Re: [Libmesh-users] Mesh Data

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John and Roy,=0A=0AThanks for your comments.  It appears that xta/xtr is re=
served for data on a mesh =0Adescribed by an xda/xdr file.  Here is the des=
cription from the MeshData example =0A(Example 12):=0A=0A     The xtr/xta f=
ormat is simply an extension of the=0Axdr/xda format to read/write also =0A=
     nodal/element-associated=0Afloating-point data.  The xtr interface of =
the MeshData=0A=0A     creates stand-alone files that may be binary or ASCI=
I.=0AYou cannot append files =0A     created by the MeshData I/O methods=0A=
to a mesh file (xdr/xda). =0AThe xtr files may =0A     be seen as a "backdr=
op", especially when=0Abinary files are preferred.  Note that unv =0A     f=
iles are always=0AASCII and may become pretty big!=0A=0ANote the last line =
which is why I'd prefer not to use unv files (but I am) except for the =0Af=
act that they can be gzip'd.  =0A=0AFor further reference, here is as I see=
 it the problem with reading in MeshData using =0Axta/xtr format.=0A=0A    =
 The problem is in xdr_io.C, subroutine read_mesh.  In particular, look=0A =
    at lines 2099-2131, which is supposed to add foreign_ids to nodes.  Thi=
s=0A     actually never happens which causes the code to crash when you try=
 to=0A     read in data to those nodes.=0A=0A     This never happens becaus=
e mesh_data is null because it is supposed to=0A     be passed in as an arg=
ument but in the call to read_mesh (line 1924 or=0A     1947) mesh_data is =
not passed in.  Fixing this is not as easy as it=0A     looks.=0A=0A     Th=
ere is more to it if you want to investigate.  Try it for a simple=0A     e=
xample (ex12) and see what happens for you.  Hopefully I've made a=0A     m=
istake and I'm wrong.=0A=0ABack to the original problem with using UNV file=
s and reading in data.  What I have =0Adone at the moment is to have all of=
 the processors read in the mesh, instead of =0Aprocessor 0 reading in mesh=
 and distributing.  This ensures close_foreign_id_maps is=0Acalled from unv=
_io.C by all processors. It seems to work for now but is obviously =0Asubop=
timal.  The other idea I had was what John proposed but requires a little b=
it of =0Awork.  I'll eventually look at this and have processor 0 read in M=
eshData and then =0Adistribute to other processors using routines similar t=
o mesh_communication.C.=0A=0AThat's all for now.  Thanks for your help.=0A=
=0ATravis=0A=0A----- Original Message ----=0AFrom: John Peterson <peterson@=
cfdlab.ae.utexas.edu>=0ATo: Travis Austin <aus...@gm...>=0ACc: Libme=
sh-...@li...=0ASent: Thursday, December 28, 2006 6:11:19 =
PM=0ASubject: [Libmesh-users]  Mesh Data=0A=0AHi!=0A=0AI'm curious...do you=
 have any idea why the MeshData class refers=0Ato it as an xta/xtr file ins=
tead of the normal xda/xdr (binary/ascii)=0Afile extensions?=0A=0AAs far as=
 the MeshData class goes, it is quite possible that it does=0Anot work in p=
arallel; this would be the case if the original=0Adevelopers only used it i=
n serial.  If you can make the entire class=0A"serial" i.e. wrap more stuff=
 in "if (libMesh::processor_id()=3D=3D0)",=0Aand then communicate the neces=
sary information using the routines=0Asimilar to those found in mesh_commun=
ication.C, that might be enough=0Ato get it working.=0A=0AI've done a very =
small amount of MPI programming, so I might be=0Aable to help out if you ha=
ve a specific question.=0A=0A-John=0A=0A=0A=0A=0ATravis Austin writes:=0A >=
 Hi,=0A > =0A > I am building reaction-diffusion problems with varying diff=
usion=0A > and reaction coefficients (each node has its own value) and I am=
=0A > currently reading in these coefficients using MeshData.  I've been=0A=
 > using MeshData because I find it is a bit more natural than using=0A > m=
ultiple EquationSystems to read in data, which was suggested=0A > previousl=
y.=0A > =0A > I originally tried to use MeshData with XTA/XDA mesh formats =
but=0A > ran into a problem that is not easily fixed.  So I've gone to usin=
g=0A > UNV mesh files (both for mesh and data).  Everything works in the=0A=
 > serial case (reading in mesh and data runs and I can access the=0A > dat=
a) but not in the parallel case.  I get the following error.=0A > =0A > (*)=
 monodomain_example_aliev: src/mesh/mesh_data.C:240: void=0A > MeshData::re=
ad(const std::string&): Assertion `_elem_id_map_closed=0A > && _node_id_map=
_closed' failed.=0A > =0A > I believe that the problem is that processor 1 =
has not closed his=0A > elem_id_map or node_id_map which is only done by pr=
ocessor 0 who=0A > reads in the mesh.=0A > =0A > See following lines in mes=
h.C and unv_io.C=0A > =0A > mesh.C:719 UNVIO(*this, *mesh_data).read (name)=
;=0A > =0A > unv_io.C:260 this->_mesh_data.close_foreign_id_maps ();=0A > =
=0A > This last line is only performed by processor 0 since only he reads=
=0A > in the mesh.  So when reading in MeshData, processor 1 causes above=
=0A > error (*).  Even if this was fixed, it doesn't look like that=0A > pr=
ocessor 0 communicates the MeshData after he reads it in so if=0A > this is=
 to work a few (hopefully just a few) bits need fixed up.=0A > =0A > My que=
stion is whether or not there is any long term support for=0A > MeshData us=
ing either UNV or XDA or any other format.  I'm worried=0A > I'm going to k=
eep running into problems using MeshData since I've=0A > found one using XT=
A/XDA and now a second using UNV with >1=0A > processors.  It seems most pe=
ople run problems using libMesh where=0A > parameters are constant so it ma=
kes me think that most people don't=0A > care about reading in data to a me=
sh.  I do and I'd like to find=0A > something reliable without redeveloping=
 something completely new.=0A > Any thoughts?=0A > =0A > Cheers, Travis Aus=
tin=0A=0A------------------------------------------------------------------=
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