[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 21:40:01 CST 2012
Thanks. I will be eagerly waiting for this.
praveen
On Thu, Nov 29, 2012 at 4:15 AM, <nek5000-users at lists.mcs.anl.gov> wrote:
> 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 <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<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<nek5000-users at lists.mcs.anl.gov>
>>> To: nek5000-users at lists.mcs.anl.**gov <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<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 <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 <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
>>>>>>
>>>>>>
>>>>>> ______________________________****_________________
>>>>>
>>>> Nek5000-users mailing list
>>>> Nek5000-users at lists.mcs.anl.****gov <Nek5000-users at lists.mcs.anl.**gov<Nek5000-users at lists.mcs.anl.gov>
>>>> >
>>>> https://lists.mcs.anl.gov/****mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users>
>>>> **<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>> **>
>>>>
>>>>
>>> ______________________________**_________________
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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.
> fax: (608) 263-4499 Madison, WI 53706
>
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