benchmark program question

[Marty Barnaby]

For my 26 GB/s rate, I don't know many of the specifics the FS itself, 
except that it what is being called /scratch_grande on our big XT3, 
Redstorm.

For reasons, I didn't choose IOR, but, instead, ran a simple, 
MPI-executable based on something which had been written by Rob Matzke, 
for our now defunct SAF IO library project.

He basically had a user input parameter for the blocksize, and, after 
the MPI_File_open, went around on a loop nrecs many times, redumping the 
same buffer with MPI_File_write_at_all, after recomputing for each 
processor, respectively, the offset based on the buffer size on the 
total processor count.

We were working on having a real user get his enormous restart in less 
time, when I decided to find the combination that got me the absolute 
fastest. I don't have an entire historgram of parameters, but I found 
that a job where the processor count was the same as the maximum LFS 
stripe-count (160), and my buffer size was 20 MB per processor, I could 
consistently get to 26 GB/s for files over 100 GB in total, final size.

I thought this had no practical value at the time, since it means having 
3.3 GB across the communicator for one, collective, field or variable 
store operation. However, now I'm seeing fields this large, and think 
that this may approach representing the second part of a properly 
applied 2-phase aggregation. Besides that already available in ROMIO, I 
am working with the CAM code from UCAR, where they have written their 
own IO package that applies the primary phase in a specific manner, 
usually involving 'rearrangement'; turning a large number of small 
buffers into a small number of larger ones, on a subset of the global 
communicators processors, then performs the writes via PNetCDF.

Marty



Wei-keng Liao wrote:
> Hi,
>
> IOR benchmark includes pnetcdf. http://sourceforge.net/projects/ior-sio
> Its pnetcdf was recently modified to use record variables. That should
> take care of the file appending I/O mode.
>
> I am interested in your results of 26 GB/s on Lustre using MPI-IO on
> shared files. My experience was about 15 GB/s top on Jaguar @ORNL using an
> application I/O kernel whose data partitioning patterns are 3D
> block-block-block. But the results were obtained when Jaguar was running
> catamount. Jaguar is currently under upgrade to new hardware and software.
> I would appreciate if you can share your results.
>
> Wei-keng
>
>
> On Tue, 26 Feb 2008, Marty Barnaby wrote:
>
>   
>> I'm new to the parallel NetCDF interface, and I don't have much
>> experience with NetCDF either. Because of new interest on our part, we
>> would like to have a straightforward, benchmark program to get byte-rate
>> metrics for writing to a Posix FS (chiefly, some large Lustre
>> deployments). I've had some reasonable experiences in this at the MPI-IO
>> level, achieving a sustained, average rate of 26 GB/s; this writing to a
>> single, shared file with an LFS stripe-count of 160. If anyone is
>> interested, I could provide them with more specifics.
>>
>> I can't find the benchmark-type code that I really need, though I've
>> been looking at the material under /test like /test_double/test_write.c
>> This I've compiled and executed successfully at the appropriate -np 4
>> level.
>>
>> There are three dynamics I would like to have that I can't see how to
>> get.
>>
>>   1. Run on any number of processors. I'm sure this is simple, but I want to
>>       know where the failure is when I attempt it.
>>
>>   2. Set the number of bytes appended to an open file in a single, atomic,
>>       collective write operation. In my MPI-IO benchmark program I merely
>>       got this number by having a buffer size on each processor, and
>> the total
>>       was the product of this times the number of processors. At the higher
>>       level of PNetCDF I'm not sure which value I'm getting in the def_var
>>       and put_var.
>>
>>   3. Be able to perform any number of equivalent, collective write operations,
>>       appending to the same, open file. Simply a:
>>
>>       for ( i = 0; i < NUMRECS; i++ )
>>
>>       concept. This is basically what our scientific, simulation applications
>> do in their 'dump' mode.
>>
>>
>> Thanks,
>> Marty Barnaby
>>
>>     
>
>
>   

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