Metadata-Version: 1.2
Name: petgem
Version: 0.6
Summary: Parallel python code for electromagnetic modeling in geophysics using high-order nédélec finite elements
Home-page: https://www.bsc.es/castillo-octavio
Maintainer: Octavio Castillo Reyes
Maintainer-email: octavio.castillo@bsc.es
License: GPLv3.0
Download-URL: http://petgem.bsc.es
Description: petgem
        ======
        
        PETGEM is a parallel python code for 3D Controlled-Source
        Electromagnetic Method (3D CSEM) in geophysics using high-order edge finite
        elements (Nédélec 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, 3.6.3 and 3.6.9 have been tested)
        * `Numpy <http://www.numpy.org/>`__ for arrays manipulation
        * `Scipy <http://www.scipy.org/>`__ for numerical operations
        * `Singleton-decorator <https://pypi.org/project/singleton-decorator/>`_
        * `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/>`_
        * `Mpi4py <https://pypi.org/project/mpi4py/>`__ for parallel computations on distributed-memory platforms.
        * `h5py <https://pypi.org/project/h5py/>`__ for input/output tasks.
        
        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, 3.8, 3.9, and 3.12 have been tested)
        
        * Uncompress the PETSc archive (in this example, using PETSc 3.12.0)::
        
          $ tar zxvf petsc-3.12.0.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-3.12.0
          $ 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
        
        * Further, to activate GPUs support, please add following options to previous configure line::
        
          $ --with-cuda=1 --with_cuda_dir=PATH
        
          where ``PATH`` is the directory of your CUDA libraries.
        
        * 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., García-Castillo, L. E., Cela, J. M. (2019).
          *Parallel 3D marine controlled-source electromagnetic modeling using high-order
          tetrahedral Nédélec elements*. Geophysical Journal International, ggz285,
          vol 219: 39-65. ISSN 0956-540X. https://doi.org/10.1093/gji/ggz285
        
        * Castillo-Reyes, O., de la Puente, J., Cela, J. M. (2018).
          *PETGEM: A parallel code for 3D CSEM forward modeling using edge finite
          elements*. Computers & Geosciences, vol 119: 123-136. ISSN 0098-3004,
          Elsevier. https://doi.org/10.1016/j.cageo.2018.07.005
        
        * 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, high-order edge finite elements, HPC, numerical simulation
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 :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries
Classifier: Operating System :: POSIX :: Linux
