detected non-right-handed element. >>>>>>>>>>>>> If, however, I use the full ASCII .rea file, the code runs >>>>>>>>>>>>> fine. >>>>>>>>>>>>> What >>>>>>>>>>>>> could be the problem in using .re2 file? Kindly >>>>>>>>>>>>> suggest a remedy. >>>>>>>>>>>>> I would like to mention that first I create the full ASCII .rea >>>>>>>>>>>>> file and generate >>>>>>>>>>>>> the .map file from it. Then, I use the executable >>>>>>>>>>>>> "reatore2" to >>>>>>>>>>>>> make the >>>>>>>>>>>>> .re2 file and smaller ASCII .rea file. I do not >>>>>>>>>>>>> make any change in >>>>>>>>>>>>> the smaller >>>>>>>>>>>>> ASCII .rea file. >>>>>>>>>>>>> Many thanks, >>>>>>>>>>>>> NN. >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> 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 >>>>>>> _______________________________________________ >>>>>>> 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 >> > _______________________________________________ > 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 May 19 08:57:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 13:57:52 +0000 Subject: [Nek5000-users] Resolution problems at computation of the energy spectrum In-Reply-To: References: Message-ID: David, You're at the marginally-resolved limit of the Nyquist sampling theorem. The only numerical method that will work in this regime is a Fourier one, and even then the quadratic nonlinearity will lead to aliasing or truncation of the higher wave numbers (depending on whether you dealias, or not; in Nek, we typically dealias, which implies truncation of the higher modes rather than aliasing of the same). Next point - all high-order polynomial based methods have a further under sampling that and be alternately viewed as a limit in the accuracy of the under-resolved modes --- The heuristic is that the Gauss points (all flavors) have a separation of pi/N in the middle of the reference domain [-1 1] as opposed to 2/N that you get for uniform points. The advantage gained is numerical stability and exponentially convergent dispersion for the resolved modes, which amounts to k_max < N/pi, instead of the usual Nyquist N/2. There have been many studies comparing Nek and spectral codes (e.g., ZENG, L., BALACHANDAR, S., & FISCHER, P. (2005). Wall-induced forces on a rigid sphere at finite Reynolds number. Journal of Fluid Mechanics, 536, 1-25. , for channel flows) -- There is no particular difficulty here provided you understand the resolution issues. hth, 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, May 19, 2017 7:33 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Resolution problems at computation of the energy spectrum Hi Neks, I am currently performing DNS of a 3d periodic box. It seems I might have encountered a resolution problem while working on the spectral analysis of the velocity field. In short: The high wavenumber modes appear to be insufficiently resolved by the GLL points / polynomials causing effects similar to aliasing and therefore a significant distortion of the energy spectrum, which can also be observed away from the high wavenumber end. The comparison of my energy spectra with literature values revealed that the energy in the high wavenumber end is significantly underestimated. In order to make sure that this deviation is not caused by a bug in my post processing, I bypassed the routine by analyzing the NEK output of a simple test case in MATLAB. In this simple 3d 2pi box the velocity is initialized as vx=sin(30*x), vy=vz=0.0 on a grid with N=65 (nelx=8,lx1=9). The regular grid output (ifreguo=.true.) of this initial time step (zeroth time step - no equations were solved) was compared to sin(30*x). Here is a plot of this comparison http://imgur.com/a/2c1q5. The deviations lead to a redistribution of the energy among several modes. Currently I am wondering if there is any solution which allows for a computation of a less distorted energy spectrum without increasing the number of elements or polynomial order, and to subsequently cutting off the high modes. I already increased the number of equidistant grid points by increasing lxo to 1.5*lx1, however the quality of the energy spectrum is not improved as the interpolation deviates nonetheless. I am looking forward to helpful suggestions or an interesting discussion, Daniel _______________________________________________ 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 May 19 14:51:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 19:51:02 +0000 Subject: [Nek5000-users] Low Mach configuration in Nek5000 Message-ID: Hello, I am trying to simulate two membranes that produce a synthetic jet with Nek5000. I have been using the low Mach configuration in Nek5000 (the flow conditions are low Mach). The low Mach set up in the low_mach example was helpful but I still have a few questions: - the low Mach does not seem to work for PnPn-2 formulation. Following this remark, what would be the correct set up with the low Mach approach to compute the full stress tensor with variable viscosity? - the user manual reads 'The implementation of the equation if state for the Low Mach formulation is for the moment hard-coded to be the ideal gas equation of state p = ?RT. This allows for both variable density and variable viscosity.? Does that mean the density is always computed using the ideal gas equation of state? What does happen when the density is specified in uservp? - since I have a moving boundary condition ?mv? and I solve the heat equation, what would be a good boundary condition for the temperature at the membranes? I do not think ?mv? boundary type is supported for the heat equation. I have tried with ?t? and ?I? without noticing any significant differences in the numerical solution. Thanks, Marco From nek5000-users at lists.mcs.anl.gov Fri May 19 16:56:34 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 19 May 2017 21:56:34 +0000 Subject: [Nek5000-users] Low Mach configuration in Nek5000 In-Reply-To: References: Message-ID: Marco, > - the low Mach does not seem to work for PnPn-2 formulation. Following this remark, what would be the correct set up with the low Mach approach to >compute the full stress tensor with variable viscosity? You will have to use the Pn-Pn formulation with IFSTRS set to true. > - the user manual reads 'The implementation of the equation if state for the Low Mach formulation is for the moment hard-coded to be the ideal gas >equation of state p = ?RT. This allows for both variable density and variable viscosity.? Does that mean the density is always computed using the ideal gas >equation of state? What does happen when the density is specified in uservp? For variable density, the RHS of the velocity constraint is non-zero, i.e. div u = -1/rho (D rho/D t) . This was implemented in Nek5000 assuming an ideal gas equation of state regardless of what you prescribe in uservp. You will need to modify qthermal.f to account for whatever equation of state you need. -Dillon -----Original Message----- From: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: Friday, May 19, 2017 2:51 PM To: Nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Low Mach configuration in Nek5000 Hello, I am trying to simulate two membranes that produce a synthetic jet with Nek5000. I have been using the low Mach configuration in Nek5000 (the flow conditions are low Mach). The low Mach set up in the low_mach example was helpful but I still have a few questions: - the low Mach does not seem to work for PnPn-2 formulation. Following this remark, what would be the correct set up with the low Mach approach to compute the full stress tensor with variable viscosity? - the user manual reads 'The implementation of the equation if state for the Low Mach formulation is for the moment hard-coded to be the ideal gas equation of state p = ?RT. This allows for both variable density and variable viscosity.? Does that mean the density is always computed using the ideal gas equation of state? What does happen when the density is specified in uservp? - since I have a moving boundary condition ?mv? and I solve the heat equation, what would be a good boundary condition for the temperature at the membranes? I do not think ?mv? boundary type is supported for the heat equation. I have tried with ?t? and ?I? without noticing any significant differences in the numerical solution. Thanks, Marco _______________________________________________ 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 Sat May 20 02:19:59 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 20 May 2017 09:19:59 +0200 Subject: [Nek5000-users] Low Mach configuration in Nek5000 In-Reply-To: References: Message-ID: You can provide your own implementation of the thermal divergence in userqtl in the .rea file. It's no longer hardcoded. The MV boundary condition is currently not supported with PnPn. On 19 May 2017, at 23:55, "nek5000-users at lists.mcs.anl.gov " > wrote: Marco, >??? - the low Mach does not seem to work for PnPn-2 formulation. Following this remark, what would be the correct set up with the low Mach approach to >compute the full stress tensor with variable viscosity? ?????? You will have to use the Pn-Pn formulation with IFSTRS set to true. >??? - the user manual reads 'The implementation of the equation if state for the Low Mach formulation is for the moment hard-coded to be the ideal gas >equation of state p = ?RT. This allows for both variable density and variable viscosity.? Does that mean the density is always computed using the ideal gas >equation of state? What does happen when the density is specified in uservp? ?????? For variable density, the RHS of the velocity constraint is non-zero, i.e. div u = -1/rho (D rho/D t) .? This was implemented in Nek5000 assuming an ideal gas equation of state regardless of what you prescribe in uservp.? You will need to modify qthermal.f to account for whatever equation of state you need. -Dillon -----Original Message----- From: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov ] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: Friday, May 19, 2017 2:51 PM To: Nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Low Mach configuration in Nek5000 Hello, I am trying to simulate two membranes that produce a synthetic jet with Nek5000. I have been using the low Mach configuration in Nek5000 (the flow conditions are low Mach). The low Mach set up in the low_mach example was helpful but I still have a few questions: ??? - the low Mach does not seem to work for PnPn-2 formulation. Following this remark, what would be the correct set up with the low Mach approach to compute the full stress tensor with variable viscosity? ??? - the user manual reads 'The implementation of the equation if state for the Low Mach formulation is for the moment hard-coded to be the ideal gas equation of state p = ?RT. This allows for both variable density and variable viscosity.? Does that mean the density is always computed using the ideal gas equation of state? What does happen when the density is specified in uservp? ??? - since I have a moving boundary condition ?mv? and I solve the heat equation, what would be a good boundary condition for the temperature at the membranes? I do not think ?mv? boundary type is supported for the heat equation. I have tried with ?t? and ?I? without noticing any significant differences in the numerical solution. Thanks, Marco ??? ??? _______________________________________________ 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 Sun May 21 20:22:06 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 09:22:06 +0800 (GMT+08:00) Subject: [Nek5000-users] Turbulence Model in Nek5000? In-Reply-To: References: Message-ID: Hi all, I find some options about k-e turbulence model in Nek5000, such as : "if (ifmodel.and.ifkeps) then call setturb" in subroutine setvar, "if (ifmodel.and.ifkeps) then call cbcturb" in subroutine setup_topo. I checked all the NekExamples and found no one uses such turbulence model (IFMODEL = F). I want to know does it have any instruction about the options about turbulence model in Nek5000 ? Best regards! Hu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 22 04:59:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 11:59:30 +0200 Subject: [Nek5000-users] Compilation problem on Blue Gene Message-ID: Hi Neks, I am facing a compilation problem on Blue Gene machine. I get the following message towards the end: I am attaching the makenek file that I am using for compilation. ld: skipping incompatible $HOME/NEK_2017/3rd_party/gslib/src/libgs.a when searching for -lgs ld: cannot find -lgs Thanks, NN. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- #!/bin/bash #------------------------------------------------------------------------------- # Nek5000 build file #------------------------------------------------------------------------------- # source path SOURCE_ROOT="$HOME/NEK_2017" SOURCE_ROOT_GSLIB="$SOURCE_ROOT/3rd_party/gslib/src" # Fortran/C compiler F77="mpixlf77_r" CC="mpixlc_r" # pre-processor list (set to "?" to get a list of available symbols) #PPLIST="" PPLIST="MPIIO" #------------------------------------------------------------------------------- # WHAT FOLLOWS ARE OPTIONAL SETTINGS #------------------------------------------------------------------------------- # optional compiler flags #FFLAGS="" #CFLAGS="" # optional linking flags #USR_LFLAGS+=" -L/usr/lib -lfoo" #USR_LFLAGS="-lmpi" # auxilliary files to compile # NOTE: source files have to located in the same directory as makenek # a makefile_usr.inc has to be provided containing the build rules #USR="foo.o" # MPI (default 1) #MPI=0 # profiling (default 1) #PROFILING=0 # VisIt in situ (default 0) #VISIT=1 # Note: you can override the lib and include paths. VISIT_LIB and VISIT_INC # If VISIT_STOP is set the simulation will stop after first step and wait # for VisIt to connect. #VISIT_INSTALL="/path/to/visit/current/linux-x86_64/" #VISIT_STOP=true ############################################################################### # DONT'T TOUCH WHAT FOLLOWS !!! ############################################################################### set -e : ${MPI:=1} : ${PROFILING:=1} : ${VISIT:=0} # assign version tag mver=17.0.0 # overwrite source path with optional 2nd argument if [ -d $2 ] && [ $# -eq 2 ]; then SOURCE_ROOT="$2" echo "change source code directory to: ", $SOURCE_ROOT fi if [ $MPI -eq 0 ]; then gslib="gsserial" else gslib="gs" fi USR_LFLAGS+=" -L$SOURCE_ROOT_GSLIB -l$gslib" # create makefile source $SOURCE_ROOT/core/makenek.inc # compile gslib if needed if [ ! -f "$SOURCE_ROOT_GSLIB/lib$gslib.a" ]; then make -j4 -B -C $SOURCE_ROOT_GSLIB MPI=0 CC="$CC" CFLAGS="$CFLAGS" ADDUS=$UNDERSCORE lib \ 2>&1 | tee compiler.out if [ $MPI -ne 0 ]; then make -j4 -B -C $SOURCE_ROOT_GSLIB MPI=1 CC="$CC" CFLAGS="$CFLAGS" ADDUS=$UNDERSCORE lib \ 2>&1 | tee compiler.out fi fi # compile nek make -j4 -f makefile 2>&1 | tee -a compiler.out exit 0 From nek5000-users at lists.mcs.anl.gov Mon May 22 05:17:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 12:17:30 +0200 Subject: [Nek5000-users] Compilation problem on Blue Gene In-Reply-To: References: Message-ID: Please post the output of makenek (compile.out) On 22 May 2017, at 11:59, "nek5000-users at lists.mcs.anl.gov " > wrote: Hi Neks, ?I am facing a compilation problem on Blue Gene machine. I get the following message towards the end: I am attaching? the makenek file that I am using for compilation. ld: skipping incompatible $HOME/NEK_2017/3rd_party/gslib/src/libgs.a when searching for -lgs ld: cannot find -lgs Thanks, NN. _______________________________________________ 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 May 22 06:54:36 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 13:54:36 +0200 Subject: [Nek5000-users] Compilation problem on Blue Gene In-Reply-To: References: Message-ID: Thanks for the follow-up of my query. Please find attached the compiler.out file with this mail. NN. On Monday 22 May 2017 12:17 PM, nek5000-users at lists.mcs.anl.gov wrote: > Please post the output of makenek (compile.out) > > On 22 May 2017, at 11:59, "nek5000-users at lists.mcs.anl.gov > " > > wrote: > >> Hi Neks, >> >> I am facing a compilation problem on Blue Gene machine. >> I get the following message towards the end: >> >> I am attaching the makenek file that I am using for compilation. >> >> ld: skipping incompatible $HOME/NEK_2017/3rd_party/gslib/src/libgs.a >> when searching for -lgs >> ld: cannot find -lgs >> >> Thanks, >> >> NN. >> >> _______________________________________________ >> >> 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: -------------- next part -------------- mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/drive.f -o obj/drive.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/drive1.f -o obj/drive1.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/drive2.f -o obj/drive2.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/plan4.f -o obj/plan4.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/bdry.f -o obj/bdry.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/coef.f -o obj/coef.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/conduct.f -o obj/conduct.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/connect1.f -o obj/connect1.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/connect2.f -o obj/connect2.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/dssum.f -o obj/dssum.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/edgec.f -o obj/edgec.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/eigsolv.f -o obj/eigsolv.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/gauss.f -o obj/gauss.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/genxyz.f -o obj/genxyz.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier1.f -o obj/navier1.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/navier1.f", line 3342.31: 1511-122 (E) Unconditional GO TO statement refers to statement inside a DO-loop, IF block, CASE construct, SELECT TYPE construct, ASSOCIATE construct, WHERE construct or FORALL construct with label 101. Transfer of control into a DO-loop, IF block, CASE construct, SELECT TYPE construct, ASSOCIATE construct, WHERE construct or FORALL construct is not permitted. mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/makeq.f -o obj/makeq.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier0.f -o obj/navier0.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier2.f -o obj/navier2.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier3.f -o obj/navier3.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier4.f -o obj/navier4.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/prepost.f -o obj/prepost.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/speclib.f -o obj/speclib.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/navier4.f", line 1157.7: 1516-023 (E) Subscript is out of bounds. mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/map2.f -o obj/map2.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/turb.f -o obj/turb.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/mvmesh.f -o obj/mvmesh.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/ic.f -o obj/ic.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/gfldr.f -o obj/gfldr.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/ssolv.f -o obj/ssolv.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/planx.f -o obj/planx.o mpixlf77_r -qsuppress=cmpmsg -c -O3 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/math.f -o obj/math.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_wrapper.f -o obj/mxm_wrapper.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/hmholtz.f -o obj/hmholtz.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/gfdm_par.f -o obj/gfdm_par.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/gfdm_op.f -o obj/gfdm_op.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/gfdm_solve.f -o obj/gfdm_solve.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/subs1.f -o obj/subs1.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/subs2.f -o obj/subs2.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/genbox.f -o obj/genbox.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/gmres.f -o obj/gmres.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/hsmg.f -o obj/hsmg.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/math.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/convect.f -o obj/convect.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/induct.f -o obj/induct.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/perturb.f -o obj/perturb.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier5.f -o obj/navier5.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier6.f -o obj/navier6.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier7.f -o obj/navier7.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/navier8.f -o obj/navier8.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/fast3d.f -o obj/fast3d.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/fasts.f -o obj/fasts.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/calcz.f -o obj/calcz.o mpixlc_r -c -O2 -DMPIIO -DMPI -DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/byte.c -o obj/byte.o mpixlc_r -c -O2 -DMPIIO -DMPI -DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/chelpers.c -o obj/chelpers.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/byte_mpi.f -o obj/byte_mpi.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/postpro.f -o obj/postpro.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/intp_usr.f -o obj/intp_usr.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/cvode_driver.f -o obj/cvode_driver.o mpixlc_r -c -O2 -DMPIIO -DMPI -DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/nek_comm.c -o obj/nek_comm.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/vprops.f -o obj/vprops.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/makeq_aux.f -o obj/makeq_aux.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/papi.f -o obj/papi.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/3rd_party/nek_in_situ.f -o obj/nek_in_situ.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/readat_new.f -o obj/readat_new.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/reader_re2.f -o obj/reader_re2.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/reader_re2.f", line 176.24: 1513-041 (W) Arguments of the wrong type were specified for the INTRINSIC procedure "mod". "/linkhome/rech/ymm/rymm003/NEK_2017/core/reader_re2.f", line 282.24: 1513-041 (W) Arguments of the wrong type were specified for the INTRINSIC procedure "mod". mpixlc_r -c -O2 -DMPIIO -DMPI -DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/3rd_party/finiparser.c -o obj/finiparser.o mpixlc_r -c -O2 -DMPIIO -DMPI -DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/3rd_party/iniparser.c -o obj/iniparser.o mpixlc_r -c -O2 -DMPIIO -DMPI -DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/3rd_party/dictionary.c -o obj/dictionary.o mpixlf77_r -qsuppress=cmpmsg -c -O3 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f -o obj/mxm_std.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/comm_mpi.f -o obj/comm_mpi.o mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/NEK_2017/core/singlmesh.f -o obj/singlmesh.o mpixlf77_r -qsuppress=cmpmsg -c -O0 -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/3rd_party/blas.f -o obj/blas.o mpixlf77_r -qsuppress=cmpmsg -c -O0 -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER /linkhome/rech/ymm/rymm003/NEK_2017/core/3rd_party/dsygv.f -o obj/dsygv.o "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. "/linkhome/rech/ymm/rymm003/NEK_2017/core/mxm_std.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. mpixlf77_r -qsuppress=cmpmsg -c -O2 -qrealsize=8 -qdpc=e -qsuffix=cpp=f -WF,-DMPIIO -WF,-DMPI -WF,-DTIMER -I/linkhome/rech/ymm/rymm003/TEST_NEK2017 -I/linkhome/rech/ymm/rymm003/NEK_2017/core -I./ /linkhome/rech/ymm/rymm003/TEST_NEK2017/WING.f -o obj/WING.o mpixlf77_r -qsuppress=cmpmsg -o nek5000 obj/WING.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/gfldr.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/intp_usr.o obj/cvode_driver.o obj/nek_comm.o obj/vprops.o obj/makeq_aux.o obj/papi.o obj/nek_in_situ.o obj/readat_new.o obj/reader_re2.o obj/finiparser.o obj/iniparser.o obj/dictionary.o obj/mxm_std.o obj/comm_mpi.o obj/singlmesh.o obj/blas.o obj/dsygv.o -L/linkhome/rech/ymm/rymm003/NEK_2017/3rd_party/gslib/src -lgs ld: skipping incompatible /linkhome/rech/ymm/rymm003/NEK_2017/3rd_party/gslib/src/libgs.a when searching for -lgs ld: cannot find -lgs make: *** [nek5000] Error 1 From nek5000-users at lists.mcs.anl.gov Mon May 22 07:29:06 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 14:29:06 +0200 Subject: [Nek5000-users] Compilation problem on Blue Gene In-Reply-To: References: Message-ID: The latest master compiles on BGQ. Not sure why it doesn't work in your case. Please try makenek realclean makenek bla -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 22nd May 2017 13:54 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Compilation problem on Blue Gene > > Thanks for the follow-up of my query. Please find attached the > compiler.out > file with this mail. > NN. > > On Monday 22 May 2017 12:17 PM, > nek5000-users at lists.mcs.anl.gov wrote: > Please post the output of makenek (compile.out) > > On 22 May 2017, at 11:59, "nek5000-users at lists.mcs.anl.gov " > > > wrote: > > Hi Neks, > ?I am facing a compilation problem on Blue Gene machine. > I get the following message towards the end: > I am attaching? the makenek file that I am using for > compilation. > > ld: skipping incompatible > $HOME/NEK_2017/3rd_party/gslib/src/libgs.a when searching > for -lgs > ld: cannot find -lgs > Thanks, > NN. > _______________________________________________ > 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 Mon May 22 08:01:51 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 15:01:51 +0200 Subject: [Nek5000-users] Contents of Nek5000-users digest, Vol 99, Issue 14 Message 1 Message-ID: Hi Paul, thank you very much for your quick and detailed answer. I have might ask you two follow up questions. 1) Is the following statement correct? In order to compare my energy spectrum with literature values, I therefore have to use pi/2 times more points to have an identical kmax. 2) Not really in the same context, but why is the energy spectrum of "coarse DNS" almost identical to a fully resolved DNS? Are Pope's resolution recommendations too conservative for NEK, so that the Kolmogorov scales can be captured with significant less points or are there some routines in the background that prevent a growing instability in the high modes, if the dissipation regime is under resolved? Thanks, Daniel From nek5000-users at lists.mcs.anl.gov Mon May 22 08:22:53 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 15:22:53 +0200 Subject: [Nek5000-users] Compilation problem on Blue Gene In-Reply-To: References: Message-ID: Thanks a lot. It worked! NN. On Monday 22 May 2017 02:29 PM, nek5000-users at lists.mcs.anl.gov wrote: > The latest master compiles on BGQ. Not sure why it doesn't work in your case. Please try > > makenek realclean > makenek bla > > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Monday 22nd May 2017 13:54 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Compilation problem on Blue Gene >> >> Thanks for the follow-up of my query. Please find attached the >> compiler.out >> file with this mail. >> NN. >> >> On Monday 22 May 2017 12:17 PM, >> nek5000-users at lists.mcs.anl.gov wrote: >> Please post the output of makenek (compile.out) >> >> On 22 May 2017, at 11:59, "nek5000-users at lists.mcs.anl.gov " >> > >> wrote: >> >> Hi Neks, >> I am facing a compilation problem on Blue Gene machine. >> I get the following message towards the end: >> I am attaching the makenek file that I am using for >> compilation. >> >> ld: skipping incompatible >> $HOME/NEK_2017/3rd_party/gslib/src/libgs.a when searching >> for -lgs >> ld: cannot find -lgs >> Thanks, >> NN. >> _______________________________________________ >> 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 Mon May 22 09:37:18 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 22 May 2017 14:37:18 +0000 Subject: [Nek5000-users] Contents of Nek5000-users digest, Vol 99, Issue 14 Message 1 In-Reply-To: References: Message-ID: Hi Daniel, Technically, you need 1.5x in each direction. This generally proves to be overly conservative, however. Yes - if you set param 103 in the .rea file to be 0.1, it will remove 10% of the energy in the Nth mode at every time step, which gives a reasonably effective grid-scale filter that is also relatively benign when you are well resolved. If your N is large ( > 8, say) then I would set param 101 = lx1/5 or lx1/6. p101 controls the number of modes, in addition to the Nth one, that are touched by the filter. The filter is applied with a parabolic round-off of the form: sigma = 1 - p103 * [ (k-k_cut) / (lx1-k_cut) ]^2 for k > k_cut, sigma = 1, otherwise, where k_cut = p101+1. So, when k=lx1, you have sigma = 1-p103 (=0.9 if p103=0.1) when k = k_cut, sigma = 1. The significance of sigma is that it is the multiplier in the modal filter basis, given by: phi_k(x) = L_k(x) - L_{k-1}(x), for k=2,...,lx1, So, expanding u(x) = \sum_k u^k phi_k we construct the filtered solution as ubar(x) = sum_k sigma_k u^k phi_k(x) Obviously, if all the sigmas = 1, then ubar == u. Common values are to run with p103=.05, p101=0, depending on resolution. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, May 22, 2017 8:01 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Contents of Nek5000-users digest, Vol 99, Issue 14 Message 1 Hi Paul, thank you very much for your quick and detailed answer. I have might ask you two follow up questions. 1) Is the following statement correct? In order to compare my energy spectrum with literature values, I therefore have to use pi/2 times more points to have an identical kmax. 2) Not really in the same context, but why is the energy spectrum of "coarse DNS" almost identical to a fully resolved DNS? Are Pope's resolution recommendations too conservative for NEK, so that the Kolmogorov scales can be captured with significant less points or are there some routines in the background that prevent a growing instability in the high modes, if the dissipation regime is under resolved? Thanks, Daniel _______________________________________________ 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 May 23 07:48:33 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 May 2017 14:48:33 +0200 Subject: [Nek5000-users] Full restart with increasing lx Message-ID: Hello Neks, Can restart a simulation by my_full_restart and also increase the lx in the SIZE file? Thank you in advance. Sincerely, Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 23 08:36:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 May 2017 13:36:02 +0000 Subject: [Nek5000-users] Full restart with increasing lx In-Reply-To: References: Message-ID: Hi Sandeep, Yes - you should be able to do that. The restart code automatically interpolates to the current resolution. 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: Tuesday, May 23, 2017 7:48 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Full restart with increasing lx Hello Neks, Can restart a simulation by my_full_restart and also increase the lx in the SIZE file? Thank you in advance. Sincerely, Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 23 15:34:01 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 May 2017 20:34:01 +0000 Subject: [Nek5000-users] Full restart with increasing lx (nek5000-users@lists.mcs.anl.gov) Message-ID: Hello, I've been able to use the full restart function increasing lx1, but in my case I had to change the timestep size (DT) in order to satisfy the CFL condition, so the solution that was saved did not work properly with the full restart because it was obtained using a different DT. So this is something for you to consider. Best, Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 23 15:56:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 23 May 2017 20:56:30 +0000 Subject: [Nek5000-users] Full restart with increasing lx (nek5000-users@lists.mcs.anl.gov) In-Reply-To: References: Message-ID: Dear Juan Diego, Good point. I guess in this case I would just use the last restart file ---- The point of "full restart" is to give a carbon copy of the preceding run. If lx1 has changed, however, then the notion of a carbon copy is lost. I do see, however, that there would be value to full restart with different lx1. 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: Tuesday, May 23, 2017 3:34 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Full restart with increasing lx (nek5000-users at lists.mcs.anl.gov) Hello, I've been able to use the full restart function increasing lx1, but in my case I had to change the timestep size (DT) in order to satisfy the CFL condition, so the solution that was saved did not work properly with the full restart because it was obtained using a different DT. So this is something for you to consider. Best, Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 24 01:48:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 24 May 2017 08:48:29 +0200 Subject: [Nek5000-users] Full restart with increasing lx (nek5000-users@lists.mcs.anl.gov) In-Reply-To: References: Message-ID: I guess the way to go, if you want to have full restart, is to first reduce the time step with the old resolution, save the three restart files (in the latest version only three files are necessary for order three) with the new time step but old resolution, and then restart... Philipp On 2017-05-23 22:56, nek5000-users at lists.mcs.anl.gov wrote: > > Dear Juan Diego, > > Good point. > > I guess in this case I would just use the last restart file ---- > > The point of "full restart" is to give a carbon copy of the preceding > run. If lx1 has changed, > however, then the notion of a carbon copy is lost. > > I do see, however, that there would be value to full restart with > different lx1. > > 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:* Tuesday, May 23, 2017 3:34 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] Full restart with increasing lx > (nek5000-users at lists.mcs.anl.gov) > > Hello, > > > I've been able to use the full restart function increasing lx1, but in > my case I had to change the timestep size (DT) in order to satisfy the > CFL condition, so the solution that was saved did not work properly with > the full restart because it was obtained using a different DT. So this > is something for you to consider. > > > Best, > > Juan Diego > > > > _______________________________________________ > 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 May 30 08:32:38 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 May 2017 15:32:38 +0200 Subject: [Nek5000-users] Read file without using load_fld nor mfi subroutines Message-ID: Hi Neks, I may have a problem when I'm trying to read velocity field (only velocity field, I don't need pressure.) so I can assign specific boundary conditions using userbc(). My questions are : 1) Is it possible to read velocity fields in nek that are contained in .f000* files without modifying the pressure "pr" nor the velocity fields "vx,vy,vz" ? 2) Is there any subroutine (besides load_fld or mfi) that would allow me to read .f000* files? When I use the mfi (in ic.f) subroutine, it looks like the pressure field is modified and hence I'm quickly running into errors like the following: 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN 1.0000E-12. If I use load_fld() I seem to me going back to the initial conditions. Thank you for your help, Arnold From nek5000-users at lists.mcs.anl.gov Tue May 30 08:54:20 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 30 May 2017 15:54:20 +0200 Subject: [Nek5000-users] Read file without using load_fld nor mfi subroutines In-Reply-To: References: Message-ID: Hi; The easies solution would be to copy your velocity and pressure to temporary arrays before reading the file and placing them back later on. e.g. real tmp_vel(lx1*ly1*lz1*lelv,ldim), tmp_pr(lx2*ly2*lz2*lelv) common /SCREV/ tmp_vel, tmp_pres integer n_tot call opcopy(tmp_vel(1,1),tmp_vel(1,2),tmp_vel(1,ndim),vx,vy,vz) n_tot = nx2*ny2*nz2*nelv call copy(tmp_pr,pr) ! read file and use variables call opcopy(vx,vy,vz,tmp_vel(1,1),tmp_vel(1,2),tmp_vel(1,ndim)) n_tot = nx2*ny2*nz2*nelv call copy(pr,tmp_pr) Regards Adam On 30/05/17 15:32, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I may have a problem when I'm trying to read velocity field (only > velocity field, I don't need pressure.) so I can assign specific > boundary conditions using userbc(). > > My questions are : 1) Is it possible to read velocity fields in nek > that are contained in .f000* files without modifying the pressure "pr" > nor the velocity fields "vx,vy,vz" ? > 2) Is there any subroutine (besides > load_fld or mfi) that would allow me to read .f000* files? > > > When I use the mfi (in ic.f) subroutine, it looks like the pressure > field is modified and hence I'm quickly running into errors like the > following: > > 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN > 1.0000E-12. > > If I use load_fld() I seem to me going back to the initial conditions. > > Thank you for your help, > > Arnold > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed May 31 03:56:47 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 31 May 2017 09:56:47 +0100 Subject: [Nek5000-users] Streamwise velocity and vorticity Message-ID: Hi nek, Is there any example using nek5000 to simulate a pipe flow. I want to output the streamwise velocity and vorticity, but I don't know how to write in usr file. Kind regards, Jian -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 31 04:44:35 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 31 May 2017 11:44:35 +0200 Subject: [Nek5000-users] Read file without using load_fld nor mfi subroutines In-Reply-To: References: Message-ID: Thank you for your solution, it works great. Thank you for your time, Best wishes, Arnold Le 30/05/2017 ? 15:54, nek5000-users at lists.mcs.anl.gov a ?crit : > Hi; > The easies solution would be to copy your velocity and pressure to > temporary arrays before reading the file and placing them back later > on. e.g. > > real tmp_vel(lx1*ly1*lz1*lelv,ldim), tmp_pr(lx2*ly2*lz2*lelv) > common /SCREV/ tmp_vel, tmp_pres > integer n_tot > > > call opcopy(tmp_vel(1,1),tmp_vel(1,2),tmp_vel(1,ndim),vx,vy,vz) > n_tot = nx2*ny2*nz2*nelv > call copy(tmp_pr,pr) > > ! read file and use variables > > call opcopy(vx,vy,vz,tmp_vel(1,1),tmp_vel(1,2),tmp_vel(1,ndim)) > n_tot = nx2*ny2*nz2*nelv > call copy(pr,tmp_pr) > > > Regards > Adam > > On 30/05/17 15:32, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Neks, >> >> I may have a problem when I'm trying to read velocity field (only >> velocity field, I don't need pressure.) so I can assign specific >> boundary conditions using userbc(). >> >> My questions are : 1) Is it possible to read velocity fields in nek >> that are contained in .f000* files without modifying the pressure >> "pr" nor the velocity fields "vx,vy,vz" ? >> 2) Is there any subroutine (besides >> load_fld or mfi) that would allow me to read .f000* files? >> >> >> When I use the mfi (in ic.f) subroutine, it looks like the pressure >> field is modified and hence I'm quickly running into errors like the >> following: >> >> 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN >> 1.0000E-12. >> >> If I use load_fld() I seem to me going back to the initial conditions. >> >> Thank you for your help, >> >> Arnold >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 31 05:59:31 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 31 May 2017 10:59:31 +0000 Subject: [Nek5000-users] Streamwise velocity and vorticity In-Reply-To: References: Message-ID: The following example simulates a flow in a pipe with periodic boundary conditions I believe: https://github.com/Nek5000/NekExamples/tree/master/pipe As for the vorticity, I have never implemented myself, but a ?grep vorticity' in the NekExamples directory should give you what you are looking for. Marco On May 31, 2017, at 4:56 AM, nek5000-users at lists.mcs.anl.gov wrote: Hi nek, Is there any example using nek5000 to simulate a pipe flow. I want to output the streamwise velocity and vorticity, but I don't know how to write in usr file. Kind regards, Jian _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 31 21:46:32 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 1 Jun 2017 10:46:32 +0800 (GMT+08:00) Subject: [Nek5000-users] Is turbulent model RANS available in Nek5000? In-Reply-To: References: Message-ID: Hi all, I found several settings about RANS in Nek5000, but no instruction about it. I checked the output settings in subroutine rdout, and found only "X","U","P","T" can be exported. I thought the turbulence kinetic energy and dissipation ratio may be contained in passive scalars, then I added two passive scalars to export ,and found the values are all zero. I really waste lots of time to read the programs.Now I am confused whether RANS is available in Nek5000? If anybody knows, please tell me is turbulent model RANS available in Nek5000? If not, then I can pay attention to other works. Thanks a lot!! Hu -------------- next part -------------- An HTML attachment was scrubbed... URL: