[Gmsh] Mesh with many volumes - memory problem

[Christophe Geuzaine]

On 19/02/10 10:36, Romain Quey wrote:
> Hello Christophe,
>
> Thanks for your quick and detailed answer.
>
> I'm glad to hear this is not due to a memory leak.
>
> As for colors, I want to use the full RGB color palette. Actually,
> this is kind of a post-processing, where the color is related to the
> value of a given physical variable - I want to visualize the field of
> this variable on the mesh.


I understand. For this you should simply use the post-processing module :-)

To visualize fields that are constant per element, the easiest is to 
create a .msh file with an "$ElementData" field.

Here's a simple example with a mesh containing 2 elements (2 quads, with 
ids 1000 and 1001), with a scalar field equal to 1.05 on element 1000 
and 3.141592 on element 1001:

$MeshFormat
2.1 0 8
$EndMeshFormat
$Nodes
6
1 0.0 0.0 0.0
2 0.1 0.0 0.0
3 0.1 0.3 0.0
4 0.0 0.3 0.0
5 0.0 0.15 0.0
6 0.1 0.15 0.0
$EndNodes
$Elements
2
1000 3  2 6 100  1 2 6 5
1001 3  2 6 100  5 6 3 4
$EndElements
$ElementData
1
"Scalar per element"
1
0.0
3
0
1
2
1000 1.05
1001 3.141592
$EndElementData

You can then play with many options (Tools->Options->View[0]) to display 
the data.



>
> Romain
>
> On 02/19/10 10:06, Christophe Geuzaine wrote:
>> On 18/02/10 20:51, Romain Quey wrote:
>>> Hi Gmsh developers, hi everyone,
>>>
>>
>> Hello Romain,
>>
>>> I'm generating meshes with a lot of element sets (or "volumes");
>>> actually, one element set for each element. It turns out that Gmsh
>>> uses much more memory than when there is only one element set (for the
>>> same mesh). Attached are examples of the same mesh made of 8807
>>> elements, but with 1 or 8807 element sets. The memory needs for
>>> loading the meshes are:
>>> - for 1 elset : 35Mb RAM (leak 5Mb, non-leak 30Mb)
>>> - for 1 elset/elt: 122Mb RAM (leak 92Mb, non-leak 30Mb)
>>>
>>> As indicated above, the memory leak reported is much higher when there
>>> are a lot of element sets (report by valgrind).
>> >
>> > With a mesh made of 157352 elements, the difference becomes very high:
>> > - 1 elset : 84Mb RAM
>> > - 1 elset/elt: 1600Mb RAM
>> >
>> > Of course, this is annoying, and I think it is due to a memory leak in
>> > Gmsh.
>>
>> * With respect to memory leaks:
>>
>> There might be some very small memory leaks in Gmsh, but the numbers you
>> report are probably not actual memory leaks. By default we do not delete
>> (free) the memory associated with the loaded models when you exit Gmsh:
>> there is no need to do this, as the OS will reclaim all the memory for
>> you automatically when the program quits. Freeing everything explicitly
>> would make exiting Gmsh much slower, with no added benefit. To detect
>> real memory leaks, you need to perform several cycles (say load a mesh,
>> delete it, load it again, etc.) and see if the actual memory usage goes
>> up. It shouldn't.
>>
>> This being said, you can free most of the memory by hand if you want by
>> adding "Delete All;" at the end of your script. This will not free
>> everything, as we always keep one empty model as well as some global
>> data in memory, but it will explicitly free most of it.
>>
>> * With respect to "element sets"
>>
>> What you call element sets are much more than that: they are actual
>> geometrical entities ("volumes"), with associated topology and geometry
>> (and many other options, like colors).
>>
>> Such a geometrical entity has a much larger memory footprint than a mesh
>> element: that's completely normal, and by design.
>>
>>>
>>> By the way, I'm generating such meshes with one element set for each
>>> element because I want to assign one particular color to every element,
>>> which is done through: "Color{R,G,B}{Volume{...};}" for each element.
>>> Is there a simpler way?
>>
>> How many different colors do you need? There is no way to assign one
>> color per element (for performance/memory reasons: cf. above), but an
>> intermediate solution could be to
>>
>> * define a single volume
>>
>> * but define several mesh partitions (cf. the additional element tags in
>> the .msh format)
>>
>> You cannot explicitly assign colors to partitions, but partitions can be
>> colored using the 20 colors of the "color carousel" (Mesh.Color.Zero,
>> Mesh.Color.One, etc.)
>>
>> Hope this helps,
>>
>> Christophe
>>
>>
>>
>>
>>>
>>> Thanks for your great software,
>>>
>>> Romain
>>>
>>>
>>>
>>> _______________________________________________
>>> gmsh mailing list
>>> gmsh at geuz.org
>>> http://www.geuz.org/mailman/listinfo/gmsh
>>
>>
>


-- 
Prof. Christophe Geuzaine
University of Liege, Electrical Engineering and Computer Science
http://www.montefiore.ulg.ac.be/~geuzaine