pytables-users

[Pytables-users] HDF5-DIAG

[<nmi...@jh...>]

I'm trying to install PyTables onto Max OS X 10.4, and it compiles and
installs fine, but when I run the tests or any examples I always get
"HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread 0.
Back trace follows." errors. The data seems to be saved properly into the
hdf5 file, i'm just not sure what the errors mean.

Naveen

---------------------------------------------------------------------
Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

- the plural of 'anecdote' is not 'data'

Re: [Pytables-users] HDF5-DIAG

[Francesc A. <fa...@ca...>]

Hi Naveen,

Can you report all the errors as well as the version of your PyTables
package? There are quite a few PyTables users on MacOSX, so this should
be a problem in your local configuration.

El dc 05 de 10 del 2005 a les 14:27 -0400, en/na nmi...@jh... va
escriure:
> I'm trying to install PyTables onto Max OS X 10.4, and it compiles and
> installs fine, but when I run the tests or any examples I always get
> "HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread 0.
> Back trace follows." errors. The data seems to be saved properly into the
> hdf5 file, i'm just not sure what the errors mean.
>=20
> Naveen
>=20
> ---------------------------------------------------------------------
> Naveen Michaud-Agrawal
> Program in Molecular Biophysics
> Johns Hopkins University
> (410) 614 4435
>=20
> - the plural of 'anecdote' is not 'data'
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
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> Pyt...@li...
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--=20
>0,0<   Francesc Altet     http://www.carabos.com/
V   V   C=E1rabos Coop. V.   Enjoy Data
 "-"

Re: [Pytables-users] HDF5-DIAG

[<nmi...@jh...>]

Hi Francesc,

This is how I set up pytables (I'm using version 1.1.1)

I downloaded hdf5-1.6.4 from the NCSA site and configured it normally
except for disabling shared libraries and enabling static libraries.
(./configure --prefix=3D$HOME/Desktop/hdf5 --disable-shared --enable-static=
)
Followed by make, make test and make install. The tests all passed.

Then I built pytables with "python setup.py --hdf5=3D$HOME/Desktop/hdf5
build" followed my an install. When I go into the test directory and try
the simplest test (which I think is test_basics.py) I get the output which
I included in the first attachment (since it's so long)

Here's the output for running tutorial1-1.py:

-**-**-**-**-**-**- file creation  -**-**-**-**-**-**-**-
Creating file: tutorial1.h5

-**-**-**-**-**- group and table creation  -**-**-**-**-**-**-**-
Group '/detector' created
HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread 0.  Back
trace follows.
  #000: H5D.c line 1072 in H5Dcreate(): not a location ID
    major(01): Function arguments
    minor(03): Inappropriate type
  #001: H5G.c line 2438 in H5G_loc(): invalid group ID
    major(01): Function arguments
    minor(05): Bad value
  #002: H5I.c line 1262 in H5I_find_id(): invalid ID
    major(07): Atom layer
    minor(32): Unable to find atom information (already closed?)
Traceback (most recent call last):
  File "tutorial1-1.py", line 46, in ?
    table =3D h5file.createTable(group, 'readout', Particle, "Readout
example")
  File
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/sit=
e-packages/tables/File.py",
line 571, in createTable
    return self._createNode(where, name, Table, doCreateNode, _log)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/sit=
e-packages/tables/File.py",
line 499, in _createNode
    setattr(parent, name, node)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/sit=
e-packages/tables/Group.py",
line 635, in __setattr__
    value._g_putUnder(self, name)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/sit=
e-packages/tables/Leaf.py",
line 232, in _g_putUnder
    self._create()
  File
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/sit=
e-packages/tables/Table.py",
line 396, in _create
    self._createTable(self._v_new_title, self.filters.complib, obversion)
  File "TableExtension.pyx", line 265, in
TableExtension.Table._createTable
tables.exceptions.HDF5ExtError: Problems creating the table

If I open the resulting hdf5 file using the interactive python intepreter
all the data seems to be there, so I'm not sure if the errors just signify
some debugging code that got compiled into the hdf5 library.

Naveen

---------------------------------------------------------------------
Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

On Thu, 6 Oct 2005, Francesc Altet wrote:

> Hi Naveen,
>
> Can you report all the errors as well as the version of your PyTables
> package? There are quite a few PyTables users on MacOSX, so this should
> be a problem in your local configuration.
>
> El dc 05 de 10 del 2005 a les 14:27 -0400, en/na nmi...@jh... va
> escriure:
> > I'm trying to install PyTables onto Max OS X 10.4, and it compiles and
> > installs fine, but when I run the tests or any examples I always get
> > "HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread 0.
> > Back trace follows." errors. The data seems to be saved properly into t=
he
> > hdf5 file, i'm just not sure what the errors mean.
> >
> > Naveen
> >
> > ---------------------------------------------------------------------
> > Naveen Michaud-Agrawal
> > Program in Molecular Biophysics
> > Johns Hopkins University
> > (410) 614 4435
> >
> > - the plural of 'anecdote' is not 'data'
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by:
> > Power Architecture Resource Center: Free content, downloads, discussion=
s,
> > and more. http://solutions.newsforge.com/ibmarch.tmpl
> > _______________________________________________
> > Pytables-users mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytables-users
> --
> >0,0<   Francesc Altet     http://www.carabos.com/
> V   V   C=E1rabos Coop. V.   Enjoy Data
>  "-"
>
>=

Re: [Pytables-users] HDF5-DIAG

[Francesc A. <fa...@ca...>]

A Dijous 06 Octubre 2005 17:11, nmi...@jh... va escriure:
> Hi Francesc,
>
> This is how I set up pytables (I'm using version 1.1.1)
>
> I downloaded hdf5-1.6.4 from the NCSA site and configured it normally
> except for disabling shared libraries and enabling static libraries.
> (./configure --prefix=3D$HOME/Desktop/hdf5 --disable-shared --enable-stat=
ic)

I'm afraid that this is the problem. I've recompiled with static HDF5
libraries and I can reproduce it :-/

Sorry, but I'm not sure what is happening here. Anyone on the list can
bring some light?

=2D-=20
>0,0<   Francesc Altet =A0 =A0 http://www.carabos.com/
V   V   C=E1rabos Coop. V. =A0=A0Enjoy Data
 "-"

[Pytables-users] Re: HDF5-DIAG

[<nmi...@jh...>]

Hi,

I was wondering if there was any resolution to the issue of compiling hdf5
statically on OS X (and maybe even other platforms). Thanks.

Naveen Michaud-Agrawal


On Wed, 5 Oct 2005 nmi...@jh... wrote:

>
> I'm trying to install PyTables onto Max OS X 10.4, and it compiles and
> installs fine, but when I run the tests or any examples I always get
> "HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread 0.
> Back trace follows." errors. The data seems to be saved properly into the
> hdf5 file, i'm just not sure what the errors mean.
>
> Naveen
>
> ---------------------------------------------------------------------
> Naveen Michaud-Agrawal
> Program in Molecular Biophysics
> Johns Hopkins University
> (410) 614 4435
>
> - the plural of 'anecdote' is not 'data'
>
>

Re: [Pytables-users] Re: HDF5-DIAG

[Francesc A. <fa...@ca...>]

Hi Naveen,

None that I'm aware of. Anyway, if you want to have a look at this,
I'm open to include anything that would be necessary to support static
libraries in the next version of PyTables.

Cheers,

A Dijous 27 Octubre 2005 00:57, nmi...@jh... va escriure:
> Hi,
>
> I was wondering if there was any resolution to the issue of compiling hdf5
> statically on OS X (and maybe even other platforms). Thanks.
>
> Naveen Michaud-Agrawal
>
> On Wed, 5 Oct 2005 nmi...@jh... wrote:
> > I'm trying to install PyTables onto Max OS X 10.4, and it compiles and
> > installs fine, but when I run the tests or any examples I always get
> > "HDF5-DIAG: Error detected in HDF5 library version: 1.6.4 thread 0.
> > Back trace follows." errors. The data seems to be saved properly into t=
he
> > hdf5 file, i'm just not sure what the errors mean.

=2D-=20
>0,0<   Francesc Altet =A0 =A0 http://www.carabos.com/
V   V   C=E1rabos Coop. V. =A0=A0Enjoy Data
 "-"