Somehow two copies of this sent earlier today didn't make it to the list. Gus Correa
> Begin forwarded message: > > From: Gustavo Correa <g...@ldeo.columbia.edu> > Subject: Re: [OMPI users] MPI advantages over PBS > Date: August 25, 2018 at 20:16:49 EDT > To: Open MPI Users <users@lists.open-mpi.org> > > Hi Diego > > I (still) have Torque/PBS version 4.something in old clusters. > [Most people at this point already switched to Slurm.] > > Torque/PBS comes with a tool named "pbsdsh" (for PBS distributed shell): > > http://docs.adaptivecomputing.com/torque/4-1-3/Content/topics/commands/pbsdsh.htm > https://wikis.nyu.edu/display/NYUHPC/PBSDSH > http://www.ep.ph.bham.ac.uk/general/support/torquepbsdsh.html > > "pbsdsh" is able to launch *serial* jobs across the nodes that you allocate > for the job. > This allows you to run so called "embarrassingly parallel" tasks: > > https://en.wikipedia.org/wiki/Embarrassingly_parallel > > Ebarrassingly parallel tasks (or programs) are those where the processes don't > need to communicate with each other (therefore would be feasible without MPI). > > The link above lists some embarrassingly parallel tasks. > A trivial example would be, for instance, to run transliterate all uppercase > letters > to lowercase in a large number of text files, i.e. to run the "tr" command > below > > tr '[:upper:]' '[:lower:]' < input${i}.txt > output{$i}.txt > > where the file name index ${i} would be distributed across the various > processes. > "pbsdsh" can do it without MPI, because there is no need for one processor to > communicate with another processor to perform this. > > However, pbsdsh is not unique at all. > There are other tools, independent of PBS, which can do the same if not more > than pbsdsh. > "Pdsh" is one of them (probably the most versatile and popular): > > https://github.com/chaos/pdsh > https://linux.die.net/man/1/pdsh > http://www.linux-magazine.com/Issues/2014/166/Parallel-Shells > https://www.rittmanmead.com/blog/2014/12/linux-cluster-sysadmin-parallel-command-execution-with-pdsh/ > > > [Some examples in the links above are "parallel system administration tasks", > some are user-level tasks.] > > *** > > *However ... not all parallelizable problems are embarrassingly parallel!!!* > Actually, most are not embarrassingly parallel. > A whole very large class of common problems in science in engineering, > is to solve partial differential equations (PDE) using finite-differences > (FD) or similar methods > (finite elements, finite volume, pseudo-spectral, etc) through domain > decomposition. > This is a typical example of a problem that is parallelizable, but not > embarrassingly parallel. > When solving PDE's with FD through domain decomposition, you have to exchange > the data on the sub-domain halos across the processors in charge of solving > the > equation on each subdomain. This requires communication across the processors, > something that pbsdsh or pdsh cannot do, but MPI can (and so did the > predecessors of > MPI: p4, PVM, etc). > This class of problems includes most of computational fluid dynamics, > structural mechanics, > weather forecast, climate/oceans/atmosphere modeling, geodynamics, etc. > Many problem solving methods in molecular dynamics and computational > chemistry are not > embarrassingly parallel either. > There are many other classes of parallelizable problems that are not > embarrassingly parallel. > > Ian Foster's book, although somewhat out of date in several aspects, > still provides some background on this: > > https://pdfs.semanticscholar.org/09ed/7308fdfb0b640077328aa4fd10ce429f511a.pdf > > [Anybody in the list can suggest a recent book that with this type of > comprehensive approach to parallel programs, please? > The ones I know are restricted to MPI, or OpenMP, and so on.] > > Do you know what type of problem you're trying to solve, > and whether it is embarrassingly parallel or not? > Which type of problem are you trying to solve? > > I hope this helps, > Gus Correa > > >> On Aug 25, 2018, at 03:06, John Hearns via users <users@lists.open-mpi.org> >> wrote: >> >> Diego, >> I am sorry but you have different things here. PBS is a resource allocation >> system. It will reserve the use of a compute server, or several compute >> servers, for you to run your parallel job on. PBS can launch the MPI job - >> there are several mechanisms for launching parallel jobs. >> MPI is an API for parallel programming. I would rather say a library, but if >> I'm not wrong MPI is a standard for parallel programming and is technically >> an API. >> >> One piece of advice I would have is that you can run MPI programs from the >> command line. So Google for 'Hello World MPI'. Write your first MPI program >> then use mpirun from the command line. >> >> If you have a cluster which has the PBS batch system you can then use PBS to >> run your MPI program. >> IF that is not clear please let us know what help you need. >> >> >> >> >> >> >> >> >> >> >> >> On Sat, 25 Aug 2018 at 06:54, Diego Avesani <diego.aves...@gmail.com> wrote: >> Dear all, >> >> I have a philosophical question. >> >> I am reading a lot of papers where people use Portable Batch System or job >> scheduler in order to parallelize their code. >> >> What are the advantages in using MPI instead? >> >> I am writing a report on my code, where of course I use openMPI. So tell me >> please how can I cite you. You deserve all the credits. >> >> Thanks a lot, >> Thanks again, >> >> >> Diego >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users
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