GenericIO

GenericIO is a write-optimized library for writing self-describing scientific data files on large-scale parallel file systems.

• Repository: git.cels.anl.gov
• Documentation: CPACdocs

Reference

Habib, et al., HACC: Simulating Future Sky Surveys on State-of-the-Art Supercomputing Architectures, New Astronomy, 2015 (http://arxiv.org/abs/1410.2805).

Obtaining the Source Code

The most recent version of source is available by cloning this repo:

git clone https://git.cels.anl.gov/hacc/genericio.git

There is also a history of code releases: 2019-04-17 / 2017-09-25 / 2016-08-29 / 2016-04-12 / 2015-06-08 /

Building Executables / C++Library

The executables and libgenericio can be built either with CMake (minimum version 3.10) or with GNUMake. The following executables will be built:

• frontend/GenericIOPrint print data to stdout (non-MPI version)
• frontend/GenericIOVerify verify and try reading data (non-MPI version)
• mpi/GenericIOBenchmarkRead reading benchmark, works on data written with GenericIOBenchmarkWrite
• mpi/GenericIOBenchmarkWrite writing benchmark
• mpi/GenericIOPrint print data to stdout
• mpi/genericIORewrite rewrite data with a different number of ranks
• mpi/genericIOVerify verify and try reading data

Using CMake

Note that the executables / libraries will be located in build/<frontend/mpi>. CMake will use the compiler pointed to in the CC and CXX environmental variables.

mkdir build && cd build
cmake ..
make -j4

Using Make

Make will create the executables / libraries under the main directory. Edit the CC, CXX, MPICC, and MPICXX variables in the GNUmakefile to change the compiler.

make

Installing the Python Library

The pygio library is pip-installable and works with mpi4py.

Requirements

• Currently, a CMake version >= 3.11.0 is required to fetch dependencies during configuration. If the system does not provide a suitable cmake version, pip should (theoretically) download cmake from the PyPI repository.
• The pygio module also requires MPI libraries to be detectable by CMake's FindMPI. The compiler needs to support C++17 (make sure that CC and CXX point to the correct compiler).

Install

The python library can be installed by running pip in the main folder:

python -m pip install .

Alternatively, the library can also directly be installed from the git URL without having to clone the repository first:

python -m pip install git+https://git.cels.anl.gov/hacc/genericio.git

It will use the compiler referred by the CC and CXX environment variable. In case the automatically detected compiler is incorrect, specify the compiler path as

CC=/path/to/gcc CXX=/path/to/g++ python -m pip install .

If the compiler supports OpenMP, the library will be threaded. Make sure to set OMP_NUM_THREADS to an appropriate variable, in particluar when using multiple MPI ranks per node.

Installing and running with VELOC support

Requirements

This mode requires a working VELOC installation. Instructions can be found here: https://veloc.readthedocs.io

Install

Set the VELOC_INSTALL_DIR variable in GNUMakefile to the root of the VELOC installation directory. Then proceed to compile and link GIO as usual.

Run

Define the GENERICIO_USE_VELOC environment variable as the path to the VELOC configuration file. An example is available here: veloc.cfg