BOINC Projects - Recent changes [en]

BOINC projects

Al Piskun — Sat, 26 Sep 2026 11:45:11 GMT

retire LODA

@@ Line 197: / Line 197: @@
+|
 | A BOINC server for LHC@home development.
 |-
@@ Line 4,416: / Line 4,403: @@
+|
 |Distributed neural-network learning techniques influenced by Hebbian learning [[Axiom Distributed AI|See more...]]
 |-
@@ Line 4,430: / Line 4,416: @@
 | [https://podcasts.apple.com/us/podcast/project-brief-ramanujan-machine-5-2-2022/id1492837872?i=1000570072053 Listen]
 | Conjecturing new mathematical formulas. [[Ramanujan Machine|See more...]]
 |}

LODA

Al Piskun — Fri, 25 Sep 2026 20:12:41 GMT

add wayback link

← Older revision		Revision as of 20:12, 25 September 2026
Line 18:		Line 18:
	}}		}}

	'''LODA BOINC''' was a [[wikipedia:Volunteer computing\|volunteer computing]] project based on the [[wikipedia:Berkeley Open Infrastructure for Network Computing\|Berkeley Open Infrastructure for Network Computing]] (BOINC) platform. It used computing resources donated by volunteers to search for programs, formulas, and algorithms for integer sequences in the [[wikipedia:On-Line Encyclopedia of Integer Sequences\|On-Line Encyclopedia of Integer Sequences]] (OEIS).<ref name="archive-home">{{cite web		'''[https://web.archive.org/web/20260921044946/https://boinc.loda-lang.org/loda/ LODA BOINC]''' was a [[wikipedia:Volunteer computing\|volunteer computing]] project based on the [[wikipedia:Berkeley Open Infrastructure for Network Computing\|Berkeley Open Infrastructure for Network Computing]] (BOINC) platform. It used computing resources donated by volunteers to search for programs, formulas, and algorithms for integer sequences in the [[wikipedia:On-Line Encyclopedia of Integer Sequences\|On-Line Encyclopedia of Integer Sequences]] (OEIS).<ref name="archive-home">{{cite web
	\|url=https://web.archive.org/web/20260921044946/https://boinc.loda-lang.org/loda/		\|url=https://web.archive.org/web/20260921044946/https://boinc.loda-lang.org/loda/
	\|title=LODA project homepage		\|title=LODA project homepage

Main Page

Al Piskun — Fri, 25 Sep 2026 20:11:03 GMT

retire LODA

← Older revision		Revision as of 20:11, 25 September 2026
Line 120:		Line 120:
	\| * [[SRBase]] Sierpinski-Riesel base search		\| * [[SRBase]] Sierpinski-Riesel base search
	\| * [[NumberFields@Home]] algebraic number field tables		\| * [[NumberFields@Home]] algebraic number field tables
	\|-
	~~\| * [[YAFU]] yet another factorisation utility~~
	~~\| * [[LODA]] integer sequence program synthesis~~
	\|-		\|-
	\| * [[Moo! Wrapper]] distributed.net RC5-72 wrapper		\| * [[Moo! Wrapper]] distributed.net RC5-72 wrapper
Line 131:		Line 128:
	\|-		\|-
	\| * [[Rakesearch]] Latin square searches		\| * [[Rakesearch]] Latin square searches
	\|		\|* [[YAFU]] yet another factorisation utility
	\|}		\|}
	</div>		</div>
Line 266:		Line 263:
	\|-		\|-
	\|* [[Leiden Classical]] submit personal classical mechanics and molecular dynamics simulations		\|* [[Leiden Classical]] submit personal classical mechanics and molecular dynamics simulations
	\|* [[~~NanoHive@Home~~]] ~~used the NanoHive-1 nanospace simulator to search for failure modes in tooltips~~		\|* [[LODA]] integer sequence program synthesis
	\|-		\|-
	\|* [[Malariacontrol.net]] simulate the transmission dynamics and health effects of malaria		\|* [[Malariacontrol.net]] simulate the transmission dynamics and health effects of malaria
	\|* [[MindModeling@Home]] computational cognitive modeling to study human performance and learning		\|* [[MindModeling@Home]] computational cognitive modeling to study human performance and learning
			\|-
			\|
			\|* [[NanoHive@Home]] used the NanoHive-1 nanospace simulator to search for failure modes in tooltips
	\|-		\|-
	\| * [[nanoHUB@Home]] nanotechnology simulation		\| * [[nanoHUB@Home]] nanotechnology simulation

LODA

Al Piskun — Fri, 25 Sep 2026 20:02:54 GMT

update completed status

Show changes

Main Page

Al Piskun — Sun, 30 Aug 2026 14:53:46 GMT

wording

← Older revision		Revision as of 14:53, 30 August 2026
(One intermediate revision by the same user not shown)
Line 25:		Line 25:
	<div class="bs-stat-label">[[BOINC projects\|Projects listed]]</div>		<div class="bs-stat-label">[[BOINC projects\|Projects listed]]</div>
	</div>		</div>
	<div class="bs-stat bs-stat-purple"><div class="bs-stat-number">97</div>		<div class="bs-stat bs-stat-purple"><div class="bs-stat-number">99</div>
	<div class="bs-stat-label">Projects documented</div>		<div class="bs-stat-label">Projects documented</div>
	</div>		</div>
Line 47:		Line 47:
	<div class="bs-definition">		<div class="bs-definition">
	<span class="bs-definition-label">What is a BOINC project?</span>		<span class="bs-definition-label">What is a BOINC project?</span>
	'''A BOINC project''' is a website and associated server set up by an individual or group to distribute applications to [https://boinc.berkeley.edu/ BOINC] volunteer computing devices. Those devices deliberately attach to receive, process, and return results for further scientific research — at no cost to the researcher, and no cost to the volunteer beyond electricity.		'''A BOINC project''' is a website and associated server set up by an individual or group to distribute applications to [https://boinc.berkeley.edu/ BOINC] volunteer computing devices. Those devices deliberately attach to receive, process, and return results for further scientific research at no cost to the researcher, and no cost to the volunteer beyond electricity.

	''BOINC'' stands for '''Berkeley Open Infrastructure for Network Computing''', developed at the University of California, Berkeley. Any researcher can create a BOINC project; any person can donate their idle CPU or GPU time to one.		''BOINC'' stands for '''Berkeley Open Infrastructure for Network Computing''', developed at the University of California, Berkeley. Any researcher can create a BOINC project; any person can donate their idle CPU or GPU time to one.
Line 66:		Line 66:
	<div class="bs-cta">		<div class="bs-cta">
	<div class="bs-cta-title">📺 BOINC Project Screensaver Archive</div>		<div class="bs-cta-title">📺 BOINC Project Screensaver Archive</div>
	<div class="bs-cta-body">Before modern power management made them obsolete, every BOINC project shipped a real-time animated screensaver showing the computation in progress, including protein chains folding, star fields sweeping and climate models spinning. All 71 known screensaver recordings, spanning projects from SETI@home to Pirates@Home, are now preserved in one place.</div>		<div class="bs-cta-body">Before modern power management made them obsolete, every BOINC project shipped a real-time animated screensaver showing the computation in progress, including protein chains folding, star fields sweeping and climate models spinning. All 71 known screensaver recordings, spanning projects from SETI@home to Pirates@Home, are now preserved in one place — with one exception: the NanoHive@Home screensaver, which survives only as a static image, its animation never recorded.</div>
	<big>'''[[BOINC project screensavers\|View the BOINC Screensaver Archive →]]'''</big>		<big>'''[[BOINC project screensavers\|View the BOINC Screensaver Archive →]]'''</big>
	</div>		</div>
Line 235:		Line 235:
	\|* [[BOINC@TACC]] routes computing jobs from TACC supercomputers to volunteer devices		\|* [[BOINC@TACC]] routes computing jobs from TACC supercomputers to volunteer devices
	\|-		\|-
	\|* [[~~CAS~~@~~home~~]] ~~hosted by the Chinese Academy~~ of ~~Sciences, best known for running the TreeThreader protein structure~~		\|* [[BRaTS@Home]] perform gravitational lensing ray-tracing simulations of galaxy clusters
	\|* [[CAS@home]] hosted by the Chinese Academy of Sciences, best known for running the TreeThreader protein structure		\|* [[CAS@home]] hosted by the Chinese Academy of Sciences, best known for running the TreeThreader protein structure
	\|-		\|-
	\|* [[~~BRaTS@Home~~]] ~~perform gravitational lensing ray~~-~~tracing simulations~~ of ~~galaxy clusters~~		\|* [[Correlizer]] studiy the organization of genomes using long-range correlation analysis of chromosomes
	\|* [[Chess@Home]] build a labeled dataset intended for training a machine-learned classifier of winning position		\|* [[Chess@Home]] build a labeled dataset intended for training a machine-learned classifier of winning position
	\|-		\|-
Line 314:		Line 314:
	\|-		\|-
	\| * [[Virtual Prairie]] simulations of clonal plant growth to inform the ecological design of sustainable prairie ecosystems		\| * [[Virtual Prairie]] simulations of clonal plant growth to inform the ecological design of sustainable prairie ecosystems
	\| * [[~~WEP-M+2 Project~~]] ~~mersenne-related prime search~~		\| * [[Volpex@Home]] run communicating parallel programs through process replication and a shared dataspace
	\|-		\|-
	\|		\|* [[WEP-M+2 Project]] mersenne-related prime search
	\|* [[uFluids@Home]] support research into satellite propellant management and lab-on-a-chip devices		\|* [[uFluids@Home]] support research into satellite propellant management and lab-on-a-chip devices
	\|}		\|}

BOINC projects

Al Piskun — Sun, 30 Aug 2026 14:22:51 GMT

add Volpex@Home and Correlizer See more...

← Older revision		Revision as of 14:22, 30 August 2026
Line 3,309:		Line 3,309:
	\| [https://web.archive.org/web/20130525113734/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ Correlizer]		\| [https://web.archive.org/web/20130525113734/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ Correlizer]
	\| [https://boinc.berkeley.edu/pubs.php#Correlizer 5]		\| [https://boinc.berkeley.edu/pubs.php#Correlizer 5]
	\|		\|2011-08-03
			2015
	\|		\|
	\|		\|
	\|		\|
	\|		\|
			\|BioQuant Centre, University of Heidelberg
	\|		\|
	\|		\|
	\|		\| Studiy the organization of genomes using long-range correlation analysis of completely sequenced chromosomes. [[Correlizer\|See more...]]
	~~\| Revealing~~ the ~~mysteries~~ of ~~genome organization~~.

	\|-		\|-
Line 3,530:		Line 3,531:
	\| [https://web.archive.org/web/20160120043345/http://volpexathome.cs.uh.edu/VolPEx/ Volpex@Home]		\| [https://web.archive.org/web/20160120043345/http://volpexathome.cs.uh.edu/VolPEx/ Volpex@Home]
	\| [https://boinc.berkeley.edu/pubs.php#Volpex@Home 9]		\| [https://boinc.berkeley.edu/pubs.php#Volpex@Home 9]
	\|		\|2011-12
			2017
	\|		\|
	\|		\|
Line 3,538:		Line 3,540:
	\|		\|
	\|		\|
	\| ~~Research in creating effective~~ parallel ~~computing~~ on ~~multiple volatile nodes~~.		\| Run communicating parallel programs on failure-prone volunteer PCs through process replication and a shared dataspace. [[Volpex@Home\|See more...]]

	\|-		\|-

Correlizer

Al Piskun — Sun, 30 Aug 2026 14:04:47 GMT

← Older revision		Revision as of 14:04, 30 August 2026
Line 35:		Line 35:
	}}		}}

	'''Correlizer''' was a scientific [[wikipedia:Volunteer computing\|volunteer computing]] project that ran on the [[wikipedia:BOINC\|BOINC]] platform and applied long-range correlation analysis to completely sequenced genomes in order to study the sequential and three-dimensional organization of [[wikipedia:Genome\|genome]]s. It was operated from the Biophysical Genomics group at the [https://www.bioquant.uni-heidelberg.de/ BioQuant] Centre of the [[wikipedia:Heidelberg University\|University of Heidelberg]] in Germany, and the underlying science was developed by Tobias A. Knoch, a researcher also affiliated with the [[wikipedia:German Cancer Research Center\|German Cancer Research Center]] (DKFZ) and the [[wikipedia:Erasmus MC\|Erasmus MC]] in Rotterdam. The project began distributing work in August 2011 and is generally regarded as a completed BOINC project, having stopped issuing work units around 2015 after its workload was folded into [http://boinc.almeregrid.nl/ AlmereGrid].<ref name="home">{{cite web \|title=Correlizer: Revealing the Mysteries of Genome Organization \|url=http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ \|work=Biophysical Genomics \|publisher=BioQuant Centre, University of Heidelberg \|access-date=30 August 2026 \|archive-url=https://web.archive.org/web/20130525113734/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ \|archive-date=25 May 2013 \|url-status=dead}}</ref><ref name="rechenkraft">{{cite web \|title=Correlizer (beendet) \|url=https://www.crogramdataboincprojectswww.rechenkraft.net/wiki/Correlizer_(beendet) \|work=Rechenkraft \|language=German \|access-date=30 August 2026}}</ref>		'''[https://web.archive.org/web/20130525113734/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ Correlizer]''' was a scientific [[wikipedia:Volunteer computing\|volunteer computing]] project that ran on the [[wikipedia:BOINC\|BOINC]] platform and applied long-range correlation analysis to completely sequenced genomes in order to study the sequential and three-dimensional organization of [[wikipedia:Genome\|genome]]s. It was operated from the Biophysical Genomics group at the [https://www.bioquant.uni-heidelberg.de/ BioQuant] Centre of the [[wikipedia:Heidelberg University\|University of Heidelberg]] in Germany, and the underlying science was developed by Tobias A. Knoch, a researcher also affiliated with the [[wikipedia:German Cancer Research Center\|German Cancer Research Center]] (DKFZ) and the [[wikipedia:Erasmus MC\|Erasmus MC]] in Rotterdam. The project began distributing work in August 2011 and is generally regarded as a completed BOINC project, having stopped issuing work units around 2015 after its workload was folded into [http://boinc.almeregrid.nl/ AlmereGrid].<ref name="home">{{cite web \|title=Correlizer: Revealing the Mysteries of Genome Organization \|url=http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ \|work=Biophysical Genomics \|publisher=BioQuant Centre, University of Heidelberg \|access-date=30 August 2026 \|archive-url=https://web.archive.org/web/20130525113734/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ \|archive-date=25 May 2013 \|url-status=dead}}</ref><ref name="rechenkraft">{{cite web \|title=Correlizer (beendet) \|url=https://www.crogramdataboincprojectswww.rechenkraft.net/wiki/Correlizer_(beendet) \|work=Rechenkraft \|language=German \|access-date=30 August 2026}}</ref>

	== Background: genome organization ==		== Background: genome organization ==

Correlizer

Al Piskun — Sun, 30 Aug 2026 14:01:15 GMT

first light

New page

{{Infobox software
| name = Correlizer
| logo = logo-Correlizer.png
| logo caption = Correlizer logo (the "Revealing the Mysteries of Genome Organization" project mark)
| screenshot =
| caption =
| description = Correlizer was a BOINC volunteer computing project run from the BioQuant Centre at the University of Heidelberg that studied the sequential and three-dimensional organization of genomes using long-range correlation analysis of completely sequenced chromosomes. It launched in 2011 and was completed around 2015, after its workload was integrated into AlmereGrid.
| status = Completed
| category = Biology
| compute = CPU
| dependencies = None
| developer = Tobias A. Knoch
| author = Tobias A. Knoch
| sponsor = BioQuant Centre, University of Heidelberg (with the German Cancer Research Center and Erasmus MC)
| maintainer = Tobias A. Knoch
| released = {{Start date and age|2011|08|03}}
| completed = c. 2015
| discontinued =
| repository =
| programming language =
| operating system = Windows, Linux, macOS (also ARM/Linux embedded)
| size =
| stats as of = {{Start date|2013|03|27}}
| average performance = 1,160 GFLOPS
| active users = 615
| total users = 1,747
| active hosts = 2,096
| total hosts = 8,349
| rac =
| credit per day =
| gpu performance = None (CPU only)
| cpu performance = 1,160 GFLOPS
| website = {{URL|http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/}}
| license =
}}

'''Correlizer''' was a scientific [[wikipedia:Volunteer computing|volunteer computing]] project that ran on the [[wikipedia:BOINC|BOINC]] platform and applied long-range correlation analysis to completely sequenced genomes in order to study the sequential and three-dimensional organization of [[wikipedia:Genome|genome]]s. It was operated from the Biophysical Genomics group at the [https://www.bioquant.uni-heidelberg.de/ BioQuant] Centre of the [[wikipedia:Heidelberg University|University of Heidelberg]] in Germany, and the underlying science was developed by Tobias A. Knoch, a researcher also affiliated with the [[wikipedia:German Cancer Research Center|German Cancer Research Center]] (DKFZ) and the [[wikipedia:Erasmus MC|Erasmus MC]] in Rotterdam. The project began distributing work in August 2011 and is generally regarded as a completed BOINC project, having stopped issuing work units around 2015 after its workload was folded into [http://boinc.almeregrid.nl/ AlmereGrid].<ref name="home">{{cite web |title=Correlizer: Revealing the Mysteries of Genome Organization |url=http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ |work=Biophysical Genomics |publisher=BioQuant Centre, University of Heidelberg |access-date=30 August 2026 |archive-url=https://web.archive.org/web/20130525113734/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/ |archive-date=25 May 2013 |url-status=dead}}</ref><ref name="rechenkraft">{{cite web |title=Correlizer (beendet) |url=https://www.crogramdataboincprojectswww.rechenkraft.net/wiki/Correlizer_(beendet) |work=Rechenkraft |language=German |access-date=30 August 2026}}</ref>

== Background: genome organization ==

The central motivation for Correlizer was a long-standing question in biology: how the informational content of a genome is related to the physical shape in which it is stored. In a human cell the genetic information is carried by a diploid set of DNA molecules, the chromosomes. The total sequence is about <math>3 \times 10^{9}</math> [[wikipedia:Base pair|base pair]]s (bp), which corresponds to roughly <math>2.80\ \text{GB}</math> of data. Laid end to end the molecule would be about <math>2\ \text{m}</math> long, yet it is folded into a cell nucleus with a typical diameter of about <math>10\ \mu\text{m}</math> and a volume of roughly <math>500\ \mu\text{m}^{3}</math>.<ref name="background">{{cite web |title=Background: Approaching the three-Dimensional Organization of the Human Genome |url=http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/background.php |work=Biophysical Genomics |publisher=BioQuant Centre, University of Heidelberg |access-date=30 August 2026 |archive-url=https://web.archive.org/web/20130430032449/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/background.php |archive-date=30 April 2013 |url-status=dead}}</ref><ref name="knoch2009">{{cite journal |last1=Knoch |first1=Tobias A. |last2=Göker |first2=Markus |last3=Lohner |first3=Rudolf |last4=Abuseiris |first4=Anis |last5=Grosveld |first5=Frank G. |title=Fine-structured multi-scaling long-range correlations in completely sequenced genomes: features, origin, and classification |journal=European Biophysics Journal |volume=38 |issue=6 |pages=757-779 |year=2009 |doi=10.1007/s00249-009-0489-y |pmc=2701493 |url=https://doi.org/10.1007/s00249-009-0489-y}}</ref>

The sequential organization of a genome, meaning the statistical relations between base pairs that are far apart along the sequence, and the way that sequence relates to the three-dimensional architecture of the chromosomes, remained largely unresolved. Correlizer treated correlation analysis as a kind of "virtual microscope" for this hidden structure. The analysis is based on the concentration profile of single nucleotides along the DNA sequence. If <math>c_{l}</math> is the concentration of a nucleotide in a window of length <math>l</math>, and the concentration in the whole sequence of length <math>L</math> is known, then the concentration-fluctuation function <math>C(l)</math> and the local correlation coefficient <math>\delta(l)</math> can be computed. For a purely random sequence <math>\delta \approx -0.5</math>, whereas values clearly above this threshold indicate positive long-range correlations; a power-law dependence such as <math>C(l) \sim l^{\delta}</math> is the signature of correlations that extend over many length scales.<ref name="knoch2009" />

== What was computed ==

Correlizer distributed this correlation analysis over the volunteer computers of its participants. The application, delivered by the project as "Correlizer Applications" (version 1.09) and an embedded build for ARM/Linux (version 1.10), used the [[wikipedia:BOINC|BOINC]] scheduler to farm out individual analysis jobs.<ref name="apps">{{cite web |title=Applications |url=http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/apps.php |work=Biophysical Genomics |publisher=BioQuant Centre, University of Heidelberg |access-date=30 August 2026 |archive-url=https://web.archive.org/web/20130430032444/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/apps.php |archive-date=30 April 2013 |url-status=dead}}</ref>

[[File:DNA Double Helix by NHGRI.jpg|thumb|right|upright=1.1|alt=A computer rendering of the DNA double helix|The genomic sequence analysed by Correlizer is carried by the [[wikipedia:DNA|DNA]] double helix.]]

The project found long-range power-law correlations on almost the entire observable scale of 132 completely sequenced chromosomes, ranging in length from <math>0.5 \times 10^{6}</math> to <math>3.0 \times 10^{7}</math> bp and spanning organisms as different as [[wikipedia:Archaea|Archaea]], [[wikipedia:Bacteria|Bacteria]], ''[[wikipedia:Arabidopsis thaliana|Arabidopsis thaliana]]'', ''[[wikipedia:Saccharomyces cerevisiae|Saccharomyces cerevisiae]]'', ''[[wikipedia:Schizosaccharomyces pombe|Schizosaccharomyces pombe]]'', ''[[wikipedia:Drosophila melanogaster|Drosophila melanogaster]]'', and ''[[wikipedia:Human|Homo sapiens]]''. The local correlation coefficients displayed a species-specific multiscaling behavior: correlations were close to random on the scale of a few base pairs, rose to a first maximum between <math>40</math> and <math>3{,}400</math> bp (split into two submaxima for ''Arabidopsis thaliana'' and ''Drosophila melanogaster''), and often showed one or more second maxima in the region from <math>10^{5}</math> to <math>3 \times 10^{5}</math> bp.<ref name="knoch2009" /><ref name="home" />

Within this multiscaling a further fine structure was present, attributable to codon usage in every species except the human sequences, where it instead reflected nucleosomal binding. The study also showed that computer-generated random sequences, designed to assume a block organization of genomes with a particular codon usage and nucleosomal binding, reproduced the observed behavior, while random reshuffling of real sequences destroyed the correlations. This suggested that the stability of the correlations is tightly controlled by evolution and closely connected to the spatial organization of the genome, particularly at large scales.<ref name="knoch2009" />

== Project history ==

Correlizer was announced to the BOINC community in August 2011 and hosted at <code>svahesrv2.bioquant.uni-heidelberg.de/correlizer</code>, with the server running on the BioQuant infrastructure at the [[wikipedia:Heidelberg University|University of Heidelberg]].<ref name="rechenkraft" /><ref>{{cite web |title=Correlizer Project (BOINC message boards) |publisher=University of California, Berkeley |url=https://boinc.berkeley.edu/dev/forum_thread.php?id=6806 |access-date=30 August 2026}}</ref> The client application was CPU-based, with builds for [[wikipedia:Microsoft Windows|Windows]], [[wikipedia:Linux|Linux]], [[wikipedia:MacOS|macOS]], and an embedded build for ARM-based Linux systems. The software could operate through a proxy and could be configured to run as a screensaver, but no GPU (CUDA or OpenCL) version was provided.<ref name="rechenkraft" /><ref name="apps" />

[[File:Human karyotype diagram showing autosomes and sex chromosomes - NHGRI.jpg|thumb|right|upright=1.15|alt=A diagram of the human karyotype|A human karyotype. The 23 pairs of chromosomes carry roughly <math>3 \times 10^{9}</math> base pairs of DNA.]]

By late 2014 the project had gone offline while the system and applications were updated, and the project's message boards noted that much of the older account and forum data had been lost. Volunteers reported over the following months that the project was no longer issuing work units, and by mid-2015 the project was widely considered inactive.<ref>{{cite web |title=Welcome back, Correlizer |publisher=University of California, Berkeley |url=https://boinc.berkeley.edu/dev/forum_thread.php?id=9855 |access-date=30 August 2026}}</ref><ref>{{cite web |title=Projects to retire from your site stats that are no longer active |publisher=BOINC Combined Statistics |url=https://boinc.netsoft-online.com/forum/general-discussion/1138/ |access-date=30 August 2026}}</ref> German-language project records list its end date as the point at which it stopped emitting work units because its workload had in the meantime been integrated into [http://boinc.almeregrid.nl/ AlmereGrid], a Dutch volunteer computing project.<ref name="rechenkraft" /> The project is consequently listed among the completed and retired BOINC projects.

=== Statistics at its last active snapshot ===

A server-status snapshot from 27 March 2013 recorded a healthy, running infrastructure. At that point the project reported about 416,000 tasks ready to send, roughly 103,500 tasks in progress, and an average work-unit runtime of about 0.26 hours. The volunteer base was small but steady, and the aggregate processing power reported was about 1,160 [[wikipedia:FLOPS|GFLOPS]], i.e. roughly <math>1.16 \times 10^{12}</math> floating-point operations per second.<ref name="status">{{cite web |title=Project status |url=http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/server_status.php |work=Biophysical Genomics |publisher=BioQuant Centre, University of Heidelberg |access-date=30 August 2026 |archive-url=https://web.archive.org/web/20130327050036/http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/server_status.php |archive-date=27 March 2013 |url-status=dead}}</ref>

== Scientific publications ==

The following publications are credited to the project on the [[wikipedia:BOINC|BOINC]] publications list.<ref name="boincpubs">{{cite web |title=Publications by BOINC Projects |publisher=University of California, Berkeley |url=https://boinc.berkeley.edu/pubs.php |access-date=30 August 2026}}</ref>

* {{cite journal |last1=Knoch |first1=Tobias A. |last2=Göker |first2=Markus |last3=Lohner |first3=Rudolf |last4=Abuseiris |first4=Anis |last5=Grosveld |first5=Frank G. |title=Fine-structured multi-scaling long-range correlations in completely sequenced genomes: features, origin, and classification |journal=European Biophysics Journal |volume=38 |issue=6 |pages=757-779 |year=2009 |doi=10.1007/s00249-009-0489-y |pmc=2701493 |url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701493/}} This is the founding paper and the one the project's own publications page highlighted.<ref name="knoch2009" />
* {{cite book |last1=Knoch |first1=Tobias |last2=Baumgärtner |first2=Volkmar |last3=de Zeeuw |first3=Luc |last4=Grosveld |first4=Frank |last5=Egger |first5=Kurt |title=Large-scale resource sharing at public funded organizations: e-Human "Grid" Ecology |year=2009 |hdl=1765/77698 |url=http://hdl.handle.net/1765/77698}} A systems and grid-architecture paper by the same investigators.
* {{cite journal |last1=Knoch |first1=Tobias A. |title=A Guided Protocol for Array Based T2C: A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture |journal=Current Protocols in Human Genetics |volume=99 |issue=1 |year=2018 |doi=10.1002/cphg.55 |url=https://onlinelibrary.wiley.com/doi/10.1002/cphg.55}}
* {{cite journal |last1=Knoch |first1=Tobias A. |title=Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments: An evaluation and review framework of the 3D genome organization |journal=Seminars in Cell & Developmental Biology |volume=90 |pages=19-42 |year=2019 |doi=10.1016/j.semcdb.2018.07.012 |url=https://linkinghub.elsevier.com/retrieve/pii/S1084952118301058}}

A fifth entry appears under the Correlizer heading on the BOINC list, "ISDEP, a fusion application deployed in the EDGeS project" by Alejandro Rivero and Dario Ferrer (2010). That entry concerns the [https://home.edges-grid.eu/home/ EDGeS@Home] project and appears to be a listing error on the aggregation page rather than a Correlizer result.<ref name="boincpubs" /><ref>{{cite web |last1=Rivero |first1=Alejandro |last2=Ferrer |first2=Dario |title=ISDEP, a fusion application deployed in the EDGeS project |url=https://www.academia.edu/758702/ |year=2010 |access-date=30 August 2026}}</ref>

== Related publications by the project investigators ==

The computational framework used by Correlizer grew out of the same research program, and the project's methods were subsequently extended in further work by its principal investigator and collaborators:

* {{cite journal |last1=Knoch |first1=Tobias A. |last2=Wachsmuth |first2=Malte |last3=Kepper |first3=Nick |last4=Lesnussa |first4=Michael |last5=Abuseiris |first5=Anis |last6=Ali Imam |first6=A. M. |last7=Kolovos |first7=Petros |last8=Zuin |first8=Jessica |last9=Kockx |first9=Christel E. M. |last10=Brouwer |first10=Rutger W. W. |last11=van de Werken |first11=Harmen J. G. |last12=van IJcken |first12=Wilfred F. J. |last13=Wendt |first13=Kerstin S. |last14=Grosveld |first14=Frank G. |title=The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes |journal=Epigenetics & Chromatin |volume=9 |issue=58 |year=2016 |doi=10.1186/s13072-016-0089-x |url=https://archiv.ub.uni-heidelberg.de/volltextserver/22432/}}
* {{cite thesis |last1=Knoch |first1=Tobias A. |title=Approaching the three-dimensional organization of the human genome: structural, scaling and dynamic properties in the simulation of interphase chromosomes and cell nuclei, long-range correlations in complete genomes |type=PhD thesis |publisher=Ruperto-Carola University of Heidelberg |year=2002}} The doctoral work that underpinned the correlation method used by the project.<ref name="knoch2009" />

== See also ==

* [[wikipedia:Berkeley Open Infrastructure for Network Computing|Berkeley Open Infrastructure for Network Computing]] (BOINC)
* [[wikipedia:Volunteer computing|Volunteer computing]]
* [[wikipedia:Genome|Genome]]
* [[wikipedia:Human genome|Human genome]]
* [[wikipedia:Chromosome|Chromosome]]
* [[wikipedia:Chromatin|Chromatin]]
* [[wikipedia:Nucleosome|Nucleosome]]
* [[wikipedia:DNA sequencing|DNA sequencing]]
* [[wikipedia:Distributed computing|Distributed computing]]

== References ==

{{Reflist}}

[[Category:BOINC projects]]
[[Category:Completed BOINC projects]]
[[Category:Volunteer computing projects]]

File:Logo-Correlizer.png

Al Piskun — Sun, 30 Aug 2026 14:00:07 GMT

Al Piskun uploaded File:Logo-Correlizer.png Correlizer logo

New page

== Summary ==
Correlizer logo

Volpex@Home

Al Piskun — Sun, 30 Aug 2026 09:41:49 GMT

add image

← Older revision		Revision as of 09:41, 30 August 2026
Line 62:		Line 62:

	=== VolpexMPI ===		=== VolpexMPI ===
			[[File:Remd.jpg\|alt=inCell@Home is an application of Volpex\|thumb\|445x445px\|inCell@Home is an application of Volpex; this project simulates how proteins behave and make function in a real cell-like environment which can be applied in biological drug design.]]
	'''VolpexMPI''' was a subset implementation of the [[wikipedia:Message_Passing_Interface\|Message Passing Interface]] (MPI) standard tailored to volatile nodes. Ordinary message-passing exchanges were converted into asynchronous Put/Get operations, and process replication provided robustness. The key fault-tolerance technique was fully distributed, sender-based message logging, which let a restarted or replacement replica reconstruct the messages it needed without a central checkpoint server.<ref name="leblanc2009" /> A later, portable variant called VolpexPyMPI was written in [[wikipedia:Python_(programming_language)\|Python]], ran on both Linux and Windows, and accepted user-level MPI programs written in C or [[wikipedia:Fortran\|Fortran]], trading some performance for ease of use and portability across heterogeneous hardware and operating systems.<ref name="leblanc2010ccgrid">{{cite conference \|last1=LeBlanc \|first1=Troy P. \|last2=Subhlok \|first2=Jaspal \|last3=Gabriel \|first3=Edgar \|title=A High-Level Interpreted MPI Library for Parallel Computing in Volunteer Environments \|book-title=2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid) \|date=2010 \|pages=405-414 \|doi=10.1109/CCGRID.2010.85 \|url=https://ieeexplore.ieee.org/document/5493405}}</ref>		'''VolpexMPI''' was a subset implementation of the [[wikipedia:Message_Passing_Interface\|Message Passing Interface]] (MPI) standard tailored to volatile nodes. Ordinary message-passing exchanges were converted into asynchronous Put/Get operations, and process replication provided robustness. The key fault-tolerance technique was fully distributed, sender-based message logging, which let a restarted or replacement replica reconstruct the messages it needed without a central checkpoint server.<ref name="leblanc2009" /> A later, portable variant called VolpexPyMPI was written in [[wikipedia:Python_(programming_language)\|Python]], ran on both Linux and Windows, and accepted user-level MPI programs written in C or [[wikipedia:Fortran\|Fortran]], trading some performance for ease of use and portability across heterogeneous hardware and operating systems.<ref name="leblanc2010ccgrid">{{cite conference \|last1=LeBlanc \|first1=Troy P. \|last2=Subhlok \|first2=Jaspal \|last3=Gabriel \|first3=Edgar \|title=A High-Level Interpreted MPI Library for Parallel Computing in Volunteer Environments \|book-title=2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid) \|date=2010 \|pages=405-414 \|doi=10.1109/CCGRID.2010.85 \|url=https://ieeexplore.ieee.org/document/5493405}}</ref>

Line 68:		Line 68:

	=== Volpex Simulation ===		=== Volpex Simulation ===

	[[File:BOINC project architecture.png\|thumb\|alt=A diagram of the BOINC client-server architecture showing a server feeding work to many volunteer clients over the Internet\|The BOINC client-server architecture that Volpex extended with its Dataspace communication layer.<ref name="rohit2011" />\|360x360px]]

	A third thrust, '''Volpex Simulation''', built a virtual model of a real-world desktop grid, complete with realistic node and network characteristics, to estimate how parallel applications would perform under different network parameters and configurations before deployment.<ref name="about" /> Using a measurement and simulation tool chain on the NAS benchmarks, the researchers found that running on a realistic volunteer campus pool produced slowdowns by factors of roughly <math>2</math> to <math>10</math> compared with a dedicated cluster, depending on the benchmark code.<ref name="nandagudi2012">{{cite conference \|last1=Nandagudi \|first1=Girish \|last2=Subhlok \|first2=Jaspal \|last3=Gabriel \|first3=Edgar \|last4=Gimenez \|first4=Judit \|title=Estimation of MPI Application Performance on Volunteer Environments \|book-title=Euro-Par 2011: Parallel Processing Workshops, Lecture Notes in Computer Science \|volume=7155 \|date=2012 \|pages=511-520 \|publisher=Springer \|doi=10.1007/978-3-642-29737-3_56 \|url=https://link.springer.com/chapter/10.1007/978-3-642-29737-3_56}}</ref>		A third thrust, '''Volpex Simulation''', built a virtual model of a real-world desktop grid, complete with realistic node and network characteristics, to estimate how parallel applications would perform under different network parameters and configurations before deployment.<ref name="about" /> Using a measurement and simulation tool chain on the NAS benchmarks, the researchers found that running on a realistic volunteer campus pool produced slowdowns by factors of roughly <math>2</math> to <math>10</math> compared with a dedicated cluster, depending on the benchmark code.<ref name="nandagudi2012">{{cite conference \|last1=Nandagudi \|first1=Girish \|last2=Subhlok \|first2=Jaspal \|last3=Gabriel \|first3=Edgar \|last4=Gimenez \|first4=Judit \|title=Estimation of MPI Application Performance on Volunteer Environments \|book-title=Euro-Par 2011: Parallel Processing Workshops, Lecture Notes in Computer Science \|volume=7155 \|date=2012 \|pages=511-520 \|publisher=Springer \|doi=10.1007/978-3-642-29737-3_56 \|url=https://link.springer.com/chapter/10.1007/978-3-642-29737-3_56}}</ref>
Line 86:		Line 84:

	== How volunteers participated ==		== How volunteers participated ==

			[[File:BOINC project architecture.png\|thumb\|alt=A diagram of the BOINC client-server architecture showing a server feeding work to many volunteer clients over the Internet\|The BOINC client-server architecture that Volpex extended with its Dataspace communication layer.<ref name="rohit2011" />\|360x360px]]

	Volunteers attached their BOINC client to the project's URL, and the BOINC server recruited hosts for each parallel job. Because a communicating job needs a fixed number of processes running at the same time, the server waited until enough hosts had been recruited and then started them together; recruited hosts that were waiting their turn temporarily idled and released the CPU rather than running the task.<ref name="faq" /> Some hosts were designated as spare nodes that stood by to replace a failed node mid-job.<ref name="faq" />		Volunteers attached their BOINC client to the project's URL, and the BOINC server recruited hosts for each parallel job. Because a communicating job needs a fixed number of processes running at the same time, the server waited until enough hosts had been recruited and then started them together; recruited hosts that were waiting their turn temporarily idled and released the CPU rather than running the task.<ref name="faq" /> Some hosts were designated as spare nodes that stood by to replace a failed node mid-job.<ref name="faq" />

File:Remd.jpg

Al Piskun — Sun, 30 Aug 2026 09:36:48 GMT

Al Piskun uploaded File:Remd.jpg how proteins behave

New page

== Summary ==
how proteins behave

Volpex@Home

Al Piskun — Sun, 30 Aug 2026 09:33:24 GMT

fix links and images

Show changes

Volpex@Home

Al Piskun — Sun, 30 Aug 2026 09:11:22 GMT

Created page with "{{Infobox software | name = Volpex@Home | logo = VolpexLogo.png | logo caption = Volpex@Home logo | screenshot = | caption = | description = Volpex@Home (Volpex@UH) was a completed volunteer computing project at the University of Houston that used BOINC to run communicating parallel programs on ordinary, failure-prone volunteer PCs through process replication and a shared dataspace. | status..."

New page

{{Infobox software
| name = Volpex@Home
| logo = VolpexLogo.png
| logo caption = Volpex@Home logo
| screenshot =
| caption =
| description = Volpex@Home (Volpex@UH) was a completed volunteer computing project at the University of Houston that used BOINC to run communicating parallel programs on ordinary, failure-prone volunteer PCs through process replication and a shared dataspace.
| status = Completed
| category = Computer science
| compute = CPU
| dependencies = [[BOINC]] client 6.12 or later
| developer = [https://en.wikipedia.org/wiki/University_of_Houston University of Houston] Department of Computer Science; Parallel Software Technologies Laboratory (PSTL)
| author = Jaspal Subhlok; Edgar Gabriel
| sponsor = [https://en.wikipedia.org/wiki/National_Science_Foundation National Science Foundation] (awards CNS-0834750 and MCB-0919974)
| maintainer = Volpex team
| released = {{Start date and age|2011|12}}
| completed = 2017
| discontinued =
| repository = {{URL|https://github.com/PSTL-UH/VolpexMPI}}
| programming language = C, [https://en.wikipedia.org/wiki/Python_(programming_language) Python], C++
| operating system = Windows, Linux
| size =
| stats as of = {{Start date and age|2012|01|05}}
| average performance = 17.2 GFLOPS
| active users = 135
| total users = 292
| active hosts = 404
| total hosts = 824
| rac = 3,449
| credit per day =
| gpu performance = None (CPU-only)
| cpu performance =
| website = {{URL|http://volpexathome.cs.uh.edu/VolPEx/}}
| license = Source-available (source code available on request)
}}

'''Volpex@Home''' (originally '''Volpex@UH''') was a [https://en.wikipedia.org/wiki/Volunteer_computing volunteer computing] project run by the Department of Computer Science at the [https://en.wikipedia.org/wiki/University_of_Houston University of Houston] that used the [[BOINC]] middleware to execute communicating [https://en.wikipedia.org/wiki/Parallel_computing parallel] programs on ordinary, Internet-connected personal computers. The name Volpex stands for '''Parallel Execution on Volatile Nodes''', and the project's central goal was to make the idle time of everyday "volatile" desktop machines usable as a virtual [https://en.wikipedia.org/wiki/Computer_cluster cluster] for [https://en.wikipedia.org/wiki/Message_passing message passing] parallel applications that the standard BOINC model could not run.<ref name="nsf-volpex">{{cite web |title=Award Abstract #0834750: CSR-PSCE, SM: Collaborative Research: VOLPEX: A Framework for Parallel Execution on Volatile Nodes |publisher=National Science Foundation |url=https://www.nsf.gov/awardsearch/showAward?AWD_ID=0834750 |access-date=2026-08-30}}</ref><ref name="homepage">{{cite web |title=Volpex@Home (archived project homepage) |publisher=University of Houston |url=https://web.archive.org/web/20160120043345/http://volpexathome.cs.uh.edu/VolPEx/ |access-date=2026-08-30}}</ref>

The project also hosted a biological application called '''inCell@Home''', which ran [https://en.wikipedia.org/wiki/Parallel_tempering replica-exchange] [https://en.wikipedia.org/wiki/Molecular_dynamics molecular dynamics] simulations of protein behavior inside a crowded, cell-like environment in support of drug-design research.<ref name="homepage" /> The framework research was funded by two [https://en.wikipedia.org/wiki/National_Science_Foundation National Science Foundation] grants, and the project reached about 1,700 volunteers before it was completed and retired in 2017.<ref name="nsf-volpex" /><ref name="nsf-cheung">{{cite web |title=Award Abstract #0919974: Effects of macromolecular crowding on protein structure, folding, and interactions |publisher=National Science Foundation |url=https://www.nsf.gov/awardsearch/showAward?AWD_ID=0919974 |access-date=2026-08-30}}</ref><ref name="frwiki">{{cite web |title=Liste des projets BOINC (Volpex@UH statistics) |publisher=French Wikipedia |url=https://fr.wikipedia.org/wiki/Liste_des_projets_BOINC |access-date=2026-08-30}}</ref>

[[File:Volpex concept diagram.jpg|thumb|alt=A diagram captioned VOLPEX showing a scientific application in the center linked by arrows to a volunteer environment, parallel execution, and heterogeneous devices|The Volpex concept: a scientific application runs on a heterogeneous, volunteer, parallel computing environment.<ref name="homepage" />]]

== Overview ==

Most desktop computers sit idle for much of the day, representing a large pool of unused processing, storage, and communication capacity that grows with the spread of [https://en.wikipedia.org/wiki/Multi-core_processor multi-core] machines. The difficulty is that these machines are ''volatile'': their owners can switch them off, disconnect them, or reclaim them at any time and without warning.<ref name="about">{{cite web |title=About VOLPEX |publisher=University of Houston (archived) |url=https://web.archive.org/web/20150524061949/http://volpexathome.cs.uh.edu/VolPEx/volpexinfo.php |access-date=2026-08-30}}</ref> Platforms such as BOINC and [https://en.wikipedia.org/wiki/HTCondor Condor] handle this volatility well for independent, non-communicating tasks (the so-called [https://en.wikipedia.org/wiki/Embarrassingly_parallel "bag-of-tasks" or master-slave] model), but they do not natively support tightly coupled, message-passing parallel programs in which tasks must exchange data as they run.<ref name="nsf-volpex" /><ref name="faq">{{cite web |title=Volpex@Home Frequently Asked Questions |publisher=University of Houston (archived) |url=https://web.archive.org/web/20150524023014/http://volpexathome.cs.uh.edu/VolPEx/faq.php |access-date=2026-08-30}}</ref>

Volpex was designed to remove exactly that limitation, so that a broader class of scientific applications could run on volunteer hardware and many more research projects could benefit from free, donated compute time.<ref name="faq" /> Rather than relying only on [https://en.wikipedia.org/wiki/Application_checkpointing checkpointing], which the researchers argued is inadequate in environments with very high failure rates, Volpex used managed redundancy: it ran two or more replicas of every parallel process and regenerated failed replicas on demand from healthy ones, so that the application progressed at the rate of the fastest surviving replicas and continued seamlessly as long as at least one replica of each process remained alive.<ref name="nsf-volpex" /><ref name="about" />

== History ==

The Volpex framework began as academic computer-science research. A collaborative [https://en.wikipedia.org/wiki/National_Science_Foundation National Science Foundation] grant, "VOLPEX: A Framework for Parallel Execution on Volatile Nodes" (award CNS-0834750), started on 1 September 2008 with Jaspal Subhlok as principal investigator and Rong Zheng and Edgar Gabriel as co-principal investigators at the University of Houston.<ref name="nsf-volpex" /> The associated MPI library, VolpexMPI, was first described in a 2009 paper by Troy LeBlanc, Rakhi Anand, Edgar Gabriel, and Jaspal Subhlok.<ref name="leblanc2009">{{cite journal |last1=LeBlanc |first1=Troy |last2=Anand |first2=Rakhi |last3=Gabriel |first3=Edgar |last4=Subhlok |first4=Jaspal |title=VolpexMPI: An MPI Library for Execution of Parallel Applications on Volatile Nodes |journal=Recent Advances in Parallel Virtual Machine and Message Passing Interface (EuroPVM/MPI 2009), Lecture Notes in Computer Science |volume=5759 |pages=124-133 |date=2009 |publisher=Springer |doi=10.1007/978-3-642-03770-2_19 |url=https://link.springer.com/chapter/10.1007/978-3-642-03770-2_19}}</ref>

The public BOINC project, initially named Volpex@UH, was online by late 2011, when volunteer teams began joining, and it was announced on the official BOINC news page on 22 December 2012 as a University of Houston project seeking alpha testers for parallel computing across multiple hosts.<ref name="boinc-news">{{cite web |title=BOINC News archive: New project seeks testers (Volpex@UH) |publisher=BOINC, UC Berkeley |date=2012-12-22 |url=https://boinc.berkeley.edu/old_news.php |access-date=2026-08-30}}</ref><ref name="boincstats-early">{{cite web |title=BOINCstats project statistics for Volpex (archived, 5 January 2012) |url=https://web.archive.org/web/20120105232519/http://boincstats.com/stats/project_graph.php?pr=volpex |access-date=2026-08-30}}</ref> The project later moved to the address volpexathome.cs.uh.edu and became known as Volpex@Home.<ref name="homepage" />

The team upgraded their BOINC server to a newer release in March 2013 and recovered from a full server disk in April 2015; new work jobs were still being posted as late as June 2015.<ref name="homepage" /> The biological side of the work was supported by a second NSF award to Margaret S. Cheung (MCB-0919974, "Effects of macromolecular crowding on protein structure, folding, and interactions"), which began 1 July 2009 and used the distributed simulations to study proteins in cell-like conditions.<ref name="nsf-cheung" /> The project was completed and retired around 2017, and it is listed among finished BOINC projects.<ref name="frwiki" /><ref name="bcwiki">{{cite web |title=BOINC-Projekte/en, Finished projects: Volpex@UH |publisher=BC-Wiki |url=https://wiki.bc-team.org/index.php?title=BOINC-Projekte/en |access-date=2026-08-30}}</ref>

== Technical design ==

Volpex provided two complementary programming interfaces for application developers, plus a simulation effort to predict performance.<ref name="about" />

[[File:Volpex testbeds.jpg|thumb|alt=A network diagram titled Volpex Testbeds showing the Volpex server connected through the UH network and Internet to a Shark cluster, Condor clusters, a NASA virtualized cluster, corporate networks, and home PCs|The Volpex testbeds: campus clusters, a NASA virtualized cluster, and home PCs linked through the University of Houston network and the public Internet.<ref name="about" />]]

=== Volpex Dataspace ===

The central component was the '''Volpex Dataspace''', an abstract global data layer that let tasks exchange data objects asynchronously through anonymous ''Put/Get'' operations. Instead of volunteer machines contacting one another directly, tasks read and wrote data objects through the project's central server, which acted as an intermediary; the project noted that this design meant there was no direct peer-to-peer security exposure for volunteers.<ref name="rohit2011">{{cite conference |last1=Rohit |first1=Eshwar |last2=Nguyen |first2=Hien |last3=Kanna |first3=Nagarajan |last4=Subhlok |first4=Jaspal |last5=Gabriel |first5=Edgar |last6=Wang |first6=Qian |last7=Cheung |first7=Margaret S. |last8=Anderson |first8=David |title=A Robust Communication Framework for Parallel Execution on Volunteer PC Grids |book-title=2011 11th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) |date=2011 |pages=443-453 |doi=10.1109/CCGrid.2011.72 |url=https://ieeexplore.ieee.org/document/5948604}}</ref><ref name="faq" /> The Dataspace extended BOINC's independent-task model to allow inter-task communication while preserving consistent results even when redundancy or checkpointing caused a single operation to be invoked several times.<ref name="rohit2011" /> The team described this, integrated with BOINC, as the first comprehensive solution for reliably running communicating parallel codes on volunteer nodes.<ref name="ccgrid2011pdf">{{cite web |title=A Robust Communication Framework for Parallel Execution on Volunteer PC Grids (preprint PDF) |publisher=University of Houston |url=https://www2.cs.uh.edu/~jaspal/papers/11ccgrid.pdf |access-date=2026-08-30}}</ref>

=== VolpexMPI ===

'''VolpexMPI''' was a subset implementation of the [https://en.wikipedia.org/wiki/Message_Passing_Interface Message Passing Interface] (MPI) standard tailored to volatile nodes. Ordinary message-passing exchanges were converted into asynchronous Put/Get operations, and process replication provided robustness. The key fault-tolerance technique was fully distributed, sender-based message logging, which let a restarted or replacement replica reconstruct the messages it needed without a central checkpoint server.<ref name="leblanc2009" /> A later, portable variant called VolpexPyMPI was written in [https://en.wikipedia.org/wiki/Python_(programming_language) Python], ran on both Linux and Windows, and accepted user-level MPI programs written in C or [https://en.wikipedia.org/wiki/Fortran Fortran], trading some performance for ease of use and portability across heterogeneous hardware and operating systems.<ref name="leblanc2010ccgrid">{{cite conference |last1=LeBlanc |first1=Troy P. |last2=Subhlok |first2=Jaspal |last3=Gabriel |first3=Edgar |title=A High-Level Interpreted MPI Library for Parallel Computing in Volunteer Environments |book-title=2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid) |date=2010 |pages=405-414 |doi=10.1109/CCGRID.2010.85 |url=https://ieeexplore.ieee.org/document/5493405}}</ref>

Because each process had several replicas, a receiving process had to decide which sender replica to contact first. The group developed communication target-selection algorithms for this; a hybrid strategy gave performance close to that of an all-fast-machine configuration, and evaluations used the [https://en.wikipedia.org/wiki/NAS_Parallel_Benchmarks NAS Parallel Benchmarks] across heterogeneous network and processor configurations.<ref name="anand2010">{{cite conference |last1=Anand |first1=Rakhi |last2=Gabriel |first2=Edgar |last3=Subhlok |first3=Jaspal |title=Communication Target Selection for Replicated MPI Processes |book-title=Recent Advances in the Message Passing Interface (EuroMPI 2010), Lecture Notes in Computer Science |volume=6305 |date=2010 |pages=181-190 |publisher=Springer |doi=10.1007/978-3-642-15646-5_21 |url=https://link.springer.com/chapter/10.1007/978-3-642-15646-5_21}}</ref>

=== Volpex Simulation ===

A third thrust, '''Volpex Simulation''', built a virtual model of a real-world desktop grid, complete with realistic node and network characteristics, to estimate how parallel applications would perform under different network parameters and configurations before deployment.<ref name="about" /> Using a measurement and simulation tool chain on the NAS benchmarks, the researchers found that running on a realistic volunteer campus pool produced slowdowns by factors of roughly <math>2</math> to <math>10</math> compared with a dedicated cluster, depending on the benchmark code.<ref name="nandagudi2012">{{cite conference |last1=Nandagudi |first1=Girish |last2=Subhlok |first2=Jaspal |last3=Gabriel |first3=Edgar |last4=Gimenez |first4=Judit |title=Estimation of MPI Application Performance on Volunteer Environments |book-title=Euro-Par 2011: Parallel Processing Workshops, Lecture Notes in Computer Science |volume=7155 |date=2012 |pages=511-520 |publisher=Springer |doi=10.1007/978-3-642-29737-3_56 |url=https://link.springer.com/chapter/10.1007/978-3-642-29737-3_56}}</ref>

=== Reliability model ===

The central trade-off in the Volpex design is between the cost of redundancy and the probability that a parallel job survives. If each process is replicated <math>r</math> times and an individual volunteer node remains available for the duration of a job with probability <math>p</math>, then a given process group survives only as long as at least one of its replicas is alive. With independent failures, the probability that a job requiring <math>n</math> distinct processes completes is

:<math>P_{\text{job}} = \big(1 - (1-p)^{r}\big)^{n}.</math>

Increasing the replica count <math>r</math> sharply raises survival probability, but it also inflates the total compute demand: the aggregate redundant work relative to a single execution scales approximately as

:<math>W_{\text{total}} \approx r \cdot n \cdot W_{\text{process}}.</math>

Much of the project's research concerned managing this tension efficiently, for example through on-demand regeneration of lost replicas, sender-based message logging, and optimized checkpointing intervals for inter-dependent replicated processes.<ref name="nsf-volpex" /><ref name="leblanc2009" /><ref name="rahman2016">{{cite conference |last1=Rahman |first1=Mohammad Tanvir |last2=Nguyen |first2=Hien |last3=Subhlok |first3=Jaspal |last4=Pandurangan |first4=Gopal |title=Checkpointing to Minimize Completion Time for Inter-Dependent Parallel Processes on Volunteer Grids |book-title=2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) |date=2016 |pages=510-519 |doi=10.1109/CCGrid.2016.78 |url=https://ieeexplore.ieee.org/document/7515706}}</ref>

== How volunteers participated ==

Volunteers attached their BOINC client to the project's URL, and the BOINC server recruited hosts for each parallel job. Because a communicating job needs a fixed number of processes running at the same time, the server waited until enough hosts had been recruited and then started them together; recruited hosts that were waiting their turn temporarily idled and released the CPU rather than running the task.<ref name="faq" /> Some hosts were designated as spare nodes that stood by to replace a failed node mid-job.<ref name="faq" />

This model produced a few unusual behaviors that the project documented for volunteers: tasks could appear as "Waiting to run (Scheduler wait)" during recruitment, a task could be terminated deliberately once the overall job had finished, and the CPU could sit idle while a process waited for data from another process. Tasks were also given short deadlines and run at high BOINC priority so that all processes of a coordinated job stayed reachable, since one unavailable process could stall a computation involving hundreds of processes.<ref name="faq" /><ref name="rechenkraft">{{cite web |title=Volpex@UH (beendet) |publisher=Rechenkraft.net wiki |url=https://www.rechenkraft.net/wiki/Volpex@UH |access-date=2026-08-30}}</ref> Uniquely for a BOINC project, credit was granted periodically in proportion to the time a host spent on a task, rather than only when a task completed successfully.<ref name="faq" />

Work was available for Windows and Linux machines on x86 and x86-64 CPUs; there was no GPU application, and clients older than BOINC 6.12 were not supported because the project relied on the client reporting its task name for identification.<ref name="apps">{{cite web |title=Volpex@Home Applications (archived) |publisher=University of Houston |url=https://web.archive.org/web/20141008180240/http://volpexathome.cs.uh.edu/VolPEx/apps.php |access-date=2026-08-30}}</ref><ref name="faq" />

[[File:BOINC project architecture.png|thumb|alt=A diagram of the BOINC client-server architecture showing a server feeding work to many volunteer clients over the Internet|The BOINC client-server architecture that Volpex extended with its Dataspace communication layer.<ref name="rohit2011" />]]

== Applications ==

By 2014 the project served two CPU applications, each available for Windows and Linux on Intel x86 (and Linux on x86-64):<ref name="apps" />

* '''REMD Protein Folding''' (version 1.35), the inCell@Home replica-exchange molecular dynamics application; and
* '''Sieve''' (version 1.08), a lightweight test and benchmarking application used to exercise and validate the Volpex framework.

=== inCell@Home ===

[[File:inCell REMD crowded environment.jpg|thumb|alt=Molecular visualization of several protein replicas (red, white, and blue structures) surrounded by a dense field of grey spheres representing crowding macromolecules|Replica-exchange molecular dynamics of proteins (colored structures) inside a densely crowded, cell-like environment of macromolecules (grey spheres), as simulated by inCell@Home.<ref name="homepage" />]]

'''inCell@Home''' was the flagship scientific application of Volpex and a collaboration with the research group of Margaret S. Cheung at the University of Houston. It simulated how proteins behave and function inside a realistic, crowded cell-like environment rather than in dilute solution, with the results intended to inform biological drug design.<ref name="homepage" /><ref name="nsf-cheung" /> The application ran replica-exchange molecular dynamics (REMD), a method in which many copies (replicas) of a system are simulated at different temperatures and periodically exchange configurations to overcome the kinetic trapping that makes protein folding hard to sample; the loosely coupled, communication-light nature of REMD made it well suited to a replicated, volatile environment and to the Volpex Dataspace.<ref name="ccgrid2011pdf" /><ref name="rohit2011" />

This tied the computer-science framework directly to a biophysics question: experimental and computational work by the Cheung group showed that [https://en.wikipedia.org/wiki/Macromolecular_crowding macromolecular crowding] dramatically affects protein structure, folding, and activity, for example compacting the enzyme phosphoglycerate kinase and increasing its activity under crowded conditions that mimic the inside of a cell.<ref name="cheung-research">{{cite web |title=Cheung Group Research: Protein structure, function, and dynamics under cell-like conditions (archived) |publisher=University of Houston |url=https://web.archive.org/web/20120303170028/http://mynsm.uh.edu/groups/cheunggroup/wiki/f569a/Research.html |access-date=2026-08-30}}</ref> The crowding research combined coarse-grained and atomistic molecular simulation in a multi-scale approach and was supported by NSF award MCB-0919974.<ref name="nsf-cheung" />

[[File:Crowded cytosol.png|thumb|alt=Illustration of a densely packed cell cytosol full of proteins and other macromolecules|The crowded cytosol of a cell: macromolecular crowding alters protein folding and behavior, the phenomenon studied by inCell@Home.<ref name="nsf-cheung" />]]

== Funding and statistics ==

The framework research was supported by the National Science Foundation's Computer Systems Research program under award CNS-0834750 (approximately $296,000 awarded to the University of Houston), and the biological crowding research by award MCB-0919974 (approximately $232,000 awarded).<ref name="nsf-volpex" /><ref name="nsf-cheung" />

Volpex remained a small research project throughout its life. In early January 2012 it counted 292 registered users (135 active), 824 hosts (404 active), and 64 teams across 36 countries, with about 1.1 million total credits, a recent average credit of roughly 3,449, and an average throughput of about 17.2 [https://en.wikipedia.org/wiki/FLOPS GFLOPS].<ref name="boincstats-early" /> By the time the project was retired, the French Wikipedia's BOINC project table recorded 1,746 users, 6,688 hosts, 252 teams, and 65,282,403 total credits as of 15 October 2017.<ref name="frwiki" />

== Scientific publications ==

The University of California, Berkeley list of publications arising from BOINC projects catalogs nine Volpex@Home papers, spanning the framework, its MPI and Dataspace components, message logging, performance estimation, checkpointing, and a summary journal article.<ref name="boinc-pubs">{{cite web |title=Publications by BOINC Projects: Volpex@Home |publisher=BOINC, UC Berkeley |url=https://boinc.berkeley.edu/pubs.php#Volpex@Home |access-date=2026-08-30}}</ref>

# Subhlok, Jaspal; Hien Nguyen; Edgar Gabriel; Mohammad Tanvir Rahman (2018). [https://onlinelibrary.wiley.com/doi/10.1002/cpe.4478 "Resilient parallel computing on volunteer PC grids"]. ''Concurrency and Computation: Practice and Experience''. DOI: 10.1002/cpe.4478.
# Rahman, Mohammad Tanvir; Hien Nguyen; Jaspal Subhlok; Gopal Pandurangan (2016). [https://ieeexplore.ieee.org/document/7515706 "Checkpointing to Minimize Completion Time for Inter-Dependent Parallel Processes on Volunteer Grids"]. ''2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)''. DOI: 10.1109/CCGrid.2016.78.
# Islam, Md Tarikul; Hien Nguyen; Jaspal Subhlok; Edgar Gabriel (2015). [https://ieeexplore.ieee.org/document/7284289 "Efficient Message Logging to Support Process Replicas in a Volunteer Computing Environment"]. ''2015 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW)''. DOI: 10.1109/IPDPSW.2015.91.
# Nguyen, Hien; Eshwar Pedamallu; Jaspal Subhlok; Edgar Gabriel; Qian Wang; Margaret S. Cheung; David Anderson (2012). [http://ieeexplore.ieee.org/document/6337577/ "An Execution Environment for Robust Parallel Computing on Volunteer PC Grids"]. ''2012 41st International Conference on Parallel Processing (ICPP)''. DOI: 10.1109/ICPP.2012.18.
# Rohit, Eshwar; Hien Nguyen; Nagarajan Kanna; Jaspal Subhlok; Edgar Gabriel; Qian Wang; Margaret S. Cheung; David Anderson (2011). [https://ieeexplore.ieee.org/document/5948604 "A Robust Communication Framework for Parallel Execution on Volunteer PC Grids"]. ''2011 11th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)''. DOI: 10.1109/CCGrid.2011.72.
# Anand, Rakhi; Edgar Gabriel; Jaspal Subhlok (2010). [https://link.springer.com/chapter/10.1007/978-3-642-15646-5_21 "Communication Target Selection for Replicated MPI Processes"]. ''Recent Advances in the Message Passing Interface (EuroMPI 2010), Lecture Notes in Computer Science'', vol. 6305, pp. 181-190. Springer. DOI: 10.1007/978-3-642-15646-5_21.
# LeBlanc, Troy P.; Jaspal Subhlok; Edgar Gabriel (2010). [https://ieeexplore.ieee.org/document/5493405/ "A High-Level Interpreted MPI Library for Parallel Computing in Volunteer Environments"]. ''2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid)'', pp. 405-414. DOI: 10.1109/CCGRID.2010.85.
# Kanna, Nagarajan; Jaspal Subhlok; Edgar Gabriel; Eshwar Rohit; David Anderson (2010). [https://link.springer.com/chapter/10.1007/978-3-642-13374-9_1 "A Communication Framework for Fault-Tolerant Parallel Execution"]. ''Languages and Compilers for Parallel Computing (LCPC), Lecture Notes in Computer Science''. Springer. DOI: 10.1007/978-3-642-13374-9_1.
# LeBlanc, Troy; Rakhi Anand; Edgar Gabriel; Jaspal Subhlok (2009). [https://link.springer.com/chapter/10.1007/978-3-642-03770-2_19 "VolpexMPI: An MPI Library for Execution of Parallel Applications on Volatile Nodes"]. ''Recent Advances in Parallel Virtual Machine and Message Passing Interface (EuroPVM/MPI 2009), Lecture Notes in Computer Science'', vol. 5759, pp. 124-133. Springer. DOI: 10.1007/978-3-642-03770-2_19.

== Related publications ==

Additional Volpex-related papers not listed in the BOINC publications index include a performance-estimation study and the journal version of the VolpexMPI work reported on the project's NSF award page:<ref name="nsf-volpex" /><ref name="nandagudi2012" />

* Nandagudi, Girish; Jaspal Subhlok; Edgar Gabriel; Judit Gimenez (2012). [https://link.springer.com/chapter/10.1007/978-3-642-29737-3_56 "Estimation of MPI Application Performance on Volunteer Environments"]. ''Euro-Par 2011: Parallel Processing Workshops, Lecture Notes in Computer Science'', vol. 7155, pp. 511-520. Springer. DOI: 10.1007/978-3-642-29737-3_56.
* Anand, Rakhi; Troy LeBlanc; Edgar Gabriel; Jaspal Subhlok (2011). [https://doi.org/10.1007/s10723-010-9172-x "A Robust and Efficient Message Passing Library for Volunteer Computing Environments"]. ''Journal of Grid Computing'', vol. 9, no. 3, p. 325. DOI: 10.1007/s10723-010-9172-x.

== See also ==

* [[BOINC]] (Berkeley Open Infrastructure for Network Computing)
* [https://en.wikipedia.org/wiki/Volunteer_computing Volunteer computing]
* [https://en.wikipedia.org/wiki/Distributed_computing Distributed computing]
* [https://en.wikipedia.org/wiki/Grid_computing Grid computing]
* [https://en.wikipedia.org/wiki/Desktop_grid Desktop grid]
* [https://en.wikipedia.org/wiki/Message_Passing_Interface Message Passing Interface]
* [[Rosetta@home]]

== References ==

{{Reflist}}

[[Category:Volunteer computing projects]]
[[Category:BOINC projects]]
[[Category:University of Houston]]
[[Category:Computer science projects]]
[[Category:Molecular dynamics software]]

File:VolpexLogo.png

Al Piskun — Sun, 30 Aug 2026 09:07:18 GMT

Al Piskun uploaded File:VolpexLogo.png Volpex Logo

New page

== Summary ==
Volpex Logo