From 3280051fd424337a066b71eb49aab0cdbb2f033e Mon Sep 17 00:00:00 2001 From: fizban007 Date: Thu, 21 Jul 2016 21:05:31 -0400 Subject: [PATCH 1/4] Changed txt to md for better github display --- packages.md | 160 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 160 insertions(+) create mode 100644 packages.md diff --git a/packages.md b/packages.md new file mode 100644 index 0000000..08e0a9a --- /dev/null +++ b/packages.md @@ -0,0 +1,160 @@ + + +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 + + + 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. + From 689bea6df9ab48a6b731be355295ad6a2708f4ce Mon Sep 17 00:00:00 2001 From: fizban007 Date: Thu, 21 Jul 2016 21:13:52 -0400 Subject: [PATCH 2/4] cleaned up the md file a bit --- packages.md | 175 +++++++++++++++++++++++++++++----------------------- 1 file changed, 97 insertions(+), 78 deletions(-) diff --git a/packages.md b/packages.md index 08e0a9a..e0f2b8a 100644 --- a/packages.md +++ b/packages.md @@ -1,5 +1,3 @@ - - 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. @@ -11,38 +9,39 @@ 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 + 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: + and to get a updated version with the latest additions: - cd pitp2016 - git pull + cd pitp2016 + git pull -gcc +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) + 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: + 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 @@ -55,106 +54,126 @@ ipython 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 - + 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. + + 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/ + + 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/ + + 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 + 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. + + 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. + This is the Gnu Scientific Library. Use your package manager to install it, e.g. + In Ubuntu linux: + + sudo apt install libgsl-dev - Lecture notes are here: http://yt-project.org/pitp2016_demo/yt_tutorial.slides.html +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: + 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) + 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 + 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/ +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 + + 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. + 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 + + 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 - - Makefile - make - mpirun -n 1 ./tristan-mp2d - Iseult/iseult.py + 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 + + + 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. + Here it is important to have an MPI enabled compiler !!! See the "openmpi" comments + earlier in this document. From d39b5a67e546b3738eeb46ee3f6a657c5e816530 Mon Sep 17 00:00:00 2001 From: fizban007 Date: Thu, 21 Jul 2016 21:17:05 -0400 Subject: [PATCH 3/4] Further styling of the md --- packages.md | 35 ++++++++++++++++------------------- 1 file changed, 16 insertions(+), 19 deletions(-) diff --git a/packages.md b/packages.md index e0f2b8a..9792e66 100644 --- a/packages.md +++ b/packages.md @@ -13,7 +13,7 @@ own directory within /data/pitp/ and work within that. UNIX COMMANDS: -git +## git we also use this to distribute notes, scripts, software for PITP 2016. To get a copy of the PITP notes: @@ -27,17 +27,14 @@ git git pull -gcc -g++ -gfortran +## 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 +## 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. @@ -53,7 +50,7 @@ ipython glueviz -ffmpeg +## 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. @@ -62,16 +59,16 @@ ffmpeg sudo apt install ffmpeg imagemagick vlc -gnuplot +## gnuplot A simple, basic but effective way to plot data. -ygraph +## ygraph Another simple and basic graph plotter. See for example http://cactuscode.org/documentation/visualization/yGraph/ -visit +## visit A more graphical based visualization environment See https://wci.llnl.gov/simulation/computer-codes/visit/ @@ -80,7 +77,7 @@ visit -------------------------------------------------------------------------------- UNIX LIBRARIES: -openmpi +## openmpi This is one of the ways to implement MPI, and probably our preferred way. On Ubuntu/Linux: @@ -93,7 +90,7 @@ openmpi brew install openmpi --enable-mpi-thread-multiple brew install hdf5 --with-fortran --with-mpi -mpich +## mpich This is another MPI library: On Ubuntu/Linux: @@ -102,14 +99,14 @@ mpich but not experimented with this yet, as openmpi seems to work. -gsl +## 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) +## yt (ZuHone) Versatile visualization environment in python. Probably easiest to install within your python environment via the commands @@ -138,19 +135,19 @@ yt (ZuHone) wget -r --no-parent http://yt-project.org/pitp2016_demo/examples -d3js (Ericson) +## 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) +## athena (Stone) http://www.astro.princeton.edu/~jstone/downloads/papers/stone_hw.pdf Use athena4.2.tar.gz -harmpi (Tchekhovskoy) +## harmpi (Tchekhovskoy) GitHub repo: https://github.com/atchekho/harmpi.git Tutorial: https://github.com/atchekho/harmpi/blob/master/tutorial.md @@ -158,11 +155,11 @@ harmpi (Tchekhovskoy) The code is 3D and is parallelized using MPI, results can be obtained rather quickly. -iharm2d_v3 (Gammie) +## iharm2d_v3 (Gammie) more instructions will follow -tristan (Spitovsky) +## tristan (Spitovsky) Homework at: http://www.astro.princeton.edu/~anatoly/PICHW2016.html Code at: https://github.com/ntoles/tristan-mp-pitp From 7a6866df0be88159d63dec990eb1265f936c4fa2 Mon Sep 17 00:00:00 2001 From: fizban007 Date: Thu, 21 Jul 2016 21:19:06 -0400 Subject: [PATCH 4/4] Further styling of md file --- packages.md | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/packages.md b/packages.md index 9792e66..a8797b4 100644 --- a/packages.md +++ b/packages.md @@ -15,7 +15,7 @@ UNIX COMMANDS: ## git - we also use this to distribute notes, scripts, software for PITP 2016. + 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 @@ -30,14 +30,14 @@ UNIX COMMANDS: ## 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. + 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. + an integrated scientific python environment, e.g. via anaconda. Within python, the following modules are recommended: numpy @@ -52,7 +52,7 @@ UNIX COMMANDS: ## ffmpeg - This tool creates movies from still images that simulations often create on the fly. + 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: @@ -65,12 +65,12 @@ UNIX COMMANDS: ## ygraph - Another simple and basic graph plotter. + Another simple and basic graph plotter. See for example http://cactuscode.org/documentation/visualization/yGraph/ ## visit - A more graphical based visualization environment + A more graphical based visualization environment See https://wci.llnl.gov/simulation/computer-codes/visit/ @@ -79,7 +79,7 @@ UNIX LIBRARIES: ## openmpi - This is one of the ways to implement MPI, and probably our preferred way. + 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 @@ -92,7 +92,7 @@ UNIX LIBRARIES: ## mpich - This is another MPI library: + This is another MPI library: On Ubuntu/Linux: apt install mpich @@ -101,21 +101,22 @@ UNIX LIBRARIES: ## gsl - This is the Gnu Scientific Library. Use your package manager to install it, e.g. + 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 + 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: @@ -138,20 +139,20 @@ UNIX LIBRARIES: ## d3js (Ericson) This is a JavaScript based visualization toolkit. Great to present your research online - for outreach, collaborators etc. + for outreach, collaborators etc. See https://d3js.org/ ## athena (Stone) - http://www.astro.princeton.edu/~jstone/downloads/papers/stone_hw.pdf + 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 + 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. @@ -161,16 +162,15 @@ UNIX LIBRARIES: ## tristan (Spitovsky) - Homework at: http://www.astro.princeton.edu/~anatoly/PICHW2016.html - Code at: https://github.com/ntoles/tristan-mp-pitp + 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 - 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. + Here it is important to have an MPI enabled compiler !!! See the "openmpi" + comments earlier in this document.