H5FD_sec2_write failed to write error EINVAL

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H5FD_sec2_write failed to write error EINVAL

Ruxandra Marasescu

Hello,

 

We have a similar issue with the one mentioned here:

http://stackoverflow.com/questions/32077579/exception-appending-dataframe-chunk-with-string-values-to-large-hdf5-file-using

 

Was there a solution to it please?

5FD_sec2_write

file write failed: time = Tue Aug 18 18:26:17 2015

, filename = 'large_file.h5', file descriptor = 4, errno = 22, error message = 'Invalid argument', buf = 0000000066A40018, total write size = 262095, bytes this sub-write = 262095, bytes actually written = 18446744073709551615, offset = 47615949533

 

 

The error we are having is:

#000: C:\dev\hdf5-1.8.17\src\H5Dio.c line 271 in H5Dwrite(): can't prepare for writing data

    major: Dataset

    minor: Write failed

  #001: C:\dev\hdf5-1.8.17\src\H5Dio.c line 347 in H5D__pre_write(): can't write chunk directly

    major: Dataset

    minor: Write failed

  #002: C:\dev\hdf5-1.8.17\src\H5Dchunk.c line 392 in H5D__chunk_direct_write(): unable to write raw data to file

    major: Dataset

    minor: Write failed

  #003: C:\dev\hdf5-1.8.17\src\H5Fio.c line 171 in H5F_block_write(): write through metadata accumulator failed

    major: Low-level I/O

    minor: Write failed

  #004: C:\dev\hdf5-1.8.17\src\H5Faccum.c line 825 in H5F__accum_write(): file write failed

    major: Low-level I/O

    minor: Write failed

  #005: C:\dev\hdf5-1.8.17\src\H5FDint.c line 260 in H5FD_write(): driver write request failed

    major: Virtual File Layer

    minor: Write failed

  #006: C:\dev\hdf5-1.8.17\src\H5FDsec2.c line 802 in H5FD_sec2_write(): file write failed: time = Tue Feb 28 10:00:02 2017

, filename = 'C:\hdf_file.fast5', file descriptor = 4, errno = 22, error message = 'Invalid argument', buf = 00000000C4F6D950, total write size = 41681, bytes this sub-write = 41681, bytes actually written = 18446744073709551615, offset = 142297119656

    major: Low-level I/O

    minor: Write failed

 

Thank you,

Ruxandra

 


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Re: H5FD_sec2_write failed to write error EINVAL

bljones

Hello Ruxandra,

 

I saw in the stackoverflow issue that you referenced, that the user had contacted hdfgroup’s support. So, I went through old helpdesk issues and found the issue from the user.  We never actually determined what his issue was, but we did determine that the problem was specific to his machine.

 

I had sent him an HDF5 C example program that created a 100+ GB file. When he compiled and ran the program on his machine, it too failed. However, he could run the program successfully on another windows machine.

 

I still have the example program, and  attached it to this message in case you might find it helpful (h5cmpstr.c).

 

-Barbara

[hidden email]

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of Ruxandra Marasescu
Sent: Tuesday, February 28, 2017 9:40 AM
To: [hidden email]
Subject: [Hdf-forum] H5FD_sec2_write failed to write error EINVAL

 

Hello,

 

We have a similar issue with the one mentioned here:

http://stackoverflow.com/questions/32077579/exception-appending-dataframe-chunk-with-string-values-to-large-hdf5-file-using

 

Was there a solution to it please?

5FD_sec2_write

file write failed: time = Tue Aug 18 18:26:17 2015

, filename = 'large_file.h5', file descriptor = 4, errno = 22, error message = 'Invalid argument', buf = 0000000066A40018, total write size = 262095, bytes this sub-write = 262095, bytes actually written = 18446744073709551615, offset = 47615949533

 

 

The error we are having is:

#000: C:\dev\hdf5-1.8.17\src\H5Dio.c line 271 in H5Dwrite(): can't prepare for writing data

    major: Dataset

    minor: Write failed

  #001: C:\dev\hdf5-1.8.17\src\H5Dio.c line 347 in H5D__pre_write(): can't write chunk directly

    major: Dataset

    minor: Write failed

  #002: C:\dev\hdf5-1.8.17\src\H5Dchunk.c line 392 in H5D__chunk_direct_write(): unable to write raw data to file

    major: Dataset

    minor: Write failed

  #003: C:\dev\hdf5-1.8.17\src\H5Fio.c line 171 in H5F_block_write(): write through metadata accumulator failed

    major: Low-level I/O

    minor: Write failed

  #004: C:\dev\hdf5-1.8.17\src\H5Faccum.c line 825 in H5F__accum_write(): file write failed

    major: Low-level I/O

    minor: Write failed

  #005: C:\dev\hdf5-1.8.17\src\H5FDint.c line 260 in H5FD_write(): driver write request failed

    major: Virtual File Layer

    minor: Write failed

  #006: C:\dev\hdf5-1.8.17\src\H5FDsec2.c line 802 in H5FD_sec2_write(): file write failed: time = Tue Feb 28 10:00:02 2017

, filename = 'C:\hdf_file.fast5', file descriptor = 4, errno = 22, error message = 'Invalid argument', buf = 00000000C4F6D950, total write size = 41681, bytes this sub-write = 41681, bytes actually written = 18446744073709551615, offset = 142297119656

    major: Low-level I/O

    minor: Write failed

 

Thank you,

Ruxandra

 


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

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Re: H5FD_sec2_write failed to write error EINVAL

Samer Afach-4
Hi all:

I wanna add that we had a similar issue with h5py. It used to crash when we write certain things/strings. Nothing reasonable fixed it! Not even upgrading to Windows 10. Eventually we formatted the machine and that fixed the problem. I would say that the problem had something to do with shared library linking. Because it also created some other problems with PyQt. I don't know if this is related really, but when I read this, I was betting it's Windows 7, and I won the bet.

Cheers,
Samer Afach

On March 6, 2017 9:56:32 PM GMT+01:00, Barbara Jones <[hidden email]> wrote:

Hello Ruxandra,

 

I saw in the stackoverflow issue that you referenced, that the user had contacted hdfgroup’s support. So, I went through old helpdesk issues and found the issue from the user.  We never actually determined what his issue was, but we did determine that the problem was specific to his machine.

 

I had sent him an HDF5 C example program that created a 100+ GB file. When he compiled and ran the program on his machine, it too failed. However, he could run the program successfully on another windows machine.

 

I still have the example program, and  attached it to this message in case you might find it helpful (h5cmpstr.c).

 

-Barbara

[hidden email]

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of Ruxandra Marasescu
Sent: Tuesday, February 28, 2017 9:40 AM
To: [hidden email]
Subject: [Hdf-forum] H5FD_sec2_write failed to write error EINVAL

 

Hello,

 

We have a similar issue with the one mentioned here:

http://stackoverflow.com/questions/32077579/exception-appending-dataframe-chunk-with-string-values-to-large-hdf5-file-using

 

Was there a solution to it please?

5FD_sec2_write

file write failed: time = Tue Aug 18 18:26:17 2015

, filename = 'large_file.h5', file descriptor = 4, errno = 22, error message = 'Invalid argument', buf = 0000000066A40018, total write size = 262095, bytes this sub-write = 262095, bytes actually written = 18446744073709551615, offset = 47615949533

 

 

The error we are having is:

#000: C:\dev\hdf5-1.8.17\src\H5Dio.c line 271 in H5Dwrite(): can't prepare for writing data

    major: Dataset

    minor: Write failed

  #001: C:\dev\hdf5-1.8.17\src\H5Dio.c line 347 in H5D__pre_write(): can't write chunk directly

    major: Dataset

    minor: Write failed

  #002: C:\dev\hdf5-1.8.17\src\H5Dchunk.c line 392 in H5D__chunk_direct_write(): unable to write raw data to file

    major: Dataset

    minor: Write failed

  #003: C:\dev\hdf5-1.8.17\src\H5Fio.c line 171 in H5F_block_write(): write through metadata accumulator failed

    major: Low-level I/O

    minor: Write failed

  #004: C:\dev\hdf5-1.8.17\src\H5Faccum.c line 825 in H5F__accum_write(): file write failed

    major: Low-level I/O

    minor: Write failed

  #005: C:\dev\hdf5-1.8.17\src\H5FDint.c line 260 in H5FD_write(): driver write request failed

    major: Virtual File Layer

    minor: Write failed

  #006: C:\dev\hdf5-1.8.17\src\H5FDsec2.c line 802 in H5FD_sec2_write(): file write failed: time = Tue Feb 28 10:00:02 2017

, filename = 'C:\hdf_file.fast5', file descriptor = 4, errno = 22, error message = 'Invalid argument', buf = 00000000C4F6D950, total write size = 41681, bytes this sub-write = 41681, bytes actually written = 18446744073709551615, offset = 142297119656

    major: Low-level I/O

    minor: Write failed

 

Thank you,

Ruxandra

 


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Hdf-forum is for HDF software users discussion.
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