repo migration
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<html>
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<head>
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<title>Put your title here!!</title>
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<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
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<meta name="keywords" content="scientific visualization">
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<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
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<div id="maincenter">
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<head>
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<title>Building H5Part</title>
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</head>
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<body bgcolor="#F0F0F0">
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<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
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<UL>
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<LI><a href="#Quickstart">Quickstart guide for the impatient.</a>
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<LI><a href="#Details">Details of the Configuration Script</a>
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<!-- <LI><a href="UsingC++.html">Using the C++ interface</a> -->
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<LI><a href="#ConfigOptions">Important Configure Options</a>
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<LI><a href="#EnvVariables">Important Environment Variables</a>
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</UL>
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<hr>
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<a name="Quickstart">
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<h2>Quickstart <i>for the impatient</i></h2>
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</a>
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<OL>
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<LI><b>Configure</b>:<br>
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For the serial implementation
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<pre>
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./configure
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</pre>
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For the parallel implementation configure with
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<pre>
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./configure --enable-parallel
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</pre>
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If you also want to build fortran bindings, add the
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<code>--enable-fortran</code> flag to the configure line.
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</LI><p>
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<LI><b>Make the Library</b>:<br>
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Type <code>make</code> to build the library. The libraries are
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named accordingly.
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<UL>
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<LI>libH5Part.a: Serial C/C++ Library.</LI>
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<LI>libpH5Part.a: Parallel C/C++ library.</LI>
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<LI>libH5PartF.a: Serial F77/F90 library.</LI>
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<LI>libpH5PartF.a: Parallel F77/F90 library.</LI>
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</UL>
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</LI><p>
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<LI><b>Make Regression Tests and Examples</b>:<br>
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Just type <code>make tests</code> to build regression tests
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and/or example programs for H5Part. These tests are
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<UL>
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<LI>H5PartF: Fortran example (only build if --enable-fortran
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is specified).</LI>
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<LI>H5PartFpar: Parallel Fortran example (only built if both
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--enable-fortran and --enable-parallel are specified).</LI>
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<LI>H5PartTest: Serial C example. This test writes a sample
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datafile and then reopens it for reading. It demonstrates
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the most basic reading/writing capabilities.</LI>
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<LI>H5PartTestP: Parallel C example (only built if
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--enable-parallel is specified). This program only works
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as an MPI/parallel program.</LI>
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<LI>Bench: This program will only be built if
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--enable-parallel is specified. It compares the
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performance of raw binary
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I/O (one file per processor), raw binary MPI-IO based
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parallel I/O to a single file, and the parallel H5Part/HDF5 to
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a single file. Generally, H5Part should be very close to the
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MPI-IO implementation in terms of performance, but slower
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than one-file-per-processor. If HDF5 is slower the
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MPI-IO, it would indicate that some performance tuning
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will be required for your platform (contact us, and we will
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see what we can do!).</LI>
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</UL>
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</LI><p>
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<LI><b>Building Your Own Programs</b>:<br>
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There are many different subtleties to linking on various
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computer platforms, but typically one does the following.
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<UL>
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<LI>C/C++ Serial:
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<br><code>#include
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< H5Part.h > </code> into your
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source file.
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<br><code>$CC -I<i>path_to_H5Part.h</i>
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-I<i>path_to_hdf5.h</i> -o outfile
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MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
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-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
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</LI>
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<LI>C/C++ Parallel:
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<br><code>#include
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< H5Part.h > </code> into your
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source file.
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<br><code>$MPICC -I<i>path_to_H5Part.h</i>
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-I<i>path_to_hdf5.h</i> -DPARALLEL_IO
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-DH5_HAVE_PARALLEL -o outfile
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MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
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-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
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</LI>
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<LI>Fortran Serial:
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<br><code>include
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'H5Part.inc'</code> into your
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source file.
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<br><code>$FC -I<i>path_to_H5Part.h</i>
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-I<i>path_to_hdf5.h</i> -o outfile
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MyFile.cc -L<i>path_to_libH5PartF.a</i> -lH5PartF
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-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
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</LI>
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<LI>Fortran Parallel:
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<br><code>include
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'H5Part.inc'</code> into your
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source file.
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<br><code>$MPIF90 -I<i>path_to_H5Part.h</i>
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-o outfile
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MyFile.cc -L<i>path_to_libpH5PartF.a</i> -lpH5PartF
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-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
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</LI><p>
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</UL>
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</OL>
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<hr>
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<a name="Details">
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<h1>Details for H5Part Configure and Build</h1>
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</a>
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<a name="ConfigOptions">
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<h2>Configure Options</h2>
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</a>
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H5Part uses GNU Autoconf to generate a Makefile from the makefile
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template called <code>Makefile.in</code>.
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The configure script pays attention to the following
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configure options;<p>
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<UL>
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<LI><b>--prefix=PREFIX</b> Install files in PREFIX</LI>
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<LI><b>--enable-fortran</b> By default H5part will make no attempt to
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build Fortran bindings. If you add the
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<code>--enable-fortran</code> flag to the ./configure line, it
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will create a small test program to determine how to generate
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the fortran bindings and then create a library that includes
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those bindings. You may need to set the fortran compiler by
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setting the <code>FC</code> environment variable in your shell.</LI>
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<LI><b>--enable-parallel</b> The version of HDF5 that you build for
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Parallel I/O differs from the library you would build for
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serial I/O. Consequently, the H5Part libraries must be built
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specifically for the kind of I/O you have in mind (parallel or
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serial). The configure script will attempt to find an
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<code>mpicc</code> if it is available. If no
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<code>mpicc</code> is available it will use the regular
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C-compiler and will try to locate the location of the MPI
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include files and libraries. You can assist the configure
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program in its search by setting the <code>MPIROOT</code>
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environment variable.</LI>
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<LI><b>--enable-tools</b> Builds the currently available tools
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<br>
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<b>h5pAttrib</b>, an inspection tool that prints the number of timesteps in a file
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the file attributes, the step attributes, the dataset names and their values.
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<br>
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<b>h5pToGNUplot</b>, a converter to two column ASCII format to load in GNUplot.
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</LI>
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<LI><b>--enable-python</b><font color=red> Under construction</font> Option to build python bindings. It has not been tested.
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</LI>
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<LI><b>--help</b> Prints configure options.
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</LI>
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</UL>
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<p>
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<a name="MakeOptions">
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<h2>Make Options</h2>
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</a>
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<UL>
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<LI>make</LI>builds the libraries and test programs
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<LI>make install</LI>builds and installs
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<LI>make clean</LI>removes extraneous object files
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<LI>make distclean</LI>returns configuration to unconfigured state
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</UL>
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<a name="EnvVariables">
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<h2>Environment Variables for Configure</h2>
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</a>
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The
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configuration script is of limited intelligence. Sometimes, you
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have to define the following environment variables in order to
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help it on its way. You will often only need to tell it where to
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find the HDF5 libraries (<code>H5ROOT</code> for serial or
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<code>PHDF5ROOT</code> for parallel builds). All of these
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environment variables can also be overidden in the Makefile that
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is generated by the autoconfigure script.
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The configure script pays attention to the following
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environment variables;
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<p>
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<UL>
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<LI><b>CC</b>: Use the <code>CC</code> environment variable to tell the
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configure script where to find the C compiler. You can
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also directly modify this variable in the
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<code>Makefile</code> that is generated by the autoconfigure</LI>
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<LI><b>CXX</b>: Use the <code>CXX</code> environment variable to tell the
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configure script where to find the C++ compiler. You can
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also directly modify this variable in the
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<code>Makefile</code> that is generated by the autoconfigure</LI>
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<LI><b>FC</b>: Use the <code>FC</code> environment variable to tell the
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configure script where to find the fortran compiler. You can
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also directly modify this variable in the
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<code>Makefile</code> that is generated by the autoconfigure</LI>
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<LI><b>MPICC</b>: If you are building for parallel C I/O, then it is
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useful to tell the configure script where to find the
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<code>mpicc</code> script. Normally, <code>mpicc</code> is
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merely a wrapper script for a build using a regular C-compiler.
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If no <code>mpicc</code> is available, then the
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<code>configure</code> script will attempt to locate the mpi
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header files and libraries. In that case, it may be useful to
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define the <code>MPI_HOME</code> environment variable.</LI>
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<LI><b>MPICXX</b>If you are building for parallel C++</LI>
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<LI><b>MPIFC</b>: If you are building for parallel Fortran I/O, then it is
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useful to tell the configure script where to find the parallel fortran compiler.
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<LI><b>MPIROOT</b>: Set this environment variable to help the
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configure script to locate the MPI libraries that should be
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used to build the parallel version of the libraries. This
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variable will be ignored if configured only to build the
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serial implementation of the library.</LI>
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<LI><b>HDF5ROOT</b>: Find the path to your serial HDF5 installation. If you
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are building the serial version of H5part, then you should set
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the <code>PHDF5ROOT</code> environment variable.</LI>
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</UL><p>
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<h3>Common compiler environemt variables for NERSC platforms</h3>
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<UL>
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<LI><b>DaVinci</b>: Linux ia64 </LI>
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CC=icc CXX=icc F90=ifort MPICC=icc MPIFC=ifort MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include
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<LI><b>Bassi</b>: AIX</LI>
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CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r
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<LI><b>Jacquard</b>: Linux x86_64</LI>
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CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90
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<LI><b>Starsky.lbl.gov:</b> (Darwin) PowerPC</LI>
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CC=gcc CXX=g++ FC=g95
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</UL>
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<br>
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NOTE: You might need to set the MPI library path (MPILIB) and MPI includes (MPIIINC) if they are in non standard places. For example: <br>
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MPILIB=-L/usr/lpp/ppe.poe/lib -lmpi_r MPIINC=-I/usr/lpp/ppe.poe/include/thread
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<h3>How to set the variables for configure:</h3>
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It is very simple just call env with the variables together with configure. Notice the quotes in MPILIB.
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<pre>
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% env CC=icc CXX=icc F90=ifort MPICC=icc MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include ./configure (configure options follow here)
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</pre>
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In the worst case, you can edit the <code>src/Makefile.am</code> and <code>test/Makefile.am</code> as
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needed to perform the proper build.
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</div>
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