This is an archival copy of the Visualization Group's web page 1998 to 2017. For current information, please vist our group's new web page.
- DAGR
- Description:
DAGR is a scalable framework for implementing analysis pipelines using parallel
design patterns. DAGR abstracts the pipeline concept into a state machine
composed of connected algorithmic units. Each algorithmic unit is written to do
a single task resulting in highly modularized, reusable code. DAGR provides
infrastructure for control, communication, and parallelism, you provide the
kernels to implement your analyses.
Written in modern C++ and designed to leverage MPI+threading for parallelism,
DAGR can leverage the latest HPC hardware including many-core architectures and
GPUs. The framework supports a number of parallel design patterns including
distributed data, map-reduce, and task based parallelism.
- Project page:
https://github.com/LBL-EESA/dagr
- SENSEI Generic Data Interface
- Description:
The SENSEI generic data interface provides a framework for science code teams
and analysis algorithm developers to write code once and
use it anywhere within the four major in situ analysis
frameworks (ADIOS, GLEAN, ParaView/Catalyst and VisIt/libsim). Furthermore,
since ParaView/Catalyst and VisIt/Libsim both are treated as analysis routines
under SENSEI, these visualizations can be run in situ, or in transit
using ADIOS or GLEAN transparently.
- Project page:
https://gitlab.kitware.com/sensei/sensei-pub
- Brain Modulyzer
- Description:
Brain Modulyzer is an interactive visual exploration tool for functional
magnetic resonance imaging (fMRI) brain scans, aimed at analyzing the
correlation between different brain regions when resting or when performing
mental tasks. Integrated methods from graph theory and analysis, such as
community detection and derived graph measures, make it possible to explore the
modular and hierarchical organization of functional brain networks.
- Project page:
https://github.com/sugeerth/BrainModulyzer
- ECoG ClusterFlow
- Description:
ECoG ClusterFlow is an interactive visual analysis tool for the exploration of
high-resolution Electrocorticography (ECoG) data. ECoG Clusterflow detects and
visualizes dynamic high-level structures, such as communities, using the
time-varying spatial connectivity network derived from high-resolution ECoG
data. ECoG ClusterFlow makes it possible 1) to compare the spatio-temporal
evolution patterns for continuous and discontinuous time-frames, 2) to
aggregate data to compare and contrast temporal information at varying levels
of granularity, 3) to investigate the evolution of spatial patterns without
occluding the spatial context information.
- Project page:
https://github.com/sugeerth/ECoG-ClusterFlow
- Henson
- Description:
Henson uses coroutines and position-independent executables to enable
cooperative multitasking between simulation and analysis, allowing the same
executables to post-process simulation output, as well as to process it on the
fly, both in situ and in transit. Our design differs significantly from the
existing frameworks and offers an efficient and robust approach to integrating
multiple codes on modern supercomputers.
- Project page:
https://github.com/mrzv/henson
- DIY
- Description:
DIY is a block-parallel library for implementing scalable algorithms that can
execute both in-core and out-of-core. The same program can be executed with one
or more threads per MPI process, seamlessly combining distributed-memory
message passing with shared-memory thread parallelism. The abstraction enabling
these capabilities is block 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. Complex communication patterns,
including neighbor exchange, merge reduction, swap reduction, and all-to-all
exchange, are possible in- and out-of-core in DIY.
- Project page:
https://github.com/diatomic/diy
- zorder-lib
- Description:
zorder-lib is a C-language library callable from C or C++ programs that
provides a simple-to-use API for implementing an altnerative to traditional
row-major order in-memory layout, one based on a Morton-order space-filling
curve (SFC), specifically, a Z-order variant of the Morton order curve.
The library enables programmers to, after a simple initialization step,
to convert a multidimensional array from row-major to Z-order layouts,
then use a single, generic API call to access data from any arbitrary
(i,j,k) location from within the array, whether it it be stored in
row-major or z-order format.
- Project page:
(coming soon)
- Download software:
https://codeforge.lbl.gov/projects/z-order/
- wesBench
- Description:
wesBench is a standalone software application used for benchmarking the
performance of vertex and fragment operations on modern graphics processing
units (GPUs). It has been carefully engineered to produce reliable and
correct results for vertex and fragment operations under a variety of
user-specifiable scenarios commonly used by contemporary OpenGL-based
graphics applications.
- Project page:
(coming soon)
- Download software:
https://codeforge.lbl.gov/projects/wesbench/
- H5hut, H5part
- OpenMSI
- Description: OpenMSI is an advanced web-based gateway for management and storage of MSI data, the visualization of the hyper-dimensional contents of the data, and the statistical analysis.
- Project page: https://openmsi.nersc.gov
- Reference:Oliver Ruebel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen,
"OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging"
Analytical Chemistry 2013 85 (21), 10354-10361, DOI: 10.1021/ac402540a.
[BibTeX][Online at ACS]
- OMAAT: OpenMSI Arrayed Analysis Toolkit
- svPerfGL
- Description:
svPerfGL is an OpenGL benchmark intended to measure "real world"
performance of scientific visualization applications. These applications
are characterized by relatively high payload (i.e., lots of triangles)
with relatively few OpenGL state changes. This application takes as input
disjoint triangle payload contained in files in netCDF format, renders
the frames over a user-specified time duration, rotates the entire scene
by one degree per frame, then computes and reports a "triangles per second"
performance metric upon exit.
- Project page: /Research/svPerfGL
- Download software:
https://codeforge.lbl.gov/projects/svperfgl/.
Note: the svPerfGL application requires sample data as input. Please visit
the svPerfGL project page for more information
about accessing sample data.
- mpiReadWriteTest
- Description: mpiReadWriteTest is an MPI-based
application that can be used to measure the parallel I/O performance
of a computational platform. While it is not as efficient as a low-level
utility that reads/writes disk blocks, it is representative of
the type of performance one could reasonably expect from a "garden
variety parallel application." We have used this benchmark extensively
on our parallel systems to characterize I/O performance and as part
of filesystem tuning.
- Project page:
No project page at the present time. The source code tarball
contains a README file with build and execute instructions.
- Download software:
https://codeforge.lbl.gov/projects/mpirwt
- semViewer
- Description: The semViewer software was
developed as part of an LBNL LDRD project during the period
1999-2001. It is used to perform distance and angular measurements
of perceived 3D objects present in pairs of images obtained from
scanning electron microscopy.
- Project page:
/Research/caliper/index.html
- Download software:
https://codeforge.lbl.gov/projects/semviewer
- Visapult
- WarpIV
- Description:WarpIV is a python application that enables efficient, parallel visualization and analysis of simulation data while it is being generated by the Warp simulation framework. WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analytics to facilitate query and feature-based data analytics and efficient large-scale data analysis.
- Project page: https://bitbucket.org/berkeleylab/warpiv
- Sources:https://bitbucket.org/berkeleylab/warpiv
- Reference: O. Ruebel, B. Loring, J.-L. Vay, D. P. Grote, R. Lehe, S. Bulanov, H. Vincenti, and E.~W. Bethel, "WarpIV: In Situ Visualization and Analysis of Ion Accelerator Simulations," IEEE Computer Graphics & Applications, Scientific Visualization, pp. 22-35, May/June, 2016. LBNL-1005718
- TECA
- Description:
TECA(Toolkit for Extreme Climate Analysis). A collection of climate analysis algorithms geared toward extreme event detection and tracking implemented in a scalable parallel framework. The core is written in modern c++ and uses MPI+thread for parallelism. The framework supports a number of parallel design patterns including distributed data parallelism and map-reduce. Python bindings make the high performance c++ code easy to use. TECA has been used up to 750k cores.
- Project page:
/Software/TECA/
- Download software:
https://bitbucket.org/lbl-cascade/teca
- Xi-CAM
- Description:
Xi-CAM: A versatile interface for visualization and data analysis providing workflow for local and remote computing, data management, and seamless integration of plugins.
- Project page:
http://www.camera.lbl.gov/xi-cam-interface
- Download software:
Xi-cam is a continuing development project in an early beta stage. If interested in collaborative development or to receive development beta releases, please contact Ron Pandolfi (ronpandolfi@lbl.gov) and Alex Hexemer (ahexemer@lbl.gov).
- SHARP
- Description:
Sharp Camera is used to obtain images from ptychography experiments in real-time. It uses parallelization and GPU computing to achieve the necessary speed. It is designed to reconstruct an image from a set of far-field diffraction patterns, recorded at known sample translations, obtained in an X-ray ptychography experiment.
- Project page:
http://www.camera.lbl.gov/downloads-ptycho
- Download software:
For the further information, please contact the Sharp development team (sharp-access@lists.lbl.gov)
- F3D
- Description:
F3D is a Fiji plugin, designed for high-resolution 3D image, and written in OpenCL. F3D plugin achieves platform-portable parallelism on modern multi-core CPUs and many-core GPUs. The interface and mechanisms to access F3D accelerated kernes are written in Java to be fully integrated with other tools available within Fiji/ImageJ. F3D delivers several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilize resources and can process data out of core and scale efficiently across multiple accelerators. Optimized for data parallel filters, F3D streams data out of core to efficiently manage resources, such as memory, over complex execution sequence of filters. This has greatly expedited several scientific workflows dealing with high-resolution images.
F3D preforms two main types of 3D image processing operations: non-linear filtering, such as bilateral and median filtering, and morphological operators (MM) with varying 3D structuring elements.
- Project page:
http://www.camera.lbl.gov/downloads--imaging-
- Download software:
https://github.com/CameraIA/F3D