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packages.md

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+The following packages we are likely to need at PITP 2016. Each UNIX
+distro (linux and mac alike) have different ways how to install
+them. Some example are given here how to do them.
+
+You can find copies of codes on either our published URL's , or
+within the directory /data/pitp on the IAS cluster where all participants
+have an account. Look in /data/pitp/software.
+If you want to work on one of the cluster nodes, be sure to create your
+own directory within /data/pitp/ and work within that.
+
+
+--------------------------------------------------------------------------------
+UNIX COMMANDS:
+
+
+## git
+
+  we also use this to distribute notes, scripts, software for PITP 2016.  
+  To get a copy of the PITP notes:
+
+    git clone http://github.com/teuben/pitp2016
+    cd pitp2016
+
+  and to get a updated version with the latest additions:
+
+    cd pitp2016
+    git pull
+
+
+## gcc/g++/gfortran
+
+  The C/C++/Fortran(90) compiler suite.  Others may be available as well that work
+  also, e.g. "clang", the Intel compiler and the PGI compiler.  
+  The C compiler needs to suport OpenMP (which gcc does)
+
+
+## python/ipython
+
+  Although the python command may be present for you, what we really want here is
+  an integrated scientific python environment, e.g. via anaconda.  
+  Within python, the following modules are recommended:
+
+	numpy
+	scipy
+	matplotlib
+	yt
+	astropy
+	pandas
+	scikit-learn
+	glueviz
+
+
+## ffmpeg
+
+  This tool creates movies from still images that simulations often create on the fly.  
+  Great for presentations. We will use this for a few of the homeworks.
+
+  In ubuntu linux:
+
+    sudo apt install ffmpeg imagemagick vlc
+
+## gnuplot
+
+  A simple, basic but effective way to plot data.
+
+## ygraph
+
+  Another simple and basic graph plotter.   
+  See for example http://cactuscode.org/documentation/visualization/yGraph/
+
+## visit
+
+  A more graphical based visualization environment  
+  See https://wci.llnl.gov/simulation/computer-codes/visit/
+
+
+--------------------------------------------------------------------------------
+UNIX LIBRARIES:
+
+## openmpi 
+
+  This is one of the ways to implement MPI, and probably our preferred way.  
+  On Ubuntu/Linux:
+
+    apt install openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
+
+  On mac/homebrew:
+
+    brew install gcc
+    brew install openmpi --enable-mpi-thread-multiple
+    brew install hdf5 --with-fortran --with-mpi
+
+## mpich
+
+  This is another MPI library:  
+  On Ubuntu/Linux:
+
+    apt install mpich
+
+  but not experimented with this yet, as openmpi seems to work.
+
+## gsl
+
+  This is the Gnu Scientific Library. Use your package manager to install it, e.g.  
+  In Ubuntu linux:
+
+    sudo apt install libgsl-dev
+
+## yt  (ZuHone)
+
+  Versatile visualization environment in python. Probably easiest to install
+  within your python environment via the commands
+
+    conda install yt
+    or 
+    pip install yt
+
+  depending which type of python environment you have.
+
+  Lecture notes are here:  http://yt-project.org/pitp2016_demo/yt_tutorial.slides.html
+
+  The new yt 3.3-dev (development) series can be installed as follows:  
+
+    conda install -c http://use.yt/with_conda yt                 (unix)
+    conda install -c http://conda.anaconda.org/jzuhone yt        (windows)
+		
+  or if you have another python stack (or just want to use pip):
+
+    # build from source on macOS or Linux:
+    pip install hg+https://bitbucket.org/yt_analysis/yt#egg=yt
+    # binary install on macOS or Windows:
+    pip install --pre yt
+
+	wget -r --no-parent http://yt-project.org/pitp2016_demo/data/WindTunnel
+	wget -r --no-parent http://yt-project.org/pitp2016_demo/data/DD0046
+	wget -r --no-parent http://yt-project.org/pitp2016_demo/examples
+
+
+## d3js  (Ericson)
+
+  This is a JavaScript based visualization toolkit. Great to present your research online
+  for outreach, collaborators etc.  
+  See https://d3js.org/
+
+
+## athena  (Stone)
+
+  http://www.astro.princeton.edu/~jstone/downloads/papers/stone_hw.pdf  
+  Use athena4.2.tar.gz
+
+## harmpi  (Tchekhovskoy)
+
+  GitHub repo: https://github.com/atchekho/harmpi.git  
+  Tutorial:    https://github.com/atchekho/harmpi/blob/master/tutorial.md  
+  Homework:    https://github.com/atchekho/harmpi/blob/master/exercises.md  
+
+  The code is 3D and is parallelized using MPI, results can be obtained rather quickly.
+
+## iharm2d_v3 (Gammie)
+
+  more instructions will follow
+
+## tristan (Spitovsky) 
+
+  Homework at:   http://www.astro.princeton.edu/~anatoly/PICHW2016.html  
+  Code at:       https://github.com/ntoles/tristan-mp-pitp  
+  Vis at:        https://github.com/pcrumley/Iseult
+
+    <edit> Makefile
+    make
+    mpirun -n 1 ./tristan-mp2d
+    Iseult/iseult.py
+
+  Here it is important to have an MPI enabled compiler !!! See the "openmpi"
+  comments earlier in this document.
+