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Adding several utilities and example notebooks to the container
1 parent 3ecb7eb commit 71f2ad7

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‎Dockerfile

+101-26
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FROM jupyter/scipy-notebook
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#FROM jupyter/scipy-notebook:latest
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#FROM lambda-base
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FROM nasalambda/base-notebook
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#Installing packages and updating stuff
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USER root
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RUN apt-get -y update && apt-get install -y gcc gfortran
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RUN apt-get -y update && apt-get install -y gcc gfortran gsl-bin libgsl-dev libcfitsio-bin libcfitsio-dev libfftw3-bin libfftw3-dev git-svn libccfits0v5 libccfits-dev libclhep2.1v5 libclhep-dev libgcc-5-dev
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RUN pip install --upgrade pip
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# Create a Python 2.x environment using conda including at least the ipython kernel
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# and the kernda utility.
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RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython kernda
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RUN conda install -n python2 ipykernel
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RUN conda clean -tipsy
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USER root
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# Create a global kernelspec in the image and modify it so that it properly activates
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# the python2 conda environment.
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#RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
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# kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
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#USER $NB_USER
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#So running python2 from command line runs the miniconda python2
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RUN ln -s $CONDA_DIR/envs/python2/bin/python $CONDA_DIR/bin/python2
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RUN ln -s $CONDA_DIR/envs/python2/bin/easy_install $CONDA_DIR/bin/easy_install2
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RUN ln -s $CONDA_DIR/envs/python2/bin/pip $CONDA_DIR/bin/pip2
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RUN python2 -m ipykernel install
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USER $NB_USER
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RUN conda install astropy healpy cython emcee
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RUN conda install -n python2 astropy healpy cython scipy numpy matplotlib emcee
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RUN conda install astropy healpy cython
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RUN conda install -n python2 astropy healpy cython
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USER $NB_USER
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#CMB Analysis Summer School jupyter notebooks
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RUN git clone https://github.com/jeffmcm1977/CMBAnalysis_SummerSchool.git /home/jovyan/work/CMBAnalysis_SummerSchool
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RUN git clone https://github.com/jeffmcm1977/CMBAnalysis_SummerSchool.git $HOME/work/CMBAnalysis_SummerSchool
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#LAMBDA code
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RUN git clone https://github.com/nasa-lambda/cmb_footprint.git /home/jovyan/.ipython/cmb_footprint
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RUN git clone https://github.com/nasa-lambda/cmb_analysis.git /home/jovyan/.ipython/cmb_analysis
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RUN cp /home/jovyan/.ipython/cmb_footprint/footprint.cfg /home/jovyan/footprint.cfg
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RUN git clone https://github.com/nasa-lambda/cmb_footprint.git $HOME/.ipython/cmb_footprint
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RUN git clone https://github.com/nasa-lambda/cmb_analysis.git $HOME/.ipython/cmb_analysis
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RUN cp $HOME/.ipython/cmb_footprint/footprint.cfg $HOME/footprint.cfg
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#Installing PyCAMB
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#RUN pip2 install --egg camb
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#RUN pip install --egg camb
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RUN git clone https://github.com/cmbant/CAMB.git /home/jovyan/camb
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WORKDIR /home/jovyan/camb/pycamb
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RUN git clone https://github.com/cmbant/CAMB.git $HOME/camb
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WORKDIR $HOME/camb/pycamb
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RUN python setup.py install --user
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RUN python2 setup.py install --user
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USER $NB_USER
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#CLASS and its python wrapper
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RUN git clone https://github.com/lesgourg/class_public.git /home/jovyan/class
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WORKDIR /home/jovyan/class
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COPY Makefile_class /home/jovyan/class/Makefile
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RUN git clone https://github.com/lesgourg/class_public.git $HOME/class
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WORKDIR $HOME/class
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COPY Makefile_class $HOME/class/Makefile
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RUN make
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RUN make clean
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COPY Makefile_class_py3 /home/jovyan/class/Makefile
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COPY setup_class_py3.py /home/jovyan/class/python/setup.py
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COPY Makefile_class_py3 $HOME/class/Makefile
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COPY setup_class_py3.py $HOME/class/python/setup.py
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RUN make
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WORKDIR /home/jovyan/work
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WORKDIR $HOME/work
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#ACTPol Python Likelihood
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RUN git clone https://github.com/ACTCollaboration/actpols2_like_py.git /home/jovyan/work/actpols2
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RUN git clone https://github.com/ACTCollaboration/actpols2_like_py.git $HOME/work/actpols2
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#CMB power spectrum plotting
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RUN git clone https://github.com/nasa-lambda/cmbpol_plotting.git
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#Healpix
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WORKDIR $HOME
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RUN wget https://downloads.sourceforge.net/project/healpix/Healpix_3.31/Healpix_3.31_2016Aug26.tar.gz
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RUN tar -zxvf Healpix_3.31_2016Aug26.tar.gz
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COPY Makefile_healpix $HOME/Healpix_3.31/Makefile
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WORKDIR $HOME/Healpix_3.31
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RUN mkdir bin
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RUN mkdir lib
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RUN mkdir include
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RUN make
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#Hammurabi
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WORKDIR $HOME
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RUN git svn clone https://svn.code.sf.net/p/hammurabicode/code/trunk hammurabi
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WORKDIR $HOME/hammurabi
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COPY Makefile_hammurabi $HOME/hammurabi/Makefile
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RUN make
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ENV PYTHONPATH $HOME/hammurabi
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RUN cp $HOME/hammurabi/hampy/Hampy_quick-start.ipynb $HOME/work
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RUN cp "$HOME/hammurabi/hampy/Polarized CMB foregrounds.ipynb" $HOME/work/Polarized_CMB_foregrounds.ipynb
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WORKDIR $HOME/hammurabi/hampy
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RUN wget https://downloads.sourceforge.net/project/hammurabicode/supplementary/hampy_test.tgz
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RUN tar -zxvf hampy_test.tgz
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#PyGSM
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USER root
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WORKDIR $HOME
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RUN git clone https://github.com/telegraphic/PyGSM
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WORKDIR $HOME/PyGSM
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RUN python setup.py install
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RUN conda install -n python2 h5py
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RUN python2 setup.py install
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USER $NB_USER
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#Cosmosis
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#WORKDIR $HOME
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#RUN pip install emcee
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#RUN git clone http://bitbucket.org/joezuntz/cosmosis
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#WORKDIR $HOME/cosmosis
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#RUN git clone http://bitbucket.org/joezuntz/cosmosis-standard-library
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#WORKDIR $HOME/cosmosis/cosmosis-standard-library
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#RUN git checkout
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#WORKDIR $HOME/cosmosis
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#COPY setup-my-cosmosis $HOME/cosmosis/setup-my-cosmosis
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#RUN source setup-my-cosmosis
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#RUN make
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#BICEP Likelihood
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WORKDIR $HOME
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COPY b1_hl_likelihood_example.ipynb $HOME/work
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COPY bicep1_util.py $HOME/work
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RUN wget http://bicep.rc.fas.harvard.edu/bicep1_3yr/b1_hl_likelihood.tgz
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RUN mkdir $HOME/work/b1_hl_likelihood
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RUN tar -xvzf b1_hl_likelihood.tgz -C $HOME/work/b1_hl_likelihood
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#Copying notebooks to working directory
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COPY Introduction.ipynb /home/jovyan/work/
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COPY plot_footprints.ipynb /home/jovyan/work/
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COPY CAMBDemo.ipynb /home/jovyan/work
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COPY ClassDemo.ipynb /home/jovyan/work
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COPY actpol_likelihood_example_v4.ipynb /home/jovyan/work
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COPY Introduction.ipynb $HOME/work/
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COPY plot_footprints.ipynb $HOME/work/
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COPY CAMBDemo.ipynb $HOME/work/
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COPY ClassDemo.ipynb $HOME/work/
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COPY actpol_likelihood_example.ipynb $HOME/work/
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WORKDIR $HOME/work
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#COPY sets owner to root so this needs to be changed for files to
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#be editable and downloadable
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USER root
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RUN chown $NB_USER:users Introduction.ipynb plot_footprints.ipynb CAMBDemo.ipynb ClassDemo.ipynb actpol_likelihood_example_v4.ipynb
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RUN chown $NB_USER:users Introduction.ipynb plot_footprints.ipynb CAMBDemo.ipynb ClassDemo.ipynb actpol_likelihood_example.ipynb
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RUN chown $NB_USER:users b1_hl_likelihood_example.ipynb bicep1_util.py
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USER $NB_USER

‎Makefile_hammurabi

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#--------------------------------------------------------
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#--------------------------------------------------------
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#
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# This is the hammurabi Makefile. The first part needs to be configured for your system.
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#
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# You can choose to build:
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#
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# hammurabi: by default, the basic hammurabi, pure C++, for constant or grid TEs and simple analytic models for CREs
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# hammurabi.ne2001: including linking to the (smooth) NE2001 Fortran code using cfortran.h
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# hammurabi.galprop: including both NE2001 and Galprop to simulate the CRE propagation with the hammurabi magnetic field first.
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# hammurabi.debug: including all code, debug flags.
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# all: builds all of these.
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#
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#--------------------------------------------------------
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#--------------------------------------------------------
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#
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# Give the locations of the various libraries. Should containt include and lib subdirectories.
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#
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BASE_DIR = $(HOME)/
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HAMMURABI_HOME = $(BASE_DIR)/hammurabi
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GSL = /usr
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FFTW = /usr
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CFITSIO = /usr
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HEALPIX = $(HOME)/Healpix_3.31
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HEALPIX_TARGET = basic_gcc
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SUBDIR = x86_64-linux-gnu
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#
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# These are needed if you build with Galprop
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#
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#GALPROP = $(BASE_DIR)/galprop/galprop/build
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CCFITS = /usr
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CLHEP = /usr
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#
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# What c++ compiler you are using?
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#
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CXX = g++
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#
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# On OSX, maybe
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#CXX = g++-mp-5
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#
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# Compile options? 64bit system (-m64), optimization (-O2), openMP (-fopenmp), warnings (-Wall), etc.
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#
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#CXXFLAGS = -m64 -O2 -fopenmp -Wall
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#
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# With OSX g++-mp-4.3
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CXXFLAGS = -fopenmp -O2 -fno-inline-functions -Wall -Wextra -Wno-unknown-pragmas -ansi
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#
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# Which Fortran compiler you are using? Only if compiling with NE2001 and/or Galprop
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#
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FC = gfortran
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#
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# On OSX, maybe
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#FC = gfortran-mp-5
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# For gfortran
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FCFLAGS = -O2 -ffixed-form -ffixed-line-length-132 -c
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#
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# For ifort
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#FCFLAGS =-O -extend-source -c
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#
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# For f77 ?
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#FCFLAGS =
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#
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# For linking to C++ with gcc
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#
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LFORTFLAGS= -Df2cFortran
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#
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# Additional options depending on how you want to run:
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#
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# Use openMP. Right now, this is mandatory. (Contact
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# [email protected] for help compiling without if for some reason you
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# need it.)
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#LFLAGS_CUSTOM = -fopenmp
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#
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# OSX with gfortran-mp-4.3
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LFLAGS_CUSTOM = -fopenmp
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#
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#
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#
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# For J. West using f77 and gcc 4.1.2?
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#
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#LFORTFLAGS += -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lgcc -lg2c
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#LFLAGS_CUSTOM += -lgcc_s
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#------------------------------------------------------------
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#------------------------------------------------------------
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#
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# From here onwards, nothing should need to be changed.
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#
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#------------------------------------------------------------
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#------------------------------------------------------------
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hammurabi.debug: CXXFLAGS=-m64 -g -Wall
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hammurabi: ALL_INC = -I$(CFITSIO)/include -I$(GSL)/include -I. -I$(FFTW)/include -I$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/include/
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#hammurabi: ALL_INC = -I$(CFITSIO)/include -I$(GSL)/include -I. -I$(FFTW)/include -I$(HEALPIX)/src/cxx/cxxsupport
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hammurabi.ne2001: ALL_INC = -I$(CFITSIO)/include -I$(GSL)/include -I. -I$(FFTW)/include -I$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/include/
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hammurabi.galprop: ALL_INC = -I$(CFITSIO)/include -I$(GALPROP)/.. -I$(GALPROP)/include/ -I$(CCFITS)/include/ -I$(CLHEP)/include -I$(GSL)/include -I. -I$(FFTW)/include -I$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/include/
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hammurabi.debug: ALL_INC = -I$(CFITSIO)/include -I$(GALPROP)/.. -I$(GALPROP)/include/ -I$(CCFITS)/include/ -I$(CLHEP)/include -I$(GSL)/include -I. -I$(FFTW)/include -I$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/include/
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libhamprop.a: ALL_INC = -I$(CFITSIO)/include -I$(GALPROP)/.. -I$(GALPROP)/include/ -I$(GSL)/include -I. -I$(FFTW)/include -I$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/include/
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hammurabi: ALL_L = -L$(CFITSIO)/lib/$(SUBDIR) -L$(GSL)/lib/$(SUBDIR) -L$(FFTW)/lib/$(SUBDIR) -L$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/lib/ -L.
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hammurabi.ne2001: ALL_L = -L$(CFITSIO)/lib/$(SUBDIR) -L$(GSL)/lib/$(SUBDIR) -L$(FFTW)/lib/$(SUBDIR) -L$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/lib/ -L.
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hammurabi.galprop: ALL_L = -L$(CFITSIO)/lib/$(SUBDIR) -L$(GALPROP)/lib/ -L$(CCFITS)/lib/$(SUBDIR) -L$(CLHEP)/lib/$(SUBDIR) -L$(GSL)/lib/$(SUBDIR) -L$(FFTW)/lib/$(SUBDIR) -L$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/lib/ -L.
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hammurabi.debug: ALL_L = -L$(CFITSIO)/lib/$(SUBDIR) -L$(GALPROP)/lib/ -L$(CCFITS)/lib/$(SUBDIR) -L$(CLHEP)/lib /$(SUBDIR) -L$(GSL)/lib/$(SUBDIR) -L$(FFTW)/lib/$(SUBDIR) -L$(HEALPIX)/src/cxx/$(HEALPIX_TARGET)/lib/ -L.
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hammurabi : CXXFLAGS+= $(ALL_INC) -c
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hammurabi.ne2001: CXXFLAGS+= $(ALL_INC) -c -DNE2001
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hammurabi.galprop: CXXFLAGS+= $(ALL_INC) -c -DGALDEF_PATH=\"./GALDEF\" -DFITSDATA_PATH=\"./FITS/\" -DDATA_PATH=\"./DATA\" -DGALPROP -DNE2001
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hammurabi.debug : CXXFLAGS+= $(ALL_INC) -c -DGALDEF_PATH=\"./GALDEF\" -DFITSDATA_PATH=\"./FITS/\" -DDATA_PATH=\"./DATA\" -DGALPROP -DNE2001 -g -Wall
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# Turns off sanity check to avoid some circularity. See Galprop README.tess
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libhamprop.a: CXXFLAGS+= $(ALL_INC) -c -DGALDEF_PATH=\"./GALDEF\" -DFITSDATA_PATH=\"./FITS/\" -DDATA_PATH=\"./DATA\" -DLIBHAMPROP -DGALPROP -DNE2001
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hammurabi: LFLAGS = $(ALL_L) -lhammurabi -lhealpix_cxx -lcxxsupport -lc_utils -lfftpack -lcfitsio -lgsl -lgslcblas -lm -lfftw3 -lfftw3_threads $(LFLAGS_CUSTOM)
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hammurabi.ne2001: LFLAGS = $(ALL_L) -lhammurabi -lNE2001 -lhealpix_cxx -lcxxsupport -lc_utils -lfftpack -lcfitsio -lgsl -lgslcblas -lm -lfftw3 -lfftw3_threads -lgfortran $(LFLAGS_CUSTOM)
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hammurabi.debug: LFLAGS = $(ALL_L) -lhammurabi -lNE2001 -lhealpix_cxx -lcxxsupport -lc_utils -lfftpack -lcfitsio -lgsl -lgslcblas -lm -lfftw3 -lfftw3_omp -lgfortran -lgalprop -lskymap -lCCfits -lCLHEP $(LFLAGS_CUSTOM)
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hammurabi.galprop: LFLAGS = $(ALL_L) -lhammurabi -lNE2001 -lhealpix_cxx -lcxxsupport -lc_utils -lfftpack -lcfitsio -lgsl -lgslcblas -lm -lfftw3 -lfftw3_omp -lgfortran -lgalprop -lskymap -lCCfits -lCLHEP $(LFLAGS_CUSTOM)
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default:
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make hammurabi
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all:
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make clean ; make hammurabi ; make clean ; make hammurabi.ne2001; make clean; make hammurabi.galprop ; make clean ; make hammurabi.debug
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%.o : %.cpp
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$(CXX) $(CXXFLAGS) -o $@ $<
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%.o : %.cc
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$(CXX) $(CXXFLAGS) -o $@ $<
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%.o : %.c
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$(CXX) $(CXXFLAGS) -o $@ $<
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%.o : %.f
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$(FC) $(FCFLAGS) -o $@ $<
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class_TE_density.o: class_TE_density.cpp
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$(CXX) $(CXXFLAGS) $(LFORTFLAGS) -o $@ $<
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NE2001_OBJ = dmdsm.NE2001.o density.NE2001.o neclumpN.o nevoidN.o neLISM.NE2001.o
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HAMMURABI_OBJ = class_Integrator.o class_List.o class_B_field2.o tess_tools.o class_TE_density.o class_CRE.o namespace_Vec_Handling.o class_Dust.o
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run:
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mkdir run
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$(HAMMURABI_OBJ): hammurabi.h CGS_units_file.h proto*.h tess_tools.h
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libNE2001.a: $(NE2001_OBJ)
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ar rc $@ $(NE2001_OBJ)
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ranlib $@
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hammurabi: $(HAMMURABI_OBJ) libhammurabi.a run hammurabi.o
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$(CXX) -o run/hammurabi hammurabi.o $(LFLAGS) $(LFORTFLAGS)
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hammurabi.ne2001: $(HAMMURABI_OBJ) $(NE2001_OBJ) $(NE2001_DATA) libNE2001.a libhammurabi.a run hammurabi.o
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$(CXX) -o run/hammurabi.ne2001 hammurabi.o $(LFLAGS) $(LFORTFLAGS)
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hammurabi.galprop: $(HAMMURABI_OBJ) $(NE2001_OBJ) $(NE2001_DATA) libNE2001.a libhammurabi.a run hammurabi.o
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$(CXX) -o run/hammurabi.galprop hammurabi.o $(LFLAGS) $(LFORTFLAGS)
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hammurabi.debug: $(HAMMURABI_OBJ) $(NE2001_DATA) libNE2001.a libhammurabi.a run hammurabi.o
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$(CXX) -o run/hammurabi.debug hammurabi.o $(LFLAGS) $(LFORTFLAGS)
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ifeq ($(OSTYPE),darwin)
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install_name_tool -change "@rpath/libCLHEP-2.3.3.1.dylib" "$(CLHEP)/lib/libCLHEP-2.3.3.1.dylib" run/hammurabi.debug
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endif
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print_constants: print_constants.o
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$(CXX) -o run/print_constants print_constants.o
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# To link in B_field to galprop, use this:
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libhamprop.a: class_B_field2.o tess_tools.o namespace_Vec_Handling.o
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ar cru libhamprop.a class_B_field2.o tess_tools.o namespace_Vec_Handling.o
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libhammurabi.a: $(HAMMURABI_OBJ)
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ar cru libhammurabi.a $(HAMMURABI_OBJ)
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clean:
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rm *.a *.o
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test:
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(cd unit_test; ./test.csh)
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test_big:
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(cd unit_test; ./test.csh big)
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tarfile:
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tar cvzf hammurabi.tgz *cpp *h Makefile *.f README hampy
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unittar:
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tar cvzf hammurabi_unit_test.tgz unit_test/inputs unit_test/GALDEF unit_test/FITS unit_test/negrid_n400.bin unit_test/ref.mini unit_test/ref unit_test/ref.big

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