[Nek5000-users] Nek5000-users Digest, Vol 35, Issue 9
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Thu Jan 12 14:34:35 CST 2012
Hi Katie;
Thanks for updating the page. I did exactly the same as it's suggested
in the updated page. After ./run of the script in amg_matlab I got
this error:
#########################################################
Computing Lagrange multiplier governing matrix skeleton ... nnz = 25.
Computing Lagrange multiplier governing matrix (C code) ... done.
CG to obtain Lagrange multipliers ... 1 iterations.
Computing interpolation weights (C code) ... done.
Sparsifying R_f A P: compression = 0
simple_sparsify: nnzs 4/4 (1)
Level 6, dim(A) = 2
Computing S = I - D^{-1/2} A D^{-1/2} ... done, nnz(S) = 2.
Running coarsening heuristic ...
ratio = 0, n = 0, max Gershgorin radius = 1
ratio = 0.5, n = 1, max Gershgorin radius = 0
connectivity = ??? Error using ==> fprintf
Function is not defined for sparse inputs.
Error in ==> coarse_par at 37
fprintf(1,'%g\n',max(lanczos(sparse(D*S*D))));
Error in ==> amg_setup at 30
[C F] = coarse_par(A,tolc);
Error in ==> go at 20
data = amg_setup(A, full(0*A(:,1)+1),ctol, tol, stol, wtol);
############################################################
I tried it for turbChannel test case as well as some other simplified
test cases. I have got the same errors.
Regards
Azad
Quoting nek5000-users-request at lists.mcs.anl.gov:
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> 1. Re: run-time hang up in gs_setup (nek5000-users at lists.mcs.anl.gov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Jan 2012 14:09:12 -0600
> From: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
> To: nek5000-users at lists.mcs.anl.gov
> Message-ID:
> <CAFTrYW+ctDhLYVdJCh8mOpA6bB7j361o=vn7WaATYkEDCifYsw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Azad,
>
> Earlier you had asked if a step was missing in the wiki with regards to the
> amg files/scripts. The has just been updated.
>
> Can you tell me exactly what you did to run the turbChannel test? And what
> output you had from the amg_matlab/run step?
>
> thanks,
> Katie
>
> On Thu, Jan 12, 2012 at 1:38 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>
>> Hi Stefan;
>>
>> Unfortunately it does not work. first of all, ./run in amg_matlab does not
>> produce anything (latest version). Using my version of the files (running
>> turbChannel), the simulation crashed giving me this error:
>>
>> ##############################**#################
>> AMG level 8: 3 iterations with rho = 0.680429
>> AMG level 9: 2 iterations with rho = 0.560188
>> AMG: 144540 rows
>> AMG: reading through row 1200, pass 1/121
>> ERROR (proc 0000,
>> /scratch/azad/codes/late/nek5_**svn/trunk/nek/jl/amg.c:875):
>> AMG: data
>> has more rows than given problem
>>
>> call exitt: dying ...
>> ##############################**#################
>>
>> Regards
>> Azad
>>
>> Quoting
>> nek5000-users-request at lists.**mcs.anl.gov<nek5000-users-request at lists.mcs.anl.gov>
>> :
>>
>> Send Nek5000-users mailing list submissions to
>>> nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
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>>>
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>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of Nek5000-users digest..."
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>>>
>>> Today's Topics:
>>>
>>> 1. Re: run-time hang up in gs_setup
>>> (nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>> )
>>>
>>>
>>> ------------------------------**------------------------------**
>>> ----------
>>>
>>> Message: 1
>>> Date: Thu, 12 Jan 2012 18:09:48 +0100
>>>
>>> From: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>
>>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>>> To: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>
>>> Message-ID:
>>> <CAGTrLsaGQkuowxvfpK3AxvCtgCEk**as9YBJkX024qF2Sh7RcmdA at mail.**
>>> gmail.com<CAGTrLsaGQkuowxvfpK3AxvCtgCEkas9YBJkX024qF2Sh7RcmdA at mail.gmail.com>
>>> >
>>>
>>> Content-Type: text/plain; charset=ISO-8859-1
>>>
>>> Hi Azad,
>>>
>>> can you try to run the turbChannel example using AMG and the latest
>>> version of the repo. Let me know if this works for you.
>>>
>>> Stefan
>>>
>>> On 1/11/12,
>>> nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>> <nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>>
>>> wrote:
>>>
>>>> Dear Stefan and Aleks;
>>>>
>>>> Thanks for updating the wiki webpage regarding the AMG, although, I
>>>> persume there must be another step also there exist, namely: copy the
>>>> generated files from the amg_matlb to the running directory? (Or they
>>>> should be remained there and one puts the generated .dat files after
>>>> running the 3rd step?). By the way non of the versions I tried working
>>>> (even 707!) despite the fact that I had a range of matlab versions
>>>> tried. Hanging with the old version I had I compiled again and have
>>>> got the four files which was rather fast (with the message at the end:
>>>> Error contraction factor: 0.47...) I used them and every time during
>>>> the run-time it crashed simply:
>>>> ##############################**##############################**
>>>> ###############
>>>> AMG: reading through row 144540, pass 121/121
>>>> AMG: reading 0.071106 MB of W
>>>> AMG: reading 0.115601 MB of AfP
>>>> AMG: reading 0.132477 MB of Aff
>>>> AMG level 1 F-vars: 440159
>>>> AMG level 2 F-vars: 55146
>>>> AMG level 3 F-vars: 28480
>>>> AMG level 4 F-vars: 17051
>>>> AMG level 5 F-vars: 7524
>>>> AMG level 6 F-vars: 5711
>>>> AMG level 7 F-vars: 5763
>>>> AMG level 8 F-vars: 28583
>>>> AMG level 9 F-vars: 5380
>>>> AMG level 10 F-vars: 5737
>>>> Application 731033 exit codes: 139
>>>> Application 731033 exit signals: Killed
>>>> Application 731033 resources: utime ~417s, stime ~3s
>>>> ##############################**##############################**
>>>> ##############
>>>>
>>>> Can you help me with that cause I believe this case still doable with
>>>> correct AMG scheme.
>>>>
>>>> Many thanks
>>>> Azad
>>>>
>>>>
>>>>
>>>>> Hi Azad,
>>>>>
>>>>> I believe old AMG files should work up to and including revision 707
>>>>> in case >you want to check AMG quickly.
>>>>>
>>>>> Best.
>>>>> Aleks
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>> From: nek5000-users at lists.mcs.anl.gov
>>>>> To: nek5000-users at lists.mcs.anl.gov
>>>>> Sent: Tuesday, January 10, 2012 10:58:47 AM
>>>>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>>>>>
>>>>> Hi Azad,
>>>>>
>>>>> your choice of lx1=8 is fine (it's our preferred sweet spot). If you
>>>>> have a large element count (say > 300'000) the factorization in the
>>>>> XXt setup phase may take hours. I guess that's why it looks like it's
>>>>> hanging. Again, there is a known bug which looks the same. So can't
>>>>> tell exactly what's causing your problem.
>>>>>
>>>>> I just updated the Wiki: https://nek5000.mcs.anl.gov/**
>>>>> index.php/Amg_matlab <https://nek5000.mcs.anl.gov/index.php/Amg_matlab>
>>>>>
>>>>> Can you verify that it still fails.
>>>>>
>>>>> -Stefan
>>>>>
>>>>> Quoting
>>>>> nek5000-users-request at lists.**mcs.anl.gov<nek5000-users-request at lists.mcs.anl.gov>
>>>>> :
>>>>>
>>>>> Send Nek5000-users mailing list submissions to
>>>>> nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>>>>
>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>>
>>>>> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>>> or, via email, send a message with subject or body 'help' to
>>>>>
>>>>> nek5000-users-request at lists.**mcs.anl.gov<nek5000-users-request at lists.mcs.anl.gov>
>>>>>
>>>>> You can reach the person managing the list at
>>>>>
>>>>> nek5000-users-owner at lists.mcs.**anl.gov<nek5000-users-owner at lists.mcs.anl.gov>
>>>>>
>>>>> When replying, please edit your Subject line so it is more specific
>>>>> than "Re: Contents of Nek5000-users digest..."
>>>>>
>>>>>
>>>>> Today's Topics:
>>>>>
>>>>> 1. Re: run-time hang up in gs_setup (nek5000-users at lists.mcs.anl.**
>>>>> gov <nek5000-users at lists.mcs.anl.gov>)
>>>>> 2. Re: run-time hang up in gs_setup (nek5000-users at lists.mcs.anl.**
>>>>> gov <nek5000-users at lists.mcs.anl.gov>)
>>>>> 3. Re: run-time hang up in gs_setup (nek5000-users at lists.mcs.anl.**
>>>>> gov <nek5000-users at lists.mcs.anl.gov>)
>>>>>
>>>>>
>>>>> ------------------------------**------------------------------**
>>>>> ----------
>>>>>
>>>>> Message: 1
>>>>> Date: Tue, 10 Jan 2012 06:01:29 -0600 (CST)
>>>>> From: nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>>>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>>>>> To: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>
>>>>> Message-ID:
>>>>> <Pine.LNX.4.64.1201100557250.**6026 at v8.mcs.anl.gov<Pine.LNX.4.64.1201100557250.6026 at v8.mcs.anl.gov>
>>>>> >
>>>>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>>>>
>>>>>
>>>>> Hi Azad,
>>>>>
>>>>> You are in record-setting territory for element counts! :)
>>>>>
>>>>> Are you using the amg-based coarse-grid solver?
>>>>> It is certain that you will need to do this (and,
>>>>> therefore, you will need matlab to process the AMG
>>>>> operators). There is some discussion of the steps
>>>>> on the wiki page. We can walk you through this process
>>>>> if you have any questions.
>>>>>
>>>>> What value of lx1 are you using?
>>>>>
>>>>> I would recommend fewer elements and a higher value of lx1.
>>>>> I think it will be easier to manage the data, etc.
>>>>>
>>>>> Paul
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, 10 Jan 2012,
>>>>> nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>wrote:
>>>>>
>>>>> Dear NEKs;
>>>>>>
>>>>>> I am trying to run a simulation of a turbulent flow in a straight pipe
>>>>>> in high Reynolds number (Re_tau = 1000). After generating the grid with
>>>>>> PRENEK and extrude it using n2to3, the mesh ended up with 4,495,920
>>>>>> elements. It compiled properly; however, trying to run it, hanged up in
>>>>>> the last stage:
>>>>>> ##############################**##############################**
>>>>>> ############
>>>>>>
>>>>>> verify mesh topology
>>>>>> -1.000000000000000 1.000000000000000 Xrange
>>>>>> -1.000000000000000 1.000000000000000 Yrange
>>>>>> 0.000000000000000 25.00000000000000 Zrange
>>>>>> done :: verify mesh topology
>>>>>>
>>>>>> E-solver strategy: 1 itr
>>>>>> mg_nx: 1 3
>>>>>> mg_ny: 1 3
>>>>>> mg_nz: 1 3
>>>>>> call usrsetvert
>>>>>> done :: usrsetvert
>>>>>>
>>>>>> gs_setup: 866937 unique labels shared
>>>>>> pairwise times (avg, min, max): 0.000241442 0.00019722 0.000265908
>>>>>> crystal router : 0.000458177 0.000445795 0.000471807
>>>>>> used all_to_all method: pairwise
>>>>>> setupds time 5.6048E-02 seconds 1 2 4565612 4495920
>>>>>> setvert3d: 4 86046564 122013924 86046564 86046564
>>>>>> call usrsetvert
>>>>>> done :: usrsetvert
>>>>>>
>>>>>> gs_setup: 8041169 unique labels shared
>>>>>> pairwise times (avg, min, max): 0.00050716 0.000427103 0.00056479
>>>>>> crystal router : 0.0040165 0.00392921 0.00411811
>>>>>> used all_to_all method: pairwise
>>>>>> setupds time 1.0465E+00 seconds 2 4 86046564 4495920
>>>>>> setup h1 coarse grid, nx_crs= 2
>>>>>> call usrsetvert
>>>>>> done :: usrsetvert
>>>>>>
>>>>>> gs_setup: 866937 unique labels shared
>>>>>> pairwise times (avg, min, max): 0.000233683 0.000197816 0.00024941
>>>>>> crystal router : 0.000466869 0.00045588 0.000478101
>>>>>> used all_to_all method: pairwise
>>>>>> ##############################**##############################**
>>>>>> ############
>>>>>>
>>>>>>
>>>>>> I was wondering if you could help me with that. I attached the run
>>>>>> logfile and also genmap.out.
>>>>>>
>>>>>> Many thanks
>>>>>> Azad
>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 2
>>>>> Date: Tue, 10 Jan 2012 13:35:22 +0100
>>>>> From: nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>>>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>>>>> To: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>
>>>>> Message-ID:
>>>>> <CAGTrLsaexkteQN1Y1NQ3FYz7Q2ab**b5YSLzOv+zeTwdvYXpD3Fw at mail.**
>>>>> gmail.com<CAGTrLsaexkteQN1Y1NQ3FYz7Q2abb5YSLzOv%2BzeTwdvYXpD3Fw at mail.gmail.com>
>>>>> >
>>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>>
>>>>> Hi Azad,
>>>>>
>>>>> We have seen similar situations. I think this has to do with a known
>>>>> bug. Unfortunately this bug is hard to reproduce and we haven't
>>>>> managed to fix it yet.
>>>>>
>>>>> -Stefan
>>>>>
>>>>> On 1/10/12,
>>>>> nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>>>> <nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> Hi Azad,
>>>>>>
>>>>>> You are in record-setting territory for element counts! :)
>>>>>>
>>>>>> Are you using the amg-based coarse-grid solver?
>>>>>> It is certain that you will need to do this (and,
>>>>>> therefore, you will need matlab to process the AMG
>>>>>> operators). There is some discussion of the steps
>>>>>> on the wiki page. We can walk you through this process
>>>>>> if you have any questions.
>>>>>>
>>>>>> What value of lx1 are you using?
>>>>>>
>>>>>> I would recommend fewer elements and a higher value of lx1.
>>>>>> I think it will be easier to manage the data, etc.
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, 10 Jan 2012,
>>>>>> nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>wrote:
>>>>>>
>>>>>> Dear NEKs;
>>>>>>>
>>>>>>> I am trying to run a simulation of a turbulent flow in a straight pipe
>>>>>>> in high Reynolds number (Re_tau = 1000). After generating the grid
>>>>>>> with
>>>>>>> PRENEK and extrude it using n2to3, the mesh ended up with 4,495,920
>>>>>>> elements. It compiled properly; however, trying to run it, hanged up
>>>>>>> in
>>>>>>> the last stage:
>>>>>>> ##############################**##############################**
>>>>>>> ############
>>>>>>>
>>>>>>> verify mesh topology
>>>>>>> -1.000000000000000 1.000000000000000 Xrange
>>>>>>> -1.000000000000000 1.000000000000000 Yrange
>>>>>>> 0.000000000000000 25.00000000000000 Zrange
>>>>>>> done :: verify mesh topology
>>>>>>>
>>>>>>> E-solver strategy: 1 itr
>>>>>>> mg_nx: 1 3
>>>>>>> mg_ny: 1 3
>>>>>>> mg_nz: 1 3
>>>>>>> call usrsetvert
>>>>>>> done :: usrsetvert
>>>>>>>
>>>>>>> gs_setup: 866937 unique labels shared
>>>>>>> pairwise times (avg, min, max): 0.000241442 0.00019722 0.000265908
>>>>>>> crystal router : 0.000458177 0.000445795 0.000471807
>>>>>>> used all_to_all method: pairwise
>>>>>>> setupds time 5.6048E-02 seconds 1 2 4565612 4495920
>>>>>>> setvert3d: 4 86046564 122013924 86046564 86046564
>>>>>>> call usrsetvert
>>>>>>> done :: usrsetvert
>>>>>>>
>>>>>>> gs_setup: 8041169 unique labels shared
>>>>>>> pairwise times (avg, min, max): 0.00050716 0.000427103 0.00056479
>>>>>>> crystal router : 0.0040165 0.00392921 0.00411811
>>>>>>> used all_to_all method: pairwise
>>>>>>> setupds time 1.0465E+00 seconds 2 4 86046564 4495920
>>>>>>> setup h1 coarse grid, nx_crs= 2
>>>>>>> call usrsetvert
>>>>>>> done :: usrsetvert
>>>>>>>
>>>>>>> gs_setup: 866937 unique labels shared
>>>>>>> pairwise times (avg, min, max): 0.000233683 0.000197816 0.00024941
>>>>>>> crystal router : 0.000466869 0.00045588 0.000478101
>>>>>>> used all_to_all method: pairwise
>>>>>>> ##############################**##############################**
>>>>>>> ############
>>>>>>>
>>>>>>>
>>>>>>> I was wondering if you could help me with that. I attached the run
>>>>>>> logfile and also genmap.out.
>>>>>>>
>>>>>>> Many thanks
>>>>>>> Azad
>>>>>>>
>>>>>>> ______________________________**_________________
>>>>>> Nek5000-users mailing list
>>>>>> Nek5000-users at lists.mcs.anl.**gov <Nek5000-users at lists.mcs.anl.gov>
>>>>>> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 3
>>>>> Date: Tue, 10 Jan 2012 17:58:47 +0100
>>>>> From: nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>>>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>>>>> To: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>
>>>>> Message-ID:
>>>>> <1326214727.2600.282.camel@**damavand.mech.kth.se<1326214727.2600.282.camel at damavand.mech.kth.se>
>>>>> >
>>>>> Content-Type: text/plain; charset="UTF-8"
>>>>>
>>>>> Dear Paul and Stefan;
>>>>>
>>>>> Thanks very much for looking into it. I use polynomial order 7th
>>>>> (lx1=8). For the coarse-grid solver I actually used XXt. I also tried to
>>>>> use AMG, but unfortunately neither v619 nor the latest version could
>>>>> have compiled its matlab files and always gives me this error (in
>>>>> matlab/R2011a):
>>>>> ##############################**################
>>>>> ...
>>>>> sparsification tolerance [1e-4]: stol = 0.0001
>>>>>
>>>>> ------------------------------**------------------------------**
>>>>> ------------
>>>>> Segmentation violation detected at Tue Jan 10 15:56:46 2012
>>>>> ------------------------------**------------------------------**
>>>>> ------------
>>>>> ....
>>>>> Abnormal termination:
>>>>> Segmentation violation
>>>>> ....
>>>>> ##############################**###############
>>>>> I have been in the web page: "amg_matlab Matlab based tool to generate
>>>>> AMG solver inputfiles" (http://nek5000.mcs.anl.gov/**
>>>>> index.php/Amg_matlab <http://nek5000.mcs.anl.gov/index.php/Amg_matlab>)
>>>>> which gives me an empty link.
>>>>>
>>>>> I had an old version of the .dat files needed to run AMG, which I tried
>>>>> those as (amg_Aff.dat, amgdmp_i.dat, amg.dat, amg_AfP.dat, amgdmp_p.dat,
>>>>> amgdmp_j.dat, amg_W.dat) and I have got this error:
>>>>>
>>>>> ##############################**##############
>>>>> ...
>>>>> AMG: reading through row 142800, pass 119/121
>>>>> AMG: reading through row 144000, pass 120/121
>>>>> AMG: reading through row 144540, pass 121/121
>>>>> ERROR (proc
>>>>> 0000,
>>>>> /afs/pdc.kth.se/home/a/**anoorani/codes/latest_nek/**
>>>>> nek5_svn/trunk/nek/jl/amg.c:**468<http://pdc.kth.se/home/a/anoorani/codes/latest_nek/nek5_svn/trunk/nek/jl/amg.c:468>
>>>>> ):
>>>>> AMG: missing data for some
>>>>> rows
>>>>>
>>>>> call exitt: dying ...
>>>>> ##############################**##############
>>>>>
>>>>> I think AMG could be a possibility to overcome this problem, though I
>>>>> could not manage to get a run with that one. I look into the problem
>>>>> with higher polynomial order to see if it reduces the number of elements
>>>>> dramatically, or at least resolve this issue.
>>>>>
>>>>> Best regards
>>>>> Azad
>>>>>
>>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%**%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>>
>>>>>> Hi Azad,
>>>>>>
>>>>>> We have seen similar situations. I think this has to do with a known
>>>>>> bug. Unfortunately this bug is hard to reproduce and we haven't
>>>>>> managed to fix it yet.
>>>>>>
>>>>>> -Stefan
>>>>>>
>>>>>> On 1/10/12, nek5000-users at lists.mcs.anl.gov
>>>>>> <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>
>>>>>>
>>>>>> Hi Azad,
>>>>>>
>>>>>> You are in record-setting territory for element counts! :)
>>>>>>
>>>>>> Are you using the amg-based coarse-grid solver?
>>>>>> It is certain that you will need to do this (and,
>>>>>> therefore, you will need matlab to process the AMG
>>>>>> operators). There is some discussion of the steps
>>>>>> on the wiki page. We can walk you through this process
>>>>>> if you have any questions.
>>>>>>
>>>>>> What value of lx1 are you using?
>>>>>>
>>>>>> I would recommend fewer elements and a higher value of lx1.
>>>>>> I think it will be easier to manage the data, etc.
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, 10 Jan 2012, nek5000-users at lists.mcs.anl.gov wrote:
>>>>>>
>>>>>> Dear NEKs;
>>>>>>
>>>>>> I am trying to run a simulation of a turbulent flow in a straight pipe
>>>>>> in high Reynolds number (Re_tau = 1000). After generating the grid with
>>>>>> PRENEK and extrude it using n2to3, the mesh ended up with 4,495,920
>>>>>> elements. It compiled properly; however, trying to run it, hanged up in
>>>>>> the last stage:
>>>>>> ##############################**##############################**
>>>>>> ############
>>>>>>
>>>>>> verify mesh topology
>>>>>> -1.000000000000000 1.000000000000000 Xrange
>>>>>> -1.000000000000000 1.000000000000000 Yrange
>>>>>> 0.000000000000000 25.00000000000000 Zrange
>>>>>> done :: verify mesh topology
>>>>>>
>>>>>> E-solver strategy: 1 itr
>>>>>> mg_nx: 1 3
>>>>>> mg_ny: 1 3
>>>>>> mg_nz: 1 3
>>>>>> call usrsetvert
>>>>>> done :: usrsetvert
>>>>>>
>>>>>> gs_setup: 866937 unique labels shared
>>>>>> pairwise times (avg, min, max): 0.000241442 0.00019722 0.000265908
>>>>>> crystal router : 0.000458177 0.000445795 0.000471807
>>>>>> used all_to_all method: pairwise
>>>>>> setupds time 5.6048E-02 seconds 1 2 4565612 4495920
>>>>>> setvert3d: 4 86046564 122013924 86046564 86046564
>>>>>> call usrsetvert
>>>>>> done :: usrsetvert
>>>>>>
>>>>>> gs_setup: 8041169 unique labels shared
>>>>>> pairwise times (avg, min, max): 0.00050716 0.000427103 0.00056479
>>>>>> crystal router : 0.0040165 0.00392921 0.00411811
>>>>>> used all_to_all method: pairwise
>>>>>> setupds time 1.0465E+00 seconds 2 4 86046564 4495920
>>>>>> setup h1 coarse grid, nx_crs= 2
>>>>>> call usrsetvert
>>>>>> done :: usrsetvert
>>>>>>
>>>>>> gs_setup: 866937 unique labels shared
>>>>>> pairwise times (avg, min, max): 0.000233683 0.000197816 0.00024941
>>>>>> crystal router : 0.000466869 0.00045588 0.000478101
>>>>>> used all_to_all method: pairwise
>>>>>> ##############################**##############################**
>>>>>> ############
>>>>>>
>>>>>>
>>>>>> I was wondering if you could help me with that. I attached the run
>>>>>> logfile and also genmap.out.
>>>>>>
>>>>>> Many thanks
>>>>>> Azad
>>>>>>
>>>>>>
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