[Nek5000-users] CUBIT/Moab

[nek5000-users at lists.mcs.anl.gov]

Hi Tim,Aleks:

I was able to successfully convert our test mesh from a .cub to a .h5m
using mbconvert.

Now the issue is running it with Nekton.

I am trying to run the "moab" example in the nek repo (I'm using 724),
which appears to be a simple pipe.  In the makenek file, I put "MOAB"
in the PPLIST, and I specify the moab directory (see attached makenek
file).  When I try to compile, I get issues with moab.f--essentially,
variables such as iBase_REGION, iMesh_HEXAHEDRON, etc have no implicit
type, which makes me think it is not finding these variables like it
should...

I found where these variables are defined (iMesh_f.h), and it looks
like the compiler is looking in the correct include directory (for me,
this is ${HOME}/moab/trunk/TRIAL1/include ), so I'm not sure why my
compilation of Nek is not seeing these variables.  As a sanity check,
I copied all the include files from moab to the nek/3rd_party
directory, but I get the same result.

I included my makenek file and the compiler logfile, Any help here
would be greatly appreciated!

Thanks, and let me know if you need any more information

Josh



On Tue, Sep 20, 2011 at 1:50 PM,  <nek5000-users at lists.mcs.anl.gov> wrote:
> I sent these instructions to a different Nek user a few days back:
>
> Ok.  I think in the repo version of Nek, you have to name your mesh input
> "input.h5m", which you get by translating from .cub to .h5m (the latter is
> the hdf5-based native file representation MOAB uses).  If you want to run
> this in parallel, you also need to run a partitioner on the file (using
> tools/mbzoltan in moab), and change the code at the beginning of
> nek/3rd_party/moab.f, nekMOAB_load subroutine, to use
> PARTITION=PARALLEL_PARTITION option.  Finally, you'll need to change the
> value used for lelt in the SIZE file (set it to the number of elements in
> the mesh).
>
>
> - tim
>
>
> On 09/20/2011 01:39 PM, Aleksandr Obabko wrote:
>>
>> Hi Josh,
>>
>> I have been told that the way to convert .cub file into MOAB's native .h5m
>> file is using mbconvert utility which should be in MOAB's bin directory.
>>
>> (https://svn.mcs.anl.gov/repos/ITAPS/MOAB/tags/preVersion4.0/README.IO).
>>
>>
>> Please, try
>>
>> mbconvert blah.cub blah.h5m
>>
>> Best,
>> Aleks
>>
>>
>>
>>
>> ----- Original Message -----
>> From: nek5000-users at lists.mcs.anl.gov
>> To: "nek5000-users"<nek5000-users at lists.mcs.anl.gov>
>> Sent: Monday, September 19, 2011 12:33:44 PM
>> Subject: [Nek5000-users] CUBIT/Moab
>>
>> Neks,
>>
>> We are interested in using CUBIT meshes in our Nek runs.  I took a
>> look at the "moab" example in the source, but I'm still unsure of the
>> proper process of getting a CUBIT-generated mesh into Nek.
>>
>> I have created a CUBIT mesh (.cub), and have also downloaded,
>> compiled, and installed MOAB.  I see in the example that a .h5m file
>> is used (the native format of MOAB), but I don't know how to generate
>> it through MOAB (from my .cub file).
>>
>> I realize that this is probably more of a MOAB question than a Nek
>> question, but are there some simple instructions/examples to help me
>> in understanding how to use a CUBIT mesh in Nek?  Any help would be
>> appreciated!
>>
>> Thanks,
>>
>
> --
> ================================================================
> "You will keep in perfect peace him whose mind is
>  steadfast, because he trusts in you."               Isaiah 26:3
>
>             Tim Tautges            Argonne National Laboratory
>         (tautges at mcs.anl.gov)      (telecommuting from UW-Madison)
>         phone: (608) 263-8485      1500 Engineering Dr.
>           fax: (608) 263-4499      Madison, WI 53706
>
> _______________________________________________
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> Nek5000-users at lists.mcs.anl.gov
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>



-- 
Josh Camp

"All that is necessary for the triumph of evil is that good men do
nothing" -- Edmund Burke
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