% /*@@
%   @file      RunningCactus.tex
%   @date      27 Jan 1999
%   @author    Tom Goodale, Gabrielle Allen, Gerd Lanferman
%   @desc 
%   How to run Cactus part of the Cactus User's Guide
%   @enddesc 
%   @version $Header$      
% @@*/
\begin{cactuspart}{1}{Installation and Running}{$RCSfile$}{$Revision$}
\renewcommand{\thepage}{\Alph{part}\arabic{page}}



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\chapter{Installation} 
\label{cha:in}

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\section{Required software}
\label{sec:reqo}

In general, Cactus {\em requires} the following set of software to function
in single processor mode. Please refer to the architecture section
\ref{sec:suar} for architecture specific items.
\begin{Lentry}
\item[{\tt Perl5.0}] Perl is used extensively during the Cactus
  thorn configuration phase. Perl is available for nearly all
  operating systems known to man and can be obtained at
  {\tt http://www.perl.org}
\item[{\tt GNU make}] The make
  process works with the GNU make utility (referred to as {\bf gmake} 
  henceforth). While other make utilities may also work, this is not 
  guaranteed. Gmake can be obtained from your favorite GNU site or
  from {\tt www.gnu.org}
\item[{\tt C/C++}] C and C++ compiler. For example, the GNU compilers. These
 are available for most supported platforms.  Platform specific compilers 
 should also work. 
\item[{\tt CVS}] The {\em ``Concurrent Versioning System''} is not needed
  to run/compile Cactus, but you are strongly encourage to install
  this software to take advantage of the update procedures. It can be
  downloaded from your favorite GNU site.  Tar files of each release are
  also available.
\end{Lentry}

\noindent
To use Cactus, with the default driver ({\tt CactusPUGH/PUGH}) on multiple
processors you also need:
\begin{Lentry}
\item[{\tt MPI}] the {\it Message Passing Interface (MPI)} 
which provides inter-processor communication. 
Supercomputering sites often supply a native {\tt MPI} implementation with
which Cactus is very likely to be compatible. Otherwise there are
various freely available ones available, e.g. the {\tt MPICH}
version of {\tt MPI} is available for various architectures and operating
systems at {\tt http://www-unix.mcs.anl.gov/mpi/}. 
\end{Lentry}

\noindent
If you are using any thorns containing routines 
written in {\tt FORTRAN} you also need
\begin{Lentry}
\item[{\tt F90/F77}] For routines written in F77, either an F90 or an F77
 compiler can be used. For routines written in F90 a F90 compiler is
 obviously
 required. There is a very limited set of free F90 compilers available
 for the different architectures.
\end{Lentry}

\noindent
While not required for compiling or running Cactus, for thorn development
it is useful to install
\begin{Lentry}
\item[{\tt ctags/etags}] The program Tags enables you browse through the calling structure
  of a program by help of function call database. Navigating the flesh and
  arrangements becomes very easy. Emacs and vi both support this method. See
  \ref{sec:usta} for a short guide to ``tags''.
\end{Lentry}

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\section{Supported architectures}
\label{sec:suar}

Cactus runs on many machines, under a large number of Unix operating
systems. Here we list all the machines we have compiled and verified
Cactus on, including some architecture specific notes. 
\begin{Lentry} 
\item[{\bf SGI Origin 2000} running Irix]
\item[{\bf SGI} 32 or 64 bit running Irix]
\item[{\bf Cray T3E}] 
\item[{\bf Dec Alpha}]  Dec operating system and Linux. Single processor
  mode and {\tt MPI} supported. The Decs need to have the GNU {\tt C/C++} 
  compilers installed 
\item[{\bf Intel Linux}] There is a
  free Linux F90 compiler available from  {\tt http://www.psrv.com}
  -- the only free we know of. Single processor mode and {\tt MPICH}, {\tt LAM}
  supported.
\item[{\bf Windows NT}] Compiles with Cygwin version B20, Digital Fortran Compiler and Microsoft Visual C++ compiler. Single processor mode and {\tt WMPI}, 
{\tt HPVM} supported.
\end{Lentry}

The following machines are only partially supported
\begin{Lentry}
\item[{\bf SP2}]
\item[{\bf HP Exemplar}] 
\end{Lentry}

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\section{Checkout procedure}
\label{sec:chpr}

Cactus is distributed, extended, and maintained using the free CVS
software. CVS  allows many
people to work on a large software project together without getting
into a tangle. For the beginner, we summarize the basics in appendix
\ref{sec:uscv}, please refer to this section for a short description of
the CVS syntax.

The space required for an installation depends on the arrangements and
thorns used. The flesh on its own requires less than 5 MB.

\begin{Lentry}
\item[{\bf Login}] Prior to any CVS operation, you need to log into the Cactus
  repository. For an anonymous checkout, type:\\
  {\tt
    cvs -d :pserver:cvs\_anon@cvs.cactuscode.org:/cactus login
    }
  You will be prompted for a password which is {\bf anon}. 
\item[{\bf Checkout}] To obtain a fresh copy of Cactus, move to a directory
  which does not contain a previously checked out version, and type
  {\t
    cvs -d :pserver:cvs\_anon@cvs.cactuscode.org:/cactus checkout Cactus
    }
  The CVS checkout procedure will create a directory called {\bf
  Cactus} and install the code inside this directory.  From now on we
  will reference all directory names relative to {\bf Cactus}. 

\noindent
  If you want to compile Cactus with thorns, you now need to checkout 
  separately the required arrangements (or {\it arrangements} 
   into the {\bf arrangements} directory. To see  the 
  available Cactus arrangements and thorns type
  {\t 
    cvs -d :pserver:cvs\_anon@cvs.cactuscode.org:/cactus checkout -s
  }
  To check out a arrangement or thorn type go to the arrangements directory,  {\t cd arrangements},
  and  for a arrangement type
{\t 
  cvs checkout <arrangement\_name>
  }
        or for just one thorn
{\t 
cvs checkout <arrangement\_name/thorn\_name>
}
 
To simplify this procedure you may use {\t gmake checkout} in the Cactus
home directory which provides menus to pick arrangements and thorns from.
  
  
\item[{\bf Update}] to update an existing Cactus checkout (to patch in
  possible changes, etc.), do the following {\em within} the {\tt Cactus} directory.
  {\t
    cvs update
    }
  The update process will operate recusrively downwards from your current position
  within the Cactus tree. To update only on certain directories, change
  into these directories and issue the update command.
\item{\bf CVS status}: to obtain a status report on the ``age'' of your
  Cactus or arrangement routines (from your current directory position
  downward), type
  {\t
    cvs status
    }
\item[{\bf non-anonymous CVS}] if you have an account at the central
  repository ({\tt cvs.cactuscode.org}) and would like to perform 
  any of the operation above
  {\em non-anonymously}, replace {\tt cvs\_anon} by your login name
  and provide the appropriate password during the CVS login
  process. Depending on your permissions, you may then make commits to Cactus
  or its arrangements.
\item[{\bf Commits}] you need to perform a personalized login and have
  proper permissions to commit code to the repository. 
\end{Lentry}
For more CVS commands on how to add files, etc. please refer to appendix 
\ref{sec:uscv}.


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\section{Directory structure}
\label{sec:dist}

A fresh checkout creates a directory {\tt Cactus} with the
following subdirectories:

\begin{Lentry}

\item[{\tt CVS}] the CVS book-keeping directory, present in every subdirectory.

\item[{\tt doc}] Cactus documentation

\item[{\tt lib}] contains libraries.

\item[{\tt src}] contains the source code for Cactus

\item [{\tt arrangements}] contains the Cactus arrangements. The arrangements
  (the actual ``physics'') are not supplied by checking out just Cactus. 
  If the arrangements you want to use are standard Cactus arrangements, or
  reside on our CVS repository ({\tt cvs.cactuscode.org}), 
  they can be checked out in similar way to the Flesh. 
\end{Lentry}

When Cactus is first compiled it creates a new directory {\tt
Cactus/configs}, which will contain all the source code, object files and
libraries created during the build process.  Disk space may be a problem 
on supercomputers where home directories are small. 

A workaround is to first create a
configs directory on scratch space, say {\tt scratch/cactus\_configs/} (where
{\tt scratch/} is your scratch directory), and then either
\begin{itemize}
\item{} set the environment variable {\tt CONFIGS\_DIR} to point to 
this directory
\end{itemize}
or
\begin{itemize}
\item{}  soft link this directory ({\tt ln -s
scratch/cactus\_configs Cactus/configs/}) to the Cactus directory.
\end{itemize}

Configurations are descibed in detail in section \ref{sec:coaco}.

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\section{Getting help}
\label{sec:gehe}

For tracking problem reports and bugs we use GNATS, which is a bugtracking 
system published under the GNU license. We have set up a web interface at 
{\tt http://www.cactuscode.org} which allows easy submission and browsing 
of problem reports.    

A description of the GNATS categories which we use is provided in the appendix 
\ref{sec:usgn}.

% OK, there is NO emacs at the moment, because the GNATS setup is really stupid
% and sendpr handles like c.... besides the fact, that the user has to go 
% through a make-process which installs stuff somewhere on his HD. gerd.
% \begin{itemize}
% \item {\tt A web interface}
% \item {\tt SendPR}
% {FIXME: Mention the emacs thing here too...}
% \end{itemize}

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\chapter{Compilation} 

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Cactus can be built in different configurations from the same copy of
the source files, and these different configurations coexist in the
{\tt Cactus/configs} directory. Here are several instances in which
 this can be useful:

\begin{enumerate}
\item{}Different configurations can be for {\em different
architectures}. You can keep executables for multiple architecures
based on a single copy of source code, shared on a common file
system.
\item{} You can compare different {\em compiler options, debug-modes}.
  You might want to compile different communication protocols
  (e.g. {\tt MPI} or {\tt GLOBUS}) or leave them out all together.
\item{} You can have different configurations for {\em different thorns
    collections} compiled into your executable.
\end{enumerate}

Once a configuration has been created, by {\tt gmake <config>} as described
in detail in the next section, a single call to {\tt gmake <config>}
will compile the code.  The first time will display your compile 
{\tt ThornList},  and give you the chance to edit it before continuing.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Creating a configuration}
\label{sec:coaco}

At its simplest, this is done by {\tt gmake <config>}.  This will generate
a configuration with the name {\tt config}, doing its best to automatically
determine the default compilers and compilation flags suitable for the current 
architecture.

There are a number of additional command line arguments which may be supplied 
to override some parts of the procedure.

\subsection{Configuration options}

There are two ways to pass options to the configuration process from the
gmake command line.  
\begin{enumerate}
\item{} Add the options to a configuration file and use,

{\tt gmake <config>-config  options=<filename>} 

All available configuration options may be set in the file {\tt filename}, 
any which are not set will take a default value. The options file
should contain lines of the form:

{\tt <option> [=] ...}

The equals sign is optional.

\item{} Pass the options individually  on the command line,

{\tt gmake <configuration name>-config  <option name>=<chosen value>, ...}
Not all configuration options can be set on the command line. Those than can
be set are indicated in the table below.

\end{enumerate}

Note that if a configuration file is used, and options are also passed
on the command line, the configuration file will currently override the command line
options, although this behaviour will soon change.

It is important to note that these methods cannot be used to, for example add
options to the default values for {\tt CFLAGS}. Setting {\tt CFLAGS} in the
configuration file, or the command line will overwrite completely the 
default values.

\subsection{Available options}

There is a plethora of available options.

\begin{itemize}
\item {\tt Compiler and tool specification}

These are used to specify which compilers and other tools to use. Entries followed
by * may be specified on the command line.

\begin{Lentry}
\item [{\tt CC}]
* The C compiler.
\item [{\tt CXX}]
The C++ compiler
\item [{\tt F90}]
* The Fortran 90 compiler
\item [{\tt F77}]
* The FORTRAN 77 compiler.
\item [{\tt CPP}]
  The preprocessor used to generate dependencies and to preprocess Fortran code
\item [{\tt LD}]
* The linker.
\item [{\tt AR}]
The archiver used for generating libraries.
\item [{\tt RANLIB}]
The archive indexer to use.
\item [{\tt MKDIR}]
The program to use to create a directory.
\item [{\tt SHELL}]
The shell to use.
\item [{\tt PERL}]
The name of the perl executable

\end{Lentry}

\item {\tt Compilation and tool flags}

Flags which are passed to the compilers and the tools.

\begin{Lentry}
\item [{\tt CFLAGS}]
Flags for the C compiler

\item [{\tt CXXFLAGS}]
Flags for the C++ compiler

\item [{\tt F90FLAGS}]
* Flags for the Fortran 90 compiler

\item [{\tt F77FLAGS}]
* Flags for the FORTRAN 77 compiler

\item [{\tt MKDIRFLAGS}]
  Flags for MKDIR so that no error is given if the directory exists
\item [{\tt LDFLAGS}]
* Flags for the linker

\item [{\tt ARLAGS}]
Flags for the archiver

\item [{\tt DEBUG}]
Specifies what type of debug mode should be used. The only
option currently available is {\tt yes}. The default is no debugging.

\item [{\tt OPTIMISE}]
Specifies what type of optimisation should be used. The only option
currently available is {\tt no}. The default is to use optimisation.

\end{Lentry}

\item {\tt Library flags}

Used to specify auxiliary libraries and directories to find them in.

\begin{Lentry}

\item [{\tt LIBS}]
The additional libraries.

\item [{\tt LIBDIRS}]
Any other library directories.

\end{Lentry}

\item {\tt Extra include directories}

\begin{Lentry}
\item [{\tt SYS\_INC\_DIRS}]
Used to specify any additional directories for system include files
\end{Lentry}


\item {\tt Precision options}

Used to specify the precision of the default real and integer data types,
specified as the number of bytes the data takes up.  Note that not all
values will be valid on all architectures.

\begin{Lentry}

\item [{\tt REAL\_PRECISION}]
* Allowed values are 16,8,4 .

\item [{\tt INTEGER\_PRECISION}]
* Allowed values are 8,4 and 2 .

\end{Lentry}

\item {\tt Executable name}

\begin{Lentry}
\item [{\tt EXE\_DIR}] The directory in which to place the executable
\item [{\tt EXE}]
The name of the executable.
\end{Lentry}

\item{\tt Extra packages}

Compiling with extra packages is described fully in 
Section \ref{sec:cowiexpa},
which should be consulted for the full range of configuration options.

\begin{Lentry}
\item [{\tt MPI} *] The {\tt MPI} package to use, if required. Supported values are
        {\tt CUSTOM}, {\tt NATIVE}, {\tt MPICH} or {\tt LAM}

\item [{\tt HDF5}]
Supported values are YES

\end{Lentry}

\end{itemize}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsection{Compiling with extra packages}
\label{sec:cowiexpa}


\subsubsection{MPI: Message Passing Interface}

{\tt MPI} (the {\it Message Passing Interface}) can provides inter-processor 
communication. It can either be implemented natively on a machine
(this is usual on most supercomputers), or through a standard package
such as {\tt MPICH}, {\tt MPICH-G}, {\tt LAM}, or {WMPI}.  

To compile with MPI, the configure option is
\newline
\newline
{\tt MPI = <MPI\_TYPE>}
\newline
\newline
where {\tt <MPI\_TYPE>} can take the values (entries followed by * 
may be specified on the configuration command line):

\begin{Lentry}

\item[{\tt CUSTOM}] For a custom {\tt MPI} configuation set the variables
  \begin{Lentry}
  \item [{\tt MPI\_LIBS} *] libraries
  \item [{\tt MPI\_LIB\_DIRS} *] library directories
  \item [{\tt MPI\_INC\_DIRS} *] include file directories
  \end{Lentry}

\item[{\tt NATIVE}] Use the native {\tt MPI} for this machine, as indicated in
        the {\tt known-architectures} directory 
	({\tt lib/make/known-architectures})

\item[{\tt MPICH}] 
Use MPICH ({\tt http://www-unix.mcs.anl.gov/mpi/mpich}). This is controlled
by the options
  \begin{Lentry}
  \item [{\tt MPICH\_DIR} *] directory in which {\tt MPICH} is installed.
        If this option is not defined it will be searched for.
  \item [{\tt MPICH\_DEVICE} *] the device used by {\tt MPICH}. If not 
        defined, the configuration process will search for this in a 
        few defined places.
        Supported devices are currently {\tt ch\_p4}, {\tt ch\_shmem}, 
	and {\tt globus}, and they are searched for in this order.
  \end{Lentry}

If {\tt MPICH\_DEVICE} is chosen to be Globus, (www.globus.org), 
an additional variable must be set
  \begin{Lentry}
  \item[{\tt GLOBUS\_LIB\_DIR} *] directory in which Globus libraries are installed
  \end{Lentry}

\item[{\tt LAM}]
Use {\tt LAM} (Local Area Multicomputer, {\tt http://www.mpi.nd.edu/lam/}). This is 
controlled by the variable 
  \begin{Lentry}
  \item[{\tt LAM\_DIR} *] directory in which {\tt LAM} is installed. This 
     will be searched for, in a few provided places,  if not given.
  \end{Lentry}

\item[{\tt WMPI}] 
Use WMPI (Win32 Message Passing Interface, {\tt http://dsg.dei.uc.pt/w32mpi/intro.html}). This is controlled by the variable
  \begin{Lentry}
  \item[{\tt WMPI\_DIR} *] directory in which {\tt WMPI} is installed.
  \end{Lentry}

\end{Lentry}

Note that the searches for libraries etc. mentions above use the 
locations given in the files in {\tt lib/make/extras/MPI}.


\subsubsection{HDF5: Hierarchical Data Format version 5}

To compile with HDF5 ({\tt http://hdf.ncsa.uiuc.edu/whatishdf5.html}),
the configure options are
\newline
\newline
{\tt HDF5 = YES [HDF5\_DIR = <dir>] [LIBZ\_DIR = <dir>]}
\newline
\newline
If HDF5\_DIR is not given the configuration process will search for an
installed HDF5 package in some standard places (defined in
{\tt lib/make/extras/HDF5}). If the found HDF5 library was compiled with
libz.a, the configuration process also searches for that library and adds it 
to the linker flags. You may also point directly to an installation of libz.a
by setting LIBZ\_DIR.\\






\subsection{File layout after a configuration has been created }

The configuration process sets up various subdirectories and files in the 
{\tt configs} directory to contain the configuration specific files, these
are placed in a directory with the name of the configuration.

\begin{Lentry}

\item [{\tt config-data}] contains the files created by the configure
script:

The most important ones are

\begin{Lentry}

\item [{\tt make.config.defn}] 
contains compilers and compilation flags for a configuration.  

\item [{\tt make.extra.defn}]
contains details about extra packages used in the configuration.

\item [{\tt cctk\_Config.h}]
The main configuration header file, containing architecture specific
definitions.

\item [{\tt cctk\_Archdefs.h}]
An architecture specific header file containing things which cannot be
automatically detected, and have thus been hand-coded for this architecture.
\end{Lentry}

These are the first files which should be checked or modified to suite any
peculiarities of this configuration.

In addition the following files may be informative:

\begin{Lentry}
\item [{\tt fortran\_name.pl}] 
A perl script used to determine how the Fortran compiler names subroutines.  
This is used to make some C routines callable from Fortran, and Fortran 
routines callable from C.

\item [{\tt make.config.deps}]
Initially empty.  Can be edited to add extra architecture specific dependencies
needed to generate the executable.

\item [{\tt make.config.rule}] 
Make rules for generating object files from source files.

\end{Lentry}

Finally, autoconf generates the following files.

\begin{Lentry}

\item [{\tt config.log}]
A log of the autoconf process.

\item [{\tt config.status}]
A scrit which may be used to regenerate the configuration.

\item [{\tt config.cache}]
An internal file used by autoconf.

\end{Lentry}

\item [{\tt lib}] 
An empty directory which will contain the libraries created for each thorn.

\item [{\tt build}] 
An empty directory which will contain the object files generated for this 
configuration, and preprocessed source files.

\end{Lentry}


\section{Building and Administering a configuration}
\label{sec:buanadaco}

Once you have created a new configuration, the command
\\ \\ 
{\tt gmake <configuration name>}
\\ \\
will build an executable, prompting you along the way for the 
thorns which should be included. There is a range of  gmake 
targets and options which are detailed in the following sections.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{gmake targets for building and adminstering configurations}
\label{sec:gmtafobuanadco}

A target for {\tt gmake} can be naively thought of as an argument
that tells it which of several things listed in the {\tt Makefile} it
is to do. The command {\tt gmake help} lists all gmake targets.

\begin{Lentry}

\item [{\tt gmake <config>}] 
	builds a configuration. If the configuation doesn't exist
        it will create it.

\item [{\tt gmake <config>-clean}] removes all object and dependency files from
  a configuration. 

\item [{\tt gmake <config>-cleandeps}] removes all dependency files from
  a configuration. 

\item [{\tt gmake <config>-cleanobjs}] removes all object files from
  a configuration. 

\item [{\tt gmake <config>-config}] creates a new configuration or reconfigures an old one.

\item [{\tt gmake <config>-delete}] deletes a configuration ({\tt rm -r configs/<config>}).

\item [{\tt gmake <config>-editthorns}] edits the ThornList

\item [{\tt gmake <config>-realclean}] removes from a configuration
  all object and dependency files, 
  as well as files generated from the CST (that is, only the files
  generated by configure and the ThornList files remain).

\item [{\tt gmake <config>-rebuild}] rebuilds a configuration (reruns the CST -- the perl scripts which parse the thorn configuration files).

\item [{\tt gmake <config>-testsuite}] runs the test programs associated with
 each thorn in the configuration. See section \ref{sec:te} for information about the 
 testsuite mechanism.

\item [{\tt gmake <config>-thornlist}] regenerates the ThornList for a configuration.

\item [{\tt gmake <config>-thornparfiles}] copies all the example parameter files relevant for this configuration to the directory {\tt thornparfiles} in the Cactus home directory. If a file of the same name is already there, it will not overwrite it.

\end{Lentry}



\subsection{Compiling in thorns}
\label{sec:cointh}

Cactus will try to compile all thorns listed in 
{\tt configs/<config>/ThornList}.
The {\tt ThornList} file is simply a list of the form
{\t <arrangement>/<thorn>}.  All text after a \# sign
one a line is treated as a comment and ignored.
The first time that you compile a configuration, 
you will be shown a list of all the thorns in your arrangement
directory, and asked if you with to edit them. You can regenerate
this list at anytime by typing

\begin{verbatim}
gmake <config>-thornlist
\end{verbatim}

or you can edit it using

\begin{verbatim}
gmake <config>-editthorns
\end{verbatim}

Instead of using the editor to specify the thorns you want to
  have compiled, you can {\em edit} the {\em ThornList} outside
  the make process. It is located in {\tt configs/<config>/ThornList},
  where {\tt <config>} refers to the name of your configuration.
  The directory, {\tt ./configs}, exists {\em
    after} the very first  make phase for the first configuration.

\subsection{Notes and Caveats}
\begin{itemize}
\item{} If during the build you see the error ``{\tt missing
    separator}'' you are probably not using GNU make. 
\item{} {\em The EDITOR environment variable}. You may not be aware of
  this, but this thing very often exists and may be set  by default to
  something scary like {\tt vi}. If you don't know how to use {\tt vi}
  or wish to
  use your favorite editor instead, reset this environment variable.
  (To exit {\tt vi} type {\tt <ESC> :q!})
\end{itemize}

\subsection{gmake options for building configurations}
\label{sec:gmopfobuco}

An {\it option} for gmake can be thought of as an argument which tells
it how it should make a {\tt target}. Note that the final result is always
the same.

\begin{Lentry}

\item [{\tt gmake <target> FJOBS=<number>}] compile in parallel, across files within each thorn
\item [{\tt gmake <target> THORNLIST=<file> [THORNLIST\_DIR=<dir>]}] uses the file {\tt dir/file} as the ThornList for the configuration. The directory defaults to the current directory
\item [{\tt gmake <target> SILENT=no}] print the commands that gmake is executing
\item [{\tt gmake <target> TJOBS=<number>}] compile in parallel, across thorns 
\item [{\tt gmake <target> WARN=yes}] show compiler warnings during compilation.

\end{Lentry}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Other gmake targets}

\begin{Lentry}

\item [{\tt gmake help}] lists all make options

\item [{\tt gmake checkout}] allows you to easily checkout Cactus arrangements and thorns.

\item [{\tt gmake default}] creates a new configuration with a default name.

\item [{\tt gmake distclean}] delete your {\tt configs} directory and hence all your configurations.

\item [{\tt gmake doc}] places a postscript version of the Users Guide documentation in your Cactus home directory.

\item [{\tt gmake downsize}] removes non essential files as documents
  and testsuites to allow for minimal installation size.

\item [{\tt gmake newthorn}] creates a new thorn, prompting for the necessary 
  information and creating template files.

\item [{\tt gmake TAGS}] creates an Emacs style TAGS file. See section
  \ref{sec:usta} for using TAGS within Cactus.

\item [{\tt gmake tags}] creates a {\tt vi} style tags file. See section
  \ref{sec:usta} for using TAGS within Cactus.

\item [{\tt gmake thorninfo}] give information about all available thorns.

\end{Lentry}


\section{Testing} 
\label{sec:te}

Some thorns come with a testsuite, consisting of example parameter files
and the output files generated by running these. To run the testsuites
for the thorns you have compiled use
\newline

{\tt gmake <configuration>-testsuite}
\newline

These testsuites serve the dual purpose of

\begin{Lentry}
\item [Regression testing]
i.e. making sure that changes to the thorn or the flesh don't affect the
output from a known parameter file.
\item [Portability testing]
i.e. checking that the results are independent of the architecture - this
is also of use when trying to get Cactus to work on a new architecture.
\end{Lentry}

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\chapter{Running Cactus}

This chapter covers all aspects for running your Cactus executable.
These include: command line options; parameter file syntax; understanding
screen output and environment variables.

\section{Command Line Options}
\label{sec:coliop}

The cactus executable accepts numerous command line arguments:
\newline

{\tt
\begin{tabular}{|l|l|}
\hline
Short Version & Long Version \\
\hline
 -O & -describe-all-parameters \\
\hline
 -o <param> & -describe-parameter <param> \\
\hline
 -T & -list-thorns\\
\hline
 -t <arrangement/thorn>& -test-thorn-compiled <arrangement/thorn>\\
\hline
 -h,-? & -help\\
\hline
 -v & -version \\
\hline
 -x [<nprocs>] & -test-parameters [<nprocs>] \\
\hline
 -W <level> & -warning-level <level> \\
\hline
 -E <level> & -error-level <level> \\
\hline
 -r & -redirect-stdout \\
\hline
\end{tabular}
}
\newline

\begin{Lentry}
\item [{\tt -O} or {\tt -describe-all-parameters}]
Produces a full list of all parameters from all thorns which were compiled,
along with descriptions and allowed values.
\item [{\tt -o <param>} or {\tt -describe-parameter <param>}] 
Produces the description and allowed values for a given parameter - takes one
argument.
\item [{\tt -T} or {\tt -list-thorns}] 
Produces a list of all the thorns which were compiled in.
\item [{\tt -t <arrangement or thorn>} or {\tt -test-thorn-compiled <arrangement or thorn>} ] 
Checks if a given thorn was compiled in - takes one argument.
\item [{\tt -h}, {\tt -?} or {\tt -help}]
Produces a help message.
\item [{\tt -v} or {\tt -version}] 
Produces version information of the code.
\item [{\tt -x <nprocs>} or {\tt -test-parameters <nprocs>}] 
Runs the code far enough to check the consistency of the parameters.  If
given a numeric argument it will attempt to simulate being on that number 
of processors. [To be implemented]
\item [{\tt -W <level>} or {\tt -waring-level <level>}]
Sets the warning level of the code.  All warning messages are given a level--
the lower the level the greater the severity.  This parameter controls the
level of messages to be seen.  The default is a warning level of 1, with 
0 indicating the only those messages which are (by default) fatal should 
be seen.
\item [{\tt -E <level} or {\tt -error-level <level>}]
This works in concert with {\tt -W} - it controls which warning level is
treated as a fatal error.  This cannot be set to a higher value than 
{\tt -W}. The default value is zero.
\item [{\tt -r} or {\tt -redirect-stout}]
This redirects the standard output of each processor to a file.  By default
the output from processors other than processor 0 is discarded.
\end{Lentry}

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\section{Parameter File Syntax}

The parameter file is used to control the behaviour of the code at runtime.
It is of a text file with lines which are either comments, denoted
by a `\#', or parameter statements. A parameter statement consists 
of one or more parameter names, followed by
and `=', followed by the value(s) for this (these) parameter(s).

The name of a parameter consists of:

\begin{Lentry}
\item [{\tt Global parameters}]
Just name of the parameter itself.
\item [{\tt Restricted parameters}]
The name of the {\em implementation} which defined the parameter, two colons,
and the name of the parameter --- e.g. {\tt driver::global\_nx}.
\item [{\tt Private parameters}]
The name of the {\em thorn} which defined the parameter, two colons,
and the name of the parameter --- e.g. {\tt wavetoy::amplitude}.
\end{Lentry}

In addition there is a parameter {\tt ActiveThorns} which tells the code
which {\em thorns} are to be activated.  Only parameters from active thorns can
be set  (and only those routines {\it scheduled} by active thorns are run).  
By default all thorns are inactive.  {\bf This should be the first
parameter in your parameter file.}
\newline

Note that you can obtain lists of the parameters associated with
each thorn using the command line options {\tt -o} and {\tt -O}
(Section~\ref{sec:coliop}).


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\chapter{Getting and looking at output}


\section{Screen output}

As your Cactus executable runs, standard output and standard error
are usually written to the screen. Standard output provides you
with information about the run, and standard error reports warnings
and errors from the flesh and thorns.

As the program runs, the normal output provides the following information

\begin{Lentry}

\item [Active thorns]
	A report is made as each of the thorns in the {\tt ActiveThorns} parameters from the parameter file is attempted to be activated. This report 
shows whether the activation was successful, and if successful gives the 
thorns implementation. For example

{\tt
\begin{verbatim}
Activating thorn idscalarwave...Success -> active implementation idscalarwave
\end{verbatim}
}

\item [Failed parameters] 
 	If any of the parameters in the parameter file does not belong to any of the active thorns, or if the parameter value is not in the allowed range, an
error is registered. For example, if the parameter is not recognised

{\tt
\begin{verbatim}
Unknown parameter time::ddtfac�
\end{verbatim}
}
or if the parameter value is not in the allowed range

{\tt
\begin{verbatim}
Unable to set keyword CartGrid3D::type - ByMouth not in any active rangey
\end{verbatim}
}

\item [Scheduling information]
	A complete list of all scheduled routines is given, in the 
order that they will be executed. For example

{\tt
\begin{verbatim}
----------------------------------------------------------------------
  Startup routines
    Cactus: Register banner for Cactus
    CartGrid3D: Register GH Extension for GridSymmetry
    CartGrid3D: Register coordinates for the Cartesian grid
    IOASCII: Startup routine
    IOBasic: Startup routine
    IOUtil: IOUtil startup routine
    PUGH: Startup routine.
    WaveToyC: Register banner

  Parameter checking routines
    CartGrid3D: Check coordinates for CartGrid3D
    IDScalarWave: Check parameters

  Initialisation
    CartGrid3D: Set up spatial 3D Cartesian coordinates on the GH
    PUGH: Report on PUGH set up
    Time: Set timestep based on speed one Courant condition
    WaveToyC: Schedule symmetries
    IDScalarWave: Initial data for 3D wave equation

  do loop over timesteps
    WaveToyC: Evolution of 3D wave equation
    t = t+dt
    if (analysis)
    endif
  enddo
----------------------------------------------------------------------
\end{verbatim}
}

\item [Thorn banners]
	Any banners registered from the thorns are displayed

\end{Lentry}


\section{Output}
Output methods in Cactus are all provided by thorns. Any number
of output methods can be used for each run. The behaviour of 
the output thorns in the standard arrangements are described in
those thorns documentation. In general, these thorns decide
what to output by parsing a string parameter containing the 
names of those grid variables, or groups of variables, for 
which output is required. The names should be fully qualified
with the {\tt implementation} and {\tt group} or {\tt variable} names. 
There is usually a parameter for each method to denote how often, in evolution
iterations, this output should be performed.  There is also usually
a parameter to define the directory in which the output should be
placed, defaulting to the directory from which the executable is 
run.


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\section{Checkpointing}

Checkpointing is defined as writing all data from a run to a file,
so that the run can be restarted from reading all the data from the
file. Checkpointing methods in Cactus are provided by thorns.

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\end{cactuspart}