[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 15:12:23 CST 2012
Hi Azad,
This error means that your version of matlab doesn't like the fprint() in
coarse_par.f, line 37.
Since this is just a print statement, you can comment this out by adding %
in front of line 37. So it should look like:
% fprintf(1,'%g\n',max(lanczos(sparse(D*S*D))));
Then this should work, at least for turbChannel.
good luck,
Katie
On Thu, Jan 12, 2012 at 2:34 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>
> 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<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
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>> 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>
>>
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>> 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>
>> )
>>
>>
>> ------------------------------**------------------------------**
>> ----------
>>
>> Message: 1
>> Date: Thu, 12 Jan 2012 14:09:12 -0600
>> 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:
>> <CAFTrYW+**ctDhLYVdJCh8mOpA6bB7j361o=vn7W**
>> aATYkEDCifYsw at mail.gmail.com <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<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 <http://mcs.anl.gov>
>>> <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 <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>
>>>> **<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 <http://mcs.anl.gov><
>>>> 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@**
>>>> 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<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 <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 <nek5000-users at lists.mcs.anl.gov>>
>>>> Message-ID:
>>>> <**CAGTrLsaGQkuowxvfpK3AxvCtgCEk****as9YBJkX024qF2Sh7RcmdA at mail.*
>>>> ***
>>>> gmail.com<CAGTrLsaGQkuowxvfpK3**AxvCtgCEkas9YBJkX024qF2Sh7Rcmd**
>>>> A 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 <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<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<http://mcs.anl.gov>
>>>>>> <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 <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>
>>>>>> **<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<http://mcs.anl.gov>
>>>>>> <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@*
>>>>>> *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<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<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<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 <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 <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<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 <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 <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 <nek5000-users at lists.mcs.anl.gov>>
>>>>>> Message-ID:
>>>>>> <**CAGTrLsaexkteQN1Y1NQ3FYz7Q2ab***
>>>>>> *b5YSLzOv+zeTwdvYXpD3Fw at mail.****
>>>>>> gmail.com<CAGTrLsaexkteQN1Y1NQ**3FYz7Q2abb5YSLzOv%**
>>>>>> 2BzeTwdvYXpD3Fw at mail.gmail.com<CAGTrLsaexkteQN1Y1NQ3FYz7Q2abb5YSLzOv%252BzeTwdvYXpD3Fw 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 <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 <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 <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>
>>>>>>> **<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 <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 <nek5000-users at lists.mcs.anl.gov>>
>>>>>> Message-ID: <1326214727.2600.282.camel@**d**amavand.mech.kth.se<http://damavand.mech.kth.se>
>>>>>> <1326214727**.2600.282.camel at 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<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/**<http://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<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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>>>>>>
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