Unless things have changed since my day, it is possible to read pnetcdf
files with the netCDF library. It must be built with --enable-pnetcdf and
with-pnetcdf=/some/location, IIRC.
On Fri, Oct 17, 2014 at 6:33 AM, Samrat Rao <samrat.rao@xxxxxxxxx> wrote:
> Hi,
>
> I'm sorry for the late reply.
>
> I have no classic/netcdf-3 datasets --- datasets are to be generated. All
> my codes are also new.
>
> Initially i tried with pnetcdf, wrote a few variables, but found that the
> format was CDF-5 which 'normal' netcdf would not read.
>
> I also need to read some bits of netcdf data in Matlab, so i thought of
> sticking to the usual netcdf-4 compiled for parallel io. It is also likely
> that i will have to share my workload with others in my group and/or leave
> the code for future people to work on.
>
> Does matlab read cdf-5 files?
>
> So i preferred the usual netcdf. Rob, i hope you are not annoyed.
>
> But most of the above is for another day. Currently i am stuck elsewhere.
>
> With a less no of processors, 216, the single netcdf file gets created (i
> create i single netcdf file for each variable), but for anything above that
> i get these errors:
> NetCDF: Bad chunk sizes.
> Not sure where these errors come from.
>
> Then i shifted to dumping outputs from each processor in simple binary ---
> this works till about 1500 processors. Above this number the code gets
> stuck and eventually aborts.
>
> This issue is not new. My colleague too had problems with running his code
> on 1500+ procs.
>
> Today i came to know that opening a large number of files (each proc
> writes 1 file) can overwhelm the system --- solving this requires more than
> rudimentary techniques of writing --- or understanding the system's
> inherent parameters/bottlenecks.
>
> So netcdf is probably out of bounds for now --- will try again if the
> simple binary write from each processor gets sorted out.
>
> Does anyone have any suggestion?
>
> Thanks,
> Samrat.
>
>
> On Thu, Oct 2, 2014 at 7:52 PM, Rob Latham <robl@xxxxxxxxxxx> wrote:
>
>>
>>
>> On 10/02/2014 01:24 AM, Samrat Rao wrote:
>>
>>> Thanks for your replies.
>>>
>>> I estimate that i will be requiring approx 4000 processors and a total
>>> grid resolution of 2.5 billion for my F90 code. So i need to
>>> think/understand which is better - parallel netCDF or the 'normal' one.
>>>
>>
>> There are a few specific nifty features in pnetcdf that can let you get
>> really good performance, but 'normal' netCDF is a fine choice, too.
>>
>> Right now I do not know how to use parallel-netCDF.
>>>
>>
>> It's almost as simple as replacing every 'nf' call with 'nfmpi' but you
>> will be just fine if you stick with UCAR netCDF-4
>>
>> Secondly, i hope that the netCDF-4 files created by either parallel
>>> netCDF or the 'normal' one are mutually compatible. For analysis I will
>>> be extracting data using the usual netCDF library, so in case i use
>>> parallel-netCDF then there should be no inter-compatibility issues.
>>>
>>
>> For truly large variables, parallel-netcdf introduced, with some
>> consultation from the UCAR folks, a 'CDF-5' file format. You have to
>> request it explicitly, and then in that one case you would have a pnetcdf
>> file that netcdf tools would not understand.
>>
>> In all other cases, we work hard to keep pnetcdf and "classic" netcdf
>> compatible. UCAR NetCDF has the option for an HDF5-based backend -- and in
>> fact it's not an option if you want parallel I/O with NetCDF-4 -- is not
>> compatible with parallel-netcdf. By now, your analysis tools surely are
>> updated to understand the new HDF5-based backend?
>>
>> I suppose it's possible you've got some 6 year old analysis tool that
>> does not understand NetCDF-4's HDF5-based file format. Parallel-netcdf
>> would allow you to simulate with parallel i/o and produce a classic netCDF
>> file. But I would be shocked and a little bit angry if that was actually a
>> good reason to use parallel-netcdf in 2014.
>>
>>
>> ==rob
>>
>>
>> --
>> Rob Latham
>> Mathematics and Computer Science Division
>> Argonne National Lab, IL USA
>>
>
>
>
> --
>
> Samrat Rao
> Research Associate
> Engineering Mechanics Unit
> Jawaharlal Centre for Advanced Scientific Research
> Bangalore - 560064, India
>
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