Install ISIS on Mac
This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.
Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).
1. Install Xcode (latest version) and Xquartz
To check whether Xcode is installed execute: \\
xcode-select -p
on command line
If you see /Applications/Xcode.app/Contents/Developer it should be installed.
Use the App Store to update or install Xcode
Execute xcode-select --install
on command line to install the Xcode command line tools
Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the web. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in /opt/X11/
2. Install Mac Ports or Homebrew
Fink could also work, the differences should be some package names and the location of some libraries which should be /opt/local/ for Mac Ports or /sw/local/ for Fink.
This instruction assumes that Mac Ports is installed. It is also possible to use Homebrew.
3. Install packages with Mac Ports
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
sudo port selfupdate sudo port upgrade outdated # repeat this until it does nothing sudo port install gcc12 sudo port install gsl sudo port install fig2dev sudo port install z sudo port install git sudo port install texlive # only if latex is not available yet sudo port install texlive-latex-extra # if sltikz will be used
These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not /usr/bin/gcc, which is a only "frontend" that can parse gcc), set the following in your ~/.bash_profile:
export GCC="/opt/local/bin/gcc-mp-12" export CC="/opt/local/bin/gcc-mp-12" export CXX="/opt/local/bin/g++-mp-12" export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
Then type source ~/.bash_profile in the terminal.
4. Install HEADAS
This is not necessary if only the "stellar_isisscripts" will be used.
- Download the latest version of HEASOFT (source)
- Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
- create a directory in your $HOME called Software
- unpack the HEADAS tar file in this directory
- Install HEASOFT from source but use the following configurations
./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include make sudo make install
- Add the following to your ~/.bash_profile (change this according to your terminal type and username)
export HEADAS="/Users/username/path/to/heasoft/" alias heainit="source $HEADAS/headas-init.sh heainit
The HEADAS path could/should look something like this:
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
- apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
source ~/.bash_profile in your command line
5. Install slang / slang modules / isis / isisscripts
First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
git clone https://github.com/houckj/isis git clone git://git.jedsoft.org/git/slang.git git clone git://git.jedsoft.org/git/slxfig.git git clone git://git.jedsoft.org/git/slgsl.git git clone git://git.jedsoft.org/git/jed.git git clone git://git.jedsoft.org/git/slirp.git git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
Install slang. Go to the slang directory.
./configure --with-png=/opt/local/ make sudo make install
Install isis. Go to the isis directory
./configure --with-headas=$HEADAS make sudo make install
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
sudo port install wget sudo port install pgplot sudo port install cfitsio ./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/ make sudo make install
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
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib make clean make sudo make install
Install slgsl. Go to the slgsl directory
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/ make sudo make install
Install slxfig. Go to the slxfig directory
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib make sudo make install
Install slirp. Go to the slirp directory
./configure make sudo make install
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"); };
This allows the easy access to require("isisscripts") in isis.
(6. 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
In the Makefile, change these two lines to read:
SLANGINC = -I/usr/local/include -I/opt/local/include SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. 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 *~
Edit the .isisrc file in your $HOME directory and add the following lines
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
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 * /opt/local/bin
To test if the scripts work, try for example:
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
7. Possible problems with other software
XMM SAS
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our xmmscripts rely on the ftools, this behavior is highly inconvenient. As a workaround install the HEASOFT wrapper by following the instructions here.
This will create a new directory with the executables of HEASOFT. Add this directory to your $PATH variable (in front of the rest of $PATH)!