Installing wasora

This file contains brief instructions to download, and/or compile and/or install wasora. The detailed discussed is deferred to the full documentation (see directory doc).

Getting wasora

The wasora code can be obtained essentially in either source or binary form. The v0.3.x series uses Mercurial as the version control system and the repository is hosted at Bitbucket (v0.2.x series used Bazaar and Launchpad]). Tarballs containing either sources or binaries are periodically prepared from the repository sources and may be downloaded from http://www.talador.com.ar/jeremy/wasora/.

In order of decreasing level of user expertise, to get wasora either

The provided binaries are statically linked to the required libraries to avoid having a user that expects to run wasora out of the box dealing with unresolved library dependences. However, there may be some libraries that are not available in a certain configuration. A full source compilation is recommended.

Note that using wasora in non-free operating systems is highly discouraged. Please try switching to GNU/Linux.

Bootstrapping

Skip this section if you did not clone the repository.

The repository development tree has to be bootstrapped by autoconf & friends to be able to configure and make the code. The script autogen.sh generates the files that autoconf needs to produce a working configure script:

$ ./autogen.sh 
cleaning... done
getting hg revision id... done
building changelog... done
formatting readme & install... done
building configure.ac... done
building src/Makefile.am... done
calling autoreconf... 
configure.ac:21: installing './compile'
configure.ac:16: installing './config.guess'
configure.ac:16: installing './config.sub'
configure.ac:18: installing './install-sh'
configure.ac:18: installing './missing'
parallel-tests: installing './test-driver'
src/Makefile.am: installing './depcomp'
done
$ 

At this point, a tree similar to the source distribution tarball is obtained, which can be configured and compiled as described in the section Compiling below. The bootstrapped files are listed in .hgignore so Mercurial should not report any changes in the status of the working tree after executing autogen.sh:

$ hg status
$

To clean the working tree and revert it to a fresh-clone status, the autoclean.sh script should be executed:

$ ./autoclean.sh

Note that autogen.sh calls autoclean.sh first.

Compiling

Skip this section if you downloaded a binary tarball.

wasora follows the standard GNU ./configure && make procedure. So uncompress the downloaded tarball into a proper location within your home directory:

$ tar xvzf wasora-0.3.4.tar.gz
$ cd wasora

Then execute the configure script so it can check the environment is able to build wasora:

$ ./configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
[...]
config.status: creating src/Makefile
config.status: executing depfiles commands

## --------------------- ##
## Configuration summary ##
## --------------------- ##
  GSL library (required): yes, version 1.16

  IDA library (optional): yes, version unknown
    differential-algebraic systems will be solved

  Readline library (opt): yes, version 6.3
    run-time debugging-like capabilities will be provided

Now proceed to compile with 'make'

$

If any error is reported, there may be likely problems with finding one or more libraries. See the section Required libraries below to see how the error can be fixed.

Once the configure step successfully tells us to proceed to compile with make, that is what we do:

$ make

The executable binary will be located in the current directory and called wasora. At this point you may want to check if wasora actually works by executing the test suite:

$ make check

If gnuplot is installed, some graphical windows should pop up. See the README for a full list of the test involved.

The usual way to finish the compilation of a program that follows the GNU standard is to perform a system-wide installation by executing (as root):

# make install

This would leave the executable wasora available to be executed by any user of the system. However, other workflows may be used to run wasora. See the section Installing for details.

By default, configure sets CFLAGS=-O2. To obtain a binary with debugging symbols, call either ./configure or make with CFLAGS=-g, i.e.

$ ./configure CFLAGS=-g
$ make

or

$ ./configure
$ make CFLAGS=-g

Required libraries

The code depends on a few libraries (and its development headers). Some of them are mandatory and some of the are optional. The name in parenthesis refers to the Debian-based package name

Therefore, in Debian-based GNU/Linux boxes, one would do

# apt-get install libgsl0-dev libsundials-serial-dev libreadline-dev

and all the required libraries (and development headers) should be detected by configure. Note that some wasora plugins (such as milonga) may need further additional libraries (for instance PETSc and SLEPc).

If configure is still unable to detect the GSL, it can be instructed to download and compile it in a local subdirectory using the --enable-download-gsl option:

$ ./configure --enable-download-gsl

If no Internet connection is available, the file gsl-1.16.tar.gz may be separately obtained (for example from http://ftpmirror.gnu.org/gsl/) and copied into the wasora directory.

When giving the --enable-download-gsl option, the generated binary will be statically linked against the downloaded library.

By default, configure checks for the optional libraries. However, they can be explicitly disabled by using the --without-ida and --without-readline options in configure:

$ ./configure --without-ida --without-readline 
[...]
config.status: creating src/Makefile
config.status: executing depfiles commands

## --------------------- ##
## Configuration summary ##
## --------------------- ##
  GSL library (required): yes, version 1.16

  IDA library (optional): no
    differential-algebraic systems will NOT be solved

  Readline library (opt): no
    run-time debugging-like capabilities will NOT be provided

WARNING: there is at least one optional library missing.
If this was not the desired result, check config.log for clues.

Now proceed to compile with 'make'

$

Call ./configure --help to see all the available options. Which libraries wasora was finally linked against to can be checked by executing it with the -v option:

$ ./wasora -v
wasora 0.3.5 default (2014-08-17 03:11 -0300)
wasora's an advanced suite for optimization & reactor analysis

 revision id d033f6fa994d319b4d60978c073dcb8aaa6a221a
 last commit on 2014-08-17 03:11 -0300 (rev 5)

 compiled on 2014-08-17 12:20:38 by jeremy@tom (linux-gnu x86_64)
 with gcc (Debian 4.9.1-4) 4.9.1 using -O2 and linked against
  GNU Scientific Library version 1.16
  GNU Readline version 6.3
  SUNDIALs Library version 2.5.0


 wasora is copyright (C) 2009-2014 jeremy theler
 licensed under GNU GPL version 3 or later.
 wasora is free software: you are free to change and redistribute it.
 There is NO WARRANTY, to the extent permitted by law.
$ 

If something goes wrong and the compilation fails, please feel free to ask for help at the wasora mailing list at .

Installing

Further information

See the file README for a description of wasora and the test suite.
See the contents of directory doc for full documentation.

Home page: http://www.talador.com.ar/jeremy/wasora
Mailing list and bug reports:

wasora is copyright (C) 2009--2014 jeremy theler
wasora is licensed under GNU GPL version 3 or (at your option) any later version.
wasora is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
See the file COPYING for copying conditions.

The text below the cutting line corresponds to the original FSF instructions for installing software (as wasora) that follows the GNU configure & make convention.


Installation Instructions

Copyright (C) 1994-1996, 1999-2002, 2004-2012 Free Software Foundation, Inc.

Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without warranty of any kind.

Basic Installation

Briefly, the shell commands ./configure; make; make install should configure, build, and install this package. The following more-detailed instructions are generic; see the README file for instructions specific to this package. Some packages provide this INSTALL file but do not implement all of the features documented below. The lack of an optional feature in a given package is not necessarily a bug. More recommendations for GNU packages can be found in *note Makefile Conventions: (standards)Makefile Conventions.

The configure shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a Makefile in each directory of the package. It may also create one or more .h files containing system-dependent definitions. Finally, it creates a shell script config.status that you can run in the future to recreate the current configuration, and a file config.log containing compiler output (useful mainly for debugging configure).

It can also use an optional file (typically called config.cache and enabled with --cache-file=config.cache or simply -C) that saves the results of its tests to speed up reconfiguring. Caching is disabled by default to prevent problems with accidental use of stale cache files.

If you need to do unusual things to compile the package, please try to figure out how configure could check whether to do them, and mail diffs or instructions to the address given in the README so they can be considered for the next release. If you are using the cache, and at some point config.cache contains results you don`t want to keep, you may remove or edit it.

The file configure.ac (or configure.in) is used to create configure by a program called autoconf. You need configure.ac if you want to change it or regenerate configure using a newer version of autoconf.

The simplest way to compile this package is:

  1. cd to the directory containing the package's source code and type ./configure to configure the package for your system.

    Running configure might take a while. While running, it prints some messages telling which features it is checking for.

  2. Type make to compile the package.

  3. Optionally, type make check to run any self-tests that come with the package, generally using the just-built uninstalled binaries.

  4. Type make install to install the programs and any data files and documentation. When installing into a prefix owned by root, it is recommended that the package be configured and built as a regular user, and only the make install phase executed with root privileges.

  5. Optionally, type make installcheck to repeat any self-tests, but this time using the binaries in their final installed location. This target does not install anything. Running this target as a regular user, particularly if the prior make install required root privileges, verifies that the installation completed correctly.

  6. You can remove the program binaries and object files from the source code directory by typing make clean. To also remove the files that configure created (so you can compile the package for a different kind of computer), type make distclean. There is also a make maintainer-clean target, but that is intended mainly for the package`s developers. If you use it, you may have to get all sorts of other programs in order to regenerate files that came with the distribution.

  7. Often, you can also type make uninstall to remove the installed files again. In practice, not all packages have tested that uninstallation works correctly, even though it is required by the GNU Coding Standards.

  8. Some packages, particularly those that use Automake, provide make distcheck, which can by used by developers to test that all other targets like make install and make uninstall work correctly. This target is generally not run by end users.

Compilers and Options

Some systems require unusual options for compilation or linking that the configure script does not know about. Run ./configure --help for details on some of the pertinent environment variables.

You can give configure initial values for configuration parameters by setting variables in the command line or in the environment. Here is an example:

 ./configure CC=c99 CFLAGS=-g LIBS=-lposix

*Note Defining Variables::, for more details.

Compiling For Multiple Architectures

You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their own directory. To do this, you can use GNU make. cd to the directory where you want the object files and executables to go and run the configure script. configure automatically checks for the source code in the directory that configure is in and in ... This is known as a "VPATH" build.

With a non-GNU make, it is safer to compile the package for one architecture at a time in the source code directory. After you have installed the package for one architecture, use make distclean before reconfiguring for another architecture.

On MacOS X 10.5 and later systems, you can create libraries and executables that work on multiple system types--known as "fat" or "universal" binaries--by specifying multiple -arch options to the compiler but only a single -arch option to the preprocessor. Like this:

 ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
             CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
             CPP="gcc -E" CXXCPP="g++ -E"

This is not guaranteed to produce working output in all cases, you may have to build one architecture at a time and combine the results using the lipo tool if you have problems.

Installation Names

By default, make install installs the packages commands under/usr/local/bin, include files under/usr/local/include, etc. You can specify an installation prefix other than/usr/localby givingconfigurethe option--prefix=PREFIX`, where PREFIX must be an absolute file name.

You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you pass the option --exec-prefix=PREFIX to configure, the package uses PREFIX as the prefix for installing programs and libraries. Documentation and other data files still use the regular prefix.

In addition, if you use an unusual directory layout you can give options like --bindir=DIR to specify different values for particular kinds of files. Run configure --help for a list of the directories you can set and what kinds of files go in them. In general, the default for these options is expressed in terms of ${prefix}, so that specifying just --prefix will affect all of the other directory specifications that were not explicitly provided.

The most portable way to affect installation locations is to pass the correct locations to configure; however, many packages provide one or both of the following shortcuts of passing variable assignments to the make install command line to change installation locations without having to reconfigure or recompile.

The first method involves providing an override variable for each affected directory. For example, make install prefix=/alternate/directory will choose an alternate location for all directory configuration variables that were expressed in terms of ${prefix}. Any directories that were specified during configure, but not in terms of ${prefix}, must each be overridden at install time for the entire installation to be relocated. The approach of makefile variable overrides for each directory variable is required by the GNU Coding Standards, and ideally causes no recompilation. However, some platforms have known limitations with the semantics of shared libraries that end up requiring recompilation when using this method, particularly noticeable in packages that use GNU Libtool.

The second method involves providing the DESTDIR variable. For example, make install DESTDIR=/alternate/directory will prepend /alternate/directory before all installation names. The approach of DESTDIR overrides is not required by the GNU Coding Standards, and does not work on platforms that have drive letters. On the other hand, it does better at avoiding recompilation issues, and works well even when some directory options were not specified in terms of ${prefix} at configure time.

Optional Features

If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving configure the option --program-prefix=PREFIX or --program-suffix=SUFFIX.

Some packages pay attention to --enable-FEATURE options to configure, where FEATURE indicates an optional part of the package. They may also pay attention to --with-PACKAGE options, where PACKAGE is something like gnu-as or x (for the X Window System). The README should mention any --enable- and --with- options that the package recognizes.

For packages that use the X Window System, configure can usually find the X include and library files automatically, but if it doesnt, you can use theconfigureoptions--x-includes=DIRand--x-libraries=DIR` to specify their locations.

Some packages offer the ability to configure how verbose the execution of make will be. For these packages, running ./configure --enable-silent-rules sets the default to minimal output, which can be overridden with make V=1; while running ./configure --disable-silent-rules sets the default to verbose, which can be overridden with make V=0.

Particular systems

On HP-UX, the default C compiler is not ANSI C compatible. If GNU CC is not installed, it is recommended to use the following options in order to use an ANSI C compiler:

 ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"

and if that doesn`t work, install pre-built binaries of GCC for HP-UX.

HP-UX make updates targets which have the same time stamps as their prerequisites, which makes it generally unusable when shipped generated files such as configure are involved. Use GNU make instead.

On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot parse its <wchar.h> header file. The option -nodtk can be used as a workaround. If GNU CC is not installed, it is therefore recommended to try

 ./configure CC="cc"

and if that doesn`t work, try

 ./configure CC="cc -nodtk"

On Solaris, dont put/usr/ucbearly in yourPATH. This directory contains several dysfunctional programs; working variants of these programs are available in/usr/bin. So, if you need/usr/ucbin yourPATH, put it _after_/usr/bin`.

On Haiku, software installed for all users goes in /boot/common, not /usr/local. It is recommended to use the following options:

 ./configure --prefix=/boot/common

Specifying the System Type

There may be some features configure cannot figure out automatically, but needs to determine by the type of machine the package will run on. Usually, assuming the package is built to be run on the same architectures, configure can figure that out, but if it prints a message saying it cannot guess the machine type, give it the --build=TYPE option. TYPE can either be a short name for the system type, such as sun4, or a canonical name which has the form:

 CPU-COMPANY-SYSTEM

where SYSTEM can have one of these forms:

 OS
 KERNEL-OS

See the file config.sub for the possible values of each field. If config.sub isn`t included in this package, then this package doesn't need to know the machine type.

If you are building compiler tools for cross-compiling, you should use the option --target=TYPE to select the type of system they will produce code for.

If you want to use a cross compiler, that generates code for a platform different from the build platform, you should specify the "host" platform (i.e., that on which the generated programs will eventually be run) with --host=TYPE.

Sharing Defaults

If you want to set default values for configure scripts to share, you can create a site shell script called config.site that gives default values for variables like CC, cache_file, and prefix. configure looks for PREFIX/share/config.site if it exists, then PREFIX/etc/config.site if it exists. Or, you can set the CONFIG_SITE environment variable to the location of the site script. A warning: not all configure scripts look for a site script.

Defining Variables

Variables not defined in a site shell script can be set in the environment passed to configure. However, some packages may run configure again during the build, and the customized values of these variables may be lost. In order to avoid this problem, you should set them in the configure command line, using VAR=value. For example:

 ./configure CC=/usr/local2/bin/gcc

causes the specified gcc to be used as the C compiler (unless it is overridden in the site shell script).

Unfortunately, this technique does not work for CONFIG_SHELL due to an Autoconf limitation. Until the limitation is lifted, you can use this workaround:

 CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash

configure Invocation

configure recognizes the following options to control how it operates.

--help -h Print a summary of all of the options to configure, and exit.

--help=short --help=recursive Print a summary of the options unique to this packagesconfigure, and exit. Theshortvariant lists options used only in the top level, while therecursive` variant lists options also present in any nested packages.

--version -V Print the version of Autoconf used to generate the configure script, and exit.

--cache-file=FILE Enable the cache: use and save the results of the tests in FILE, traditionally config.cache. FILE defaults to /dev/null to disable caching.

--config-cache -C Alias for --cache-file=config.cache.

--quiet --silent -q Do not print messages saying which checks are being made. To suppress all normal output, redirect it to /dev/null (any error messages will still be shown).

--srcdir=DIR Look for the packages source code in directory DIR. Usuallyconfigure` can determine that directory automatically.

--prefix=DIR Use DIR as the installation prefix. *note Installation Names:: for more details, including other options available for fine-tuning the installation locations.

--no-create -n Run the configure checks, but stop before creating any output files.

configure also accepts some other, not widely useful, options. Run configure --help for more details.