ISIS Installation Guide

For more information about isis, see: http://space.mit.edu/cxc/isis/

Send bug reports, comments and suggestions to: isis-users@space.mit.edu

Overview

The easiest way to set up a new isis installation is to run an installation script that will automatically download and install isis and a few commonly used modules. This installation method is documented in Part I, Scripted Installation.

For those who prefer greater control and customization, full details of the isis installation process are documented in Part II, Manual Installation.

Once isis is installed, a number of optional components are available to support a variety of specialized tasks. For details, see Part III, Optional Components.

I. Scripted Installation

This installation method is intended to simplify the most common situation in which isis is being installed for use as a spectral analysis tool with support for using the XSPEC spectral model library.

For The Impatient: assuming certain requirements are met, the following steps should be sufficient to install isis into directory DIR:

   wget http://space.mit.edu/cxc/isis/install-isis.sh
   setenv HEADAS /usr/local/headas/x86_64-unknown-linux-gnu-libc2.7/
   sh install-isis.sh DIR

If reading instructions just isn’t for you, then by all means go ahead and try that now, substituting the HEADAS path appropriate for your system.

The next section explains the process and requirements in a little more detail.

Requirements

Before running the installation script, the following programs must be available on your system:

wget
tar
make
C compiler (eg. gcc)
Fortran compiler (eg. gfortran)

See below for advice on choosing C and Fortran compilers.

To verify that each of these programs is available on your command search path, use which:

    > which wget
    /usr/bin/wget

The simplest way to obtain the XSPEC spectral model library is to install XSPEC itself. Isis also uses the cfitsio and pgplot libraries that come with XSPEC. For these reasons, the isis installation script assumes that XSPEC has been installed on your system; XSPEC is available from:
http://heasarc.gsfc.nasa.gov/docs/software/lheasoft/

When installing XSPEC, we strongly recommend compiling it from source code.

Installation

Once the above requirements are satisfied, isis installation can proceed as follows:

Move to a working directory where you have at least 200 MB of space to download and compile the software, then download the isis installation script into that directory:
```
   cd isis-src
   wget http://space.mit.edu/cxc/isis/install-isis.sh
```
Set the HEADAS environment variable to provide the path to your XSPEC installation. To set it, (t)csh users should type something like:
```
   setenv HEADAS /usr/local/headas/x86_64-unknown-linux-gnu-libc2.7/
```
while users of bash, ksh, etc.. should type something like
```
   HEADAS=/usr/local/headas/x86_64-unknown-linux-gnu-libc2.7/
   export HEADAS
```
Set any compiler environment variables CC, CFLAGS, FC, FFLAGS, and LDFLAGS necessary to properly define your build environment (Important Note for Mac Users).
Run the installation script to install everything into directory DIR
```
   sh install-isis.sh DIR
```
If no directory DIR is provided on the script command line, then everything will be installed into the current directory.

If all goes well, the script will download, compile and install isis along with a few commonly used modules. When the script finishes, it will provide the path to the isis executable, e.g. DIR/bin/isis. When you run isis, you should see something like this:

> DIR/bin/isis

Welcome to ISIS Version 1.6.2
Copyright (C) 1998-2016 Massachusetts Institute of Technology

          Isis web page: http://space.mit.edu/cxc/isis/
   Mailing list archive: http://space.mit.edu/cxc/isis/archive/
 Send questions to the mailing list: <isis-users@space.mit.edu>.
     For a summary of recent changes, type:  "help changes"

isis>

To run isis by typing isis at the unix command prompt instead of DIR/bin/isis, consider adding the DIR/bin directory to your command search path. Alternatively, you might consider putting an appropriate symbolic link into a bin directory that’s already on your path. For example, if $HOME/bin is on your command search path, consider putting a symbolic link there:

    ln -s DIR/bin/isis $HOME/bin/isis

Now that isis is working, you may want to consider installing some of the optional software mentioned in Part III.

II. Manual Installation

The manual installation method is available for those who want more control over the installation process.

Requirements

The S-Lang library is required (version 2.2.4 or newer). This library is available from:
http://www.jedsoft.org/slang/

To build isis with support for fitting XSPEC spectral models, the XSPEC spectral model library must be installed somewhere on your system. This library is part of HEASoft, which is available from:
http://heasarc.gsfc.nasa.gov/docs/software/lheasoft/

Along with the spectral model library, the HEASoft installation also provides the cfitsio and pgplot libraries; if you choose not to install HEASoft, then cfitsio and pgplot must be installed.

Installing from source code
Installation suggestions for specific architectures
- Linux
- Mac OS X
- Solaris
TROUBLESHOOTING

1. Installing from source code

a. Choosing compilers

It is important to build isis and S-Lang using the same C and Fortran compilers that were used to build XSPEC. For this reason, the HEASoft compiler recommendations also apply to isis. For details, see:

http://heasarc.gsfc.nasa.gov/docs/software/lheasoft/supported_platforms.html

http://heasarc.gsfc.nasa.gov/docs/software/lheasoft/install.html

Ideally, your C and Fortran compilers should be part of a matched set and their version numbers should match exactly. For example, using the C compiler gcc and the Fortran compiler gfortran, one can check the version numbers like so:

  > gcc --version
  gcc (Debian 4.3.2-1.1) 4.3.2

  > gfortran --version
  GNU Fortran (Debian 4.3.2-1.1) 4.3.2

The compilers shown in this example are likely to be compatible because they have the same version number and because they came from the same Linux distribution (Debian).

To specify which compilers to use when building isis, set the CC and FC environment variables. For example, to set these environment variables, (t)csh users should type:

  setenv CC gcc-4.3
  setenv FC gfortran-4.3

while bash, ksh, etc. users should type:

  CC=gcc-4.3
  export CC

  FC=gfortran-4.3
  export FC

b. Recommended installation method

Important

Be sure to build isis and S-Lang using the same C and Fortran compilers that were used to build XSPEC. If your compilers are incompatible, the build may fail.

If S-Lang has been installed in a standard location such as /usr/local, the isis installation process may be as simple as:

    ./configure --with-headas=$HEADAS
    make
    make check
    make install

The HEADAS environment variable gives the path to your local HEASoft installation. To set it, (t)csh users should type something like:

   setenv HEADAS /usr/local/headas/x86_64-unknown-linux-gnu-libc2.7/

while users of bash, ksh, etc.. should type something like:

   HEADAS=/usr/local/headas/x86_64-unknown-linux-gnu-libc2.7/
   export HEADAS

Note that the exact directory path depends on the details of your system.

By default, isis files will be installed in /usr/local/isis and a symbolic link to the isis executable will be placed in /usr/local/bin/isis. If /usr/local/bin is already in your command search path then, after isis is installed, you should be able to run it by typing isis at the unix prompt:

   > isis

To install isis in DIR instead of /usr/local, include the --prefix configure option:

  --prefix=DIR

If S-Lang has been installed in a non-standard location it may be necessary to specify its location using the --with-slang configure option:

  --with-slang=DIR

To make use of the APED spectroscopy database, include the --with-atomdb configure option:

  --with-atomdb=DIR

c. INSTALLATION EXAMPLE

To step through a complete installation example, suppose that your compilers are in /usr/local/bin, you want to unpack the source code in /soft/src, and you want to install everything in /soft, with HEASoft in /soft/headas and isis in /soft/isis. To create this setup, perform the following steps:

Note	To make this example concrete, specific software version numbers appear in the relevant URLs and command-lines. When performing a new installation, it is usually best to choose the newest available version of each package.

Create the /soft/src directory:
```
  mkdir -p /soft/src
```
Note that creating this directory requires root permission. However, it is unwise to compile software as root. Only the last step (make install) should be performed as root.

If you do not have root permission and cannot create the /soft/src directory, that’s ok, just choose a directory where you have write permission and enough space to hold all the files. The disk space requirement is determined primarily by the size of HEASoft; S-Lang and ISIS require very little space in comparison.
Download S-Lang, isis, and HEASoft:

S-Lang source code is available from:
ftp://space.mit.edu/pub/davis/slang/v2.2/

ISIS source code is available from:
ftp://space.mit.edu/pub/cxc/isis/

HEASoft source code is available from:
http://heasarc.gsfc.nasa.gov/lheasoft/download.html

After downloading the source code tar files, move the files to /soft/src:
```
       mv slang-2.2.4.tar.gz /soft/src
       mv isis-1.6.2.tar.gz /soft/src
       mv heasoft-6.11.1.tar.gz /soft/src
```

Specify compilers:

In C shell variants, such as csh, tcsh, type:

       setenv CC /usr/local/bin/gcc
       setenv FC /usr/local/bin/gfortran
       setenv CXX /usr/local/bin/g++

In Bourne shell variants, such as bash, ksh, etc. type:

       CC=/usr/local/bin/gcc
       export CC

       FC=/usr/local/bin/gfortran
       export FC

       CXX=/usr/local/bin/g++
       export CXX

Install S-Lang:

       cd /soft/src
       gunzip -c slang-2.2.4.tar.gz | tar xf -
       cd slang-2.2.4
       ./configure --prefix=/soft
       make
       make install

Install HEASoft:
```
       cd /soft/src
```
Follow the installation instructions in
http://heasarc.gsfc.nasa.gov/docs/software/lheasoft/install.html
Be sure to run the HEASoft configure script with the appropriate --prefix option so that HEASoft will be installed in the directory chosen for this example, /soft/src/headas:
./configure --prefix=/soft/src/headas ...
Once HEASoft is installed, the HEADAS environment variable should be set to
/soft/src/headas/<platform-string>/
as shown above.

Install isis:

       cd /soft/src
       gunzip -c isis-1.6.2.tar.gz | tar xf -
       cd isis-1.6.2
       ./configure --prefix=/soft --with-slang=/soft \
                   --with-headas=$HEADAS
       make
       make check
       make install

At this point, /soft/bin/isis should be a symbolic link to the isis executable. When you run it, you should see something like this:

> /soft/bin/isis

Welcome to ISIS Version 1.6.2
Copyright (C) 1998-2016 Massachusetts Institute of Technology

          Isis web page: http://space.mit.edu/cxc/isis/
   Mailing list archive: http://space.mit.edu/cxc/isis/archive/
 Send questions to the mailing list: <isis-users@space.mit.edu>.
     For a summary of recent changes, type:  "help changes"

isis>

Once isis is working, you may want to consider installing some of the optional software mentioned in Part III.

For a complete list of supported configure options, do:

  ./configure --help

Many of these configure options are described in the next section.

d. Configure options

--with-prefix=DIR

Use this option to install isis files in DIR/isis/$version.

--with-subdir=DIR

Use this option to install isis files in $prefix/isis/DIR instead of $prefix/isis/$version. If DIR="" (the empty string) then isis files will be installed in $prefix/isis.

--with-headas=$HEADAS

Use this option to provide the path to the xspec libraries. When the cfitsio and pgplot libraries are present in $HEADAS/lib, it is usually best to use them when building isis, rather than any other versions of these libraries that may be available on your system. For this reason, it is usually best to avoid combining the --with-headas option with any of the --with-cfitsio or --with-pgplot options.

--with-atomdb=$ATOMDB

Use this option to provide the path to the ATOMDB spectroscopy database, available from: http://www.atomdb.org/

--with-xspec-version=nn

When your local HEASoft installation includes both xspec11 and xspec12, use this option to specify which version of the xspec libraries to link to isis. If this configure option is absent, and both xspec versions are present, isis will use xspec12.

--with-xspec-static

Use this option to indicate that the xspec libraries should be statically linked to the isis executable.

--with-xspec-modelsonly=DIR

Use this option to provide the path to your xspec modelsonly library installation. When this option is used, the CCfits library must also be installed on your system. The location of the CCfits library should be specified unless the library is installed in'$prefix' or another standard location.

--with-local-setup=FILE

Use this option to indicate that the S-Lang script in FILE should be loaded when isis starts up. This file can be used to define site-local customizations that may be helpful for all users at your site.

--with-slang=DIR

Use this option to indicate that libslang is in DIR/lib and slang.h is in DIR/include

--with-slanglib=LIB_DIR

--with-slanginc=INC_DIR

Use these options to indicate that libslang is in LIB_DIR and slang.h is in INC_DIR. If you use these options, do not use the --with-slang option.

--with-cfitsio=DIR

Use this option to indicate that libcfitsio is in DIR/lib and fitsio.h is in DIR/include.

--with-cfitsiolib=LIB_DIR

--with-cfitsioinc=INC_DIR

Use these options to indicate that libcfitsio is in LIB_DIR and fitsio.h is in INC_DIR. If you use these options, do not use the --with-cfitsio option.

--with-pgplot=DIR

Use this option to indicate that libpgplot is in DIR/lib and cpgplot.h is in DIR/include

--with-pgplotlib=LIB_DIR

--with-pgplotinc=INC_DIR

Use these options to indicate that libpgplot is in LIB_DIR and cpgplot.h is in INC_DIR. If you use these options, do not use the --with-pgplot option.

--with-CCfits=DIR

Use this option to indicate that libCCfits is in DIR/lib and CCfits.h is in DIR/include

--with-CCfitslib=LIB_DIR

--with-CCfitsinc=INC_DIR

Use these options to indicate that libCCfits is in LIB_DIR and CCfits.h is in INC_DIR. If you use these options, do not use the --with-CCfits option.

--with-dep=DIR

Use this option to indicate that slang and cfitsio are installed in DIR/lib and DIR/include, and that pgplot is installed in DIR/pgplot.

--with-readline[=arg]

Use this option to select which readline library to use:

arg=gnu means use GNU readline
arg=DIR means use GNU readline (from DIR/lib and DIR/include)
arg=slang means use S-Lang readline only

--with-fclibs="…"

Use this option to provide additional libraries that may be needed by your compilers, but that are not automatically picked up by the configure script. For example, if you choose to compile isis with a C+\+ compiler (not recommended), you may need to use --with-fclibs="-lstdc++".

--x-libraries=DIR/lib

--x-includes=DIR/include

Use these options to indicate that the X libraries and include files are installed in DIR/lib and DIR/include, respectively.

e. (optional) Installing modules

You may wish to install additional isis- or slang-related software, such as one or more of the modules available from
http://space.mit.edu/cxc/isis/modules.html.

Such modules should be installed in the same directory tree where you installed slang, so that S-Lang applications such as isis will automatically find the new modules.

For example, consider adding the histogram module to the installation described above, where both isis and slang were installed in /soft. To install the histogram module, do the following:

First, download the module source code tar file from
http://space.mit.edu/CXC/software/slang/modules/hist/src/

Then, assuming the tar file is in /soft/src, do:

   cd /soft/src
   gunzip -c slhist-0.3.2a.tar.gz | tar xf -
   cd slhist-0.3.2a
   ./configure --prefix=/soft --with-slang=/soft
   make
   make install

The histogram module can then be imported into isis like so:

   isis> require ("histogram");

If you install a module that depends on other libraries (e.g. libpvm), then those additional libraries may be installed either in a standard system location (e.g. /usr) or in the same directory tree as isis (e.g. /soft), depending on which is most convenient.

2. Installation suggestions for specific architectures

Linux systems:

Recommended compilers: use gcc-4.3 and gfortran-4.3, or newer.

Older compilers will also work, but code compiled by older versions of gfortran is not fully compatible with newer versions of gfortran. On older systems, using gcc-3.4 with g77 will work; note, however, that g77 is no longer maintained.

Mac OS X systems:

See http://space.mit.edu/cxc/isis/mac_install.html

Solaris systems:

The Solaris compilers are preferred: CC=cc and FC=f90

AIX systems:

The IBM compilers are preferred: CC=xlc and FC=xlf

3. TROUBLESHOOTING

Answers to some frequently asked questions are available from the web site:
http://space.mit.edu/cxc/isis/faq.html

If isis did not compile:

Did you build isis using the same C and Fortran compilers that were used to build the XSPEC libraries?
Are your C and Fortran compilers compatible?

III. Optional Components

Isis provides extensive support for constructing multi-component collisional ionization equilibrium spectral models using the ATOMDB spectroscopy database, available from:
http://www.atomdb.org/

A growing collection of modules and data analysis packages is available from:
http://space.mit.edu/cxc/isis/modules.html

The available data analysis packages provide support for timing analysis, automated processing of Chandra grating data, and analysis of density-dependent line ratios from He-like triplet lines.

The available modules provide support for low-level I/O of FITS and HDF5 files, interaction with the ds9 image viewer, an interface to the GSL scientific library, 3D visualization, PVM-based parallel processing, and more.

Appendix

Below, I have attached the generic INSTALL instructions included in the autoconf distribution. These instructions provide more detail on how the configure script works and also describe other installation options which may be supported by the configure script.

   This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.

Basic Installation

These are generic installation instructions.

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

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

If you need to do unusual things to compile the package, please try to figure out how configure could check whether to do them, and mail diffs or instructions to the address given in the README so they can be considered for the next release. If you are using the cache, and at some point config.cache contains results you don’t want to keep, you may remove or edit it.

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

The simplest way to compile this package is:

cd to the directory containing the package’s source code and type ./configure to configure the package for your system. If you’re using csh on an old version of System V, you might need to type sh ./configure instead to prevent csh from trying to execute configure itself.

Running configure takes awhile. While running, it prints some messages telling which features it is checking for.
Type make to compile the package.
Optionally, type make check to run any self-tests that come with the package.
Type make install to install the programs and any data files and documentation.
You can remove the program binaries and object files from the source code directory by typing make clean. To also remove the files that configure created (so you can compile the package for a different kind of computer), type make distclean. There is also a make maintainer-clean target, but that is intended mainly for the package’s developers. If you use it, you may have to get all sorts of other programs in order to regenerate files that came with the distribution.

Compilers and Options

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

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

     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix

See Defining Variables, for more details.

Compiling For Multiple Architectures

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

If you have to use a make that does not support the VPATH variable, you have to compile the package for one architecture at a time in the source code directory. After you have installed the package for one architecture, use make distclean before reconfiguring for another architecture.

Installation Names

By default, make install will install the package’s files in /usr/local/bin, /usr/local/man, etc. You can specify an installation prefix other than /usr/local by giving configure the option --prefix=PATH.

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

In addition, if you use an unusual directory layout you can give options like --bindir=PATH to specify different values for particular kinds of files. Run configure --help for a list of the directories you can set and what kinds of files go in them.

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

Optional Features

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

For packages that use the X Window System, configure can usually find the X include and library files automatically, but if it doesn’t, you can use the configure options --x-includes=DIR and --x-libraries=DIR to specify their locations.

Specifying the System Type

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

     CPU-COMPANY-SYSTEM

where SYSTEM can have one of these forms:

     OS KERNEL-OS

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

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

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

Sharing Defaults

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

Defining Variables

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

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

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

configure Invocation

configure recognizes the following options to control how it operates.

--help
-h: Print a summary of the options to configure, and exit.
--version
-V: Print the version of Autoconf used to generate the configure script, and exit.
--cache-file=FILE: Enable the cache: use and save the results of the tests in FILE, traditionally config.cache. FILE defaults to /dev/null to disable caching.
--config-cache
-C: Alias for --cache-file=config.cache.
--quiet
--silent
-q: Do not print messages saying which checks are being made. To suppress all normal output, redirect it to /dev/null (any error messages will still be shown).
--srcdir=DIR: Look for the package’s source code in directory DIR. Usually configure can determine that directory automatically.

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

ISIS Installation Guide

Overview

I. Scripted Installation

Requirements

Installation

II. Manual Installation

Requirements

Table of Contents

1. Installing from source code

a. Choosing compilers

b. Recommended installation method

c. INSTALLATION EXAMPLE

d. Configure options

e. (optional) Installing modules

2. Installation suggestions for specific architectures

Linux systems:

Mac OS X systems:

Solaris systems:

AIX systems:

3. TROUBLESHOOTING

If isis did not compile:

III. Optional Components

Appendix

Basic Installation

Compilers and Options

Compiling For Multiple Architectures

Installation Names

Optional Features

Specifying the System Type

Sharing Defaults

Defining Variables

configure Invocation