Hi all,
i have a problem with hdf5 version 1.8.6. (32 bits) and Visual c++ 2008.
i have several files which contain a 4x545869 double - matrix datasset. I can open/read/write these files on linux and mac os, but windows refuses to work with these files.
I get the following call stack:
HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dcontig.c line 520 in H5D_contig_read(): contiguous read
failed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 692 in H5D_contig_readvv(): block read fai
led
major: Low-level I/O
minor: Read failed
#006: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#007: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#008: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#009: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Is there a way to detect whats wrong with the files? like an integrity checking tool?
regards
stefan
Hello again, i have played a bit more:
Also building files on Mac/Linux using Matlab
a=zeros(545869,4);
hdf5write('testfile','/testmatrix',a);
generates files wich are not readable on windows but work perfectly on Mac/Linux. Also i tried the new hdf5 1.8.7 which has a slightly more verbose output:
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dchunk.c line 1758 in H5D_chunk_read(): chunked read fail
ed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 890 in H5D_contig_readvv(): can't perform
vectorized sieve buffer read
major: Dataset
minor: Can't operate on object
#006: ..\..\..\src\H5V.c line 1454 in H5V_opvv(): can't perform operation
major: Internal error (too specific to document in detail)
minor: Can't operate on object
#007: ..\..\..\src\H5Dcontig.c line 691 in H5D_contig_readvv_sieve_cb(): block
read failed
major: Dataset
minor: Read failed
#008: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#009: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#010: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#011: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
This looks like a HDF5 Bug to me.
regards
Stefan
···
Hi all,
i have a problem with hdf5 version 1.8.6. (32 bits) and Visual c++ 2008.
i have several files which contain a 4x545869 double - matrix datasset. I can open/read/write these files on linux and mac os, but windows refuses to work with these files.
I get the following call stack:
HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dcontig.c line 520 in H5D_contig_read(): contiguous read
failed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 692 in H5D_contig_readvv(): block read fai
led
major: Low-level I/O
minor: Read failed
#006: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#007: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#008: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#009: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Is there a way to detect whats wrong with the files? like an integrity checking tool?
regards
stefan
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Stefan,
Could you please send to help@hdfgroup.org your file and the code?
It does look like a bug.
Thank you!
Elena
···
On Jun 20, 2011, at 4:53 PM, Stefan Schiffler wrote:
Hello again, i have played a bit more:
Also building files on Mac/Linux using Matlab
a=zeros(545869,4);
hdf5write('testfile','/testmatrix',a);
generates files wich are not readable on windows but work perfectly on Mac/Linux. Also i tried the new hdf5 1.8.7 which has a slightly more verbose output:
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dchunk.c line 1758 in H5D_chunk_read(): chunked read fail
ed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 890 in H5D_contig_readvv(): can't perform
vectorized sieve buffer read
major: Dataset
minor: Can't operate on object
#006: ..\..\..\src\H5V.c line 1454 in H5V_opvv(): can't perform operation
major: Internal error (too specific to document in detail)
minor: Can't operate on object
#007: ..\..\..\src\H5Dcontig.c line 691 in H5D_contig_readvv_sieve_cb(): block
read failed
major: Dataset
minor: Read failed
#008: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#009: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#010: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#011: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
This looks like a HDF5 Bug to me.
regards
Stefan
Hi all,
i have a problem with hdf5 version 1.8.6. (32 bits) and Visual c++ 2008.
i have several files which contain a 4x545869 double - matrix datasset. I can open/read/write these files on linux and mac os, but windows refuses to work with these files.
I get the following call stack:
HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dcontig.c line 520 in H5D_contig_read(): contiguous read
failed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 692 in H5D_contig_readvv(): block read fai
led
major: Low-level I/O
minor: Read failed
#006: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#007: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#008: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#009: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Is there a way to detect whats wrong with the files? like an integrity checking tool?
regards
stefan
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Stefan,
Actually... Could you please run h5dump on your files on windows and see if you still get an error?
If yes, then it is HDF5 problem and we will need to take a look.
Thank you!
Elena
···
On Jun 20, 2011, at 4:53 PM, Stefan Schiffler wrote:
Hello again, i have played a bit more:
Also building files on Mac/Linux using Matlab
a=zeros(545869,4);
hdf5write('testfile','/testmatrix',a);
generates files wich are not readable on windows but work perfectly on Mac/Linux. Also i tried the new hdf5 1.8.7 which has a slightly more verbose output:
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dchunk.c line 1758 in H5D_chunk_read(): chunked read fail
ed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 890 in H5D_contig_readvv(): can't perform
vectorized sieve buffer read
major: Dataset
minor: Can't operate on object
#006: ..\..\..\src\H5V.c line 1454 in H5V_opvv(): can't perform operation
major: Internal error (too specific to document in detail)
minor: Can't operate on object
#007: ..\..\..\src\H5Dcontig.c line 691 in H5D_contig_readvv_sieve_cb(): block
read failed
major: Dataset
minor: Read failed
#008: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#009: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#010: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#011: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
This looks like a HDF5 Bug to me.
regards
Stefan
Hi all,
i have a problem with hdf5 version 1.8.6. (32 bits) and Visual c++ 2008.
i have several files which contain a 4x545869 double - matrix datasset. I can open/read/write these files on linux and mac os, but windows refuses to work with these files.
I get the following call stack:
HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dcontig.c line 520 in H5D_contig_read(): contiguous read
failed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 692 in H5D_contig_readvv(): block read fai
led
major: Low-level I/O
minor: Read failed
#006: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#007: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#008: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#009: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Is there a way to detect whats wrong with the files? like an integrity checking tool?
regards
stefan
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Thanks for the hint,
h5dump is still giving output... i will see if it finishes. Anyway it looks like h5dump is not reading the full dataset at once! I think that is why it might finish. My code only blows up if i am not using compression, with compression everything is fine. Hence it seems that only reading the huge amount of numbers fails. Also HDF-View fails on Windows when reading the dataset....
regards Stefan
Dr. Stefan Schiffler
Zentrum für Technomathematik
Universität Bremen
Bibliothekstr. 1
D-28359 Bremen
Tel. +49 (0)421 218-63 822
www.scils.de
···
Am 21.06.2011 um 15:50 schrieb Elena Pourmal:
Stefan,
Actually... Could you please run h5dump on your files on windows and see if you still get an error?
If yes, then it is HDF5 problem and we will need to take a look.
Thank you!
Elena
On Jun 20, 2011, at 4:53 PM, Stefan Schiffler wrote:
Hello again, i have played a bit more:
Also building files on Mac/Linux using Matlab
a=zeros(545869,4);
hdf5write('testfile','/testmatrix',a);
generates files wich are not readable on windows but work perfectly on Mac/Linux. Also i tried the new hdf5 1.8.7 which has a slightly more verbose output:
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dchunk.c line 1758 in H5D_chunk_read(): chunked read fail
ed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 890 in H5D_contig_readvv(): can't perform
vectorized sieve buffer read
major: Dataset
minor: Can't operate on object
#006: ..\..\..\src\H5V.c line 1454 in H5V_opvv(): can't perform operation
major: Internal error (too specific to document in detail)
minor: Can't operate on object
#007: ..\..\..\src\H5Dcontig.c line 691 in H5D_contig_readvv_sieve_cb(): block
read failed
major: Dataset
minor: Read failed
#008: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#009: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#010: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#011: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
This looks like a HDF5 Bug to me.
regards
Stefan
Hi all,
i have a problem with hdf5 version 1.8.6. (32 bits) and Visual c++ 2008.
i have several files which contain a 4x545869 double - matrix datasset. I can open/read/write these files on linux and mac os, but windows refuses to work with these files.
I get the following call stack:
HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
#000: ..\..\..\src\H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ..\..\..\src\H5Dio.c line 448 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ..\..\..\src\H5Dcontig.c line 520 in H5D_contig_read(): contiguous read
failed
major: Dataset
minor: Read failed
#003: ..\..\..\src\H5Dselect.c line 275 in H5D_select_read(): read error
major: Dataspace
minor: Read failed
#004: ..\..\..\src\H5Dselect.c line 210 in H5D_select_io(): read error
major: Dataspace
minor: Read failed
#005: ..\..\..\src\H5Dcontig.c line 692 in H5D_contig_readvv(): block read fai
led
major: Low-level I/O
minor: Read failed
#006: ..\..\..\src\H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed
#007: ..\..\..\src\H5Faccum.c line 254 in H5F_accum_read(): driver read reques
t failed
major: Low-level I/O
minor: Read failed
#008: ..\..\..\src\H5FDint.c line 142 in H5FD_read(): driver read request fail
ed
major: Virtual File Layer
minor: Read failed
#009: ..\..\..\src\H5FDwindows.c line 827 in H5FD_windows_read(): file read fa
iled, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Read failed
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Is there a way to detect whats wrong with the files? like an integrity checking tool?
regards
stefan
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
