Installation - Revision history

Fomels: /* Prerequisites */

2024-10-15T21:58:47Z

Prerequisites

← Older revision		Revision as of 21:58, 15 October 2024
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	#C compiler. Any ANSI-compliant compiler such as [http://gcc.gnu.org/ GCC] should work. GCC usually comes pre-installed on Linux machines.		#C compiler. Any ANSI-compliant compiler such as [http://gcc.gnu.org/ GCC] should work. GCC usually comes pre-installed on Linux machines.
	#Python interpreter. [http://www.python.org/ Python] is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. Madagascar supports ~~both Python 2.7 and~~ Python 3.		#Python interpreter. [http://www.python.org/ Python] is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. Madagascar supports Python 3.

	Each API option has [[Advanced Installation#Dependencies\|its own prerequisites]].		Each API option has [[Advanced Installation#Dependencies\|its own prerequisites]].

Fomels: typos

2024-10-15T21:58:07Z

typos

← Older revision		Revision as of 21:58, 15 October 2024
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	[[Image:Fotolia_4727725_XS.jpg\|right\|]]		[[Image:Fotolia_4727725_XS.jpg\|right\|]]
	Madagascar has been installed and is periodically tested on		Madagascar has been installed and is periodically tested on different platforms
	*~~Different~~ Linux distributions (Fedora, RedHat, Ubuntu, etc.)		*Linux distributions (Fedora, RedHat, Ubuntu, etc.)
	*Solaris
	*MacOS X		*MacOS X
	*Windows under the [http://www.cygwin.com/ Cygwin] environment.		*Windows under the [http://www.cygwin.com/ Cygwin] environment.

	~~It was previously tested on~~
	*FreeBSD
	*HP-UX
	*SGI Irix
	*Windows under Microsoft's Services for UNIX environment.

	==Precompiled binary packages==		==Precompiled binary packages==

	See the [[Download\|Madagascar download page]] for availability of binary packages.		See the [[Download\|Madagascar download page]] for the availability of binary packages.

	==Installation from source==		==Installation from source==
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	[[Windows\|Specific instructions are provided]] for '''Windows''' users.		[[Windows\|Specific instructions are provided]] for '''Windows''' users.

	~~For other platform-specific instructions, please~~ consult the [[Advanced Installation#Platform-specific_installation_advice\|Advanced Installation]] guide.		Please consult the [[Advanced Installation#Platform-specific_installation_advice\|Advanced Installation]] guide for other platform-specific instructions.

	===Prerequisites===		===Prerequisites===
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	===General instructions===		===General instructions===

	# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.		# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.
	# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.		# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.
	# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used ~~somthing~~ different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used ~~somthing~~ different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/RSFDATA/ </syntaxhighlight> to ~/.bashrc and ~/.profile .		# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used something different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used something different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/RSFDATA/ </syntaxhighlight> to ~/.bashrc and ~/.profile .

	==Uninstall==		==Uninstall==
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	checking if cc works ... failed		checking if cc works ... failed
	</pre>		</pre>
	the problem may be that your compiler is in unusual place. Try		the problem may be that your compiler is in an unusual place. Try
	<pre>		<pre>
	./configure CC=/full/path/to/cc		./configure CC=/full/path/to/cc
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	</pre>		</pre>

	~~For more information, please~~ consult the [[Advanced Installation]] guide.		Please consult the [[Advanced Installation]] guide for more information.

	==Testing and quick start==		==Testing and quick start==

	Here are a few simple tests ~~and~~ and a brief introduction to Madagascar:		Here are a few simple tests and a brief introduction to Madagascar:

	Typing any Madagascar command in a terminal window without parameters should generate a brief documentation ~~on that command~~. Try one of the following:		Typing any Madagascar command in a terminal window without parameters should generate brief documentation. Try one of the following:

	<pre>		<pre>
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	</pre>		</pre>

	If you get an error like "Command not found", you may not have your <tt>$PATH</tt> environment variable set correctly, or you may need to issue the <tt>rehash</tt> command.		If you get an error like "Command not found," you may not have your <tt>$PATH</tt> environment variable set correctly, or you may need to issue the <tt>rehash</tt> command.

	Now try making a simple Madagascar data file:		Now try making a simple Madagascar data file:
Line 92:		Line 86:
	</pre>		</pre>

	This command generates a one dimensional list of 1000 numbers, all zero except for a spike equal to one at position 300. If this generates an error like		This command generates a one-dimensional list of 1000 numbers, all zero except for a spike equal to one at position 300. If this generates an error like
	<pre>		<pre>
	Cannot write to data file /path/spike.rsf@: Bad file descriptor		Cannot write to data file /path/spike.rsf@: Bad file descriptor
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	you may need to create the directory pointed to by your <tt>$DATAPATH</tt> environment variable.		you may need to create the directory pointed to by your <tt>$DATAPATH</tt> environment variable.

	The file <tt>spike.rsf</tt> is a text header. The actual data are stored in the binary file pointed to by the <tt>in=</tt> parameter in the header. You can look at the header file directly with <tt>more</tt>, or better, examine the file properties with		The file <tt>spike.rsf</tt> is a text header. The actual data are stored in the binary file pointed to by the <tt>in=</tt> parameter in the header. You can look at the header file directly with <tt>more</tt>, or better, examine the file properties with
	<pre>		<pre>
	sfin spike.rsf		sfin spike.rsf
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	</pre>		</pre>

	If you have SCons installed, you can use it to automate Madagascar processing. Here is a simple <tt>SConstruct</tt> file to make <tt>filter.rsf</tt> and <tt>filter.vpl</tt>:		If you have SCons installed, you can use it to automate Madagascar processing. Here is a simple <tt>SConstruct</tt> file to make <tt>filter.rsf</tt> and <tt>filter.vpl</tt>:

	<syntaxhighlight lang="python">		<syntaxhighlight lang="python">
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	</pre>		</pre>

	The graphics file is now stored in the <tt>Fig</tt> subdirectory. You can view it manually with:		The graphics file is now stored in the <tt>Fig</tt> subdirectory. You can view it manually with:

	<pre>		<pre>
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	</pre>		</pre>

	When an SConstruct file makes more than one graphics file, the <tt>scons view</tt> command will display all of them in sequence.		When a SConstruct file makes more than one graphics file, the <tt>scons view</tt> command will display all of them in sequence.
	[[Image:filter.png\|frame\|center\|Welcome to Madagascar.]]		[[Image:filter.png\|frame\|center\|Welcome to Madagascar.]]
	Now edit the <tt>SConstruct</tt> file: change the title string on the <tt>Result</tt> line to "Hello World!", save the file, and rerun the scons command. You will see that scons has figured out that the file <tt>filter.rsf</tt> does not need to be rebuilt because nothing that affects it has changed. Only the file <tt>filter.vpl</tt> is rebuilt.		Now edit the <tt>SConstruct</tt> file: change the title string on the <tt>Result</tt> line to "Hello World!", save the file, and rerun the scons command. You will see that scons has figured out that the file <tt>filter.rsf</tt> does not need to be rebuilt because nothing that affects it has changed. Only the file <tt>filter.vpl</tt> is rebuilt.

Sfomel: /* Installation from source */

2024-07-08T14:27:12Z

Installation from source

← Older revision		Revision as of 14:27, 8 July 2024
Line 39:		Line 39:
	# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.		# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.
	# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.		# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.
	# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/RSFDATA/ </syntaxhighlight> to ~/.bashrc and ~/.profile after the source ~/RSFSRC/share/madagascar/etc/env.csh. You will also need to create that directory with: <syntaxhighlight lang="bash">mkdir ~/RSFDATA/ </syntaxhighlight> using the command line in a terminal window.		# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/RSFDATA/ </syntaxhighlight> to ~/.bashrc and ~/.profile .

	==Uninstall==		==Uninstall==

Sfomel: /* Prerequisites */ Python 3

2020-09-22T15:07:46Z

Prerequisites: Python 3

← Older revision		Revision as of 15:07, 22 September 2020
Line 27:		Line 27:

	#C compiler. Any ANSI-compliant compiler such as [http://gcc.gnu.org/ GCC] should work. GCC usually comes pre-installed on Linux machines.		#C compiler. Any ANSI-compliant compiler such as [http://gcc.gnu.org/ GCC] should work. GCC usually comes pre-installed on Linux machines.
	#Python interpreter. [http://www.python.org/ Python] is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. ~~The preferred~~ Python ~~version is~~ 2.7 ~~but older versions are also supported. If you experience problems~~ and ~~you have an earlier version, you should probably upgrade~~.		#Python interpreter. [http://www.python.org/ Python] is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. Madagascar supports both Python 2.7 and Python 3.

	Each API option has [[Advanced Installation#Dependencies\|its own prerequisites]].		Each API option has [[Advanced Installation#Dependencies\|its own prerequisites]].

Karl: /* General instructions */

2018-05-19T14:59:45Z

General instructions

← Older revision		Revision as of 14:59, 19 May 2018
Line 39:		Line 39:
	# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.		# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.
	# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.		# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.
	# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/~~DATAPATH~~/ </syntaxhighlight> to ~/.bashrc and ~/.profile after the source ~/RSFSRC/share/madagascar/etc/env.csh		# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/RSFDATA/ </syntaxhighlight> to ~/.bashrc and ~/.profile after the source ~/RSFSRC/share/madagascar/etc/env.csh. You will also need to create that directory with: <syntaxhighlight lang="bash">mkdir ~/RSFDATA/ </syntaxhighlight> using the command line in a terminal window.

	==Uninstall==		==Uninstall==

Karl: /* General instructions */

2018-05-19T14:49:57Z

General instructions

← Older revision		Revision as of 14:49, 19 May 2018
Line 39:		Line 39:
	# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.		# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.
	# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.		# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.
	# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.~~bash_profile~~</tt> files the line <syntaxhighlight lang="bash">source ~~$RSFROOT~~/share/madagascar/etc/env.sh</syntaxhighlight> ~~where RSFROOT is the install directory you specified~~ in the <tt>--prefix</tt> option to <tt>./configure</tt>. If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~~$RSFROOT~~/share/madagascar/etc/env.csh</syntaxhighlight> Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end.		# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.profile</tt> files the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.sh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC). If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source ~/RSFSRC/share/madagascar/etc/env.csh</syntaxhighlight> (if used somthing different in the <tt>--prefix</tt> option to <tt>./configure</tt>, use that instead of ~/RSFSRC.) Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end. e.g. add <syntaxhighlight lang="bash">export DATAPATH=~/DATAPATH/ </syntaxhighlight> to ~/.bashrc and ~/.profile after the source ~/RSFSRC/share/madagascar/etc/env.csh

	==Uninstall==		==Uninstall==

Sfomel: /* Alternative build/install procedure */

2014-04-12T12:53:28Z

Alternative build/install procedure

← Older revision		Revision as of 12:53, 12 April 2014
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	==Troubleshooting==		==Troubleshooting==
	===Alternative build/install procedure===		===Alternative build/install procedure===
	# '''Set the environment variables:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, type ~~(or uncomment)~~ <syntaxhighlight lang="bash">source env.sh</syntaxhighlight> Else, if your shell is <tt>csh</tt> or <tt>tcsh</tt>, type <syntaxhighlight lang="bash">source env.csh</syntaxhighlight>		# '''Set the environment variables:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, type <syntaxhighlight lang="bash">source env.sh</syntaxhighlight> Else, if your shell is <tt>csh</tt> or <tt>tcsh</tt>, type <syntaxhighlight lang="bash">source env.csh</syntaxhighlight>
	# '''Build:''' Type <tt>scons</tt>		# '''Build:''' Type <tt>scons</tt>
	# '''Install:''' Run <tt>scons install</tt> . If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">su; scons install </syntaxhighlight> or <syntaxhighlight lang="bash">sudo scons install</syntaxhighlight>		# '''Install:''' Run <tt>scons install</tt> . If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">su; scons install </syntaxhighlight> or <syntaxhighlight lang="bash">sudo scons install</syntaxhighlight>

Sfomel: /* General instructions */

2014-04-12T12:49:55Z

General instructions

← Older revision		Revision as of 12:49, 12 April 2014
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	===General instructions===		===General instructions===

	# '''Configuration:''' Open a terminal window ~~and~~ change to the top source directory ~~(sometimes called "RSFSRC"). Next~~, you'll have to make some changes to your .bashrc file, so open it in you're favorite editor, e.g. <syntaxhighlight lang="bash"> vim ~/.bashrc </syntaxhighlight> or <syntaxhighlight lang="bash"> gedit ~/.bashrc </syntaxhighlight> Now simply append these lines to the bottom of the .bashrc file:<ol>		# '''Configuration:''' Open a terminal window, change to the top Madagascar source directory, and run <syntaxhighlight lang="bash">./configure --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install Fortran-90 API bindings in addition to the basic package, run <syntaxhighlight lang="bash">./configure API=f90 --prefix=/directory/where/you/want/madagascar/installed</syntaxhighlight> After running <tt>./configure</tt> you may see a list of dependencies that your system does not have installed (the items that have "no" next to them). Most of them are optional. If you decide to install additional packages for your platform, rerun the <tt>./configure</tt> command.
	<syntaxhighlight lang="bash"~~>export DATAPATH=$HOME/scratch/~~
	~~export EDITOR=nedit~~
	~~export OMP_NUM_THREADS=2~~
	~~export LATEX2HTML=$HOME/texmf/latex2html~~
	~~export RSFROOT=~/madagascar~~
	~~#source $HOME/Desktop/RSFSRC/env.sh~~
	</syntaxhighlight>Notice that the "source" line of this file is commented out for now. After this directory is created during the install, we'll come back here to fix this. Another tweak you make elect to implement is changing the OMP_NUM_THREADS line to a number greater than 2 but less than or equal to the number of cores on your machine (2 is the max for a dual-core processor). Incrementing this environment variable will have benefits when running parallelized code. I also assume that you want Madagascar installed to a directory called "madagascar". Feel free to adjust the second to last line accordingly. To have the changes you just made to the file take effect, type <pre>bash</pre> into your terminal window. Now you're ready to run <bash>./configure --prefix=/directory/where/you/want/madagascar/installed</~~bash~~> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install ~~C++ and~~ Fortran-90 API bindings in addition to the basic package, run <bash>./configure API=~~c++,~~f90 --prefix=/directory/where/you/want/madagascar/installed</~~bash~~> ~~Oftentimes after~~ running "./configure ~~..."~~ you~~'ll~~ see a list of ~~things~~ that your system ~~may~~ not have installed (the items that have "no" next to them). ~~Usually they~~ are optional~~, but for the best experience with Madagascar, it is strongly recommended that~~ you install ~~these~~ packages ~~using a package manager such as yum. Example syntax is used here. Just change~~ the ~~name from "python-devel" to whatever you might be missing.~~<~~syntaxhighlight lang="bash"~~>~~yum install python-devel~~</~~syntaxhighlight~~>~~After installing this dependency, rerun the .configure~~ command ~~above and repeat this step until you have all of the desired packages installed~~.~~</ol>~~
	# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.		# '''Building and installing the package:''' Run <syntaxhighlight lang="bash">make install</syntaxhighlight> If you need "root" privileges for installing under <tt>$RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">make; su; make install</syntaxhighlight> or <syntaxhighlight lang="bash">make; sudo make install</syntaxhighlight> If <tt>make</tt> does not exist on your system, an alternative procedure can be found in the [[#Troubleshooting\|Troubleshooting]] section.
	# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.bash_profile</tt> files the line <syntaxhighlight lang="bash">source $RSFROOT/share/madagascar/etc/env.sh</syntaxhighlight> where RSFROOT is the install directory you specified in the <tt>--prefix</tt> option to <tt>./configure</tt>. If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source $RSFROOT/share/madagascar/etc/env.csh</syntaxhighlight> Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end.		# '''User setup:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, add to your <tt>$HOME/.bashrc</tt> and <tt>$HOME/.bash_profile</tt> files the line <syntaxhighlight lang="bash">source $RSFROOT/share/madagascar/etc/env.sh</syntaxhighlight> where RSFROOT is the install directory you specified in the <tt>--prefix</tt> option to <tt>./configure</tt>. If your shell is <tt>(t)csh</tt>, add to your <tt>$HOME/.cshrc</tt> file the line <syntaxhighlight lang="bash">source $RSFROOT/share/madagascar/etc/env.csh</syntaxhighlight> Please be aware that, on some systems, the default value for DATAPATH set in the script above may get automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> in your resource file to another location where you have write access and that allows large files. Remember that the value of DATAPATH should have a slash at the end.

Sfomel: /* Prerequisites */

2014-04-12T12:33:36Z

Prerequisites

← Older revision		Revision as of 12:33, 12 April 2014
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	#C compiler. Any ANSI-compliant compiler such as [http://gcc.gnu.org/ GCC] should work. GCC usually comes pre-installed on Linux machines.		#C compiler. Any ANSI-compliant compiler such as [http://gcc.gnu.org/ GCC] should work. GCC usually comes pre-installed on Linux machines.
	#Python interpreter. [http://www.python.org/ Python] is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. ~~Madagascar currently attempts to support~~ Python ~~versions~~ 2.~~2 through 2.6. Versions before 2~~.~~2 are not common, but if~~ you experience problems and you have an earlier version you should probably upgrade.		#Python interpreter. [http://www.python.org/ Python] is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. The preferred Python version is 2.7 but older versions are also supported. If you experience problems and you have an earlier version, you should probably upgrade.
	#SCons is also required, but it is included with Madagascar and the configure scripts will attempt to install it for you if you don't have it already. Alternatively you can get it through yum with "yum install scons" in a terminal window. For more information see the [[Advanced Installation#Prerequisites\|Advanced Installation]] guide.

	Each API option has [[Advanced Installation#Dependencies\|its own prerequisites]].		Each API option has [[Advanced Installation#Dependencies\|its own prerequisites]].

Sfomel: /* General instructions */

2014-04-08T21:33:47Z

General instructions

← Older revision		Revision as of 21:33, 8 April 2014
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	===General instructions===		===General instructions===

	# '''Configuration:''' Open a terminal window and change to the top source directory (sometimes called "RSFSRC"). Next, you'll have to make some changes to your .bashrc file, so open it in you're favorite editor, e.g. <syntaxhighlight lang="bash"> vim ~/.bashrc </~~bash~~> or <bash> gedit ~/.bashrc </syntaxhighlight> Now simply append these lines to the bottom of the .bashrc file:<ol>		# '''Configuration:''' Open a terminal window and change to the top source directory (sometimes called "RSFSRC"). Next, you'll have to make some changes to your .bashrc file, so open it in you're favorite editor, e.g. <syntaxhighlight lang="bash"> vim ~/.bashrc </syntaxhighlight> or <syntaxhighlight lang="bash"> gedit ~/.bashrc </syntaxhighlight> Now simply append these lines to the bottom of the .bashrc file:<ol>
	<syntaxhighlight lang="bash">export DATAPATH=$HOME/scratch/		<syntaxhighlight lang="bash">export DATAPATH=$HOME/scratch/
	export EDITOR=nedit		export EDITOR=nedit