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-rw-r--r--MANIFEST18
-rw-r--r--doc/html/study.html172
-rw-r--r--doc/html/study_1000x1000.gifbin6594 -> 0 bytes
-rw-r--r--doc/html/study_250x250.gifbin6914 -> 0 bytes
-rw-r--r--doc/html/study_499x499.gifbin10429 -> 0 bytes
-rw-r--r--doc/html/study_5000x1000.gifbin10653 -> 0 bytes
-rw-r--r--doc/html/study_500x500.gifbin6842 -> 0 bytes
-rw-r--r--doc/html/study_p1.gifbin6550 -> 0 bytes
-rw-r--r--doc/html/study_p1.obj113
9 files changed, 10 insertions, 293 deletions
diff --git a/MANIFEST b/MANIFEST
index 8112a82..129bd01 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -58,6 +58,16 @@
./doc/html/Attributes.html
./doc/html/Big.html
./doc/html/Caching.html
+./doc/html/Chunking.html
+./doc/html/Chunk_f1.gif
+./doc/html/Chunk_f1.obj _DO_NOT_DISTRIBUTE_
+./doc/html/Chunk_f2.gif
+./doc/html/Chunk_f2.obj _DO_NOT_DISTRIBUTE_
+./doc/html/Chunk_f3.gif
+./doc/html/Chunk_f4.gif
+./doc/html/Chunk_f5.gif
+./doc/html/Chunk_f6.gif
+./doc/html/Chunk_f6.obj _DO_NOT_DISTRIBUTE_
./doc/html/CodeReview.html _DO_NOT_DISTRIBUTE_
./doc/html/Coding.html
./doc/html/Copyright.html
@@ -132,14 +142,6 @@
./doc/html/review1.html _DO_NOT_DISTRIBUTE_
./doc/html/review1a.html _DO_NOT_DISTRIBUTE_
./doc/html/storage.html _DO_NOT_DISTRIBUTE_
-./doc/html/study.html _DO_NOT_DISTRIBUTE_
-./doc/html/study_1000x1000.gif _DO_NOT_DISTRIBUTE_
-./doc/html/study_250x250.gif _DO_NOT_DISTRIBUTE_
-./doc/html/study_499x499.gif _DO_NOT_DISTRIBUTE_
-./doc/html/study_5000x1000.gif _DO_NOT_DISTRIBUTE_
-./doc/html/study_500x500.gif _DO_NOT_DISTRIBUTE_
-./doc/html/study_p1.gif _DO_NOT_DISTRIBUTE_
-./doc/html/study_p1.obj _DO_NOT_DISTRIBUTE_
./doc/html/symtab _DO_NOT_DISTRIBUTE_
./doc/html/version.gif
./doc/html/version.obj _DO_NOT_DISTRIBUTE_
diff --git a/doc/html/study.html b/doc/html/study.html
deleted file mode 100644
index f9e192d..0000000
--- a/doc/html/study.html
+++ /dev/null
@@ -1,172 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
-<html>
- <head>
- <title>Testing the chunked layout of HDF5</title>
- </head>
-
- <body>
- <h1>Testing the chunked layout of HDF5</h1>
-
- <p>This is the results of studying the chunked layout policy in
- HDF5. A 1000 by 1000 array of integers was written to a file
- dataset extending the dataset with each write to create, in the
- end, a 5000 by 5000 array of 4-byte integers for a total data
- storage size of 100 million bytes.
-
- <p>
- <center>
- <img alt="Order that data was written" src="study_p1.gif">
- <br><b>Fig 1: Write-order of Output Blocks</b>
- </center>
-
- <p>After the array was written, it was read back in blocks that
- were 500 by 500 bytes in row major order (that is, the top-left
- quadrant of output block one, then the top-right quadrant of
- output block one, then the top-left quadrant of output block 2,
- etc.).
-
- <p>I tried to answer two questions:
- <ul>
- <li>How does the storage overhead change as the chunk size
- changes?
- <li>What does the disk seek pattern look like as the chunk size
- changes?
- </ul>
-
- <p>I started with chunk sizes that were multiples of the read
- block size or k*(500, 500).
-
- <p>
- <center>
- <table border>
- <caption align=bottom>
- <b>Table 1: Total File Overhead</b>
- </caption>
- <tr>
- <th>Chunk Size (elements)</th>
- <th>Meta Data Overhead (ppm)</th>
- <th>Raw Data Overhead (ppm)</th>
- </tr>
-
- <tr align=center>
- <td>500 by 500</td>
- <td>85.84</td>
- <td>0.00</td>
- </tr>
- <tr align=center>
- <td>1000 by 1000</td>
- <td>23.08</td>
- <td>0.00</td>
- </tr>
- <tr align=center>
- <td>5000 by 1000</td>
- <td>23.08</td>
- <td>0.00</td>
- </tr>
- <tr align=center>
- <td>250 by 250</td>
- <td>253.30</td>
- <td>0.00</td>
- </tr>
- <tr align=center>
- <td>499 by 499</td>
- <td>85.84</td>
- <td>205164.84</td>
- </tr>
- </table>
- </center>
-
- <hr>
- <p>
- <center>
- <img alt="500x500" src="study_500x500.gif">
- <br><b>Fig 2: Chunk size is 500x500</b>
- </center>
-
- <p>The first half of Figure 2 shows output to the file while the
- second half shows input. Each dot represents a file-level I/O
- request and the lines that connect the dots are for visual
- clarity. The size of the request is not indicated in the
- graph. The output block size is four times the chunk size which
- results in four file-level write requests per block for a total
- of 100 requests. Since file space for the chunks was allocated
- in output order, and the input block size is 1/4 the output
- block size, the input shows a staircase effect. Each input
- request results in one file-level read request. The downward
- spike at about the 60-millionth byte is probably the result of a
- cache miss for the B-tree and the downward spike at the end is
- probably a cache flush or file boot block update.
-
- <hr>
- <p>
- <center>
- <img alt="1000x1000" src="study_1000x1000.gif">
- <br><b>Fig 2: Chunk size is 1000x1000</b>
- </center>
-
- <p>In this test I increased the chunk size to match the output
- chunk size and one can see from the first half of the graph that
- 25 file-level write requests were issued, one for each output
- block. The read half of the test shows that four times the
- amount of data was read as written. This results from the fact
- that HDF5 must read the entire chunk for any request that falls
- within that chunk, which is done because (1) if the data is
- compressed the entire chunk must be decompressed, and (2) the
- library assumes that a chunk size was chosen to optimize disk
- performance.
-
- <hr>
- <p>
- <center>
- <img alt="5000x1000" src="study_5000x1000.gif">
- <br><b>Fig 3: Chunk size is 5000x1000</b>
- </center>
-
- <p>Increasing the chunk size further results in even worse
- performance since both the read and write halves of the test are
- re-reading and re-writing vast amounts of data. This proves
- that one should be careful that chunk sizes are not much larger
- than the typical partial I/O request.
-
- <hr>
- <p>
- <center>
- <img alt="250x250" src="study_250x250.gif">
- <br><b>Fig 4: Chunk size is 250x250</b>
- </center>
-
- <p>If the chunk size is decreased then the amount of data
- transfered between the disk and library is optimal for no
- caching, but the amount of meta data required to describe the
- chunk locations increases to 250 parts per million. One can
- also see that the final downward spike contains more file-level
- write requests as the meta data is flushed to disk just before
- the file is closed.
-
- <hr>
- <p>
- <center>
- <img alt="499x499" src="study_499x499.gif">
- <br><b>Fig 4: Chunk size is 499x499</b>
- </center>
-
- <p>This test shows the result of choosing a chunk size which is
- close to the I/O block size. Because the total size of the
- array isn't a multiple of the chunk size, the library allocates
- an extra zone of chunks around the top and right edges of the
- array which are only partially filled. This results in
- 20,516,484 extra bytes of storage, a 20% increase in the total
- raw data storage size. But the amount of meta data overhead is
- the same as for the 500 by 500 test. In addition, the mismatch
- causes entire chunks to be read in order to update a few
- elements along the edge or the chunk which results in a 3.6-fold
- increase in the amount of data transfered.
-
- <hr>
- <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
-<!-- Created: Fri Jan 30 21:04:49 EST 1998 -->
-<!-- hhmts start -->
-Last modified: Fri Jan 30 23:51:31 EST 1998
-<!-- hhmts end -->
- </body>
-</html>
diff --git a/doc/html/study_1000x1000.gif b/doc/html/study_1000x1000.gif
deleted file mode 100644
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+++ /dev/null
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diff --git a/doc/html/study_499x499.gif b/doc/html/study_499x499.gif
deleted file mode 100644
index 0d2038b..0000000
--- a/doc/html/study_499x499.gif
+++ /dev/null
Binary files differ
diff --git a/doc/html/study_5000x1000.gif b/doc/html/study_5000x1000.gif
deleted file mode 100644
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--- a/doc/html/study_5000x1000.gif
+++ /dev/null
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diff --git a/doc/html/study_500x500.gif b/doc/html/study_500x500.gif
deleted file mode 100644
index 38dd7d6..0000000
--- a/doc/html/study_500x500.gif
+++ /dev/null
Binary files differ
diff --git a/doc/html/study_p1.gif b/doc/html/study_p1.gif
deleted file mode 100644
index 938d133..0000000
--- a/doc/html/study_p1.gif
+++ /dev/null
Binary files differ
diff --git a/doc/html/study_p1.obj b/doc/html/study_p1.obj
deleted file mode 100644
index 6fbf583..0000000
--- a/doc/html/study_p1.obj
+++ /dev/null
@@ -1,113 +0,0 @@
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