ElmerGrid segmentation fault with more than 2 subdomains

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desoza
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ElmerGrid segmentation fault with more than 2 subdomains

Post by desoza »

Hi,

I'm using Elmer compiled from svn (r5596) and I'm having trouble partitioning meshes in more than 2 subdomains. I had to comment a checking part in ElmerGrid source (femelmer.c) to workaround this.

Here's the traceback of the crash.

Code: Select all

desoza@claut621:~/AFFAIRE_TI/CODES/ELMER/CUBE$ gdb ElmerGrid
GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /opt/elmer_mpi_dbg/bin/ElmerGrid...done.
(gdb) run 2 2 cube -metis 4 2
Starting program: /opt/elmer_mpi_dbg/bin/ElmerGrid 2 2 cube -metis 4 2
[Thread debugging using libthread_db enabled]

Starting program Elmergrid
Elmergrid reading in-line arguments
The mesh will be partitioned with Metis to 4 partitions.
Output will be saved to file cube.

Elmergrid loading data:
-----------------------
Loading mesh in ElmerSolver format from directory cube.
Loading header from mesh.header
Maximum elementtype index is: 808
Allocating for 1331 knots and 1000 elements.
Loading 1331 Elmer nodes from mesh.nodes
Loading 1000 bulk elements from mesh.elements
Loading 200 boundary elements from mesh.boundary
All done

Elmergrid creating and manipulating meshes:
-------------------------------------------

Elmergrid partitioning meshes:
------------------------------
Making a Metis partitioning for 1331 nodes in 3-dimensions.
Creating a dual graph of the finite element mesh
There are at maximum 26 connections in dual graph.
There are at all in all 28460 connections in dual graph.
Starting graph partitioning METIS_PartGraphRecursive.
Finished Metis graph partitioning call.
Set the element partitions by the dominating nodal partition
There are from 247 to 257 elements in the 4 partitions.
Succesfully made a Metis partition using the dual graph.
Optimizing the partitioning at boundaries.
Ownership of 0 parents was changed at BCs
Creating a table showing all parenting partitions of nodes.
Nodes belong to 4 partitions in maximum
There are 313 shared nodes which is 23.52 % of all nodes.
The initial owner was not any of the elements for 0 nodes
Checking partitioning before optimization
Checking for partitioning
Information on partition bandwidth
Distribution of elements, nodes and shared nodes
     partition  elements   nodes      shared    
     1          247        332        79        
     2          248        333        78        
     3          248        333        83        
     4          257        333        101       
Maximum deviation in ownership 1
Average deviation in ownership 0.43
Checking for problematic sharings

Program received signal SIGSEGV, Segmentation fault.
0x000000000041b0c8 in OptimizePartitioning (data=0x7ffffff86b80, bound=0x6e1ae0, noopt=1, partbw=0, info=1) at femelmer.c:3507
3507            elemparts[j] = 0;
(gdb) where
#0  0x000000000041b0c8 in OptimizePartitioning (data=0x7ffffff86b80, bound=0x6e1ae0, noopt=1, partbw=0, info=1) at femelmer.c:3507
#1  0x0000000000481a12 in main (argc=7, argv=0x7fffffffdb78) at fempre.c:905
Commented part in femelmer.c begins here :

Code: Select all

  3484	 optimizesharing:
  3485	  
  3486	  if(info) printf("Checking for problematic sharings\n"); 
  3487	  m = 0;
  3488	
  3489	  if(partitions > 2) {  
  3490	    do {
  3491	      
I compiled on two different machines with two different compilers (GNU and Intel) and had the same problem. Is it something you're aware of ?

Thomas
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cube.tgz
(54.61 KiB) Downloaded 336 times
raback
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Re: ElmerGrid segmentation fault with more than 2 subdomains

Post by raback »

Hi Thomas

Sorry, I could not reproduce it (using gnu 4.6.2). However, I do believe there can be problems as there are some dirty heuristics being performed. Attached is my output.

-Peter
Attachments
out.txt
Output from ElmerGrid partitioning
(3.06 KiB) Downloaded 318 times
desoza
Posts: 4
Joined: 11 Apr 2012, 15:42
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Re: ElmerGrid segmentation fault with more than 2 subdomains

Post by desoza »

Hi Peter,

Thank you for your reply. It might also come from my compile options.
Since disabling the check works, I'll cope with it for now.

Thomas
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