Hi Mark,
On May 21, 2010, at 1:57 PM, Mark Howison wrote:
> Hi Quincey, it is from:
>
>>> #008: H5FDmpio.c line 1726 in H5FD_mpio_write(): can't convert from
>>> size to size_i
Ah, sorry! It is actually in the MPI-IO VFD (and was in your original
message! :-) Hmm, that 'size' parameter is actually a length variable, not an
offset variable. Are you sure all the datasets are small?
Quincey
> Mark
>
> On Thu, May 20, 2010 at 4:15 AM, Quincey Koziol <[email protected]> wrote:
>> Hi Mark,
>> Sorry for the delay in replying...
>>
>> On May 18, 2010, at 11:31 AM, Mark Howison wrote:
>>
>>> Hi all,
>>>
>>> Chris Calderon, a user at NERSC, is receiving the errors at the bottom
>>> of the email during the following scenario:
>>>
>>> - a subset of 40 MPI tasks are each opening their own HDF5 file with
>>> MPI-IO in collective mode with the MPI_COMM_SELF communicator
>>> - each task writes about 20,000 small datasets totaling 10GB per file
>>>
>>> It's worth noting that we don't intend to use MPI-IO in independent mode, so
>>> we don't really need to fix this error to make the code operational,
>>> but we'd like to understand why the error occurred. At the lowest
>>> level, the error is "can't convert from size to size_i" and looking up
>>> the relevant code, I found:
>>>
>>> size_i = (int)size;
>>> if((hsize_t)size_i != size)
>>> HGOTO_ERROR...
>>>
>>> So my guess is that the offsets at some point become large enough to
>>> cause an int32 overflow. (Each file is about 10GB total, so the
>>> overflow probably occurs around the 8GB mark since 2 billion elements
>>> times 4 bytes per float = 8GB.) Is this a known bug in the MPI-IO VFD?
>>> This suggests that the bug will also affect independent mode, but
>>> another work around is for us to use the MPI-POSIX VFD, which should
>>> bypass this problem.
>>
>> There is a limitation in the MPI standard which specifies that an
>> 'int' type must be used for certain file operations, but we may be able to
>> relax that for the MPI-POSIX driver. Could you give me the line number for
>> the code snippet above? I'll take a look and see if it really needs to be
>> there.
>>
>> Thanks,
>> Quincey
>>
>>> I looked into using the CORE VFD per Mark Miller's suggestion in an earlier
>>> thread, but the problem is that the 10GB of data will not fit into memory,
>>> and I didn't see any API calls for requesting a "dump to file" before the
>>> file close.
>>>
>>> Thanks
>>> Mark
>>>
>>> ----
>>>
>>> HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process 16:
>>> #000: H5Dio.c line 266 in H5Dwrite(): can't write data
>>> major: Dataset
>>> minor: Write failed
>>> #001: H5Dio.c line 578 in H5D_write(): can't write data
>>> major: Dataset
>>> minor: Write failed
>>> #002: H5Dmpio.c line 552 in H5D_contig_collective_write(): couldn't
>>> finish shared collective MPI-IO
>>> major: Low-level I/O
>>> minor: Write failed
>>> #003: H5Dmpio.c line 1586 in H5D_inter_collective_io(): couldn't
>>> finish collective MPI-IO
>>> major: Low-level I/O
>>> minor: Can't get value
>>> #004: H5Dmpio.c line 1632 in H5D_final_collective_io(): optimized write
>>> failed
>>> major: Dataset
>>> minor: Write failed
>>> #005: H5Dmpio.c line 334 in H5D_mpio_select_write(): can't finish
>>> collective parallel write
>>> major: Low-level I/O
>>> minor: Write failed
>>> #006: H5Fio.c line 167 in H5F_block_write(): file write failed
>>> major: Low-level I/O
>>> minor: Write failed
>>> #007: H5FDint.c line 185 in H5FD_write(): driver write request failed
>>> major: Virtual File Layer
>>> minor: Write failed
>>> #008: H5FDmpio.c line 1726 in H5FD_mpio_write(): can't convert from
>>> size to size_i
>>> major: Internal error (too specific to document in detail)
>>> minor: Out of range
>>>
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>>
>>
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>
> _______________________________________________
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