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 <[email protected]> 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 >[email protected] > >From: Hdf-forum [mailto:[email protected]] On Behalf >Of Ruxandra Marasescu >Sent: Tuesday, February 28, 2017 9:40 AM >To: [email protected] >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 -- Sent from my Android device.
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