4. Code Installation Notes¶
4.1. Powderday on HiPerGator¶
4.1.1. Manual Installation With gcc Compilers¶
[1] As of August 2022, this is the preferred way to install (i.e., least headache). Thanks to Prerak Garg for these.:
First, load up the compilers that we’ll use throughout:
>module load gcc/9.3.0 openmpi/4.1.1 libz/1.2.11 hdf5/1.10.1 git/2.30.1
yt:
>cd $HOME
>git clone https://github.com/yt-project/yt
>cd yt
>pip install -e .
fsps and python-fsps
The development version of python-fsps now includes the Fortran FSPS source code. You can get both via:
fsps:
>cd $HOME
>git clone https://github.con/cconroy20/fsps
>cd fsps/src
in the Makefile set F90=$(FC) and this will ensure that the compilers fsps uses are what you have module loaded.:
>make clean
>make
then in your .bashrc set the analog to:
>export SPS_HOME=/Users/desika/fsps
python fsps:
>CC=gcc F90=gfortran F77=gfortran python setup.py install
hyperion
As of commit 7cae6d0, a bug has been introduced with the __version__ module. Once cloned, checkout stable commit 4170c6c:
>cd $HOME
>git clone https://github.com/hyperion-rt/hyperion.git
>cd hyperion
>git checkout 4170c6cc3009893e2b591e133baeb9927122aef1
>python setup.py install
>git submodule init
>git submodule update
>./configure --prefix=$HOME/local
>make
>make install
hyperion dust:
>cd $HOME
>wget http://pypi.python.org/packages/source/h/hyperion-dust/hyperion-dust-0.1.0.tar.gz
>tar -xzvf hyperion-dust-0.1.0.tar.gz
>cd hyperion-dust-0.1.0
>python setup.py build_dust
powderday:
>git clone https://github.com/dnarayanan/powderday.git
>conda install numpy scipy cython h5py matplotlib psutil joblib six astropy scikit-learn ipython
>cd powderday
>python setup.py install
4.1.2. Manual Installation With Intel Compilers (updated for el8 installation by Dhruv as of 9/13/2023)¶
[2] The first set of instructions for the University of Florida HiPerGator3.0 facility is to employ intel compilers, and to compile everything manually. This allows the greatest flexibility, as well as the ability to use private forks of individual codes.
First, load up the compilers that we’ll use throughout:
>module load intel/2020.0.166
>module load openmpi/4.1.5
>module load hdf5/1.14.1
>module load git
yt:
>cd $HOME
>git clone https://github.com/yt-project/yt
>cd yt
>pip install -e .
python fsps and fsps:
>cd $HOME
>git clone --recursive https://github.com/dfm/python-fsps.git
>cd python-fsps
>cd src/fsps/libfsps/src
>make clean
>make
python-fsps now comes pre-packaged with fsps, so we don’t need to install them separately anymore. The –recursive option on the git clone pulls the appropriate version of fsps as well. First let’s compile fsps. In the Makefile set F90=$(FC) and this will ensure that the compilers fsps uses are what you have module loaded.
Set in your .bashrc the analog to:
>export SPS_HOME=$HOME/python-fsps/src/fsps/libfsps
Now we can install python-fsps:
>cd $HOME/python-fsps
>CC=icc F90=ifort python setup.py install
hyperion:
>cd $HOME
>git clone https://github.com/hyperion-rt/hyperion.git
>cd hyperion
>python setup.py install
>git submodule init
>git submodule update
>./configure --prefix=$HOME/local
>make
>make install
Make sure that whatever directory you put for configure is in your $PATH. You can check whether this is true by typing $PATH in the command line and looking for the <location>/bin directory.
hyperion dust:
>cd $HOME
>wget http://pypi.python.org/packages/source/h/hyperion-dust/hyperion-dust-0.1.0.tar.gz
>tar -xzvf hyperion-dust-0.1.0.tar.gz
>cd hyperion-dust-0.1.0
>python setup.py build_dust
powderday:
>git clone https://github.com/dnarayanan/powderday.git
>cd powderday
>python setup.py install
4.1.3. Conda Installation¶
[3] The final set of instructions use gcc, and the conda installation of Hyperion. Thanks to Paul Torrey for these.:
>module load openmpi/4.1.1 libz/1.2.11 hdf5/1.10.1 conda/4.12.0 git/2.30.1 gcc
>conda install -c conda-forge hyperion
>python -c "import hyperion" (just to ensure no errors thrown)
>hyperion (just to ensure command is found)
>python -m pip install fsps
>[set $SPS_HOME variable in .bashrc)
>cd $HOME
>git clone https://github.com/dnarayanan/powderday.git
>cd powderday
>python setup.py install
then fix import six line in the equivalent of all of these:
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/model/model.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/util/validator.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/conf/conf_files.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/filter/filter.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/dust/dust_type.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/model/model_output.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/densities/flared_disk.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/densities/alpha_disk.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/densities/bipolar_cavity.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/densities/ulrich_envelope.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/densities/power_law_envelope.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/densities/ambient_medium.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/model/sed.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/model/image.py
>vi /home/paul.torrey/.conda/envs/pd_gcc/lib/python3.8/site-packages/hyperion/grid/yt3_wrappers.py
4.2. Caesar on HiPerGator¶
4.3. AREPO¶
The current best set of modules to compile AREPO for hpg2-default are:
module purge
module load intel/2020.0.166
module load openmpi/4.1.5
module load python/3.11.4
module load fftw/3.3.10
module load hdf5/1.14.1
module load grackle/3.2.1
module load gsl/2.6
Alternatively the best set of modules for hpg-default are:
module load gcc/9.3.0 openmpi/4.1.1 gsl/2.6 fftw
following this:
make build