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Re: [Libmesh-users] Please some help with the examples SOLVED
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From: Leopold P. A. <le...@wo...> - 2003-11-17 18:09:30
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Dear people,
finally I have compiled the examples!!!!! Well, without gzstream part. I have
download the cvs version and it have been compiled in a debian stable with
this options:
#!/bin/sh
export PETSC_DIR="/usr/lib/petsc";
export PETSC_ARCH="linux";
./configure --disable-gzstreams;
make clean;
make -j 30;
the examples have been compiled, but someone have some errors:
ex6:
make[2]: Entering directory `/rhome/lepalom/test_finite/libmesh/examples/ex6'
Compiling C++ (in optimized mode) ex6.C...
Linking ex6...
/rhome/lepalom/test_finite/libmesh/contrib/tecplot/lib/i686-pc-linux-gnu/
tecio.a(tecxxx.o): In function `tecini':
tecxxx.o(.text+0x1a7): the use of `mktemp' is dangerous, better use `mkstemp'
***************************************************************
* Running Example ./ex6
***************************************************************
ERROR: This example requires the library to be compiled with Infinite Element
support!
[0] ex6.C, line 82, compiled Nov 17 2003 at 18:44:15
***************************************************************
* Done Running Example ./ex6
***************************************************************
and the example 12 have done another error:
make[2]: Entering directory `/rhome/lepalom/test_finite/libmesh/examples/ex12'
Compiling C++ (in optimized mode) ex12.C...
Linking ex12...
/rhome/lepalom/test_finite/libmesh/contrib/tecplot/lib/i686-pc-linux-gnu/
tecio.a(tecxxx.o): In function `tecini':
tecxxx.o(.text+0x1a7): the use of `mktemp' is dangerous, better use `mkstemp'
***************************************************************
* Running Example ./ex12
***************************************************************
Universal file Interface:
Counting nodes and elements
Convert from "D" to "e"
Nodes : 3977
Elements: 3520
Reading nodes
Reading elements
Finished.
Finished reading the mesh. MeshData is active but empty:
---------------------------------------------------------
Mesh Information:
mesh_dimension()=3
spatial_dimension()=3
n_nodes()=3977
n_elem()=3520
n_local_elem()=3520
n_active_elem()=3520
n_subdomains()=1
n_processors()=1
processor_id()=0
MeshData Information:
object activated.
After inserting artificial data into the MeshData:
--------------------------------------------------
MeshData Information:
object activated.
Element associated data initialized.
n_val_per_elem()=0
n_elem_data()=0
Node associated data initialized.
n_val_per_node()=2
n_node_data()=3977
Writing MeshData to: data_first_out_with_default_header.unv
Attach our own MeshDataUnvHeader to the MeshData:
-------------------------------------------------
(note the warning: the number of values per node in
my_header is not correct)
Writing MeshData to: data_second_with_header_out.unv
WARNING: nvaldc=3 of attached MeshDataUnvHeader object not valid!
re-set nvaldc to 2
Before clearing the MeshData:
-----------------------------
MeshData Information:
object activated.
Element associated data initialized.
n_val_per_elem()=0
n_elem_data()=0
Node associated data initialized.
n_val_per_node()=2
n_node_data()=3977
After clearing the MeshData:
----------------------------
MeshData Information:
object activated.
After re-reading the first file:
--------------------------------
MeshData Information:
object activated.
Element associated data initialized.
n_val_per_elem()=0
n_elem_data()=0
Node associated data initialized.
n_val_per_node()=2
n_node_data()=3977
----------------------------------------------
---------- next example with MeshData --------
----------------------------------------------
Universal file Interface:
Counting nodes and elements
Convert from "D" to "e"
Nodes : 3977
Elements: 3520
Reading nodes
Reading elements
Finished.
De-activated MeshData:
----------------------
Mesh Information:
mesh_dimension()=3
spatial_dimension()=3
n_nodes()=3977
n_elem()=3520
n_local_elem()=3520
n_active_elem()=3520
n_subdomains()=1
n_processors()=1
processor_id()=0
MeshData neither active nor in compatibility mode.
Writing _Mesh_ to: mesh_with_libmesh_ids.unv
Try 'diff mesh_with_libmesh_ids.unv ../../examples/ex8/pipe-mesh.unv'
to see the differences in node numbers.
---------------------------------------
Universal file Interface:
*************************************************************************
* WARNING: MeshData neither active nor in compatibility mode. *
* Enable compatibility mode for MeshData. Use this Universal *
* file with caution: libMesh node and element ids are used. *
*************************************************************************
Writing 3977 nodes
Writing elements
Finished writing 3520 elements
Writing MeshData to: data_third_with_libmesh_ids_out.unv
----------------------------------------------------------
Writing gzip'ed MeshData to: packed_data_third_with_libmesh_ids_out.unv.gz
---------------------------------------------------------------------------
To verify the integrity of the packed version, type:
gunzip packed_data_third_with_libmesh_ids_out.unv.gz;
diff packed_data_third_with_libmesh_ids_out.unv
data_third_with_libmesh_ids_out.unv
ERROR: You must have the zlib.h header files and libraries to read and write
compressed streams.
[0] src/mesh/mesh_data_unv_support.C, line 427, compiled Nov 17 2003 at
18:19:04
make[2]: *** [run] Aborted
make[2]: Leaving directory `/rhome/lepalom/test_finite/libmesh/examples/ex12'
make[1]: *** [run] Error 2
make[1]: Leaving directory `/rhome/lepalom/test_finite/libmesh/examples'
make: *** [run_examples] Error 2
lepalom@e01:~/test_finite/libmesh$ locate zlib.h
/usr/include/zlib.h
Well, I hope that this information can help. I will try to understand the
examples.
Thank's a lot,
best regards,
Leo
A Dilluns 17 Novembre 2003 16:58, Leopold Palomo Avellaneda va escriure:
> Hi,
>
> A Dilluns 17 Novembre 2003 16:08, Benjamin S. Kirk va escriure:
> > Right, that would be my thought. If the PETSc provided for Debian
> > requires libmpe.a (which it clearly does) then it should list that
> > library in the packages file like this:
> >
> > ifeq ($(PETSC_MPI),mpich)
> > MPI_HOME = /usr/lib/mpich
> > MPI_LIB = -L${MPI_HOME}/lib/shared \
> > -L${MPI_HOME}/lib -lmpich -lmpe
> > MPIRUN = /usr/bin/mpirun.mpich
> > MPI_INCLUDE = -I${MPI_HOME}/include
> > endif
>
> In others distros, how is it?
>
> > I'm not sure about your gzstreams problem yet... I'll look at that now.
> > In the mean time you can configure the library with --disable-gzstreams
> > and everything should work OK.
>
> No OK, KO.
> if I do:
> export PETSC_DIR="/usr/lib/petsc";
> export PETSC_ARCH="linux";
> ./configure --disable-gzstreams;
>
> I have
> [....]
> Compiling C++ (in optimized mode) src/mesh/mesh_data_unv_support.C...
> Compiling C++ (in optimized mode) src/mesh/mesh_data_xdr_support.C...
> Compiling C++ (in optimized mode) src/mesh/mesh_diva_support.C...
> Compiling C++ (in optimized mode) src/mesh/mesh_exodus_support.C...
> src/mesh/mesh_data_unv_support.C:29: gzstream.h: No such file or directory
> Compiling C++ (in optimized mode) src/mesh/mesh_generation.C...
> make: *** [src/mesh/mesh_data_unv_support.i686-pc-linux-gnu.o] Error 1
>
> so, I think that the libmesh script doesn't like a debian system :-(
>
> Regards,
>
> Leo
>
> > -Ben
> >
> > Leopold Palomo Avellaneda wrote:
> > > Hi,
> > >
> > > A Dilluns 17 Novembre 2003 11:11, Jens Oeser va escriure:
> > >>as I mentioned I'm running the same configuration like you. To find out
> > >>where your problem is, I configured libmesh in the same way. If
> > >>I try to link one of the examples I get the same error messages for
> > >>undefined references to "MPE_***" but not for gzstream.
> > >
> > > Ok, it's strange.
> > >
> > >>I think you are
> > >>missing a debian package like zlib1g or zlib1g-dev, but I'm not sure.
> > >
> > > I have installed.
> > > ii zlib1g 1.1.4-1 compression library - runtime
> > > ii zlib1g-dev 1.1.4-1 compression library - development
> > >
> > >>I
> > >>could also solve the mpe problem by adding -lmpe in the packages file.
> > >>This could be point of diskussion with the debain maintainer.
> > >
> > > Ok, so it's a bug in the debian package, no?
> > >
> > > regards,
> > >
> > > Leo
> > >
> > >>On Mon, 17 Nov 2003 10:25:03 +0100
> > >>
> > >>Leopold Palomo Avellaneda <le...@wo...> wrote:
> > >>>Hi,
> > >>>
> > >>>thank's for the answer.
> > >>>
> > >>>A Divendres 14 Novembre 2003 14:35, Benjamin S. Kirk va escriure:
> > >>>>post the output of 'make echo' so I can see what your configutation
> > >>>>is. Also, the symbol MPE_Log_event is defined in the MPI library
> > >>>>libmpe.a, so that needs to be linked in as well.
> > >>>
> > >>>See the attach file.
> > >>>
> > >>>>I have never needed this library for the PETSc's I have built from
> > >>>>source, but it seems to be required by the precompiled Debian
> > >>>>packages.
> > >>>
> > >>>Yes there's a dependencies. Also, there are a change betwend the
> > >>>version 2.1.3 (woody-stable) and 2.1.6 (sarge-testing). The last one
> > >>>needs the mpich library (version mpich (>= 1.2.5-4)).
> > >>>
> > >>>>look at the file $PETSC_DIR/bmake/$PETSC_ARCH/packages and see what
> > >>>>it says about the MPI configuration. If it only has -lmpich add
> > >>>>-lmpe and let me know what happens.
> > >>>
> > >>>In this file, the lines that you are talking about are:
> > >>>
> > >>># For mpich:
> > >>>ifeq ($(PETSC_MPI),mpich)
> > >>> MPI_HOME = /usr/lib/mpich
> > >>> MPI_LIB = -L${MPI_HOME}/lib/shared -L${MPI_HOME}/lib -lmpich
> > >>> MPIRUN = /usr/bin/mpirun.mpich
> > >>> MPI_INCLUDE = -I/usr/lib/mpich/include
> > >>>endif
> > >>>
> > >>>So, I have the error. But, if I add -lmpe I have this:
> > >>>
> > >>>make[1]: Entering directory
> > >>>`/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/examples'
> > >>>make[2]: Entering directory
> > >>>`/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/examples/ex1'
> > >>>Linking ex1...
> > >>>/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/contrib/tecplot/lib/i686
> > >>>-pc-linux-gnu/tecio.a(tecxxx.o): In function `tecini':
> > >>>tecxxx.o(.text+0x1a7): the use of `mktemp' is dangerous, better use
> > >>>`mkstemp'/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/lib/i686-pc-lin
> > >>>ux-gnu_opt/libmesh.so: undefined reference to
> > >>>`gzstreambase::gzstreambase(int, char const *,
> > >>>int)'/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/lib/i686-pc-linux-g
> > >>>nu_opt/libmesh.so: undefined reference to
> > >>>`gzstreambase::~gzstreambase(void)'/rhome/lepalom/test_finite/libmesh
> > >>>-0.4.1-rc2/lib/i686-pc-linux-gnu_opt/libmesh.so: undefined reference
> > >>>to `gzstreambase type_info
> > >>>node'/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/lib/i686-pc-linux-g
> > >>>nu_opt/libmesh.so: undefined reference to `gzstreambase type_info
> > >>>function' collect2: ld returned 1 exit status
> > >>>make[2]: *** [ex1] Error 1
> > >>>make[2]: Leaving directory
> > >>>`/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/examples/ex1'
> > >>>make[1]: *** [run] Error 2
> > >>>make[1]: Leaving directory
> > >>>`/rhome/lepalom/test_finite/libmesh-0.4.1-rc2/examples'
> > >>>make: *** [run_examples] Error 2
> > >>>lepalom@e01:~/test_finite/libmesh-0.4.1-rc2$
> > >>>
> > >>>So only there are one error. This could be a bug in the petsc package,
> > >>>so please confirm that you didn't have this and I will comment it to
> > >>>the debian package mantainer.
> > >>>
> > >>>>I'm not sure what the gzstreambase stuff is yet, but try what I
> > >>>>mention above and we'll go from there.
> > >>>
> > >>>Now, we have only the error on this part of code.
> > >>>
> > >>>Best regards,
> > >>>
> > >>>Leo
> > >
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