[Nek5000-users] Setting up a case from scratch
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Nov 28 16:45:00 CST 2012
Oh, right, ok. I'd forgotten that those parts of NekCEM and Nek5000 are different.
- tim
On 11/28/2012 01:35 PM, Misun Min wrote:
>
> Hi Tim
>
> MOAB supporting 2D quad meshes have been tested for NekCEM/LBM
> codes but not tested with nek5000. I'll check with Aleks to make
> sure the updated moab routines not to conflict with nek5000 and
> commit soon.
>
> Thanks
> Misun
>
> ----- Original Message -----
> From: "Tim Tautges" <tautges at mcs.anl.gov>
> To: nek5000-users at lists.mcs.anl.gov, "Misun Min" <mmin at mcs.anl.gov>
> Sent: Wednesday, November 28, 2012 1:23:02 PM
> Subject: Re: [Nek5000-users] Setting up a case from scratch
>
> 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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>
--
================================================================
"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 (gvoice): (608) 354-1459 1500 Engineering Dr.
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