Dendro-GRCA

"Dendro" in Greek language means tree. The Dendro library is a large scale (262K cores on ORNL's Titan) distributed memory adaptive octree framework. The main goal of Dendro is to perform large scale multiphysics simulations efficeiently in mordern supercomputers. Dendro consists of efficient parallel data structures and algorithms to perform variational (finite element) methods and finite difference mthods on 2:1 balanced arbitary adaptive octrees which enables the users to perform simulations raning from black holes (binary black hole mergers) to blood flow in human body, where applications ranging from relativity, astrophysics to biomedical engineering.

Dendro-GRCA is developed originally from a team, including Hyun Lim, in University of Utah and Brigham Young University. This is a LANL disclosure version from open Dendro repository. You can find detailed information about this in Dendro-5.01

How to build Dendro?

Dendro can be installed anywhere in your system but we suggest that all repositories are downloaded in DENDRO root directory such as ${HOME}/DENDRO

Suggested directory structure

We recommend to have following directory structure:

  ${HOME}/DENDRO
  ├── Dendro-GRCA
  │   └── build
  └── local
      ├── bin
      ├── include
      ├── lib
      ├── lib64
      └── share

Below we use ${HOME}/DENDRO/local for an installation directory. Make sure to set your CMAKE prefix to this location:

% export CMAKE_PREFIX_PATH=${HOME}/DENDRO/local

Prerequisites

You will need the following tools:

• C++11 - capable compiler, such as gcc version >= 4.8;
• MPI libraries, compiled with the gcc compiler above and multithread support (--enable-mpi-thread-multiple for OpenMPI and --enable-threads=multiple for MPICH);
• cmake version > 2.8;
• Python version > 3.5; (For RHS generation scripts. Not required for building code unless you want to generate RHS during compile time)
• zlib compression library;
• BLAS and LAPACK

Building Dendro

Clone the master branch from the Dendro-GRCA git repo:

   cd $HOME/DENDRO
   git clone git@github.com:lanl/Dendro-GRCA.git

After cloning the repo, follow the configure command: (copy and paste below into your temrinal)

   cd Dendor-GRCA ;
   mkdir build ; cd build
   export CMAKE_PREFIX_PATH=${HOME}/DENDRO/local
   cmake .. \
       -DCMAKE_INSTALL_PREFIX=$CMAKE_PREFIX_PATH \
       -DALLTOALLV_FIX=OFF                       \
       -DHILBERT_ORDERING=ON                     \
       -DPROFILE_TREE_SORT=OFF                   \
       -DSPLITTER_SELECTION_FIX=ON               \
       -DNUM_NPES_THRESHOLD=2                    \
       -Who-dev

Normally, you should have the C, C++, Objective-C, Fortran, and among other compilers, as well as runtime libraries for C++, Objective-C, and Fortran if you install GCC. Sometimes, CMake complains such as

  No CMAKE_Fortran_COMPILER could be found.

In this case, you can check whether you have that compiler or not by using

which <CMake_not_found_complier>

This will show the path of complier. If this does not show anything, you should install that specific complier. If this shows the path, you can export via

export CMAKE_<Complier_name>_COMPILER = <path_to_compiler>

After that, following above configure command again. Similar argument can be applied to MPI library.

Once your configuration is successful, you will see

-- Configuring done
-- Generating done
-- Build files have been written to: ${HOME}/DENDRO/Dendro-GRCA/build

at the end of configuration.

After configuration, build and install inside of your build directory by:

     make -j 
     make install

Note that if your machine does not support parallel job, you may not use -j option during make

Note for MAC OSX user

Because of MacOS use LLVM complier, gcc (or g++) links to clang complier. This is not compatible OpenMp. (You cannot use -fopenmp as the flag). Here is two possible solution.

You can install gnu complier manually, and use gnu complier as your complier. Then, gnu links OpenMP automatically.

Mac has own version of OpenMP, called clang-omp. You can install this, and link this for using OpenMp in Mac.

Running Dendro application : Example with QG project

Once you successfully building the Dendro, you will have quadgravSolver in your build directory and/or ${HOME}/DENDRO/local/bin.

You can run quadgravSolver as follow

  mpirun -np <number of mpi tasks> ./quadgravSolver <parameter file name>.par

An example parameter file can be found in QuadGrav/par. You can create your own parameter file based on this

Details About the Code

If you are interested in learning details about this toolkit, please check the publication

Visualization

We are using Paravies as our visualization toolkit with parallel vtu output.

Contact

Please contact Hyun Lim via hyunlim@lanl.gov if you have any questions or problem.

Copyright

© 2020. Triad National Security, LLC. All rights reserved.
This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos
National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S.
Department of Energy/National Nuclear Security Administration. All rights in the program are
reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear
Security Administration. The Government is granted for itself and others acting on its behalf a
nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare
derivative works, distribute copies to the public, perform publicly and display publicly, and to permit
others to do so.