Roy, I tried what you suggested, however when I check the NumericVector type of my added vector (I add it as GHOSTED before read) after EquationSystems::Read() it changes to parallel ?!! ( I checked with NumericVector::type() it was 3 before the read and 2 after)
Is there a work around so I can make a GHOSTED NumericVector myself from this PARALLEL vector? Thanks, Ata On Dec 10, 2012, at 2:21 PM, Ataollah Mesgarnejad <[email protected]> wrote: > > On Dec 10, 2012, at 2:20 PM, Ataollah Mesgarnejad <[email protected]> > wrote: > >> >> On Dec 10, 2012, at 1:45 PM, Roy Stogner <[email protected]> wrote: >> >>> >>> On Fri, 7 Dec 2012, Ataollah Mesgarnejad wrote: >>> >>>> I managed to isolate the problem in my code: I use an added vector >>>> to a system (third order CLOUGH) as the loading for one of systems; >>>> I did two tests >>>> >>>> 1) >>>> - I used system.project_vector to initialize this vector at each time >>>> step. >>>> - Solved with this loading. >>>> >>>> 2) >>>> Code a) >>>> - I used system.project_vector to initialize this vector at each time >>>> step. >>>> - I wrote this in a binary XDR file using: >>>> equation_system.write(xdr_file_name.str(), >>>> EquationSystems::WRITE_DATA | >>>> >>>> EquationSystems::WRITE_ADDITIONAL_DATA); >>>> Code b) >>>> - I read this additional vector at the beginning of the time step using: >>>> equation_system.read(xdr_file_name.str(), >>>> EquationSystems::READ_HEADER |EquationSystems::READ_DATA | >>>> EquationSystems::READ_ADDITIONAL_DATA); >>>> - Solve with this loading. >>> >>>> even though, everything else is unchanged between case 1 and 2, the >>>> solutions are different and you can see that the solution of case 2 >>>> visibly deteriorates at mesh partition boundaries. I'm attaching the >>>> solutions at the 1st time step from both cases. >>> >>> The attachments didn't come through, but there's enough description >>> here to make me wonder at one thing that's missing: >>> >>> In what way are you handling ghost degrees of freedom for your initial >>> vector? There's code in libMesh itself to handle updating ghost >>> degrees of freedom "behind the scenes" for your solution vector, but >>> if you're creating additional vectors that will get used as inputs to >>> an assembly then you'll typically also need additional code to make >>> sure those vectors' ghost dof coefficients get communicated at the >>> appropriate times. >>> >> I add the vector as GHOSTED. In my experience it worked fine when not >> depending on XDR system::read. >> >>> It looks like we handle the communication step in library code at the >>> end of System::project_vector(), but not in library code at the end of >>> System::read*() methods. Worse yet: this isn't easy to fix without >>> changing our xda/xdr file format, our I/O for which currently >>> recreates any additional vectors as PARALLEL type, even if they were >>> written out for something of GHOSTED type. >>> >>> We'll have other reasons to change our file format in the next year or >>> so, so I'd just as soon table the problem at the library level until >>> then. For now, the user level workaround for I/O of ghosted vectors >>> would be: >>> >>> Manually create the systems containing such vectors and add the >>> vectors themselves as GHOSTED before doing EquationSystems::read() >>> (you're probably already doing this based on the above description, >>> but I mention it for others who run into this problem) >> Yes I do. >> >>> >>> After the EquationSystems::read(), call close() on any ghosted >>> vectors. (if you're not running with PETSc and --enable-ghosted, >>> you'd currently need a more complicated localize(self, send_list) call >>> instead; I'll see if we can fix that.) >> I'm running with PETSc. I'll see if it would fix the issue. >> >> PS: the images are here if anyone wants to look. > > Forgot the link > http://cl.ly/3y3U1C0z1k07 > > Sorry, > Ata > >> >> Thanks, >> Ata >> >>> --- >>> Roy >> > ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
