SGI Developer Toolbox 6.1/SGI Developer Toolbox 6.1 - Disc 4.iso/public/SciAn/src/README

Text File | 1994-08-01 | 28KB | 634 lines

***************************************************************************
*                                                                         *
*  SciAn README File                                                      *
*  Eric Pepke and Jim Lyons                                               *
*  September 15, 1993                                                     *
*                                                                         *
***************************************************************************

This file describes the process of obtaining and installing SciAn on your
workstation.  Please read it thoroughly before doing any installation.  I
know it's not always much fun to read things before jumping in and compiling,
but please do it anyway--there are some definable options that you need to
know about before you begin.

Table Of Contents

1.0  Introduction
2.0  System requirements
   2.1  FORTRAN option
   2.2  HDF option
   2.3  NetCDF option
   2.4  JPEG option
3.0  Obtaining and installing SciAn
   3.1  Installing SciAn from the SuperComputing 93 CD-ROM
   3.2  Obtaining SciAn via ftp
      3.2.1  Connecting to ftp.scri.fsu.edu
      3.2.1  Downloading the SciAn Package
   3.3  Installing SciAn
      3.3.1  Preparing the installation options
      3.3.2  Assigning font mappings
      3.3.3  Compiling and linking SciAn
      3.3.4  Releasing SciAn
      3.3.5  Local options
4.0  Obtaining the documentation
   4.1  PostScript format
   4.2  Microsoft Word format
5.0  Using the technical notes
6.0  Getting help
   6.1  Common problems and solutions

---------------------------------------------------------------------------

1.0  Introduction

SciAn is a scientific visualization and animation program for Silicon
Graphics and IBM RISC/Sytem 6000 workstations.  It was developed at the
Supercomputer Computations Research Institute at Florida State University
to help meet the daily visualization needs of our scientists.

SciAn is primarily intended to do 3-D visualizations of data in an
interactive environment with the ability to generate animations using
frame-accurate video recording devices.  A user manual, on-line help, and
technical notes will help you use the program.

As a research institution, we have always relied upon the availability of
free software to meet our needs, and we wanted to give something back to the
research community in return.  For this reason, we are making SciAn
available at no charge.

If you have problems with or suggestions about SciAn, please don't hesitate
to send us electronic mail.  However, please understand that we are a
research institution, not a software development company.  We work best in
an environment of cooperation and collaboration, and we hope that you will
join us. Send inquiries about SciAn to [e-mail]. You can also
request to be put on the SciAn mailing list, which will keep you informed
of updates.  There is no requirement to sign a license agreement for SciAn,
but it is important to keep track of who is using it, so that we can show
those who fund us that we are doing useful work for the research community.

If you use SciAn to produce images or animations for publication, please
give credit to the Supercomputer Computations Research Institute at Florida
State University.  It is a lot easier to justify continuing to put effort
into maintaining SciAn if we can point to places where it is being used to
do real work.

2.0  System requirements

SciAn currently runs on two platforms:
  1) Silicon Graphics 4D workstations
  2) IBM RISC/System 6000 workstations

Beginning with version 0.60, SciAn should run on all Silicon Graphics Power
Series, Personal IRIS, and Indigo workstations with Z-buffer capability.  It
will not run on very old workstations, such as the 1000, 2000, and 3000
series.

SciAn will run only on IBM RISC/System 6000 workstations that have 3-D
graphics accelerators that provide GL compatibility.  SciAn also requires
a Z-buffer.  If there is any question about whether your hardware provides
this, please get in touch with your system manager or IBM sales
representative.  (IBM makes a bewildering variety of hardware, and I can't
keep up, but the magic words are Z-buffer and 3-D GL compatibility.)

On all workstations, SciAn ABSOLUTELY REQUIRES a Z-buffer.  If you try
to run it on a workstation that does not have a Z-buffer, you will get
strange results.

Because SciAn is distributed as source code, you must also have access to
a C compiler to install.  Any old ANSI C will do; you don't need C++.

In addition to the basic SciAn, there are several installation options.
The automatic installation process as described in Section 3.3.2 takes
care of detecting and modifying the installation for these options.
It is necessary to have the correct libraries and languages installed
before you begin to install SciAn.

2.1  FORTRAN option

If a FORTRAN compiler is present on your system, SciAn will use it to
compile the PLOT-3D file reader to be able to read unformatted FORTRAN
data files.  If you don't have a FORTRAN compiler, the PLOT-3D file
reader will only be able to read formatted and binary files.

In order to compile using FORTRAN, there must be a FORTRAN compiler in the
/bin, /usr/bin, /usr/local/bin, or . directories.  The name of the FORTRAN
compiler is given in the flags.?.make file as described in section 3.

2.2  HDF option

SciAn may also optionally be installed using the Hierarchical Data Format
(HDF) library developed by the National Center for Supercomputing
Applications at the University of Illinois at Urbana-Champaign.  This library
is available via anonymous FTP from ftp.ncsa.uiuc.edu.  We strongly recommend
that you obtain this library, as it provides a good data format.

You must install the HDF library, libdf.a, in /lib, /usr/lib, or
/usr/local/lib before starting the SciAn installation process.  SciAn will
work with versions 3.1, 3.2, and 3.3 of the HDF library.

2.3  NetCDF option

SciAn may optionally be installed using the NetCDF library, which is
available via anonymous FTP from unidata.ucar.edu.  We strongly recommend
that you obtain this library, as it provides a good data format.

You must install the NetCDF library, libnetcdf.a, in /lib, /usr/lib, or
/usr/local/lib before starting the SciAn installation process.  There must
also be a library called librpcsvc.a, which normally comes with the system
software, in /usr/lib.  Silicon Graphics machines must also have the Sun
compatibility library, libsun.a.

2.4  JPEG option

The JPEG animation recorder driver provides an easy way to save animation
in a series of compressed JPEG files.  In order to use this, you must
install the JPEG library developed by Rodney Hoinkes at the Centre for
Landscape Research.  It is available via anonymous ftp from uceng.uc.edu.
There are several libraries available from this site; the one you need
is called libCLRjpeg4.a.  It must be installed in /lib, /usr/lib, or
/usr/local/lib.

3.0  Obtaining and installing SciAn

The next three sections describe the process of installing SciAn on your
machine. If you want to use the files on this CD, read section 3.1 and then
go on to section 3.3. If you want to obtain the very latest version of SciAn
from our ftp site, read section 3.2. Once you have the files on your
workstation, follow the instructions in section 3.3 to create a SciAn
executable file.

3.1  Installing SciAn from the SuperComputing 93 CD-ROM

This disc contains a directory named "SciAn" with five files:

README            This file, describing the installation process
RELEASE.NOTES     Notes about this version of SciAn
scian085.tar.Z    Compressed tar file of the SciAn source files
user080.ps.tar.Z  Compressed tar file of the User's Manual PostScript files
ref080.ps.tar.Z   Compressed tar file of the Reference Manual PostScript files

First, make a directory for the SciAn files on your local disk and copy all
five files to it. Then go to the directory and uncompress the source files
by entering

    uncompress scian085.tar

When the uncompress command finishes, you will have a file called scian085.tar.
To extract the individual files from the tar file, enter

    tar -xvof scian085.tar

If you get an error message, try

    tar -xvf scian085.tar

Many files will be extracted from the SciAn tar file.  Files ending in .c,
.h, and .f are the source files of SciAn.  The Makefile and files with .make
in their names are for the make program.  There is also a directory called
demo which contains demonstration files for SciAn.

If you want to print out the documentation, uncompress the two document
files and extract the individual files from them. Enter

    uncompress user080.ps.tar
    tar -xvf user080.ps.tar

and

    uncompress ref080.ps.tar
    tar -xvf ref080.ps.tar

The tar command will produce a number of PostScript files, all ending in the
.ps extension.  You can print out these PostScript files according to the
rules for the printers at your site. (Note that the manuals describe version
0.80 of the program. You may notice some minor differences from the current
release.)

If you are installing from the CD-ROM, skip to section 3.3 now.

3.2  Obtaining SciAn via ftp

SciAn is normally distributed via anonymous ftp from ftp.scri.fsu.edu.  If
you do not have access to anonymous ftp, send us mail, and we'll try to
figure out some other way to get you the program.  It is much easier to
get the program through ftp, however, and it's certainly easier to get
updates that way.


3.2.1  Connecting to ftp.scri.fsu.edu

Before you connect to the SciAn distribution machine, make sure that you are
in a directory on your machine where you want the SciAn source to reside.  You
will need a few megabytes to keep the files during the installation process.

To connect to ftp.scri.fsu.edu, start up ftp on your unix machine like
this:

    ftp ftp.scri.fsu.edu

When asked for a user name, enter anonymous.  When asked for a password,
enter your network electronic mail address.

The SciAn program and documentation are located in the SciAn subdirectory
of the pub directory.  To get into that directory, enter

    cd pub/SciAn

In that directory, you will find a README file (which is this document)
and several subdirectories.

The release subdirectory contains the release versions of SciAn.  Obtaining
SciAn from this directory is described in section 3.2.

The beta subdirectory contains versions of SciAn for our beta testers.  These
versions are not as thoroughly tested as the release versions.  When a version
passes beta test, it is moved to the "release" directory.

The patches subdirectory contains minor patches to particular versions of
SciAn which do not require the bother of recompiling the entire source.  You
will receive notice of patches through the SciAn mailing list.

The documentation subdirectory contains documentation for SciAn.  Obtaining
and printing it is described in section 4.0.

The technotes subdirectory contains technical notes for using SciAn.  These
are text files that contain information about topics that we haven't had time
to put in the manual.

3.2.1  Downloading the SciAn Package

In the "release" subdirectory (enter  cd release  to get to the directory)
you will find several files.  They will all have names of the form
scianXXX.tar.Z, where XXX is the version number of SciAn.  For example, the
file scian082.tar.Z contains SciAn version 0.82.

It is usually best to get the latest version of SciAn, unless you have
recieved a note to use an older version.

You must download the file in binary mode.  Most versions of ftp figure out
that the target machine is running UNIX and go into binary mode automatically.
Just to make sure, enter

    image

to put ftp in binary mode.  Now it is time to download SciAn.  Let's assume
that you want to download SciAn version 0.82.  Enter

    get scian082.tar.Z

After the file has been transferred, you can get out of ftp by entering bye
or quit, depending on the version of ftp you have.

The SciAn distribution is a compressed tar file.  The first step in getting
the file ready is to uncompress it.  Enter

    uncompress scian082.tar

When the uncompress command finishes, you will have a file called scian082.tar.
To extract the individual files from the tar file, enter

    tar -xvof scian082.tar

If you get an error message, try

    tar -xvf scian082.tar

Many files will be extracted from the SciAn tar file.  Files ending in .c,
.h, and .f are the source files of SciAn.  (Currently, you don't need the
FORTRAN compiler to compile SciAn.)  The Makefile and files with .make
in their names are for the make program.  There is also a directory called
demo which contains demonstration files for SciAn.  There may also be a file
called RELEASE.NOTES.  Look in this file to determine special features of the
version you have just downloaded.

3.3  Installing SciAn

Before SciAn can be installed, it must be configured to your machine.  In
order to understand the process of configuration, you must first understand
how the SciAn source is structured.

One copy of the SciAn source is used to produce all versions of SciAn.  Which
version is being compiled depends on constants defined in the file machine.h.
At compile time, the file tests constants to see if it is running on an IBM
or a Silicon Graphics machine and adjusts automatically.  However, there are
several options that you need to set by hand.

There are four basic steps in installing SciAn:

1) Prepare the installation options by entering make INSTALL.  Read everything
   the computer prints to the console.  If there is an error which will cause
   problems later on in the installation, it will be described in a message,
   and you will need to fix the error and repeat this step.
2) Assign font mappings for special characters according to the fonts on
   your computer.
3) Compile and link SciAn by entering make scian (or pmake scian on Silicon
   Graphics machines with more than one processor).
4) Release SciAn by moving the scian executable and the demo files to the
   appropriate directories.

These steps are described in the following four sections, 3.3.1 through
3.3.4.  They should work for nearly all installations.  Some sites may have
local options, such as locally developed additions to SciAn.  Information
on this is described in section 3.3.5.

3.3.1  Preparing the installation options

When all the supplemental libraries as described in section 2 have been
installed, the first basic step in installation is to prepare the
installation options.  This is an extremely important step, and if you
forget to do it, you may get link errors later.  Enter

    make INSTALL

A program called ScianPreInstall will go through the options defined in
machine.h and check to make sure that the libraries that are needed are
present on your system.

When ScianPreInstall runs, it will ask you questions and print some messages
to the console.  Read everything it prints!  ScianPreInstall will tell you if
there is anything that needs to be changed in the optional libraries.
Do not proceed to the next step until ScianPreInstall tells you that it is OK
to do so.

ScianPreInstall also writes several important files, which will be included
into the source code and make file when you make scian.

If and only if make INSTALL has given you the go-ahead to compile, you can go
on to the next step.

3.3.2  Assigning font mappings

The next step in the installation is to assign font mappings.  SciAn uses
some characters in the Silicon Graphics font library which are outside the
normal range of ASCII characters.  Unfortunately, which characters are
which has changed as new versions of the operating system and the font
manager have come out.  It is necessary for you to tell SciAn what the
mappings are.  To do this, enter

make FONTS

at the console.  If you are running on a Silicon Graphics workstation,
you MUST be at a graphics console when doing this.  On all other machines
this will just produce a message and generate a file, and you can go on
to the next step.  On the Silicon Graphics, this will run a program that
will put up a window which will ask you to find the various characters.
Follow the directions given to you by the program, and then you will be
able to go on to compiling SciAn.

This step really only needs to be done when you install SciAn for the first
time, or when you do an upgrade of the operating system which changes the
characters in the fonts.  If you are having any trouble with special
characters within SciAn, e.g., the copyright C in a circle doesn't appear
on the Copyright help screen, then you must do this step and recompile
SciAn.

You can omit this step entirely, in which case a set of default mappings will
be used.  The default mappings will probably work on your system, unless you
are running an old version of the operating system.  If not, the worst that
can happen is that you won't be able to see some special characters.

3.3.3  Compiling and linking SciAn

To make SciAn, enter

    make scian

If you are making on a Silicon Graphics machine with more than one processor,
you can do a parallel make instead by entering

    pmake scian

The makefile will compile and link SciAn resulting in an executable named
scian.  If you get any kind of error, make sure that the configuration is
set up correctly as described in sections 3.3.1 and 3.3.2.  If that doesn't
help, read through section 6.1.  If you still cannot figure out what is
wrong, send mail to us at [e-mail].

When scian has been made, test it out by typing ./scian.  The user manual
has a brief tour, but if you don't have a copy of the manual, you can get
on-line help by clicking the mouse in the title window.

3.3.4  Releasing SciAn

The final step in installing SciAn is to release it to the users of your
machine.

First copy the scian executable file to a place where users can reach it.
One good place to put it is in /usr/local/bin.

Then copy or move the demo directory to some directory where users can reach
it and tell your users where it is.  The user manual refers to this directory,
so your users need to know its location.

The executable of the Silicon Graphics version of SciAn should run on any
Silicon Graphics workstation.  However, the IBM RS/6000 version will probably
only run on workstations configured in a similar way to the workstation where
it was compiled.  If you are running in a heterogeneous environment with
several different versions of AIX, you may need to keep several executables
of SciAn.

3.3.5  Local options

Although the standard installation process works for most people, some
sites may have unusual setups that require modification to work.  This
section gives some hints for possible configuration requirements.

In order to understand how to do this, you need to know a little about
how the installation process works.  Running make INSTALL compiles and
executes a program called ScianPreInstall.  This program determines
what kind of machine it has been compiled on (using the include file
machine.h).  Currently, two machine types are recognized: IBM RS/6000
workstations, and Silicon Graphics workstations.  These are called
"ibm6k" and "sgi4d" respectively.

Once SciAn PreInstall determines the basic machine type, it looks at a
number of installation source files, each containing the name of the
machine type.  Currently, these files are the following:

flags.ibm6k.make
flags.sgi4d.make
flfiles.ibm6k.make
flfiles.sgi4d.make
lfiles.ibm6k.make
lfiles.sgi4d.make

The flags.*.make files contain symbol definitions that are included in
the Makefile.  These give the names of the C and FORTRAN compilers and
compilation and linking options.

The lfiles.*.make files contain the names of link libraries,
one per line, that are required for standard linking.  The flfiles.*.make
files contain the names of link libraries, one per line, that are required
for linking when FORTRAN has been used.  All libraries are the names that
will be used with the -l flag when linking.  For example, a library that
appears in flags.sgi4d.make as gl_s refers to the library libgl_s.a and
results in a flag -lgl_s on the link line.

The search paths for link libraries and compilers, as well as the names of
the optional libraries, are currently hard-coded into the beginning of
ScianPreInstall.c.

In addition, ScianPreInstall reads the file machine.local.h, if present.
This contains lines to be included into the C source, such as #define
constants.

ScianPreInstall.c produces a number of files (lfiles.make, flfiles.make,
and flags.make) that are directly included in the Makefile.  In addition,
it produces a number of include files (machine.extras.h, machine.hdf.h,
machine.jpeg.h, etc.) which specify compilation options for SciAn.

The names of the C and FORTRAN compilers are specified in the flags.sgi4d.
make or flags.ibm6k.make, whichever is appropriate.  By default they are
cc and f77, respectively.  To change the names, change them in this file
and make INSTALL again.  The C compiler is also used to link SciAn.

To add to the search path for header files or libraries, change the CFLAGS,
FFLAGS, or LFLAGS symbols in flags.<machinetype>.make and make INSTALL
again.  If the new search path is used for one of the SciAn optional
libraries such as HDF, you may also need to edit the ScianPreInstall
source code before  doing make INSTALL.

If you are compiling on an IBM RS/6000 machine, you may need to define the
MENUSFROM0 constant in machine.h.  The numbering of menu items in GL is
supposed to start at 1.  However, some versions of the IBM GL emulation,
such as with AIX 3.1.5, start at 0.  There isn't really any way to tell
this beforehand, but if you compile SciAn and notice that the wrong menu
items are getting grayed, you will need to go back and change this.

4.0  Obtaining the documentation

Documentation can be downloaded in two forms: PostScript files and Macintosh
files for Microsoft Word 5.

4.1  PostScript format

PostScript files for the manuals are located in the documentation subdirectory.
The name of the user manual is of the form userXXX.ps.tar.Z, and the name
of the reference manual is of the form refXXX.ps.tar.Z, where XXX is the
version of SciAn.  For example, for version 0.80 of SciAn, there is a user
manual named user080.ps.tar.Z and a reference manual named ref080.ps.tar.Z.
There may also be a file of the form colorXXX.ps.tar.Z, which contains a
color plate that can be printed out on a color PostScript printer.

Each file is a compressed tar file, similar to the file containing the
SciAn software, as described in section 3.  Make sure that ftp is using
the binary format by typing 'image' and then download the files.  After you
exit ftp, uncompress the files using the uncompress command.  Then use the
tar command to extract the files from the archive.  For example:

uncompress user080.ps.tar
tar xvf user080.ps.tar

The tar command will produce a number of PostScript files, all ending in the
.ps extension.  You can print out these PostScript files according to the
rules for the printers at your site.

4.2  Microsoft Word format

Microsoft Word files are located in the documentation subdirectory.  The
name of the user manual is of the form userXXX.msw.sit.hqx, and the name
of the reference manual is of the form refXXX.msw.sit.hqx, where XXX is
the version of SciAn.  For example, version 0.80 of SciAn has a user manual
named user080.msw.sit.hqx and a reference manual named ref080.msw.sit.hqx.
There may also be a file of the form color080.msw.sit.hqx, which contains a
color plate that can be printed out on a color printer.

The manual is in Macintosh Word 5 format and has been compressed and
encoded with Stuffit.  Use BinHex4 or StuffIt to decode the file and
then use StuffIt to extract the archive.  When printing the manual, be
sure to check "Color/Grayscale" in the print dialog. Printing the manual
requires a lot of memory, so it may be necessary to increase the amount of
memory used by Word. If you use background printing, it may be necessary to
quit all other open applications. If you still have problems, try printing
the manual in sections.

5.0  Using the technical notes

When we need to release information about some aspect of SciAn that cannot
wait for the long time delay in releasing a new version of the manual, we will
put a technical note in the technotes directory.  A file called INDEX will
give summaries of all the technical notes in the directory.

Technical notes are not guaranteed to be easy to understand and may cover
esoteric topics.

6.0  Getting help

We hope you enjoy SciAn.  If you have difficulty installing it, please
first check through this file to make sure that you are doing everything
correctly.  Be sure to look through section 6.1.  If you still have problems,
send a message to [e-mail].

If you have suggestions for new features for SciAn, please send them to
[e-mail].  Please keep in mind that we are a research program
and not a software house, and we work better in collaboration with you.

6.1  Common problems and solutions

This section contains some problems that a few people have had during
installation or printing of the manual.  Please check this section if you
have a problem.

PROBLEM: I get link errors.

SOLUTION: About 95% of the time this is due to forgetting to do make INSTALL
before doing make scian.  Make INSTALL is a very, very important part of
the installation process.  It will set up the link files to link properly
if it can and will tell you what to do to fix it if it can't.


PROBLEM: When I link, I see a message saying that ScianFontMapper.h can't
be found.

SOLUTION: This indicates that you haven't gone through the 'make FONTS'
process to generate the font mappings.  See section 3.3.3


PROBLEM: When I link, I get DFSDgetmaxmin or DFSDgetrange undefined.

SOLUTION: Between versions 3.1 and 3.2 of the NCSA HDF library, they changed
the name of one of the routines from DFSDgetmaxmin to DFSDgetrange.  SciAn
can link using either, but you have to specify in machine.h.  Look for
constants beginning with the letters HDF.  The make INSTALL process will tell
you if SciAn is correctly configured for the right version of HDF.


PROBLEM: When I print the manual, the figures come out funny!

SOLUTION: Make sure you are using the latest version of the Apple laser
printer drivers, and turn background printing off.


PROBLEM: SciAn compiles fine on the IBM, but when I run it, I get an error
and it exits.

SOLUTION: This one can mean a wide range of things, from trivial to
disastrous.  In ascending order of difficulty, these are some of the things
we have run into:

1) When a user brings up X, some versions of AIX assume that the user "owns"
   the GL emulator and does not allow anyone else to use it.  Make sure that
   you are the user that ran xinit.
2) Binaries compiled under different versions of the operating system will
   not run on other versions.  (Also see MENUSFROM0 in machine.h.)  Make
   sure that you have compiled and run on the same machine.
3) There are some software configurations that prevent you from using the
   GL emulator from within X.  Check with your system manager to see if this
   is the case.
4) If you have multiple versions of the X library, the search path specified
   may get the wrong one.  If this is the case, change the order of the
   directories in lfiles.ibm6k.make and rerun make INSTALL.  DO NOT change
   lfiles.make; it is written by make INSTALL.
5) SciAn does not run on every IBM system, only on those with graphics
   accelerators that can do 3-D GL emulation, have Z-buffers, and can
   do RGB color.

PROBLEM: When I try to run it on the IBM, the wrong menu items appear to
highlight, and the fonts don't work in text boxes on the screen.

SOLUTION: This probably means that you have compiled under AIX 3.1.5 without
defining MENUSFROM0 in machine.h.  Take a look at machine.h, run "make INSTALL"
again, and try to make again.  This problem is further explained in section
3.3.1.