H5FD_sec2_write failed to write error EINVAL

Hdf-forum archives
1

Hello,

We have a similar issue with the one mentioned here:

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

2

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
help@hdfgroup.org

h5cmpstr.c (3.45 KB)

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Ruxandra Marasescu
Sent: Tuesday, February 28, 2017 9:40 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] H5FD_sec2_write failed to write error EINVAL

Hello,

We have a similar issue with the one mentioned here:

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

3

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 <bljones@hdfgroup.org> 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
help@hdfgroup.org

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf
Of Ruxandra Marasescu
Sent: Tuesday, February 28, 2017 9:40 AM
To: hdf-forum@lists.hdfgroup.org
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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