This cookbook is intended to install Tom Marsh's software with the aim of using the Doppler tomography software that he ported to python. In his website, he has a very detailed explanation of every step (I will not repeat it). If you want to understand the "why" of every step, please feel free to check the documentation. However, it is known (even by Tom Marsh himself) that sometimes there are things that go wrong (expect it to happen). This cookbook compiles (pun intended) some of the lessons learnt in the process by Aarran Shaw and myself to successfully install this fantastic code. The cookbook is designed as if you are installing the software from scratch in a brand new machine. Some of the steps might be redundant but for completeness sake, I have added every single step in my log. Hope this helps anyone who wants to install it.
First let's install all the dependencies required:
Sometimes, the astropy and cython versions are not the latest ones and will have conflicts when running the Doppler scripts. Therefore, let's force an update to the latest version:
sudo apt-get install autoconf automake libtool git gfortran libreadline-dev sudo apt-get install libxerces-c-dev libpcre3-dev libfftw3-dev libcfitsio-dev sudo apt-get install libcurl4-gnutls-dev xorg-dev csh libpng-dev sudo apt-get install g++ libpcre3 libpcre3-dev python-plplot python-pip sudo apt-get install python-sphinx python-numpy python-astropy python-matplotlib sudo apt-get install ipython python-scipy cython
sudo pip install --upgrade astropy sudo pip install --upgrade cython
We need to add environment variables for the different compilers as well as directions to PGPLOT and the installation directories.
# Compilers export CC=/usr/bin/gcc export CXX=/usr/bin/g++ export PERL=/usr/bin/perl export FC=/usr/local/bin/gfortran # PGPLOT export PGPLOT_DIR=/usr/local/lib export PGPLOT_DEV=/Xserve #TOM MARSH SOFTWARE export TRM_SOFTWARE=/home/juan/trm_software export CPPFLAGS="-I/home/juan/trm_software/include -I/usr/local/src/pgplot/include" export LDFLAGS="-L/home/juan/trm_software/lib -L/usr/local/src/pgplot/lib" export PYTHONPATH=$TRM_SOFTWARE/lib/python2.7/site-packages export LD_LIBRARY_PATH=/usr/local/src/pgplot/lib:/usr/local/lib:$TRM_SOFTWARE/lib:$LD_LIBRARY_PATH
Now, the trickiest part of the whole installation: PGPLOT. First, let's create following folders:
Then, let's download the latest version of pgplot from here. The filename should be something like pgplot5.2.tar.gz. Once you have this, then you need to download Tom's script to install pgplot. Go here to download PGPLOT_INSTALL.sh. Go to the directory where you save the script and run the following commands. Make sure to point towards the directory where pgplot5.2.tar.gz resides.
sudo mkdir /usr/local/src sudo mkdir /usr/local/src/pgplot sudo mkdir /usr/local/pgplot sudo mkdir /usr/local/src/pgplot/lib sudo mkdir /usr/local/src/pgplot/include
chmod u+x PGPLOT_INSTALL.csh sudo ./PGPLOT_INSTALL.csh /home/juan/Downloads/pgplot5.2.tar.gz /usr/local/src/pgplot/ /usr/local/pgplot/ gfortran
At this point two things might have happened:
Whatever happens, try the demo to check if pgplot works
cd /usr/local/src/pgplot/lib sudo ln -sf /usr/local/pgplot/libpgplot.so sudo ln -sf /usr/local/pgplot/libpgplot.a sudo ln -sf /usr/local/pgplot/libcpgplot.a cd ../include/ sudo ln -sf /usr/local/pgplot/cpgplot.h
cd /usr/local/pgplot ./pgdemo1
The next step is to install SLALIB. For this you need to send kind email to Tom Marsh so he can provide you with a link to the download file. Check the documentation to see why this is. Anyway, once you have it. Go to the directory where you saved it and run the following code:
tar -zxvf sla.tar.gz cd sla-1.0.4 ./configure make sudo make install sudo updatedb
At this point, you are ready to install all the software.