[Dune] FW: H5Fed into Dune as a grid manager, comments, ideas ???
Oswald Benedikt
Benedikt.Oswald at psi.ch
Sun Nov 15 15:41:58 CET 2009
Hi Oliver, indeed, you're right. H5Fed initially was designed as a standard for storing finite element meshes
and associated data only, including hierarchically refined grids with hanging nodes.
When we then proceeded with its development we realized that optimum use of H5Fed in our
codes requires tight integration into Dune; for example we need checkpoint-restart capability, especially for
larger machines such as the Cray where run time is often limited to 48 hours, larger jobs then must be
resubmitted to go through.
Also, we do need the capability of reading large meshes and associated dats (volume id, boundary id)
NOW, especially for larger macro grids (large meaning n * 10^5 tets). While we intensely use
the DGF format, this does not scale as other users have come to realize. Eventually, this prevents
us from running the problems that we must run: waiting for hours sometimes until the mesh
and its parameters are read, is just not an option.
Further, we think that reading large meshes should really be done in parallel, i.e. not reading
the whole mesh on the master node (memory bottleneck, especially on future supercomputers
which may have hundreds of thousands of cores but quite little memory per core; e.g. our
Cray XT5 in Manno has 22 kCores but only 1.3 GByte per core...)
Eventually, H5Fed will not stop short of only having tets as elements. Whereas we now focus
on tetrahedra, we foresee its extension to hexahedra and maybe also hybrid meshes,
combining tets and hexahedra.
To make a long story short, we need a grid manager and a data storage format that can handle
practical meshes (while the macro grid may have some 10^5 tets, the leaf grid may have hundreds
of millions of tets eventually, this number may sound huge but it is foreseeable).
Let me make one point very clear: we would like to contribute the Dune community
to this actively in order to make it a success. In no way this is designed to introduce
competition, but really it is intended to solve our comp. needs, together with Dune
since we think Dune to be one of the greatest project, if not the greatest , in this field
Have a nice weekend! Benedikt
------------------------------------------------------------------------------------------------------------------
Benedikt Oswald, Dr. sc. techn., dipl. El. Ing. ETH, www.psi.ch, Computational Accelerator Scientist
Paul Scherrer Institute (PSI), CH-5232 Villigen, Suisse, benedikt.oswald at psi.ch, +41(0)56 310 32 12
"Passion is required for any great work, and for the Revolution passion and audacity are required in big doses.",
Ernesto 'Che' Guevara, Letter to his parents.
http://maxwell.psi.ch/amaswiki/index.php/User:BenediktOswald
------------------------------------------------------------------------------------------------------------------
-----Original Message-----
From: Oliver Sander [mailto:sander at mi.fu-berlin.de]
Sent: Fri 13.11.2009 16:05
To: Oswald Benedikt
Cc: dune at dune-project.org
Subject: Re: [Dune] FW: H5Fed into Dune as a grid manager, comments, ideas ???
Hi Benedikt!
So far I thought that what you guys did was developing a general
and powerful file format for fe grids and data. Now all of a sudden
it is a grid. My impression reading your email below is that you are
reinventing the wheel. What can your grid do that ALUGrid or UGGrid
cannot do already? Why spend the time to write yet another grid
manager (yagm)? If the problem is that there is currently no way to
get a hierarchical grid from your file into a ALU/Alberta/UGGrid then
we should discuss the possibility of extending the GridFactory interface.
Yours,
Oliver
Oswald Benedikt schrieb:
>
> Hi Christian, yes, local refinement with hanging nodes is is already
> available in the current H5Fed (which has no connection to Dune yet)
> including tags and adjacencies; i.e. we can attach and read / write
> data to any top. entity on any level; data may be scalar, vector and
> matrices of type double, complex, integer.
>
> Maybe we should use derive from the grid factory class
> and add additional member functions ?
>
> Benedikt
>
>
>
>
> -----Original Message-----
> From: Christian Engwer [mailto:christi at uni-hd.de]
> Sent: Fri 13.11.2009 14:03
> To: Oswald Benedikt
> Cc: Markus Blatt; dune at dune-project.org
> Subject: Re: [Dune] H5Fed into Dune as a grid manager, comments, ideas ???
>
> On Fri, Nov 13, 2009 at 01:56:26PM +0100, Oswald Benedikt wrote:
>
>> indeed yes, the idea is to fully connect/integrate H5Fed into Dune so that we can also use
>> H5Fed as a grid manager. So far H5Fed works in serial mode, without connection to Dune,
>> and has been tested up to about 2 million tets, but tests are ongoing and of course this
>> number of tets makes more sense in parallel aynway.
>>
>> One of the questions is then if we should adhere to the grid factory approach as do the
>> other grid managers ?
>>
>
> Well, the grid factory is only for coarse grid creation. I suggest to
> support this interface, but you will need more. Do you intend to
> implement a full grid manager with local refinement etc? In this case
> you will also want to add read/write methods for your "internal" data
> format.
>
> Christian
>
>
>> Greetings, Benedikt
>>
>>
>>
>> -----Original Message-----
>> From: dune-bounces+benedikt.oswald=psi.ch at dune-project.org on behalf of Markus Blatt
>> Sent: Fri 13.11.2009 13:51
>> To: dune at dune-project.org
>> Subject: Re: [Dune] H5Fed into Dune as a grid manager, comments, ideas ???
>>
>> Hi,
>>
>> On Thu, Nov 12, 2009 at 05:17:06PM +0100, Oswald Benedikt wrote:
>>
>>> NOW, we want to integrate H5Fed into Dune as a (parallel) grid manager,
>>> in a way like other grid managers are connected to Dune:
>>>
>>>
>> Up to now I thought that you are just concerned about reading and
>> writing data. Do I interpret your comment correctly in sense that you
>> will provide a full Dune grid based on H5fed? Or am I just not
>> comprehending your sentence?
>>
>> Markus
>>
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>
>
>
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--
************************************************************************
* Oliver Sander ** email: sander at mi.fu-berlin.de *
* Freie Universität Berlin ** phone: + 49 (30) 838 75348 *
* Institut für Mathematik ** URL : page.mi.fu-berlin.de/~sander *
* Arnimallee 6 ** -------------------------------------*
* 14195 Berlin, Germany ** Member of MATHEON (www.matheon.de) *
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