Thanks, it works.
On 29/08/16 18:49, Guyer, Jonathan E. Dr. (Fed) wrote: > phi1.globalValue will return the value over the entire domain > >> On Aug 29, 2016, at 10:50 AM, ronghai wu <ronghai...@fau.de> wrote: >> >> >> >> On 29/08/16 15:06, Guyer, Jonathan E. Dr. (Fed) wrote: >>> Hard to say. Diagnosing parallel race conditions is neither easy nor >>> entertaining. >>> >>> Could be that you just need a comm.Barrier() call before the comm.bcast() >>> calls. >>> >>> One possible issue is that FiPy automatically partitions the mesh when it >>> detects that it is running in parallel, so the result of your run() routine >>> is that phi1 gets solved only on partition 1, phi2 only on partition 2, >>> etc. and so it may be waiting for the solutions on the other partitions >>> that are never going to come. >>> >> As I print the shape of phi1...phi4, I found the reason is that: I want to >> solve four equations with each equation (in whole mesh) one core. However, >> once running with $mpiexec -n 4 python script.py, Fipy will automatically >> divide the mesh and cellvariables into four subdomains. Besides, it seems >> that the user defined communicator cannot control fipy communicator. >> Anyway, if I do not do any tricky thing, just write normal code and run in >> four-core parallel, for example the following code: >> >> ############# >> nx = >> 200 >> >> ny = nx >> dx = >> 1. >> >> dy = >> 1. >> >> mesh = fp.PeriodicGrid2D(nx=nx, ny=ny, dx=dx, dy=dy) >> eq1 = fp.TransientTerm(var=phi1, coeff=1.) == fp.DiffusionTerm(var=phi1, >> coeff=1. >> ) >> eq2 = fp.TransientTerm( >> var=phi2, coeff=1.) == fp.DiffusionTerm(var=phi2, coeff=1. >> ) >> eq3 = fp.TransientTerm( >> var=phi3, coeff=1.) == fp.DiffusionTerm(var=phi3, coeff=1. >> ) >> eq4 = fp.TransientTerm( >> var=phi4, coeff=1.) == fp.DiffusionTerm(var=phi4, coeff=1. >> ) >> eq = eq1 & eq2 & eq3 & eq4 >> res = >> 1.e4 >> >> while res > 1.e-3 >> : >> eq.cacheMatrix() >> eq.cacheRHSvector() >> res = eq.sweep( >> dt=1, solver >> =solver()) >> >> mat >> = eq.matrix >> >> vec >> = eq.RHSvector >> >> phi1.updateOld() >> phi2.updateOld() >> phi3.updateOld() >> phi4.updateOld() >> >> print 'phi1 shape = ' >> , np.shape(phi1.value) >> >> >> ############# I notice the np.shape(phi1.value) is not the whole mesh >> shape (200*200), but (10400) ,(10400), (10800) and (10800) in four >> subdomains. The question is, how to gather phi1 in subdomains to make it a >> complete one in the whole domain (with shape 40000)? Thanks >>>> On Aug 28, 2016, at 11:50 AM, ronghai wu <ronghai...@fau.de> >>>> wrote: >>>> >>>> >>>> Dear Fipy developers and users, >>>> >>>> The official parallel running way works for me, however, I would like to >>>> try an different way shown in the attached script. When running by $time >>>> mpiexec -n 4 python My_Fipy_Parallel.py, it gets stuck at time step 179 >>>> without any error message pop out, four cores are full but enough memory >>>> left. The bigger the mesh is, the sooner it will get stuck. Does any know >>>> why and how to solve this problem? Thanks. >>>> >>>> Regards >>>> Ronghai >>>> <My_Fipy_Parallel.py>_______________________________________________ >>>> fipy mailing list >>>> >>>> fipy@nist.gov >>>> http://www.ctcms.nist.gov/fipy >>>> >>>> [ NIST internal ONLY: >>>> https://email.nist.gov/mailman/listinfo/fipy >>>> ] >>>> >>> _______________________________________________ >>> fipy mailing list >>> >>> fipy@nist.gov >>> http://www.ctcms.nist.gov/fipy >>> >>> [ NIST internal ONLY: >>> https://email.nist.gov/mailman/listinfo/fipy >>> ] >>> >> -- >> ------------------------------------------ >> Ronghai Wu >> >> Institute of Materials Simulation (WW8) >> Department of Materials Science and Engineering >> University of Erlangen-Nürnberg >> Dr.-Mack-Str. 77, 90762 Fürth, Germany >> >> Tel. +49 (0)911 65078-65064 >> >> _______________________________________________ >> fipy mailing list >> fipy@nist.gov >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] -- ------------------------------------------ Ronghai Wu Institute of Materials Simulation (WW8) Department of Materials Science and Engineering University of Erlangen-Nürnberg Dr.-Mack-Str. 77, 90762 Fürth, Germany Tel. +49 (0)911 65078-65064 _______________________________________________ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
