[Swift-commit] r3922 - text/parco10submission

[noreply at svn.ci.uchicago.edu]

Author: wilde
Date: 2011-01-09 15:10:57 -0600 (Sun, 09 Jan 2011)
New Revision: 3922

Modified:
   text/parco10submission/paper.bib
   text/parco10submission/paper.tex
Log:
Revised glass science text with revised text from Glen. Added one ref on the glass app.

Modified: text/parco10submission/paper.bib
===================================================================
--- text/parco10submission/paper.bib	2011-01-09 01:38:14 UTC (rev 3921)
+++ text/parco10submission/paper.bib	2011-01-09 21:10:57 UTC (rev 3922)
@@ -26,6 +26,15 @@
   url = {http://people.cs.uchicago.edu/~iraicu/publications/2008_NOVA08_book-chapter_Swift.pdf},
 }
 
+ at article{GlassMethods_2008,
+ title = {{Thermodynamic signature of growing amorphous order in glass-forming liquids}},
+ author = {G Biroli and J P Bouchaud and A Cavagna and  T S Grigera and P Verrocchio},
+ journal = {{Nature Physics}},
+ volume = {4},
+ year = 2008,
+ pages = {771-775}
+}
+
 @article{PTMap_2010,
  title = {{The first global screening of protein substrates bearing protein-bound 3,4-Dihydroxyphenylalanine in Escherichia coli and human mitochondria.}},
  author = {S Lee and Y Chen and H Luo and A A Wu and M Wilde and P T Schumacker and Y Zhao},

Modified: text/parco10submission/paper.tex
===================================================================
--- text/parco10submission/paper.tex	2011-01-09 01:38:14 UTC (rev 3921)
+++ text/parco10submission/paper.tex	2011-01-09 21:10:57 UTC (rev 3922)
@@ -1277,20 +1277,36 @@
 
 \subsection{Simulation of glass cavity dynamics and thermodynamics.}
 
-A recent study of the glass transition in model systems has focused on calculating from theory or simulation what is known as the ``Mosaic length''.
+Many recent studies of the glass transition in model systems have focused
+on calculating from theory or simulation what is known as the ÓMosaic
+lengthÓ. Glen Hocky of the Reichman Group at Columbia is evaluating a new
+cavity method \cite{GlassMethods_2008} for measuring this length scale, where particles are
+simulated by molecular dynamics or Monte Carlo methods within cavities
+having amorphous boundary conditions.
 
-Glen Hocky of the Reichman Group at Columbia applied a new cavity method for measuring this length scale, where particles are simulated by molecular dynamics or Monte Carlo methods within cavities having amorphous boundary conditions. Various correlation functions are calculated at the interior of cavities of varying sizes and averaged over many independent simulations to determine a thermodynamic length. Hocky is using simulations of this method to investigate the differences between three different glass systems which all have the same structure but which differ in other subtle ways to determine if this thermodynamic length causes the variations between the three systems.
+In this method, various correlation functions are
+calculated at the interior of cavities of varying sizes and averaged over
+many independent simulations to determine a thermodynamic length. Hocky is
+using simulations of this method to investigate the differences between
+three different glass systems which all have the same structure but which
+differ in other subtle ways to determine if this thermodynamic length causes
+the variations between the three systems.
 
-Hocky's application code performs 100,000 Monte-Carlo steps in about 1-2 hours. Ten jobs are used to generate the 1M simulation steps needed for each configuration. The input data to each simulation is a file of about 150KB representing initial glass structures. Each simulation returns three new structures of 150KB each, a 50 KB log file, and a 4K file describing which particles are in the cavity.
+The glass cavity simulation code performs
+100,000 Monte-Carlo steps in 1-2 hours. Jobs of this length are run in
+succession and strung together to make longer simulations tractable across a
+variety of systems. The input data to each simulation is a file of
+about 150KB representing initial glass structures and a 4K file describing
+which particles are in the cavity. Each simulation returns three new
+structures of 150KB each, a 50 KB log file, and the same 4K file
+describing which particles are in the cavity.
 
-Each script run covers a simulation space of 7 radii by 27 centers by 10 models, requiring 1690 jobs per run. Three methods are simulated (``kalj'', ``kawka'', and  ``pedersenipl'') for total of 90 runs. Swift mappers enable metadata describing these aspects to be encoded in the data files of the campaigns to assist in managing the large volume of file data.
+Each script run covers a simulation space of 7 radii by 27 centers by
+10 models, requiring 1690 jobs per run. Three different model systems are
+investigated for total of 90 runs. Swift mappers enable metadata describing
+these aspects to be encoded in the data files of the campaigns to assist in
+managing the large volume of file data.
 
-As the simulation campaigns are quite lengthy (the first ran from October through December 2010) Hocky chose to leverage Swift ``external'' mappers to determine what simulations need to be performed at any point in the campaign. His input mappers assume an application run was complete if all the returned ``\verb|.final|'' files exist.  In the case of script restarts, results that already existed were not (re)computed.
-
-Roughly 152,000 jobs are executed in a simulation campaign, defined by a set of parameter files defining molecular radii and centroids, and set set of ``run'' scripts that perform the execution of the {\tt swift} command with appropriately varying science parameters. Most runs were performed using the "User Engagement" virtual organization (VO) of the Open Science Grid (OSG) \cite{OSG, OSGEngage}. Some runs were done on other resources including University of Chicago ``PADS'' cluster and TeraGrid resources. The only change necessary to run on OSG was configuring the OSG sites to run the science application.
-
-The approximate OSG usage was over 100,000 cpus hours with about 100,000 tasks of 1-2 hours completed. The simulation campaign has been successfully run on about 18 OSG sites, with the majority of runs have been completed on about 6 primary  sites that tend to provide the most compute-hour opportunities for members of the Engagement VO.
-
 Example 2 shows a slightly reformatted version of the glass simulation script that was in use in Dec. 2010. Its key aspects are as follows.
 Lines 1-3 define the mapped file types; these files are used to compose input and output structures at lines 5-15. (At the moment, the input structure is a degenerate single-file structure, but Hocky has experimented with various multi-file input structures in prior versions of this script). The output structure reflects the fact that the simulation is restartable in 1-2 hour increments, and works together with the Swift script to create a simple but powerful mechanism for managing checkpoint/restart across a long-running large-scale simulation campaign.
 
@@ -1650,7 +1666,7 @@
 Leadership Computing Facility, TeraGrid, the Open Science Grid, the UChicago / Argonne Computation Institute
 Petascale Active Data Store, and the Amazon Web Services Education allocation program.
 
-The quantum glass example in the article is the work of Glen Hocky of the Reichman Lab of the Columbia University Department of Chemistry. We thank Glen for many contributions and extremely valuable feedback to the Swift project. We gratefully acknowledge the contributions of current and former Swift team members and collaborators Sarah Kenny, Allan Espinosa, Zhao Zhang, David Kelly, Milena Nokolic, Jon Monette, Aashish Adhikari, Marc Parisien, Michael Andric, Steven Small, John Dennis, Mats Rynge,  Michael Kubal, Tibi Stef-Praun, Xu Du, Zhengxiong Hou, and Xi Li. The initial implementation of Swift was the work of Yong Zhao and Mihael Hategan.
+The quantum glass example in the article is the work of Glen Hocky of the Reichman Lab of the Columbia University Department of Chemistry. We thank Glen for many contributions to the text and code of Sec. 4 and valuable feedback to the Swift project. We gratefully acknowledge the contributions of current and former Swift team members and collaborators Sarah Kenny, Allan Espinosa, Zhao Zhang, David Kelly, Milena Nokolic, Jon Monette, Aashish Adhikari, Marc Parisien, Michael Andric, Steven Small, John Dennis, Mats Rynge,  Michael Kubal, Tibi Stef-Praun, Xu Du, Zhengxiong Hou, and Xi Li. The initial implementation of Swift was the work of Yong Zhao and Mihael Hategan; Karajan was designed and implemented by Hategan. Tim Armstrong provided helpful comments on the text.
 
 %% \section{TODO}