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NetCDF Benchmark Tool

Introduction

NetCDF Performance Benchmark Tool (NetCDF-Bench) was developed to measure NetCDF performance on devices ranging from notebooks to large HPC systems. It mimics the typical I/O behavior of scientific climate applications and captures the performance on each node/process. In the end, it aggregates the data to human readable summary.

The data layout is inspired by simulation where a 3D object changes its shape over time. Therefore, it creates a 3-dimensional space and several time steps. Furthermore, we assume that a scientific application is executed on several processes on multiple nodes, and processes the time steps in sequential order.

NetCDF-Bench is parallel bechmark. It supports independent I/O, collective I/O and chunked I/O modes. If necessary, it can pre-fill the variables with some value.

Domain decomposition

NetCDF-Bench supports various access patterns on a 4D dataset (one time dimension and three data dimensions). The short notation of the geometry is (t:x:y:z), e.g., (10:1000:1000:500).

The pictures shows an example of data with geometry (3:6:4:3).

Domain decomposition: 3:6:4:3

Data size vs. Block size

The data is written in blocks to the shared file. The block size can be customized, but there are some restrictions. Assume, that

  • t:x:y:z is the data size
  • t is a multiple of some integer value s
  • nn is the number of nodes
  • ppn the number of processes per node
  • px and py are integer values, that satisfies the condition: px · py = nn · ppn

Then (s:x/px:y/py:z) is a valid block size. (Default block size is (1:x/nn:y/ppn:z).)

Each process allocates (s:x/px:y/py:z) * type_size memory space.

The data is read/written in timesteps.

Usage

NetCDF-Bench is designed in that way that it can run without any parameters, but for advanced usage our tool provides a number of parameters.

Benchtool (datatype: int) 
Synopsis: ./benchtool [-n] [-p] [-d] [-b] [-c] [-r] [-w] [-t] [-u] [-f] [-x] [-F] [--verify]  [Optional Args]

Flags
-r, --read                    Enable read benchmark
-w, --write                   Enable write benchmark
-u, --unlimited               Enable unlimited time dimension
-F, --use-fill-value          Write a fill value
--verify                      Verify that the data read is correct (reads the data again)

Optional arguments
-n, --nn=0                    Number of nodes
-p, --ppn=0                   Number of processes
-d, --data-geometry=STRING    Data geometry `(t:x:y:z)`
-b, --block-geometry=STRING   Block geometry `(t:x:y:z)`
-c, --chunk-geometry=STRING   Chunk geometry `(t:x:y:z|auto)`
-t, --io-type=ind             Independent / Collective I/O (ind|coll)
-f, --testfile=STRING         Filename of the testfile
-x, --output-format=human     Output-Format (parser|human)

Example output

NetCDF-Bench aggregates the result of all processes and creates a summary. Here is an example output:

$ mpiexec -n 1 ./benchtool 
[1494497686.787267] [mlogin103:1936 :0]         sys.c:744  MXM  WARN  Conflicting CPU frequencies detected, using: 2501.00
Benchtool (datatype: int) 
Data geometry (t:x:y:z x sizeof(type))     100:100:100:10 x 4 bytes               
Block geometry (t:x:y:z x sizeof(type))      1:100:100:10 x 4 bytes               
Datasize                                             40000000 bytes                (40.0 MB)
Blocksize                                              400000 bytes                (400.0 kB)
I/O Access                                        independent
Storage                                            contiguous
File length                                             fixed
File value                                                 no
                                                                               min                  avg                  max                     
benchmark:write      Open time                                        0.2811507931         0.2811507931         0.2811507931 secs                
benchmark:write      I/O time                                         0.1901479111         0.1901479111         0.1901479111 secs                
benchmark:write      Close time                                       0.3576489800         0.3576489800         0.3576489800 secs                
benchmark:write      I/O Performance (w/o open/close)               200.6173638152       200.6173638152       200.6173638152 MiB/s               
benchmark:write      I/O Performance                                 46.0185526612        46.0185526612        46.0185526612 MiB/s

On-going work

We plan to extend the tool with the following features.

  1. Drop caches - Cached data can influence the results of I/O performance, therefore it must be cleared before benchmark runs. This features must run in user space.
  2. Compression - This feature is useful to benchmark the NetCDF compression, but also for people who are working on new compression methods.
  3. CSV output - Detailed information about the benchmark run for analysis with third party tools.