Package: pumapy
Porous Microstructure Analysis (PuMA)The stable releases of PuMA can be found on theofficial NASA Github repository,
whereas the latest development can be found on thedevelopment Gitlab repository.A few useful resources:Documentationdetailing the use of each functionCommunity chatto ask questions or to get in touchYouTube channelwith the video tutorialsTutorialswith examples for both python and C++Software descriptionThe Porous Microstructure Analysis (PuMA) software has been developed to
compute effective material properties and perform material response simulations on
digitized microstructures of porous media. PuMA is able to import digital three-dimensional
images obtained from X-ray microtomography or to generate artificial microstructures
that mimic real materials. PuMA also provides a module for interactive 3D visualizations.
Version 3 includes modules to compute simple morphological properties such as porosity,
volume fractions, pore diameter, and specific surface area. Additional capabilities include
the determination of effective thermal and electrical conductivity (both radiative and solid conduction -
including the ability to simulate local anisotropy for the latter); effective diffusivity and
tortuosity from the continuum to the rarefied regime; techniques to determine the local material orientation,
as well as the mechanical properties (elasticity coefficient), and the permeability of a material.Some examples of microstructures that have been run in the past are shown in the pictures below,
together with PuMA's software architecture schematic.System requirementsUNIX (tested on MacOS 10.14.1+, Ubuntu 12.04+, RHEL, and CentOS).
On Windows, only the python distribution (pumapy) is available.Indicative recommended specs (varies depending on the material property):8 GB of ram for small simulations (5003or smaller)16-32 GB of ram for medium simulations (8003range)32+ GB of ram for large simulations (above 10003)InstallationTo install PuMA, a conda distribution must be installed on your machine.
To test whether conda is installed, run "conda" from a terminal to see if the command is recognized.
If not, conda can be installed by following the instructionshere.Binaries (UNIX and Windows)Once the conda command is working, all the PuMA components can be installed by executing
the following commands in a terminal (note that the "solving environment" step can sometimes take up to 15 mins):conda create -y --name puma -c conda-forge pumaOnUNIX(i.e. Mac or Linux), the conda command installs the PuMA C++ library, pumapy python package and GUI.
OnWindows, only the pumapy python package is available.Note: TexGen (C++ library to create artificial weaves) is only installed on UNIX, because it needs more
advanced compilation. A friendly warning will appear when TexGen is not installed and pumapy is imported.Build from source (UNIX-only)This is the recommended installation for developers that need to make modifications to the C++ part of PuMA.
The installation is broken into two sections:Installation of basic dependencies that may be missing from your systemDownload the repository, build the source code and install the binariesStep 1 of the installation varies slightly based on the system.
Open a terminal, navigate to the directory you would like PuMA installed, and execute one of the following lines:xcode-select --install                                                                 # run this on MacOS
sudo apt-get install git build-essential mesa-common-dev                               # Debian (Ubuntu)
sudo yum group install "Development Tools"; sudo yum install git gcc mesa-libGL-devel  # Fedora (CentOS, RHEL)Note: If XCode command line tools are already installed, the command will result in an error, which is not a problem.Now that the necessary dependencies have been installed, you can go ahead with Step 2 of the installation:git clone https://github.com/nasa/puma.git
cd puma; chmod +x installer.sh; ./installer.shAfter installation, close the terminal and open a new one.Uninstalling PuMATo uninstall PuMA and all the installed dependencies, execute the following command to delete the puma environment:conda remove -y --name puma --allRunning PuMAPuMA relies on a conda environment in order to manage its software dependencies and environment variables.
It is therefore important to always activate the environment before using any of PuMA's functionalities.
Once the installation is complete, the PuMA GUI can be launched by running:conda activate puma
pumaGUIYou can follow thejupyter notebook tutorials,
which show the typical function usage for both PuMA C++ and pumapy. These can also be run directly in Binder.How to setup PuMA on the NAS cluster:In order to install PuMA on the NASA supercomputing cluster, some modules need to be loaded and environment
variables need to be set. This can be achieved by adding the following commands to the ~/.profile file before the installation:module use -a /swbuild/analytix/tools/modulefiles
module load miniconda3/v4
module load /nasa/modulefiles/pkgsrc/sles12/gcc/6.2
export CONDA_PKGS_DIRS=/nobackup/$USER/.conda/pkgs
export CONDA_ENVS_PATH=/nobackup/$USER/.conda/envs
conda config --append envs_dirs /nobackup/$USER/.conda/envs
source activateCiting PuMAIf you use PuMA in your research, please use the following BibTeX entries to cite it:@article{puma2021,title={Update 3.0 to “PuMA: The Porous Microstructure Analysis software”,(PII: S2352711018300281)},author={Ferguson, Joseph C and Semeraro, Federico and Thornton, John M and Panerai, Francesco and Borner, Arnaud and Mansour, Nagi N},journal={SoftwareX},volume={15},pages={100775},year={2021},publisher={Elsevier}}@article{puma2018,title={PuMA: The porous microstructure analysis software},author={Ferguson, Joseph C and Panerai, Francesco and Borner, Arnaud and Mansour, Nagi N},journal={SoftwareX},volume={7},pages={81--87},year={2018},publisher={Elsevier}}See thepublicationsfile for a full list of papers on PuMA
and its numerical methods.Common errors and bug reportingThis is a list of the common errors encountered during the setup and how to solve them:If PuMA was partially installed but was interrupted, this can cause errors when trying to install the software.
To fix this, first follow the instructions to uninstall puma, and then repeat the installation procedureIf an error "make: Warning: File ... has modification time ... s in the future" is displayed,
then run "sudo apt install ntp" (or equivalent for your distribution)If any bugs are found, or if the software crashes for any reason, please open an issue atthis linkand/or contact either of the authors mentioned below.Contributing to PuMASince PuMA is a free open-source code, any user is welcome to contribute or collaborate however they would like.
If you are interested in significant development for your research goals, please contact either of the authors mentioned
below, either by email or on the community chat.AuthorsCreator:  Joseph Fergusonjoseph.ferguson@stanford.eduMaintainer: Federico Semerarofederico.semeraro@nasa.govContributors:
John M. Thornton,
Francesco Panerai,
Arnaud Borner,
Jeremie B. Meurisse,
Sergio Fraile Izquierdo,
Nagi N. MansourLegal / LicenseCopyright @ 2017, 2020, 2021 United States Government as represented by the Administrator of the National Aeronautics and Space Administration. All Rights Reserved.
This software may be used, reproduced, and provided to others only as permitted under the terms of the agreement under which it was acquired from the U.S. Government. Neither title to, nor ownership of, the software is hereby transferred. This notice shall remain on all copies of the software.
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