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Metadata-Version: 1.1
Name: petgem
Version: 0.30.48
Summary: Parallel python code for electromagnetic modeling in geophysics
Home-page: https://www.bsc.es/castillo-octavio
Author: Octavio Castillo Reyes
Author-email: octavio.castillo@bsc.es
License: GPLv3.0
Download-URL: http://petgem.bsc.es
Description-Content-Type: UNKNOWN
Description: petgem
======
petgem is a parallel python code for 3D Controlled-Source
Electromagnetic Method (3D CSEM) in geophysics using edge finite
elements (Nedelec finite elements).
Requirements
------------
PETGEM is known to run on various flavors of Linux clusters. Its requirements are:
* `PETSc <https://www.mcs.anl.gov/petsc/>`__ (builded version for **COMPLEX-VALUED NUMBERS**) for the use of direct/iterative parallel solvers
* `Python 3 <https://www.python.org/>`__ (versions 3.5.2 and 3.6.3 have been tested)
* `Numpy <http://www.numpy.org/>`__ for arrays manipulation
* `Scipy <http://www.scipy.org/>`__ for numerical operations
* `Blessings <https://pypi.python.org/pypi/blessings/>`_ for terminal styling and positioning
* `Sphinx <http://www.sphinx-doc.org>`__ and `LaTeX <https://www.latex-project.org/>`__ (textlive) to generate documentation
* `Petsc4py <https://bitbucket.org/petsc/petsc4py>`__ for parallel computations on distributed-memory platforms. It allows the use of parallel direct/iterative solvers from `PETSc <http://www.mcs.anl.gov/petsc/>`_
On Linux, consult the package manager of your preference. PETGEM can be
used without any installation by running the kernel from the top-level
directory of the distribution.
Install
-------
* Following commands may require root privileges
* Download `PETSc <https://www.mcs.anl.gov/petsc/>`__ (PETSc 3.7 and 3.8 have been tested)
* Uncompress the PETSc archive (in this example, using PETSc 3.8.3)::
$ tar zxvf petsc-3.8.3.tar.gz
* Configure and build PETSc. The configuration options depend on the calculations you want to perform (complex- or real-valued) as well as your compiler/MPI/Blas/Lapack setup. For PETGEM executions, **PETSC MUST BE BUILD FOR COMPLEX-VALUED NUMBERS**. In order to avoid incompatibilities between PETSC, petsc4py and PETGEM, we highly recommend the following configuration lines. Please, visit PETSc website for advanced configuration options. If you have a clean environment (not working MPI/Blas/Lapack), then run::
$ cd petsc-3.8.3
$ export PETSC_DIR=$PWD
$ export PETSC_ARCH=arch-linux2-c-debug
* If you do not want support for MUMPS, run following configure line::
$ ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack --with-scalar-type=complex
* If you want support for MUMPS, please add following options to previous configure line::
$ --download-mumps --download-scalapack --download-parmetis --download-metis --download-ptscotch --download-cmake
* Then, build and install PETSc::
$ make $PETSC_DIR $PETSC_ARCH all
$ make $PETSC_DIR $PETSC_ARCH test
$ make $PETSC_DIR $PETSC_ARCH streams
* Ensure your ``mpicc`` compiler wrapper is on your search path::
$ export PATH="${PETSC_DIR}/${PETSC_ARCH}/bin:${PATH}"
* Ensure you have a Numpy installed::
$ pip3 install numpy
* And finally, install PETGEM with its dependencies (`Scipy <http://www.scipy.org/>`_ , `Blessings <https://pypi.python.org/pypi/blessings/>`__, `Sphinx <http://www.sphinx-doc.org>`__, `Petsc4py <https://bitbucket.org/petsc/petsc4py>`__) by typing::
$ pip3 install petgem
Citations
---------
If petgem been significant to a project that leads to an academic
publication, please acknowledge that fact by citing the project:
* Castillo-Reyes, O., de la Puente, J., Cela, J.M. (2017).
*Three-Dimensional CSEM Modelling on Unstructured Tetrahedral Meshes
Using Edge Finite Elements*, Communications in Computer and
Information Science, vol 697: 247-256. ISBN 978-3-319-57971-9
Springer, Cham. https://doi.org/10.1007/978-3-319-57972-6_18
Keywords: 3D CSEM, edge finite elements, HPC, petsc, petsc4py.
Platform: Linux
Classifier: Development Status :: 3 - Alpha
Classifier: License :: Free for non-commercial use
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries
Classifier: Operating System :: POSIX :: Linux
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