[Nek5000-users] Setting up a case from scratch

Wed Nov 28 13:23:02 CST 2012

Misun and one of her students had that working recently, but I'm not sure if all her updates have been committed to the 
code.  Misun?

- tim

On 11/28/2012 11:28 AM, nek5000-users at lists.mcs.anl.gov wrote:
> It looks like Nek does not get the mesh from MOAB...
>
> Also I doubt the currecnt version of Nek/MOAB supports 2D Quad meshes -- only 3D hexes, right, Tim?
>
> Thanks.
> Aleks
>
>
> ----- Original Message -----
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Sent: Wed, 28 Nov 2012 11:23:04 -0600 (CST)
> Subject: Re: [Nek5000-users] Setting up a case from scratch
>
> Thanks. I am making little progress. Now I can compile. When running on h5m
> mesh I get
>
>   read .rea file
>   ABORT: nelv is invalid in nekmoab_proc_map
>   nelv, lelv =            0        1850
>
> But mbsize shows
>
> $ mbsize karman.h5m
> File karman.h5m:
>     type count   total     minimum     average         rms     maximum
>   std.dev.
> ------- ----- ------- ----------- ----------- ----------- -----------
> -----------
>     Edge   212     5.5   0.0063678    0.026102    0.029283    0.048844
>   0.013273
>     Quad  1832    0.89  3.8386e-05   0.0004881  0.00054375   0.0011788
>   0.00023963
> 1D Side  7328 1.8e+02   0.0037915    0.024086    0.027266    0.048844
>   0.012777
>   Vertex  7540
>
> praveen
>
> On Wed, Nov 28, 2012 at 10:27 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>
>> Hi Praven,
>>
>> use examples/moab/SIZE
>>
>> Thanks.
>> Aleks
>>
>>
>>
>> On Wed, 28 Nov 2012, nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>wrote:
>>
>>   The gmsh file does have all vertices for the higher order elements.
>>>
>>> I am now trying to compile with moab. I am doing everything in serial for
>>> now. I compiled moab succesfully and can convert from gmsh to h5m.
>>>
>>> But when compiling nek with moab I get this type of errors. This is the
>>> first one.
>>>
>>> gcc -c  -O2 -DMOAB -DPTRSIZE8 -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG
>>> /Users/praveen/Applications/**nek5_svn/trunk/nek/3rd_party/**imeshcutil.c
>>> -o
>>> obj/imeshcutil.o
>>> SIZE:5.21:
>>>     Included at
>>> /Users/praveen/Applications/**nek5_svn/trunk/nek/3rd_party/**MOABCORE:17:
>>>     Included at
>>> /Users/praveen/Applications/**nek5_svn/trunk/nek/3rd_party/**NEKMOAB:51:
>>>     Included at
>>> /Users/praveen/Applications/**nek5_svn/trunk/nek/3rd_party/**moab.f:79:
>>>
>>>       parameter (ldim=2)
>>>                      1
>>> Error: Symbol 'ldim' at (1) has no IMPLICIT type
>>>
>>> My makenek looks like this
>>>
>>> # Fortran compiler
>>> F77="gfortran"
>>>
>>> # C compiler
>>> CC="gcc"
>>>
>>> # pre-processor symbol list
>>> # (set PPLIST=? to get a list of available symbols)
>>> PPLIST="MOAB"
>>>
>>> # plug-in list
>>> PLUGIN_LIST=""
>>>
>>>
>>> # OPTIONAL SETTINGS
>>> # -----------------
>>>
>>> # enable MPI (default true)
>>> IFMPI="false"
>>>
>>> # auxilliary files to compile
>>> # NOTE: source files have to located in the same directory as makenek
>>> #       a makefile_usr.inc has to be provided containing the build rules
>>> #USR="foo.o"
>>>
>>> # linking flags
>>> #USR_LFLAGS="-L/usr/lib -lfoo"
>>>
>>>
>>> # generic compiler flags
>>> #G="-g"
>>>
>>> # optimization flags
>>> #OPT_FLAGS_STD=""
>>> #OPT_FLAGS_MAG=""
>>>
>>> # enable AMG coarse grid solver (default XXT)
>>> #IFAMG="true"
>>> #IFAMG_DUMP="true"
>>>
>>> # CVODE path
>>> #CVODE_DIR=$HOME/cvode/lib
>>>
>>> # MOAB/iMESH path
>>> MOAB_DIR="/opt/moab"
>>>
>>> # For linking to MOAB, the following might be needed:
>>> # NOTE: compiler specific, use the appropriate one depending on your
>>> compiler
>>> # GNU:
>>> USR_LFLAGS="-lmpi_cxx -lstdc++"
>>> # Intel:
>>> # USR_LFLAGS="-cxxlib"
>>> # PGI:
>>> # USR_LFLAGS="-pgcpplibs"
>>> # USR_LFLAGS=" -lmpi_cxx -lstdc++"
>>>
>>> What am I doing wrong ?
>>>
>>> Thanks
>>> praveen
>>>
>>> On Wed, Nov 28, 2012 at 8:46 PM, <nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>>
>>> wrote:
>>>
>>>   Try running 'mbsize' on the gmsh file, and check the number of vertices
>>>> to
>>>> make sure it's getting all of them.  Or, run mbsize -ll, piping the
>>>> output
>>>> to a file, and check one of the hexes to make sure it's 27-noded.  If
>>>> that's the case, we're all set (modulo how to handle the BC's).
>>>>
>>>> - tim
>>>>
>>>>
>>>   ______________________________**_________________
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>>
>
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-- 
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   steadfast, because he trusts in you."               Isaiah 26:3

              Tim Tautges            Argonne National Laboratory
          (tautges at mcs.anl.gov)      (telecommuting from UW-Madison)
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