[Nek5000-users] run-time hang up in gs_setup
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Thu Jan 12 11:09:48 CST 2012
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> 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
>>
>> Can you verify that it still fails.
>>
>> -Stefan
>>
>> Quoting nek5000-users-request at lists.mcs.anl.gov:
>>
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>> Today's Topics:
>>
>> 1. Re: run-time hang up in gs_setup (nek5000-users at lists.mcs.anl.gov)
>> 2. Re: run-time hang up in gs_setup (nek5000-users at lists.mcs.anl.gov)
>> 3. Re: run-time hang up in gs_setup (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
>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>> To: nek5000-users at lists.mcs.anl.gov
>> Message-ID: <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 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
>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>> To: nek5000-users at lists.mcs.anl.gov
>> Message-ID:
>> <CAGTrLsaexkteQN1Y1NQ3FYz7Q2abb5YSLzOv+zeTwdvYXpD3Fw 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> 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
>>>>
>>> _______________________________________________
>>> Nek5000-users mailing list
>>> Nek5000-users at lists.mcs.anl.gov
>>> 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
>> Subject: Re: [Nek5000-users] run-time hang up in gs_setup
>> To: nek5000-users at lists.mcs.anl.gov
>> Message-ID: <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)
>> 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):
>> 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
>>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>
>>
>> End of Nek5000-users Digest, Vol 35, Issue 5
>> ********************************************
>>
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