Install ISIS on Linux

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These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

1. Install basic dependencies and general things

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng. However, it might be easier to rely on HEASOFT in this case. 

sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev 
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra

or on Arch linux 

sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc: 

export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/

Then do 

source ~/.bashrc

2. Install HEASOFT

This is not required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then: 

cd heasoft-6.29/BUILD_DIR

Before I could run the configure script I had to make many files executable, so it seems easiest to make all of them executable (this is not good practice): 

find .. -name '*' | xargs chmod +x

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with --prefix=/path/to/installation/folder/. 

./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc: 

export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to include the two following lines. You need to adjust the path of course: 

export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh

for csh, use instead: 

setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

Then, in the terminal: 

source ~/.bashrc
# or source ~/.cshrc

3. Install slang / slang modules / isis / isisscripts

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories: 

git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

      • Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions: 

find . -name '*.sh' | xargs chmod +x

The following will assume you want to use root access. If that is not the case, you can use use the option 

--prefix=/path/to/installation/folder/

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory. 

bash ./configure
make
sudo make install
make clean

Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed. If "libpng16" is not installed yet (try find /usr/lib/ -name "*libpng*"), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS: 

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

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and: 

bash ./configure
make
sudo make install
make clean

If "make" has an issue with pgplot, try setting using ./configure --with-pgplot=/usr/. Add --with-slang=/path/to/slang to the following configuration set ups in case you installed slang in a different path other than /usr/local/

Install jed. Go to the jed directory 

bash ./configure
make
make xjed
sudo make install
make clean

Install slgsl. Go to the slgsl directory 

bash ./configure
make
sudo make install
make clean

Install slxfig. Go to the slxfig directory 

bash ./configure
make
sudo make install
make clean

Install slirp. Go to the slirp directory 

bash ./configure
make
sudo make install
make clean

Before building the isisscripts, install the "SLURP" perl module. 

sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit

Then go to the isisscripts directory and 

make

Create / modify the .isisrc file in your $HOME directory and add the following line 

add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
# if s-lang is not in your $PATH
# add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");

This allows the easy access to require("isisscripts") in isis.

4. Install stellar_isisscripts

Get the newest version of the stellar_isisscripts from git. If you have a Remeis/gitlab account and are at the Remeis observatory, do: 

git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts

If you have a Remeis/gitlab account and are not at the Remeis observatory, do: 

git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts

Otherwise ask Matti Dorsch. Then: 

cd stellar_isisscripts
make

Now compile some necessary C functions: 

cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile

Then: 

make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~

Create modify the .isisrc file in your $HOME directory and add the following line 

add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package: 

sudo apt-get install stilts

Only if this does not work: 

mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example: 

isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;


Known issues: 1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

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