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+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+ <head>
+ <title>Big Datasets on Small Machines</title>
+ </head>
+
+ <body>
+ <h1>Big Datasets on Small Machines</h1>
+
+ <h2>1. Introduction</h2>
+
+ <p>The HDF5 library is able to handle files larger than the
+ maximum file size, and datasets larger than the maximum memory
+ size. For instance, a machine where <code>sizeof(off_t)</code>
+ and <code>sizeof(size_t)</code> are both four bytes can handle
+ datasets and files as large as 18x10^18 bytes. However, most
+ Unix systems limit the number of concurrently open files, so a
+ practical file size limit is closer to 512GB or 1TB.
+
+ <p>Two "tricks" must be imployed on these small systems in order
+ to store large datasets. The first trick circumvents the
+ <code>off_t</code> file size limit and the second circumvents
+ the <code>size_t</code> main memory limit.
+
+ <h2>2. File Size Limits</h2>
+
+ <p>Some 32-bit operating systems have special file systems that
+ can support large (&gt;2GB) files and HDF5 will detect these and
+ use them automatically. If this is the case, the output from
+ configure will show:
+
+ <p><code><pre>
+checking for lseek64... yes
+checking for fseek64... yes
+ </pre></code>
+
+ <p>Otherwise one must use an HDF5 file family. Such a family is
+ created by setting file family properties in a file access
+ property list and then supplying a file name that includes a
+ <code>printf</code>-style integer format. For instance:
+
+ <p><code><pre>
+hid_t plist, file;
+plist = H5Pcreate (H5P_FILE_ACCESS);
+H5Pset_family (plist, 1<<30, H5P_DEFAULT);
+file = H5Fcreate ("big%03d.h5", H5F_ACC_TRUNC, H5P_DEFAULT, plist);
+ </code></pre>
+
+ <p>The second argument (<code>30</code>) to
+ <code>H5Pset_family()</code> indicates that the family members
+ are to be 2^30 bytes (1GB) each. In general, family members
+ cannot be 2GB because writes to byte number 2,147,483,647 will
+ fail, so the largest safe value for a family member is
+ 2,147,483,647. HDF5 will create family members on demand as the
+ HDF5 address space increases, but since most Unix systems limit
+ the number of concurrently open files the effective maximum size
+ of the HDF5 address space will be limited.
+
+ <p>If the effective HDF5 address space is limited then one may be
+ able to store datasets as external datasets each spanning
+ multiple files of any length since HDF5 opens external dataset
+ files one at a time. To arrange storage for a 5TB dataset one
+ could say:
+
+ <p><code><pre>
+hid_t plist = H5Pcreate (H5P_DATASET_CREATE);
+for (i=0; i&lt;5*1024; i++) {
+ sprintf (name, "velocity-%04d.raw", i);
+ H5Pset_external (plist, name, 0, (size_t)1&lt;&lt;30);
+}
+ </code></pre>
+
+ <h2>3. Dataset Size Limits</h2>
+
+ <p>The second limit which must be overcome is that of
+ <code>sizeof(size_t)</code>. HDF5 defines a new data type
+ called <code>hsize_t</code> which is used for sizes of datasets
+ and is, by default, defined as <code>unsigned long long</code>.
+
+ <p>To create a dataset with 8*2^30 4-byte integers for a total of
+ 32GB one first creates the dataspace. We give two examples
+ here: a 4-dimensional dataset whose dimension sizes are smaller
+ than the maximum value of a <code>size_t</code>, and a
+ 1-dimensional dataset whose dimension size is too large to fit
+ in a <code>size_t</code>.
+
+ <p><code><pre>
+hsize_t size1[4] = {8, 1024, 1024, 1024};
+hid_t space1 = H5Screate_simple (4, size1, size1);
+
+hsize_t size2[1] = {8589934592LL};
+hid_t space2 = H5Screate_simple (1, size2, size2};
+ </pre></code>
+
+ <p>However, the <code>LL</code> suffix is not portable, so it may
+ be better to replace the number with
+ <code>(hsize_t)8*1024*1024*1024</code>.
+
+ <p>For compilers that don't support <code>long long</code> large
+ datasets will not be possible. The library performs too much
+ arithmetic on <code>hsize_t</code> types to make the use of a
+ struct feasible.
+
+ <hr>
+ <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+<!-- Created: Fri Apr 10 13:26:04 EDT 1998 -->
+<!-- hhmts start -->
+Last modified: Wed May 13 12:36:47 EDT 1998
+<!-- hhmts end -->
+ </body>
+</html>