[Nek5000-users] Setting up a case from scratch

Wed Nov 28 11:28:58 CST 2012

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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