[Nek5000-users] run-time hang up in gs_setup

Tue Jan 10 13:25:58 CST 2012

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

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