Error when h5dwrite is executed

Hdf-forum archives
1

Hi!

We experienced this problem as well. Actually, this was when using the IDL language. In our case it seemed to be a discrepancy between the version of "zlib" installed on the system and the ones required by HDF. I recommend you check the version of zlib you got installed and which version the HDF5 lib is compiled against.

With kind regards,

Pieter van der Meer

···

--
Pieter van der Meer
Software Engineer / Scientist
E-mail: P.van.der.Meer@sron.nl
Tel. +31 (0) 30 - 2535725

SRON Netherlands Institute for Space Research
http://www.sron.nl

"Ramakrishnan Iyer" <ramakrishnan.iyer@altair.com> 06/27/08 2:37 PM >>>

All,

When writing into hdf5 I get the following error

HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0. Back
trace follows.

  #000: ..\..\src\H5Dio.c line 587 in H5Dwrite(): can't write data

    major(15): Dataset interface

    minor(25): Write failed

  #001: ..\..\src\H5Dio.c line 958 in H5D_write(): can't write data

    major(15): Dataset interface

    minor(25): Write failed

  #002: ..\..\src\H5Dio.c line 2139 in H5D_chunk_write(): file gather
failed

    major(05): Low-level I/O layer

    minor(25): Write failed

  #003: ..\..\src\H5Dselect.c line 204 in H5D_select_fgath(): read error

    major(14): Dataspace interface

    minor(24): Read failed

  #004: ..\..\src\H5Distore.c line 2025 in H5D_istore_readvv(): unable
to read raw data chunk

    major(05): Low-level I/O layer

    minor(24): Read failed

  #005: ..\..\src\H5Distore.c line 1612 in H5D_istore_lock(): data
pipeline read failed

    major(19): Data filters layer

    minor(24): Read failed

  #006: ..\..\src\H5Z.c line 997 in H5Z_pipeline(): filter returned
failure during read

    major(19): Data filters layer

    minor(24): Read failed

  #007: ..\..\src\H5Zdeflate.c line 99 in H5Z_filter_deflate():
inflateInit() failed

    major(19): Data filters layer

    minor(29): Unable to initialize object

Assertion failed: mem, file ..\..\src\H5MM.c, line 142

Can anyone let me know what could be the reason for the write failure as
also how can this error be resolved ?

Regards

Ramakrishnan

----------------------------------------------------------------------
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2

All,

HDF5 (and HDF4) shouldn't depend on the version of the zlib library (if this is the case we would like to know about it ASAP :slight_smile:

But HDF5 read will fail if zlib is not available (for example, if ZLIB was not available when library was compiled, deflate filter is not available to the library, therefore HDF5 will not be able to modify/write/read zlib compressed dataset).

Elena

···

On Jun 27, 2008, at 9:11 AM, Pieter van der Meer wrote:

Hi!

We experienced this problem as well. Actually, this was when using the IDL language. In our case it seemed to be a discrepancy between the version of "zlib" installed on the system and the ones required by HDF. I recommend you check the version of zlib you got installed and which version the HDF5 lib is compiled against.

With kind regards,

Pieter van der Meer

--
Pieter van der Meer
Software Engineer / Scientist
E-mail: P.van.der.Meer@sron.nl
Tel. +31 (0) 30 - 2535725

SRON Netherlands Institute for Space Research
http://www.sron.nl

"Ramakrishnan Iyer" <ramakrishnan.iyer@altair.com> 06/27/08 2:37 PM >>>

All,

When writing into hdf5 I get the following error

HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0. Back
trace follows.

#000: ..\..\src\H5Dio.c line 587 in H5Dwrite(): can't write data

   major(15): Dataset interface

   minor(25): Write failed

#001: ..\..\src\H5Dio.c line 958 in H5D_write(): can't write data

   major(15): Dataset interface

   minor(25): Write failed

#002: ..\..\src\H5Dio.c line 2139 in H5D_chunk_write(): file gather
failed

   major(05): Low-level I/O layer

   minor(25): Write failed

#003: ..\..\src\H5Dselect.c line 204 in H5D_select_fgath(): read error

   major(14): Dataspace interface

   minor(24): Read failed

#004: ..\..\src\H5Distore.c line 2025 in H5D_istore_readvv(): unable
to read raw data chunk

   major(05): Low-level I/O layer

   minor(24): Read failed

#005: ..\..\src\H5Distore.c line 1612 in H5D_istore_lock(): data
pipeline read failed

   major(19): Data filters layer

   minor(24): Read failed

#006: ..\..\src\H5Z.c line 997 in H5Z_pipeline(): filter returned
failure during read

   major(19): Data filters layer

   minor(24): Read failed

#007: ..\..\src\H5Zdeflate.c line 99 in H5Z_filter_deflate():
inflateInit() failed

   major(19): Data filters layer

   minor(29): Unable to initialize object

Assertion failed: mem, file ..\..\src\H5MM.c, line 142

Can anyone let me know what could be the reason for the write failure as
also how can this error be resolved ?

Regards

Ramakrishnan

----------------------------------------------------------------------
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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3

Hi Elena,
I am using zlib1.2.1 for hdf51.6.5 . It works well . When I try to write a larger information I get the error that I have given below . What could be the reason ?

Regards,
Ramakrishnan J Iyer

···

-----Original Message-----
From: Elena Pourmal [mailto:epourmal@hdfgroup.org]
Sent: Saturday, June 28, 2008 12:57 AM
To: Pieter van der Meer
Cc: Ramakrishnan Iyer; hdf-forum@hdfgroup.org
Subject: Re: [hdf-forum] Error when h5dwrite is executed

All,

HDF5 (and HDF4) shouldn't depend on the version of the zlib library
(if this is the case we would like to know about it ASAP :slight_smile:

But HDF5 read will fail if zlib is not available (for example, if
ZLIB was not available when library was compiled, deflate filter is
not available to the library, therefore HDF5 will not be able to
modify/write/read zlib compressed dataset).

Elena

On Jun 27, 2008, at 9:11 AM, Pieter van der Meer wrote:

Hi!

We experienced this problem as well. Actually, this was when using
the IDL language. In our case it seemed to be a discrepancy between
the version of "zlib" installed on the system and the ones required
by HDF. I recommend you check the version of zlib you got installed
and which version the HDF5 lib is compiled against.

With kind regards,

Pieter van der Meer

--
Pieter van der Meer
Software Engineer / Scientist
E-mail: P.van.der.Meer@sron.nl
Tel. +31 (0) 30 - 2535725

SRON Netherlands Institute for Space Research
http://www.sron.nl

"Ramakrishnan Iyer" <ramakrishnan.iyer@altair.com> 06/27/08 2:37
PM >>>

All,

When writing into hdf5 I get the following error

HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
Back
trace follows.

#000: ..\..\src\H5Dio.c line 587 in H5Dwrite(): can't write data

   major(15): Dataset interface

   minor(25): Write failed

#001: ..\..\src\H5Dio.c line 958 in H5D_write(): can't write data

   major(15): Dataset interface

   minor(25): Write failed

#002: ..\..\src\H5Dio.c line 2139 in H5D_chunk_write(): file gather
failed

   major(05): Low-level I/O layer

   minor(25): Write failed

#003: ..\..\src\H5Dselect.c line 204 in H5D_select_fgath(): read
error

   major(14): Dataspace interface

   minor(24): Read failed

#004: ..\..\src\H5Distore.c line 2025 in H5D_istore_readvv(): unable
to read raw data chunk

   major(05): Low-level I/O layer

   minor(24): Read failed

#005: ..\..\src\H5Distore.c line 1612 in H5D_istore_lock(): data
pipeline read failed

   major(19): Data filters layer

   minor(24): Read failed

#006: ..\..\src\H5Z.c line 997 in H5Z_pipeline(): filter returned
failure during read

   major(19): Data filters layer

   minor(24): Read failed

#007: ..\..\src\H5Zdeflate.c line 99 in H5Z_filter_deflate():
inflateInit() failed

   major(19): Data filters layer

   minor(29): Unable to initialize object

Assertion failed: mem, file ..\..\src\H5MM.c, line 142

Can anyone let me know what could be the reason for the write
failure as
also how can this error be resolved ?

Regards

Ramakrishnan

----------------------------------------------------------------------
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.

----------------------------------------------------------------------
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.

----------------------------------------------------------------------
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.

4

Hi Ramakrishnan,

It is hard to say why your programs fails. May be it runs out of memory. (see line 142 in H5MM.c file where assertion fails).

Have you tried 1.6.7 or 1.8.1?

Elena

···

On Jul 2, 2008, at 3:38 AM, Ramakrishnan Iyer wrote:

Hi Elena,
I am using zlib1.2.1 for hdf51.6.5 . It works well . When I try to write a larger information I get the error that I have given below . What could be the reason ?

Regards,
Ramakrishnan J Iyer

-----Original Message-----
From: Elena Pourmal [mailto:epourmal@hdfgroup.org]
Sent: Saturday, June 28, 2008 12:57 AM
To: Pieter van der Meer
Cc: Ramakrishnan Iyer; hdf-forum@hdfgroup.org
Subject: Re: [hdf-forum] Error when h5dwrite is executed

All,

HDF5 (and HDF4) shouldn't depend on the version of the zlib library
(if this is the case we would like to know about it ASAP :slight_smile:

But HDF5 read will fail if zlib is not available (for example, if
ZLIB was not available when library was compiled, deflate filter is
not available to the library, therefore HDF5 will not be able to
modify/write/read zlib compressed dataset).

Elena

On Jun 27, 2008, at 9:11 AM, Pieter van der Meer wrote:

Hi!

We experienced this problem as well. Actually, this was when using
the IDL language. In our case it seemed to be a discrepancy between
the version of "zlib" installed on the system and the ones required
by HDF. I recommend you check the version of zlib you got installed
and which version the HDF5 lib is compiled against.

With kind regards,

Pieter van der Meer

--
Pieter van der Meer
Software Engineer / Scientist
E-mail: P.van.der.Meer@sron.nl
Tel. +31 (0) 30 - 2535725

SRON Netherlands Institute for Space Research
http://www.sron.nl

"Ramakrishnan Iyer" <ramakrishnan.iyer@altair.com> 06/27/08 2:37
PM >>>

All,

When writing into hdf5 I get the following error

HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
Back
trace follows.

#000: ..\..\src\H5Dio.c line 587 in H5Dwrite(): can't write data

  major(15): Dataset interface

  minor(25): Write failed

#001: ..\..\src\H5Dio.c line 958 in H5D_write(): can't write data

  major(15): Dataset interface

  minor(25): Write failed

#002: ..\..\src\H5Dio.c line 2139 in H5D_chunk_write(): file gather
failed

  major(05): Low-level I/O layer

  minor(25): Write failed

#003: ..\..\src\H5Dselect.c line 204 in H5D_select_fgath(): read
error

  major(14): Dataspace interface

  minor(24): Read failed

#004: ..\..\src\H5Distore.c line 2025 in H5D_istore_readvv(): unable
to read raw data chunk

  major(05): Low-level I/O layer

  minor(24): Read failed

#005: ..\..\src\H5Distore.c line 1612 in H5D_istore_lock(): data
pipeline read failed

  major(19): Data filters layer

  minor(24): Read failed

#006: ..\..\src\H5Z.c line 997 in H5Z_pipeline(): filter returned
failure during read

  major(19): Data filters layer

  minor(24): Read failed

#007: ..\..\src\H5Zdeflate.c line 99 in H5Z_filter_deflate():
inflateInit() failed

  major(19): Data filters layer

  minor(29): Unable to initialize object

Assertion failed: mem, file ..\..\src\H5MM.c, line 142

Can anyone let me know what could be the reason for the write
failure as
also how can this error be resolved ?

Regards

Ramakrishnan

----------------------------------------------------------------------
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.

----------------------------------------------------------------------
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.

----------------------------------------------------------------------
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.

5

Hi Elena,
I will give this a try with hdf1.8.1 .

Regards,
Ramakrishnan

···

-----Original Message-----
From: Elena Pourmal [mailto:epourmal@hdfgroup.org]
Sent: Thursday, July 03, 2008 10:43 AM
To: Ramakrishnan Iyer
Cc: hdf-forum@hdfgroup.org
Subject: Re: [hdf-forum] Error when h5dwrite is executed

Hi Ramakrishnan,

It is hard to say why your programs fails. May be it runs out of
memory. (see line 142 in H5MM.c file where assertion fails).

Have you tried 1.6.7 or 1.8.1?

Elena

On Jul 2, 2008, at 3:38 AM, Ramakrishnan Iyer wrote:

Hi Elena,
I am using zlib1.2.1 for hdf51.6.5 . It works well . When I try to
write a larger information I get the error that I have given below .
What could be the reason ?

Regards,
Ramakrishnan J Iyer

-----Original Message-----
From: Elena Pourmal [mailto:epourmal@hdfgroup.org]
Sent: Saturday, June 28, 2008 12:57 AM
To: Pieter van der Meer
Cc: Ramakrishnan Iyer; hdf-forum@hdfgroup.org
Subject: Re: [hdf-forum] Error when h5dwrite is executed

All,

HDF5 (and HDF4) shouldn't depend on the version of the zlib library
(if this is the case we would like to know about it ASAP :slight_smile:

But HDF5 read will fail if zlib is not available (for example, if
ZLIB was not available when library was compiled, deflate filter is
not available to the library, therefore HDF5 will not be able to
modify/write/read zlib compressed dataset).

Elena

On Jun 27, 2008, at 9:11 AM, Pieter van der Meer wrote:

Hi!

We experienced this problem as well. Actually, this was when using
the IDL language. In our case it seemed to be a discrepancy between
the version of "zlib" installed on the system and the ones required
by HDF. I recommend you check the version of zlib you got installed
and which version the HDF5 lib is compiled against.

With kind regards,

Pieter van der Meer

--
Pieter van der Meer
Software Engineer / Scientist
E-mail: P.van.der.Meer@sron.nl
Tel. +31 (0) 30 - 2535725

SRON Netherlands Institute for Space Research
http://www.sron.nl

"Ramakrishnan Iyer" <ramakrishnan.iyer@altair.com> 06/27/08 2:37
PM >>>

All,

When writing into hdf5 I get the following error

HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
Back
trace follows.

#000: ..\..\src\H5Dio.c line 587 in H5Dwrite(): can't write data

  major(15): Dataset interface

  minor(25): Write failed

#001: ..\..\src\H5Dio.c line 958 in H5D_write(): can't write data

  major(15): Dataset interface

  minor(25): Write failed

#002: ..\..\src\H5Dio.c line 2139 in H5D_chunk_write(): file gather
failed

  major(05): Low-level I/O layer

  minor(25): Write failed

#003: ..\..\src\H5Dselect.c line 204 in H5D_select_fgath(): read
error

  major(14): Dataspace interface

  minor(24): Read failed

#004: ..\..\src\H5Distore.c line 2025 in H5D_istore_readvv(): unable
to read raw data chunk

  major(05): Low-level I/O layer

  minor(24): Read failed

#005: ..\..\src\H5Distore.c line 1612 in H5D_istore_lock(): data
pipeline read failed

  major(19): Data filters layer

  minor(24): Read failed

#006: ..\..\src\H5Z.c line 997 in H5Z_pipeline(): filter returned
failure during read

  major(19): Data filters layer

  minor(24): Read failed

#007: ..\..\src\H5Zdeflate.c line 99 in H5Z_filter_deflate():
inflateInit() failed

  major(19): Data filters layer

  minor(29): Unable to initialize object

Assertion failed: mem, file ..\..\src\H5MM.c, line 142

Can anyone let me know what could be the reason for the write
failure as
also how can this error be resolved ?

Regards

Ramakrishnan

----------------------------------------------------------------------

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.

----------------------------------------------------------------------
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.

----------------------------------------------------------------------
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.