Software





DIY: Do-it-Yourself Analysis


An open-source package of scalable building blocks for data movement tailored to the needs of large-scale parallel analysis workloads

Installation (Linux, Mac, IBM and Cray supercomputers):
Download DIY with the following command:

git clone https://github.com/diatomic/diy


and follow the instructions in the README.
Documentation can be found here.

Description:
Scalable, parallel analysis of data-intensive computational science relies on the decomposition of the analysis problem among a large number of data-parallel subproblems, the efficient data exchange among them, and data transport between them and the memory/storage hierarchy. The abstraction enabling these capabilities is block-based parallelism; blocks and their message queues are mapped onto processing elements (MPI processes or threads) and are migrated between memory and storage by the DIY runtime. Configurable data partitioning, scalable data exchange, and efficient parallel I/O are the main components of DIY. The current version of DIY has been completely rewritten to support distributed- and shared-memory parallel algorithms that can run both in- and out-of-core with the same code. The same program can be executed with one or more threads per MPI process and with one or more data blocks resident in main memory. Computational scientists, data analysis researchers, and visualization tool builders can all benefit from these tools.


DIY structure


Above: The DIY software structure. The master manages block placement in the memory/storage hieararchy and executes the block operations with one or more threads. The decomposer creates blocks with regularly defined decomposition patterns, and the assigner maps one or more blocks to an MPI process. Communication occurs between blocks using regular patterns. The I/O module provides collective and independent block I/O. Common tasks are provided by a set of ready-to-use algorithms.


DIY performance


DIY has demonstrated strong scaling out to 512K processes on existing machines in a diverse array of science and analysis codes, including cosmology, molecular dynamics, nuclear engineering, co-design, astrophysics, combustion, and synchrotron light source imaging. The figure above shows a benchmark of strong and weak scaling of parallel Delaunay tessellations, one of the libraries built on top of DIY. [SC14 paper]

More information and citing DIY:
Please refer to our LDAV'11 paper,
pdf bibtex
and our LDAV'16 paper,
pdf bibtex

Authors:
DIY is a collaboration between Tom Peterka of Argonne National Laboratory and Dmitriy Morozov of Lawrence Berkeley National Laboratory.



Tess: Parallel Delaunay and Voronoi Tessellation


An open-source package for parallelizing Delaunay and Voronoi tessellation over distributed-memory HPC architecture

Installation (Linux, Mac, IBM and Cray supercomputers):
Download Tess with the following command:

git clone https://github.com/diatomic/tess2


and follow the instructions in the README.

Description:
Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. Tess is a parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbor points need to be exchanged among the subdomains of a spatial decomposition. Computing tessellations at scale performs poorly when the input data is unbalanced, which is why Tess uses k-d trees to evenly distribute points among processes. The running times are up to 100 times faster using k-d tree compared with regular grid decomposition. Moreover, in unbalanced data sets, decomposing the domain into a k-d tree is up to five times faster than decomposing it into a regular grid.


Tess performance


Above: Cosmology simulations are a prime example of severe load imbalance, as dark matter particles cluster into halos and voids whose densities can vary by six orders of magnitude. The strong scaling of parallel Delaunay tessellation improves by approximately 100X by decomposing blocks in a DIY k-d tree versus a regular grid.

More information and citing Tess:
Please refer to our SC14 paper,
pdf bibtex
and our SC16 paper,
pdf bibtex

Authors:
Tess is a collaboration between Tom Peterka of Argonne National Laboratory and Dmitriy Morozov of Lawrence Berkeley National Laboratory.



Decaf: Decoupled Dataflows


An open-source package of dataflow communication for in situ HPC data analysis workflows

Installation (Linux, Mac, IBM and Cray supercomputers):
Download Decaf with the following command:

git clone https://bitbucket.org/tpeterka1/decaf

and follow the instructions in the README.

Description:
Decaf is a dataflow system for the parallel communication of coupled tasks in an HPC workflow. The dataflow can perform arbitrary data transformations ranging from simply forwarding data to complex data redistribution. Decaf does this by allowing the user to allocate resources and execute custom code in the dataflow. All communication through the dataflow is efficient parallel message passing over MPI. The runtime for calling tasks is entirely message-driven; Decaf executes a task when all messages for the task have been received. Such a message-driven runtime allows cyclic task dependencies in the workflow graph, for example, to enact computational steering based on the result of downstream tasks. Decaf includes a simple Python API for describing the workflow graph. This allows Decaf to stand alone as a complete workflow system, but Decaf can also be used as the dataflow layer by one or more other workflow systems to form a heterogeneous task-based computing environment.


Decaf structure


Above: The Decaf software structure. Decaf is a dataflow middleware for coupling HPC simulation and analytics codes. Decaf includes distributed and configurable dataflow links, standard data redistribution patterns, flow control, and automatic data filtering.


Decaf performance


Decaf has demonstrated strong scaling out to 1280 processes on existing machines in numerous science and analysis codes, including cosmology, molecular dynamics, and light source imaging. The figure above shows a benchmark of strong scaling of an HPC workflow consisting of computational cosmology, parallel Voronoi tessellation, and parallel density estimation of gravitational lensing due to dark matter.

More information and citing Decaf:
Please refer to our ISAV'15 paper,
pdf bibtex
and our Cluster'16 paper,
pdf bibtex

Authors:
Decaf is a collaboration between Tom Peterka and Matthieu Dreher of Argonne National Laboratory.