Hi,
Yes, the selections in the file and memory dataspace are both the same rank and
dimension. I am basically writing a very large vector, so rank always remains 1
and I use the same dimension for both the memory and file dataspace.
Is there something else I may need to check ?
Can I find out where exactly the problem lies ?
Regards,
Nikhil
Hi Nikhil,
> Hi,
>
> While doing paallel writes, if the size of the data being written by
> each
> processor is not the same, can it lead to the operation getting
> serialized by
> the MPI Implementation of HDF5 ?This probably shouldn't matter, the HDF5 library should just create
an MPI file view that incorporates the different sizes.> After looking at all possible reasons that may be slowing my write
> operation,
> I now think that this may be reason.Are the selections in the memory dataspaces you are using the same
rank and dimensions as the file dataspace selections?Quincey
> Regards,
> Nikhil
>
>> Hi Nikhil,
>>
>>
>>> Hi,
>>>
>>> Sorry about that. Its attached this time.
>>
>> OK, I took a look at your section of code and although it's doing
>> parallel writes, they may be getting serialized somewhere under HDF5
>> by the MPI implementation due to the [apparently] non-regular pattern
>> you are writing. It's also very likely that you are writing too
>> small
>> of an amount of data to see much benefit from parallel I/O.
>>
>> Quincey
>>
>>
>>> Regards,
>>> NIkhil
>>>
>>>> Hi Nikhil,
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> Thanks for your reply.
>>>>>
>>>>> I am attaching part of my code that does the parallel write.
>>>>> Points to notice are:
>>>>>
>>>>> 1. for 'nprocs' processors, there are 'nend' diagonal processors
>>>>> that are
>>>>> actually doing the write, where:
>>>>>
>>>>> nprocs = nend * (nend+1) / 2
>>>>>
>>>>> 2. the subroutine for parallel write, 'phdfwrite' is present in
>>>>> the
>>>>> file hdfmodule.f
>>>>>
>>>>> 3. This subroutine is called only by the diagonal processors(nend)
>>>>>
>>>>> Please find attached the source files.
>>>>
>>>> There was no attachment on your message.
>>>>
>>>> Quincey
>>>>
>>>>> I also notice that for 265875 real nos.,
>>>>> there is no speed difference even between INDEPENDENT and
>>>>> COLLECTIVE
>>>>> IO. Is this
>>>>> because of the small size of the array. Also do you find anything
>>>>> that I may be
>>>>> doing which reduces the speed ?
>>>>>
>>>>> Best Regards,
>>>>> Nikhil
>>>>>
>>>>>> Hi Nikhil,
>>>>>>
>>>>>>
>>>>>>> Hi All,
>>>>>>>
>>>>>>> I am writing a HDF5 file in parallel. But to my surprise, the
>>>>>>> performance of the
>>>>>>> parallel write isn't better compared to the serial binary write
>>>>>>> operation. To
>>>>>>> write 265875 real numbers, my HDF write takes about 0.1 seconds
>>>>>>> whereas the
>>>>>>> serial binary operation takes around 0.07 seconds. This is
>>>>>>> surprising as
>>>>>>> parallel should be atleast as fast as serial if not any faster.
>>>>>>>
>>>>>>> Can anybody give me any suggestions as to what can be done to
>>>>>>> noticably speedup
>>>>>>> this write operation ?
>>>>>>
>>>>>> Hmm, are you using collective or independent parallel I/O?
>>>>>> Also,
>>>>>> that's a pretty small dataset, so you are not likely to see much
>>>>>> difference either way.
>>>>>>
>>>>>>> Will the performance of HDF5 write be better than binary for
>>>>>>> very
>>>>>>> large arrays ?
>>>>>>
>>>>>> Our goal is to make HDF5 writes be equivalent to binary for
>>>>>> large
>>>>>> raw
>>>>>> data I/O operations, but to make the files produced self-
>>>>>> describing,
>>>>>> portable, etc. also.
>>>>>>
>>>>>>> If not how can I bring any substantial speedup ?
>>>>>>
>>>>>> This is a very hard question to answer without more
>>>>>> details...
>>>>>>
>>>>>> Quincey
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Regards,
>>>>>>> Nikhil
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------------
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> subscribe@hdfgroup.org
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
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>>>>>> .
>>>>>>
>>>>>
>>>>>
>>>>> Regards,
>>>>> Nikhil
>>>>>
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------------
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>>>>>
>>>>>
>>>>
>>>
>>>
>>> Regards,
>>> Nikhil
>>> <
>>> parallel
>>> .f
>>>>
>>> <
>>> hdfmodule
>>> .f
>>>>
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>>
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>
>
> Regards,
> Nikhil
>
>
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Regards,
Nikhil
···
On Aug 5, 2008, at 12:21 PM, Nikhil Laghave wrote:
>> On Jul 10, 2008, at 2:34 PM, Nikhil Laghave wrote:
>>>> On Jul 10, 2008, at 2:07 PM, Nikhil Laghave wrote:
>>>>>> On Jul 9, 2008, at 6:39 PM, Nikhil Laghave wrote:
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