README.md

Synopsis

Lightweight c++ wrapper for PETSc aiming to enable a more epressive and simpler usage of PETSc with minimal overhead.

int main(int main(int argc, char *argv[]){

  // Initialize Petsc
  Petscpp::App app(argc, argv);

  int const N = 1600;

  /* Wrapper for PETSc::Vec struct. Initialize a parallel vector of
   * size N, with default value of 3.1
   */
  Petscpp::Vector v1(N, 3.1);

  /* Scale `v1` and assign to a new vector with same layout as v1,
   * with contents 3.1*2
   */
  Petscpp::Vector v2 = 2*v1;

  /* Add `v1` and `v2`, and write to a new vector with same parallel
   * layout as `v1` and `v2`
   */
  Petscpp::Vector v3 = v1 + v2;

  // Create a new vector of dimension 2 for demo purposes
  Petscpp::Vector v4(2);

  /* (`v1`, `v2` , `v3`) have compatible parallel layouts. Following
   * line performs lazy evaluation: original `v4` (different layout as
   * `v1`, `v2`, `v3` is destroyed, and a new vector with compatible
   * layout to (`v1`, `v2`, `v3`) is created. No temporaries are created.
   */
  v4 = v1 + v2 + v3;

  // No need to manually clean up PETSc objects

  return 0;
}

NOTE: Treat this repo as incomplete. This was originally started in ~2015 and has not been completed or updated since.

Requirements

• PETSc (used 3.4.4; expect breaking changes in newer versions)
• MPICH
• ATLAS (recommended)
• Eigen
• c++11+ compiler

Usage

See the examples directory.

Build

1. Build Petsc
2. Build

   cd path-to-petscpp-root
   mkdir build
   cd build
   cmake ..
   make

Building PETSc

(Built with petsc-3.4.4). Note: there are or were often breaking changes between different PETSc releases)

Consider building PETSc with an optimized linear algebra system (see example below). An optimized LA system can lead to a considerable performance boost.

1. Install MPICH

• Install =MPICH=

  yum install mpich2

• Load the MPI module

  module load mpi/mpich-x86_64

  You can add the above line to ~/.bash_profile so that MPI module is loaded on login

2. Get ATLAS
   1. Download ATLAS (tested with atlas-3.10.3)
   2. Build ATLAS
      • If using INTEL CPU, boot the OS with intel_pstate disabled. This can be achieved for example by appending intel_pstate to boot options.
      • Disable CPU frequency scaling

      echo performance > /sys/devices/system/cpu/cpu0/cpufreq/scaling_governo
      echo performance > /sys/devices/system/cpu/cpu1/cpufreq/scaling_governo
      # ...

   3. Configure ATLAS. Example build process:

    cd /path/to/atlas/dir
    mkdir name_of_build_directory && cd name_of_build_directory
    ../configure --with-netlib-lapack-tarfile=/path/to/lapak/tarbal.tgz \
        -Fa alg \
        -fPIC
    make build
    make check
    make ptcheck
    make time

3. Build PETSc
4. Configure and build PETSc (tested with petsc-3.4.4). Set appropriate flags

./configure --with-c-support=1 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 \
            --with-pic \
            --with-debugging=0
            --with-blas-lapack-dir=/path/to/atlast/build/dir/lib \
            --with-x=0 \
            --with-superlu=1
            --download-superlu \
            --with-superlu_dist=1 \
            --download-superlu_dist \
            --with-parmetis=1 \
            --download-parmetis \
            --with-metis=1 \
            --download-metis \
            --with-dynamic-loading=0 \
            --with-shared-libraries=1 \
            --download-mpich
make PETSC_DIR=/opt/petsc-3.4.4 PETSC_ARCH=arch-linux2-c-opt all

2. Set needed PETSc environmental variables by adding following to ~/.bashrc

$ export PETSC_DIR=/path/to/petsc/dir
$ export PETSC_ARCH=/path/to/petsc/arch/build

3. Install cmake
4. Download Eigen
5. Add path to Eigen as an env variable in ~/.bashrc

# ...
export EIGEN_DIR=/path/to/eigen/root/dir

6. Build

cd /path/to/petscpp/root/dir/
mkdir build && cd build
cmake ..
make

7. Run PETSc tests

cd /path/to/executable
mpiexec -n <number-of-procs> ./name_of_executable

Limit the processor number up to the number of available physical cores when using MPI.