Re: [Apbs-users] Submitting async parallel jobs
Biomolecular electrostatics software
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From: Nathan B. <ba...@bi...> - 2005-10-25 16:35:39
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Hi Ryogo -- You are correct, we make the assumption that values in the overlap region are sufficient to provide accurate boundary conditions. This is the same principle as mg-para and is discussed in more detail in: Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers . IBM Journal of Research and Development 45,=20 427-438, 2001. (http://www.research.ibm.com/journal/rd/453/baker.pdf) and Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041, 2001. (http://dx.doi.org/10.1073/pnas.181342398) The concept is the same as the traditional focusing method: Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature. 330 (6143), 84-6, 1987.=20 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3DPubMed&li= st_uids=3D3313058&dopt=3DAbstract but the notion of extending this to parallel calculations (and the resulting asynchronous generalization) is based on work by Mike Holst and Randy Bank: Bank RE, Holst M. A new paradigm for parallel adaptive meshing algorithms. SIAM Review. 45 (2), 291-323, 2003.=20 http://dx.doi.org/10.1137/S003614450342061 In short, the asynchronous mode does the same operations as mg-para but leaves out the final step of reassembling to the user. Hope this helps, Nathan On 10/25/05, Ryogo Sugitani <rsu...@gm...> wrote: > Hi Todd, > > Thanks for your reply. > But the main question still remains. > How is async parallel calculatiion different from running > separate serial calculations on sub-divided region and merge them > together afterwards? > In other words, how does the values on the border of one region is > transmitted to > the other regions without any integration master process? > (I assume mergedx is just really merging dx files and don't do much > equilibration calculcation or anything.) > Do you assume the values in overlap region would give a reasonable estima= tes > of adjacent regions so that series of async parallel calculation is equiv= alent > with running a big single PB calculation? > is that the same principle used in mg-para option, too? > > If my questions is still unclear, please let me know. > > Thank you, > > Ryogo > > 2005/10/25, Todd Dolinsky <to...@cc...>: > > Hi Ryogo - > > > > The asynchronous use of APBS does just that - allows users to break up = a > > parallel calculation one processor at a time, and then asynchronously > > (one after another) run APBS. > > > > So if you have a large PQR file, for example, and it is recommended tha= t > > you use parallel processing yet you only have one processor, you would > > split the file up (as you did), and then proceed to call APBS for each > > file, just as you mentioned: > > > > apbs apbs-PARALLEL-PE0.in > > apbs apbs-PARALLEL-PE1.in > > apbs apbs-PARALLEL-PE2.in > > apbs apbs-PARALLEL-PE3.in > > > > This allows users to run APBS on large PQR files with machines with > > limited resources. Depending on what you want to get back from APBS yo= u > > can either sum energies, or merge DX files using the mergedx utility. > > The naming of the files assists with the mergedx utility. > > > > On the other hand, if you have a multiple-processor machine and want to > > run APBS in parallel, there is no need to run APBS asynchronously - you > > just need to use the mg-para keyword. > > > > Please see > > > > http://apbs.sourceforge.net/doc/user-guide/x645.html#mg-para > > http://apbs.sourceforge.net/doc/user-guide/x645.html#async > > > > for more information. > > > > Todd > > > > > > Ryogo Sugitani wrote: > > > Hello, > > > > > > After you get appropriate sets of input file from a mg-para > > > calculation input file > > > with appropriate "async {rank}" options (by using asynchronous.sh or = by hand), > > > how do we actually submit those sets of input files into ABPS? > > > > > > For example, with born example, I've got > > > apbs-PARALLEL-PE0.in > > > apbs-PARALLEL-PE1.in > > > apbs-PARALLEL-PE2.in > > > apbs-PARALLEL-PE3.in > > > after I process apbs-PARALLEL.in with asynchronous.sh > > > > > > Do we just do feed the first input file, like > > > apbs apbs-PARALLEL-PE0.in > > > > > > or some other way? > > > (In case you calculate them individually, how would each division can > > > communicate with each other?) > > > > > > I'll test the first case later today, but I don't see how apbs will > > > recognize which files to read > > > after reading the first one. Is the naming of the files the key? > > > > > > Thanks in advance, > > > > > > Ryogo > > > > > > > > > ------------------------------------------------------- > > > This SF.Net email is sponsored by the JBoss Inc. > > > Get Certified Today * Register for a JBoss Training Course > > > Free Certification Exam for All Training Attendees Through End of 200= 5 > > > Visit http://www.jboss.com/services/certification for more informatio= n > > > _______________________________________________ > > > apbs-users mailing list > > > apb...@li... > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |