[ubuntu] Configure warnings installing XOOPIC from Berkeley Plasma Physics Group

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XOOPIC source is available via www at http://langmuir.eecs.berkeley.edu/pub/codes

Most if this file is old, but here is the quickstart. Read on if you have trouble.
: This is a standard ./configure, make, make install system.
: start with the script 'run_conf.sh' - it is a nicer way to pass arguments to configure
and it is the same for xoopic and xgrafix (you need to install xgrafix first)
: once you have edited run_conf.sh to fit your needs, use it to configure xgrafix, then install it:
$> sh run_conf.sh
$> make && sudo make install # note only sudo if you need root privileges to write the destination
: then once that completes, use _the same_ run_conf.sh to configure xoopic:
$> sh run_conf.sh
$> make && cp xg/xoopic /path/to/where/I/want/xoopic

That should do it!

bash_completion generally has nice tab completion for introspection of available options to configure
($>./configure<tab><tab> will show your options)

############################
# Dependencies:
############################
building and running xgrafix/xoopic depend on the following headers/libraries/programs:
X11, Xpm, Tcl/Tk, gcc, imagemagick, bison

optional xoopic dependencies:
Fortran
MPI for parallel runs
HDF5 for parallel or high performance dump files
libpng for png diagnostics
fftw
fftw3


dependencies can be installed on Ubuntu (or likely any Debian based distro) with the command:
sudo aptitude install gcc g++ gfortran build-essential automake \
tk-dev imagemagick bison libx11-dev libxpm-dev libpng-dev \
fftw-dev libfftw3-dev h5utils hdf5-tools libhdf5-serial-*\

the first two lines are necessary, the last installs optional fftw/hdf5 dependencies

On Fedora, these dependencies can be installed with:
sudo yum install gcc gcc-gfortran gcc-c++ automake libX11-devel libXpm-devel \
ImageMagick bison tk-devel libpng-devel \
hdf5 hdf5-devel

On SUSE, install the following packages with your package manager:
gcc gcc-c++ gcc-fortran automake xorg-x11-devel make
tk-devel bison libpng-devel imagemagick hdf5 hdf5-devel


##################
# Configure / build/ install
##################
For a new install:

edit the run_conf.sh file to match your system. For a basic install, the only
thing you are likely to edit is `prefix` - the install location.

then you can do:
sh run_conf.sh # configure the build

make # build the program
# or, if you have a multiprocessor machine, this can go faster with:
make -j 4 #(that's 4 threads, you can do as many or as few as you want)

# If you are building xgrafix, do:
make install # sudo make install if you need root privileges to write to $prefix/{bin|lib|include}

test the xgrafix build with:
./ctest/xtest # from the xgrafix root dir.

Once you have built and installed xgrafix, you can build xoopic. run_conf.sh is the same for
both xoopic and xgrafix, so if you configured run_conf.sh in xgrafix, use the same one in xoopic.

The process to build xoopic is the same as xgrafix, except skip the 'make install' step, since you only
need the binary file in 'xg/xoopic'. You can test xoopic with:
./xoopic -i input/ebeam1a.inp # from the xoopic root dir

once xoopic is done, you can install it with:
cp xoopic $prefix/bin/

note that you do not need to do 'make install' for xoopic, just place the binary './xoopic' anywhere in your path

where prefix is defined as in:
prefix=/usr/local # to install for all users
or
prefix=$HOME # to install just for you (assuming ~/bin is already in your path)

**************************************
The rest of this file is pretty old...

XOOPIC has been compiled successfully on the following UNIX systems running
X11R5 or better:

OS Machine compiler library
-------------------------------------------------------------------------
HP-UX A.09.05 HP 712/80 g++2.7.2 libg++2.7.1
DEC UNIX 3.2 DEC 200/4/233 g++2.7.2 libg++2.7.1
DEC UNIX 3.2 DEC 200/4/233 CXX5.1 vendor supplied
using DEC CXX 5.1 is not recommended for XOOPIC
DEC UNIX 4.0C PWS 600AU g++2.8.0 libg++2.8.0
DEC UNIX 4.0C PWS 600AU egcs-1.0.1 egcs libraries
DEC UNIX 4.0C PWS 600AU CXX6.0 vendor supplied.
DEC UNIX 4.0D PWS 600AU CXX6.0 vendor supplied.
DEC UNIX 4.0D DEC 8400 CXX6.0 vendor supplied.
SunOS 4.1.x Sparc 2 g++2.7.2 libg++2.7.1
Solaris 2.5 UltraSPARC g++2.7.2
Solaris 2.6 UltraSPARC Sun CC 4.2 vendor supplied
AIX 3.2 IBM 590 g++2.7.2 libg++2.7.1
AIX 3.2 IBM 590 xlC 1.00 -- had to modify the code,
and turn off optimization on some
files. Furthermore, the compiled
code was 1/2 as fast as g++.
Solaris 2.4 Sparc 10 Sun c++4.0.1
(required a few simple changes)

Linux PPro g++2.7.2, g++2.8.0
Linux/Alpha 21164 g++2.7.2, g++2.8.0
FreeBSD K6 g++2.7.2
-- Most of this is outdated, but 2009 versions have been compiled on the following:
both 32/64 bit:
Ubuntu Linux 8.10 - 9.10, gcc 4.2-4.4, tcl/tk 8.4-8.5
Mac OSX 10.4.8,10.5.7,10.6.1 - using MacPorts or Fink for tcl/tk
Fedora Core 8 (64) - gcc4.1
Fedora Core 11 (32) - gcc4.4
openSUSE 11 (32) - gcc4.3

************************************************** **************************
If possible ENLIST THE AID OF YOUR SYSTEM ADMINISTRATOR FOR COMPILING XOOPIC.

WARNING: g++ 2.6.1, g++ 2.6.2, and g++ 2.6.3 are BROKEN and WILL NOT
compile XOOPIC (on most systems). I don't know about previous versions.

ALSO: g++2.7.2 on Windows NT 4.0 does NOT work.
************************************************** **************************




The rest of this file is possibly outdated:
**********
To compile and install XOOPIC, you need the following public domain
software packages which we do not maintain:


* g++ (/pub/GNU/gcc-2.7.2.tar.gz at gatekeeper.dec.com)
* libg++ (/pub/GNU/libg++-2.7.?.tar.gz at gatekeeper.dec.com)

OR DEC CXX instead of g++ and libg++

* libtcl7.4.a (or later)
* libtk4.0.a (or later)
* libXpm.a
* libXGrafix2.50 (or later) (http://ptsg.eecs.berkeley.edu)

*************************************************
*** NOTE: Requirement for the XGrafix version ***
*************************************************
Update on Aug. 16, 2005 by H.C. KIM

To make this version of xoopic work properly, the recent version
of XGrafix (later than Mar. 29, 2005) needs to be installed.
Otherwise, you may see "core dumped" when restoring from a dump file.
*************************************************

Once you have a c++ compiler, libtcl.a libtk.a libXpm.a, you are ready to
begin:

0) Get the sources:
http://ptsg.eecs.berkeley.edu

You may already have these and can omit this step.

1) Unpack the sources:
>tar -xvzf xoopic.tar.gz

You should get a directory named oopic with these files:
README Makefile physics/ advisor/ xg/ xgrafix/ input/ g++-fixes/ doc/
configure
physics/ contains the basic physical models for XOOPIC
advisor/ contains the input file reader and input sanity checking
xgrafix/ contains the graphics library used by XOOPIC
input/ contains sample input files for XOOPIC
g++-fixes/ contains any fixes you may need to make to g++ to get
it to work
doc/ contains documentation.
bench/ benchmarks of XOOPIC
+ other misc. files..

2) Compile and install XGrafix.
(XGrafix has its own instructions)

3) Run ./configure

Once you have a c++ compiler, libXGC250.a, libXpm.a, libtcl*.a, libtk*.a,
you are ready to start compiling xoopic.

To begin, run "configure", which will try to find all the libraries
and headers needed, and which will accept parameters indicating
configuration options or library locations.

In the directory where you have:
README Makefile physics/ advisor/ xg/ xgrafix/ input/

./configure

Pay attention to the messages configure gives. If it fails to
automatically find something such as libXpm.a, it will prompt
you to tell it where to find that file.

configure --help
will give you a list of configure options.

As an example, this command will cause XOOPIC to use the compiler
'cxx' instead of the default 'g++':

./configure --with-CXX=cxx

If HDF5 library is not installed in your systems,
you need to give an option of '--disable-hdf5':

./configure --disable-hdf5

Depending on how idiosyncratic your system installation is, you
might have to give a very complex configure comand such as:

./configure --with-CXX=cxx --with-tclsh=/home/tcl/bin
--x-includes=/usr/X11/include --x-libraries=/sww/X11/lib
--with-xpm=/usr/local/Xpm/lib --with-XGRAFIX-lib=/usr/local/tmp

However, that should only be necessary if your system administrator
likes to install things in non-standard locations.

Configure, when successful, should convert Makefile.in in each of
. advisor/ physics/ and xg/ and convert them to a Makefile.

4) Run make

make

This should go into each of physics/ advisor/, and xg/,
and create the binary xg/xoopic for you.

If the compile fails, complaining of missing include files
or libraries, try editing */Makefile to add the appropriate
includes or libraries.

If the link fails with missing symbols, it is likely that
the version of tcl/tk that XOOPIC is trying to use is a
mismatch to the XGrafix library. XGrafix must be configured
to use either version 7.4/4.0 of the tcl/tk libraries,
or configured to use version 7.5/4.1 or higher. If
XGrafix was configured for the wrong tcl/tk libraries,
then XOOPIC won't link!

Possible problems: the compile fails, giving errors involving
cstring.h. This is a g++2.7.0 problem.
A fix for this is in g++-fixes.

b) upon starting XOOPIC, xgrafix reports that it can't find
a tcl/tk initialization file.

Solution: Figure out where the file xgrafix is looking for is,
and fix xgrafix to find it. These are some in particular:
init.tcl in the tcl lib directory, (usually /usr/local/lib/tcl)
init.tk in the tk lib directory, (usually /usr/local/lib/tk)
xgsetup.tcl in your xgrafix directory

If the problem is with finding init.tcl, and init.tk, then probably
these libraries are misinstalled. If xgsetup.tcl is not found,
you probably didn't set XGTCL correctly when building xgrafix.
Double check this and recompile if necessary.

To run,

xoopic -i input/dring.inp

or whatever input file is appropriate for you.




Bugs: email bugreports to xoopic@langmuir.eecs.berkeley.edu

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