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224 lines
8.7 KiB
Plaintext
224 lines
8.7 KiB
Plaintext
1. Title:
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User Guide for SWMR Use Case Programs
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2. Purpose:
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This is a User Guide of the SWMR Use Case programs. It descibes the use
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case program and explain how to run them.
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2.1. Author and Dates:
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Version 2: By Albert Cheng, 2013/06/18.
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Version 1: By Albert Cheng, 2013/06/01.
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%%%%Use Case 1.7%%%%
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3. Use Case [1.7]:
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Appending a single chunk
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3.1. Program name:
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use_append_chunk
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3.2. Description:
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Appending a single chunk of raw data to a dataset along an unlimited
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dimension within a pre-created file and reading the new data back.
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It first creates one 3d dataset using chunked storage, each chunk
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is a (1, chunksize, chunksize) square. The dataset is (unlimited,
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chunksize, chunksize). Data type is 2 bytes integer. It starts out
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"empty", i.e., first dimension is 0.
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The writer then appends planes, each of (1,chunksize,chunksize)
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to the dataset. Fills each plan with plane number and then writes
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it at the nth plane. Increases the plane number and repeats till
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the end of dataset, when it reaches chunksize long. End product is
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a chunksize^3 cube.
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The reader is a separated process, running in parallel with
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the writer. It reads planes from the dataset. It expects the
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dataset is being changed (growing). It checks the unlimited dimension
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(dimension[0]). When it increases, it will read in the new planes, one
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by one, and verify the data correctness. (The nth plan should contain
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all "n".) When the unlimited dimension grows to the chunksize (it
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becomes a cube), that is the expected end of data, the reader exits.
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3.3. How to run the program:
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Simplest way is
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$ use_append_chunk
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It creates a skeleton dataset (0,256,256) of shorts. Then fork off
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a process, which becomes the reader process to read planes from the
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dataset, while the original process continues as the writer process
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to append planes onto the dataset.
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Other possible options:
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1. -z option: different chunksize. Default is 256.
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$ use_append_chunk -z 1024
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It uses (1,1024,1024) chunks to produce a 1024^3 cube, about 2GB big.
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2. -f filename: different dataset file name
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$ use_append_chunk -f /gpfs/tmp/append_data.h5
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The data file is /gpfs/tmp/append_data.h5. This allows two independent
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processes in separated compute nodes to access the datafile on the
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shared /gpfs file system.
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3. -l option: launch only the reader or writer process.
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$ use_append_chunk -f /gpfs/tmp/append_data.h5 -l w # in node X
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$ use_append_chunk -f /gpfs/tmp/append_data.h5 -l r # in node Y
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In node X, launch the writer process, which creates the data file
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and appends to it.
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In node Y, launch the read process to read the data file.
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Note that you need to time the read process to start AFTER the write
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process has created the skeleton data file. Otherwise, the reader
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will encounter errors such as data file not found.
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4. -n option: number of planes to write/read. Default is same as the
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chunk size as specified by option -z.
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$ use_append_chunk -n 1000 # 1000 planes are writtern and read.
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5. -s option: use SWMR file access mode or not. Default is yes.
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$ use_append_chunk -s 0
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It opens the HDF5 data file without the SWMR access mode (0 means
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off). This likely will result in error. This option is provided for
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users to see the effect of the neede SWMR access mode for concurrent
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access.
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3.4. Test Shell Script:
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The Use Case program is installed in the test/ directory and is
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compiled as part of the make process. A test script (test_usecases.sh)
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is installed in the same directory to test the use case programs. The
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test script is rather basic and is more for demonstrating how to
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use the program.
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%%%%Use Case 1.8%%%%
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4. Use Case [1.8]:
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Appending a hyperslab of multiple chunks.
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4.1. Program name:
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use_append_mchunks
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4.2. Description:
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Appending a hyperslab that spans several chunks of a dataset with
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unlimited dimensions within a pre-created file and reading the new
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data back.
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It first creates one 3d dataset using chunked storage, each chunk is a (1,
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chunksize, chunksize) square. The dataset is (unlimited, 2*chunksize,
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2*chunksize). Data type is 2 bytes integer. Therefore, each plane
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consists of 4 chunks. It starts out "empty", i.e., first dimension is 0.
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The writer then appends planes, each of (1,2*chunksize,2*chunksize)
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to the dataset. Fills each plan with plane number and then writes
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it at the nth plane. Increases the plane number and repeats till
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the end of dataset, when it reaches chunksize long. End product is
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a (2*chunksize)^3 cube.
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The reader is a separated process, running in parallel with
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the writer. It reads planes from the dataset. It expects the
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dataset is being changed (growing). It checks the unlimited dimension
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(dimension[0]). When it increases, it will read in the new planes, one
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by one, and verify the data correctness. (The nth plan should contain
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all "n".) When the unlimited dimension grows to the 2*chunksize (it
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becomes a cube), that is the expected end of data, the reader exits.
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4.3. How to run the program:
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Simplest way is
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$ use_append_mchunks
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It creates a skeleton dataset (0,512,512) of shorts. Then fork off
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a process, which becomes the reader process to read planes from the
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dataset, while the original process continues as the writer process
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to append planes onto the dataset.
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Other possible options:
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1. -z option: different chunksize. Default is 256.
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$ use_append_mchunks -z 512
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It uses (1,512,512) chunks to produce a 1024^3 cube, about 2GB big.
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2. -f filename: different dataset file name
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$ use_append_mchunks -f /gpfs/tmp/append_data.h5
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The data file is /gpfs/tmp/append_data.h5. This allows two independent
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processes in separated compute nodes to access the datafile on the
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shared /gpfs file system.
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3. -l option: launch only the reader or writer process.
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$ use_append_mchunks -f /gpfs/tmp/append_data.h5 -l w # in node X
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$ use_append_mchunks -f /gpfs/tmp/append_data.h5 -l r # in node Y
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In node X, launch the writer process, which creates the data file
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and appends to it.
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In node Y, launch the read process to read the data file.
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Note that you need to time the read process to start AFTER the write
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process has created the skeleton data file. Otherwise, the reader
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will encounter errors such as data file not found.
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4. -n option: number of planes to write/read. Default is same as the
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chunk size as specified by option -z.
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$ use_append_mchunks -n 1000 # 1000 planes are writtern and read.
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5. -s option: use SWMR file access mode or not. Default is yes.
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$ use_append_mchunks -s 0
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It opens the HDF5 data file without the SWMR access mode (0 means
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off). This likely will result in error. This option is provided for
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users to see the effect of the neede SWMR access mode for concurrent
|
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access.
|
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4.4. Test Shell Script:
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The Use Case program is installed in the test/ directory and is
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compiled as part of the make process. A test script (test_usecases.sh)
|
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is installed in the same directory to test the use case programs. The
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test script is rather basic and is more for demonstrating how to
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use the program.
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%%%%Use Case 1.9%%%%
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5. Use Case [1.9]:
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Appending n-1 dimensional planes
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5.1. Program names:
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use_append_chunk and use_append_mchunks
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5.2. Description:
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Appending n-1 dimensional planes or regions to a chunked dataset where
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the data does not fill the chunk.
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This means the chunks have multiple planes and when a plane is written,
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only one of the planes in each chunk is written. This use case is
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achieved by extending the previous use cases 1.7 and 1.8 by defining the
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chunks to have more than 1 plane. The -y option is implemented for both
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use_append_chunk and use_append_mchunks.
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5.3. How to run the program:
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Simplest way is
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$ use_append_mchunks -y 5
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It creates a skeleton dataset (0,512,512), with storage chunks (5,512,512)
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of shorts. It then proceeds like use case 1.8 by forking off a reader
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process. The original process continues as the writer process that
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writes 1 plane at a time, updating parts of the chunks involved. The
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reader reads 1 plane at a time, retrieving data from partial chunks.
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The other possible options will work just like the two use cases.
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5.4. Test Shell Script:
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Commands are added with -y options to demonstrate how the two use case
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programs can be used as for this use case.
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