Help regarding HDF5.

Hi,

Well, i don't understand if there are any invalid arguments. It looks ok to me.
I am also able to compile the code but the errors are coming on runtime. I made
a separate file with all the HDF5 related code to create a HDF file and a
dataset. Again I am facing the same problem at runtime.

I am attaching my source file "mychunk.f90". Could someone please let me know if
they are able to run the executable on their machine and also let me know if
there are any errors that you can see in the code.

Just a FYI, I am using h5pfc to compile the code.

I am also attaching the source file chunk.f90 from the HDF website. This is the
file that I used as a reference. I am able to run the output of chunk.f90
successfully but not mychunk.f90

Thanks for your help.

Regards,
Nikhil

mychunk.f90 (1.77 KB)

chunk.f90 (6.48 KB)

···

Hi Nikhil,

On Jun 11, 2008, at 12:00 PM, Nikhil Laghave wrote:

> Hello Everybody,
>
> I am a newbie to HDF5. I am working on a huge fortran code and
> trying to improve
> the IO performance by using HDF5.
>
> I tried to make an interface for HDF5 in the simplest possible area
> in the code.
> I am able to compile the code after using some simple operations to
> create a
> dataset and write some data to it.
>
> But when I execute the file, I get these errors. I dont understand
> what is the
> reason for this and how to overcome it. Can some please help me if
> this looks
> somewhat familiar ?

  It's pretty difficult to determine what's going on here, but I'm
guessing that the parameters you are passing to the HDF5 routines are
not valid IDs.

  Quincey

>
>
> -bash-3.00$ mpirun -np 15 ./xmfdn
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 141 in H5Dcreate2(): not a location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
> #001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5Dio.c line 403 in H5Dwrite(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5D.c line 379 in H5Dclose(): not a dataset
> major: Invalid arguments to routine
> minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
> #000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
> major: Object atom
> minor: Unable to close file
> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
> major: Object atom
> minor: Unable to find atom information (already closed?)
>
> Any help is greatly appreciated. Thanks.
>
> Regards,
> Nikhil
>
>
>
> ----------------------------------------------------------------------
> This mailing list is for HDF software users discussion.
> To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org
> .
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>
>

Nikhil,

You used rank 1 in the h5pset_chunk_f call. Chunk always has the same dimensionality as a dataset.

I also allocated integer array and assigned some data. It works with 1.8.1 using h5fc (do not have a quick access to check h5pfc).

The corrected program is attached.

Elena

t.f90 (1.87 KB)

···

On Jun 11, 2008, at 2:24 PM, Nikhil Laghave wrote:

Hi,

Well, i don't understand if there are any invalid arguments. It looks ok to me.
I am also able to compile the code but the errors are coming on runtime. I made
a separate file with all the HDF5 related code to create a HDF file and a
dataset. Again I am facing the same problem at runtime.

I am attaching my source file "mychunk.f90". Could someone please let me know if
they are able to run the executable on their machine and also let me know if
there are any errors that you can see in the code.

Just a FYI, I am using h5pfc to compile the code.

I am also attaching the source file chunk.f90 from the HDF website. This is the
file that I used as a reference. I am able to run the output of chunk.f90
successfully but not mychunk.f90

Thanks for your help.

Regards,
Nikhil

Hi Nikhil,

On Jun 11, 2008, at 12:00 PM, Nikhil Laghave wrote:

Hello Everybody,

I am a newbie to HDF5. I am working on a huge fortran code and
trying to improve
the IO performance by using HDF5.

I tried to make an interface for HDF5 in the simplest possible area
in the code.
I am able to compile the code after using some simple operations to
create a
dataset and write some data to it.

But when I execute the file, I get these errors. I dont understand
what is the
reason for this and how to overcome it. Can some please help me if
this looks
somewhat familiar ?

  It's pretty difficult to determine what's going on here, but I'm
guessing that the parameters you are passing to the HDF5 routines are
not valid IDs.

  Quincey

-bash-3.00$ mpirun -np 15 ./xmfdn
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 141 in H5Dcreate2(): not a location ID
  major: Invalid arguments to routine
  minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
  major: Invalid arguments to routine
  minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5Dio.c line 403 in H5Dwrite(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5D.c line 379 in H5Dclose(): not a dataset
  major: Invalid arguments to routine
  minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) MPI-process 0:
#000: H5F.c line 1999 in H5Fclose(): decrementing file ID failed
  major: Object atom
  minor: Unable to close file
#001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID
  major: Object atom
  minor: Unable to find atom information (already closed?)

Any help is greatly appreciated. Thanks.

Regards,
Nikhil

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Hi,

Are the intel compilers supported on linux? If I compile 1.6.7 with icc and ifort (10.1) I get the library initialization error on the call:

    CALL h5open_f(ERROR)

The C interface works OK in my other codes, it is the FORTRAN interface that does not.

If I compile the library with gcc and ifort it works. Am I not supposed to use icc?

(DS)

···

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

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With 1.8.0, I could not get all of the test to pass with icc and ifort. Gcc and ifort worked. YMMV.

Dave McCloskey

···

-----Original Message-----
From: Dominik Szczerba [mailto:domi@vision.ee.ethz.ch]
Sent: Tuesday, July 01, 2008 5:00 AM
To: HDF Forum
Subject: [hdf-forum] 1.6.7 compiled with icc and ifort

Hi,

Are the intel compilers supported on linux? If I compile 1.6.7 with icc
and ifort (10.1) I get the library initialization error on the call:

    CALL h5open_f(ERROR)

The C interface works OK in my other codes, it is the FORTRAN interface
that does not.

If I compile the library with gcc and ifort it works. Am I not supposed
to use icc?

(DS)

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

David and Dominik,

We tested those releases with Intel 9.1; currently we are using Intel 10.1 on both 32 and 64-bit Linux machines. We don't see any problems.

Could you please tell me what exactly is failing? (please send me compilation errors and output of failed tests).

Thank you!

Elena

···

On Jul 1, 2008, at 8:08 AM, McCloskey, David L. wrote:

With 1.8.0, I could not get all of the test to pass with icc and ifort. Gcc and ifort worked. YMMV.

Dave McCloskey

-----Original Message-----
From: Dominik Szczerba [mailto:domi@vision.ee.ethz.ch]
Sent: Tuesday, July 01, 2008 5:00 AM
To: HDF Forum
Subject: [hdf-forum] 1.6.7 compiled with icc and ifort

Hi,

Are the intel compilers supported on linux? If I compile 1.6.7 with icc
and ifort (10.1) I get the library initialization error on the call:

    CALL h5open_f(ERROR)

The C interface works OK in my other codes, it is the FORTRAN interface
that does not.

If I compile the library with gcc and ifort it works. Am I not supposed
to use icc?

(DS)

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

----------------------------------------------------------------------
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Hi Elena,

Simply initializing the Fortran interface fails. There is no special data files involved, no operations whatsoever, just the first line in the relevant routine:

>> CALL h5open_f(ERROR)

produces an error about wrong data type, then dataset does not exists, or so. No other hdf5 commands in the whole source file (except USE HDF5). I deleted the build, so I don't have the exact line anymore, if you really need it I can compile a test version again and tell you exactly. It was compiled with:

> ifort -V
Intel(R) Fortran Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_fc_p_10.1.015

> icc -V
Intel(R) C Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_cc_p_10.1.015

When compiled with gcc 4.2.1 the problem does not occur.

thanks a lot and best regards,
Dominik

Elena Pourmal wrote:

···

David and Dominik,

We tested those releases with Intel 9.1; currently we are using Intel 10.1 on both 32 and 64-bit Linux machines. We don't see any problems.

Could you please tell me what exactly is failing? (please send me compilation errors and output of failed tests).

Thank you!

Elena

On Jul 1, 2008, at 8:08 AM, McCloskey, David L. wrote:

With 1.8.0, I could not get all of the test to pass with icc and ifort. Gcc and ifort worked. YMMV.

Dave McCloskey

-----Original Message-----
From: Dominik Szczerba [mailto:domi@vision.ee.ethz.ch]
Sent: Tuesday, July 01, 2008 5:00 AM
To: HDF Forum
Subject: [hdf-forum] 1.6.7 compiled with icc and ifort

Hi,

Are the intel compilers supported on linux? If I compile 1.6.7 with icc
and ifort (10.1) I get the library initialization error on the call:

        CALL h5open_f(ERROR)

The C interface works OK in my other codes, it is the FORTRAN interface
that does not.

If I compile the library with gcc and ifort it works. Am I not supposed
to use icc?

(DS)

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
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Did you run FORTRAN tests when you installed your library? Did they pass?

···

On Jul 1, 2008, at 10:24 AM, Dominik Szczerba wrote:

Hi Elena,

Simply initializing the Fortran interface fails. There is no special data files involved, no operations whatsoever, just the first line in the relevant routine:

>> CALL h5open_f(ERROR)

produces an error about wrong data type, then dataset does not exists, or so. No other hdf5 commands in the whole source file (except USE HDF5). I deleted the build, so I don't have the exact line anymore, if you really need it I can compile a test version again and tell you exactly. It was compiled with:

> ifort -V
Intel(R) Fortran Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_fc_p_10.1.015

> icc -V
Intel(R) C Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_cc_p_10.1.015

When compiled with gcc 4.2.1 the problem does not occur.

thanks a lot and best regards,
Dominik

Elena Pourmal wrote:

David and Dominik,
We tested those releases with Intel 9.1; currently we are using Intel 10.1 on both 32 and 64-bit Linux machines. We don't see any problems.
Could you please tell me what exactly is failing? (please send me compilation errors and output of failed tests).
Thank you!
Elena
On Jul 1, 2008, at 8:08 AM, McCloskey, David L. wrote:

With 1.8.0, I could not get all of the test to pass with icc and ifort. Gcc and ifort worked. YMMV.

Dave McCloskey

-----Original Message-----
From: Dominik Szczerba [mailto:domi@vision.ee.ethz.ch]
Sent: Tuesday, July 01, 2008 5:00 AM
To: HDF Forum
Subject: [hdf-forum] 1.6.7 compiled with icc and ifort

Hi,

Are the intel compilers supported on linux? If I compile 1.6.7 with icc
and ifort (10.1) I get the library initialization error on the call:

       CALL h5open_f(ERROR)

The C interface works OK in my other codes, it is the FORTRAN interface
that does not.

If I compile the library with gcc and ifort it works. Am I not supposed
to use icc?

(DS)

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
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I have rebuilt the deleted malfunctioning build to find that the problem does not occur anymore even with icc+ifort, and all the tests in fortran/test pass of course. So probably this was somehow an unclean build syndrome before (and I did not try the tests of course...). Strange though, because it was functioning for months otherwise with C interface. icc and ifort versions did not change, but maybe system stuff like glibc... A little scary though. I'll let you know should the problem come back.
Thanks,
Dominik

Elena Pourmal wrote:

···

Did you run FORTRAN tests when you installed your library? Did they pass?

On Jul 1, 2008, at 10:24 AM, Dominik Szczerba wrote:

Hi Elena,

Simply initializing the Fortran interface fails. There is no special data files involved, no operations whatsoever, just the first line in the relevant routine:

>> CALL h5open_f(ERROR)

produces an error about wrong data type, then dataset does not exists, or so. No other hdf5 commands in the whole source file (except USE HDF5). I deleted the build, so I don't have the exact line anymore, if you really need it I can compile a test version again and tell you exactly. It was compiled with:

> ifort -V
Intel(R) Fortran Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_fc_p_10.1.015

> icc -V
Intel(R) C Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_cc_p_10.1.015

When compiled with gcc 4.2.1 the problem does not occur.

thanks a lot and best regards,
Dominik

Elena Pourmal wrote:

David and Dominik,
We tested those releases with Intel 9.1; currently we are using Intel 10.1 on both 32 and 64-bit Linux machines. We don't see any problems.
Could you please tell me what exactly is failing? (please send me compilation errors and output of failed tests).
Thank you!
Elena
On Jul 1, 2008, at 8:08 AM, McCloskey, David L. wrote:

With 1.8.0, I could not get all of the test to pass with icc and ifort. Gcc and ifort worked. YMMV.

Dave McCloskey

-----Original Message-----
From: Dominik Szczerba [mailto:domi@vision.ee.ethz.ch]
Sent: Tuesday, July 01, 2008 5:00 AM
To: HDF Forum
Subject: [hdf-forum] 1.6.7 compiled with icc and ifort

Hi,

Are the intel compilers supported on linux? If I compile 1.6.7 with icc
and ifort (10.1) I get the library initialization error on the call:

       CALL h5open_f(ERROR)

The C interface works OK in my other codes, it is the FORTRAN interface
that does not.

If I compile the library with gcc and ifort it works. Am I not supposed
to use icc?

(DS)

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

--
Dominik Szczerba, Ph.D.
Biomedical Simulation Group
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
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