Installation and Building¶

Downloading the Source¶

\(\texttt{HODLRlib}\) is distributed using the git version control system, and is hosted on Github. The repository can be cloned using:

git clone https://github.com/sivaramambikasaran/HODLR.git --recursive

The --recursive flag is argument to ensure that all submodules are also checked out. The Python wrappers for the library make use of pybind11 and would need to be checked out for Python functionality.

Dependencies¶

Eigen Linear Algebra Library (get it here)
(optional) An OpenMP enabled compiler (e.g. gcc4.2 or above) is required to use shared-memory parallelism.
(optional) MKL libraries (\(\texttt{HODLRlib}\) has improved performance when compiled against MKL)

NOTE: On MacOS, the default compiler is clang which doesn’t have OpenMP support. You will have to use g++ to make use of the speedups from OpenMP:

user@computer HODLR$ brew install g++-8
user@computer HODLR$ export CXX=g++

Installation¶

You can either install \(\texttt{HODLRlib}\) by using the provided install script provided or manually install and link the needed dependencies.

Install Script¶

The easiest way to get running is to install the needed dependencies by running the install.sh provided in the root level of this repository:

user@computer HODLR$ ./install.sh

The above command should create a folder deps/ in the current directory with the needed dependencies. Additionally, the script should set the environment variables that would be needed during the build and execution stages. This only needs to be done once since the environment variables are automatically written to .bash_profile.

Manually Installing¶

First set the environment variable HODLR_PATH to the root level of this repository. This is needed by some of the routines in the plotting of the low-rank structure for the specific kernel. (NOTE: The plotting is carried out using python, and requires the matplotlib package to be installed in your python environment)

Then, set the environment variable EIGEN_PATH to the location of your Eigen installation. This is needed by the CMake script.:

user@computer HODLR$ export EIGEN_PATH=path/to/eigen/

Optionally: set the environment variable MKLROOT to take advantage of speedups from MKL.:

user@computer HODLR$ export MKLROOT=path/to/mkl/

Python Installation¶

Get the dependencies and set environment variables needed for the library through the Install Script of Manual Install routes. Once these have been setup, navigate to the python subdirectory from the root level of the repository. The Python wrapper for the library can be installed by running:

user@computer python$ python setup.py install

Testing¶

C++¶

Now, we need to ensure that all the functions of the libraries function as intended. For this purpose, we will be running the script test/test_HODLR.cpp. By default, during a build this file under test/ gets compiled, and would show up under the test/ directory in your build folder. To check this on your computer, run the following lines:

user@computer HODLR$ mkdir build && cd build
user@computer build$ cmake ..
user@computer build$ ./test/test_HODLR

For a succesful test, the final line of output for this run would read:”Reached End of Test File Successfully! All functions work as intended!”.

Fortran¶

In order to ensure that the Fortran wrapper works as intended, run the Fortran file found under fortran/test/test_HODLR.f90. In order to run this and ensure correct functioning, type the following at the commandline:

user@computer HODLR$ cd fortran
user@computer fortran$ mkdir build && cd build
user@computer build$ cmake .. -DCMAKE_BUILD_TYPE=TESTING
user@computer build$ ./test_HODLR

For a succesful test, the final line of output for this run would read:”Reached End of Test File Successfully! All functions work as intended!”.

Python¶

In order to ensure that the Python wrapper works as intended, run the Python file found under python/test/test_HODLR.py. This can be executed by running the following commands from the terminal:

user@computer HODLR$ cd python/test
user@computer test$ python test_HODLR.py

For a succesful test, the final line of output for this run would read:”Reached End of Test File Successfully! All functions work as intended!”.

Building and Executing¶

C++¶

Key in the required .cpp to be used as input under INPUT_FILE in HODLRlib/CMakeLists.txt. Here you also set the name of the output executable under OUTPUT_EXECUTABLE_NAME. Then navigate to your build directory and run cmake path/to/CMakeLists.txt and run the generated Makefile to get your executable:

user@computer build$ cmake path/to/HODLR/
user@computer build$ make -j n_threads
user@computer build$ ./executable

Fortran¶

The compilation process for the fortran wrappers is similar to the process for C++: Key in the required .f90 to be used as input under INPUT_FILE in HODLRlib/fortran/CMakeLists.txt. Here you also set the name of the output executable under OUTPUT_EXECUTABLE_NAME. Then navigate to your build directory and run cmake path/to/CMakeLists.txt and run the generated Makefile to get your executable:

user@computer build$ cmake path/to/HODLR/fortran/
user@computer build$ make -j n_threads
user@computer build$ ./executable

Python¶

The process of running Python files that make use of pyhodlrlib follow the standard procedure used to run a python file:

user@computer example$ python example.py