petgem 0.9

Requirements

petgem is known to run on various flavors of Linux clusters. Its requirements are:

• PETSc (builded version for COMPLEX-VALUED NUMBERS) for the use of direct/iterative parallel solvers

• Python 3 (versions 3.5.2, 3.6.3 and 3.6.9 have been tested)

• Numpy for arrays manipulation

• Scipy for numerical operations

• Singleton-decorator

• Sphinx and LaTeX (textlive) to generate documentation

• Petsc4py for parallel computations on distributed-memory platforms. It allows the use of parallel direct/iterative solvers from PETSc

• Mpi4py for parallel computations on distributed-memory platforms.

• 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 (PETSc 3.7, 3.8, 3.9, 3.12, and 3.14 have been tested)

• Uncompress the PETSc archive (in this example, using PETSc 3.14.0):

  $ tar zxvf petsc-3.14.0.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-3.14.0
  $ 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 , Blessings, Sphinx, 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