Dear Kostas Thank you for your message. I deleted branches.
BR Tetsuo 2021年8月3日(火) 5:23 Konstantinos Poulios <[email protected]>: > Dear Tetsuo, > > Thanks for testing, mpi-fixes branch is merged to master. If you find any > other issues with MPI, please let me know. > > I see there are also some old branches of yours > > devel-tetsuo-add-truss-element-squash > devel-tetsuo-add_lumped_mass_python_interface > devel-tetsuo-add_lumped_mass_python_interface_squash > devel-tetsuo-fix-export-vtu > devel-tetsuo-hht_method > devel-tetsuo-xml > devel-tetsuo-xml02 > > Can we delete some of them if they are merged? I think you should be able > to delete your old branches yourself if you do not need them with > > git push origin --delete devel-tetsuo-..... > > BR > Kostas > > On Wed, Jul 28, 2021 at 2:31 AM Tetsuo Koyama <[email protected]> > wrote: > >> Dear Kostas >> >> Sorry for my late reply. >> My test was passed in nonlinear terms. >> Thank you for fixing it. >> >> Best regards Tetsuo >> >> 2021年7月23日(金) 20:29 Konstantinos Poulios <[email protected]>: >> >>> Dear Tetsuo, >>> >>> Have you tested the mpi-fixes branch? Should we merge it? >>> >>> Regarding unit tests, we could configure "make check" to run for example >>> test_assembly.cc with different numbers of processes and report assembly >>> times. Then we can consider also adding a check that computational times >>> are decreasing with increasing number of processes. >>> >>> Best regards >>> Kostas >>> >>> On Sun, May 23, 2021 at 4:18 PM Tetsuo Koyama <[email protected]> >>> wrote: >>> >>>> Dear Kostas >>>> >>>> Thanks. Yes, I would like to. >>>> Are there any points when adding tests? >>>> >>>> Is there a >>>> >>>> 2021年5月23日(日) 21:46 Konstantinos Poulios <[email protected]>: >>>> >>>>> Dear Tetsuo, >>>>> >>>>> You can now test the code in the mpi-fixes branch. Would you like to >>>>> help with a bit more extensive testing of MPI in GetFEM and maybe also >>>>> with >>>>> making some new unit tests for MPI? >>>>> >>>>> Best regards >>>>> Kostas >>>>> >>>>> On Sun, May 23, 2021 at 7:29 AM Tetsuo Koyama <[email protected]> >>>>> wrote: >>>>> >>>>>> Dear Kostas >>>>>> >>>>>> Thanks a lot. I will check the code. >>>>>> >>>>>> BR >>>>>> Tetsuo >>>>>> >>>>>> 2021年5月23日(日) 10:34 Konstantinos Poulios <[email protected]>: >>>>>> >>>>>>> I think I have fixed it but need to test it a bit more and tidy it >>>>>>> up. >>>>>>> BR >>>>>>> Kostas >>>>>>> >>>>>>> On Fri, May 21, 2021 at 8:42 AM Konstantinos Poulios < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> oh sorry, my fault, I can reproduce the error now. I had forgotten >>>>>>>> that I had to replace the linear term with a nonlinear one. >>>>>>>> >>>>>>>> BR >>>>>>>> Kostas >>>>>>>> >>>>>>>> On Thu, May 20, 2021 at 7:42 AM Tetsuo Koyama <[email protected]> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Sorry for lack of explanation. >>>>>>>>> >>>>>>>>> I build getfem on ubuntu:20.04 and using the configuration >>>>>>>>> command " --with-pic --enable-paralevel=2" >>>>>>>>> >>>>>>>>> I am using... >>>>>>>>> - automake >>>>>>>>> - libtool >>>>>>>>> - make >>>>>>>>> - g++ >>>>>>>>> - libqd-dev >>>>>>>>> - libqhull-dev >>>>>>>>> - libmumps-dev >>>>>>>>> - liblapack-dev >>>>>>>>> - libopenblas-dev >>>>>>>>> - libpython3-dev >>>>>>>>> - gfortran >>>>>>>>> - libmetis-dev >>>>>>>>> >>>>>>>>> I attach a Dockerfile and a Python file to reproduce. >>>>>>>>> You can reproduce by the following command. >>>>>>>>> >>>>>>>>> $ sudo docker build -t demo_parallel_laplacian_nonlinear_term.py . >>>>>>>>> >>>>>>>>> Best Regards >>>>>>>>> Tetsuo >>>>>>>>> >>>>>>>>> 2021年5月19日(水) 23:12 Konstantinos Poulios <[email protected] >>>>>>>>> >: >>>>>>>>> >>>>>>>>>> I think the instructions page is correct. What distribution do >>>>>>>>>> you build getfem on and what is your configuration command? >>>>>>>>>> Best regards >>>>>>>>>> Kostas >>>>>>>>>> >>>>>>>>>> On Wed, May 19, 2021 at 10:44 AM Tetsuo Koyama < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> Dear Kostas >>>>>>>>>>> >>>>>>>>>>> This page (http://getfem.org/tutorial/install.html) says >>>>>>>>>>> - Parallel MUMPS, METIS and MPI4PY packages if you want to use >>>>>>>>>>> the MPI parallelized version of GetFEM. >>>>>>>>>>> >>>>>>>>>>> Is there a recommended way to install Parallel Parallel MUMPS, >>>>>>>>>>> METIS and MPI4PY ? >>>>>>>>>>> I could not find the information in the page. >>>>>>>>>>> >>>>>>>>>>> If you could give me any information I will add it to the >>>>>>>>>>> following page. >>>>>>>>>>> http://getfem.org/install/install_linux.html >>>>>>>>>>> >>>>>>>>>>> BR >>>>>>>>>>> Tetsuo >>>>>>>>>>> >>>>>>>>>>> 2021年5月19日(水) 10:45 Tetsuo Koyama <[email protected]>: >>>>>>>>>>> >>>>>>>>>>>> Dear Kostast >>>>>>>>>>>> >>>>>>>>>>>> No I haven't. I am using libmumps-seq-dev of Ubuntu repository. >>>>>>>>>>>> I will use parallel version of mumps again. >>>>>>>>>>>> >>>>>>>>>>>> BR >>>>>>>>>>>> Tetsuo >>>>>>>>>>>> >>>>>>>>>>>> 2021年5月19日(水) 4:50 Konstantinos Poulios < >>>>>>>>>>>> [email protected]>: >>>>>>>>>>>> >>>>>>>>>>>>> Dear Tetsuo, >>>>>>>>>>>>> >>>>>>>>>>>>> Have you compiled GetFEM with the parallel version of mumps? >>>>>>>>>>>>> In Ubuntu/Debian you must link to dmumps instead of dmumps_seq >>>>>>>>>>>>> for example. >>>>>>>>>>>>> >>>>>>>>>>>>> BR >>>>>>>>>>>>> Kostast >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, May 18, 2021 at 2:09 PM Tetsuo Koyama < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Dear Kostas >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you for your report. >>>>>>>>>>>>>> I am happy that it runs well in your system. >>>>>>>>>>>>>> I will organize the procedure that can reproduce this error. >>>>>>>>>>>>>> Please wait. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best Regards Tetsuo >>>>>>>>>>>>>> >>>>>>>>>>>>>> 2021年5月18日(火) 18:10 Konstantinos Poulios < >>>>>>>>>>>>>> [email protected]>: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Dear Tetsuo, >>>>>>>>>>>>>>> I could not confirm this issue. On my system the example >>>>>>>>>>>>>>> runs well both on 1 and 2 processes (it doesn't scale well >>>>>>>>>>>>>>> though) >>>>>>>>>>>>>>> BR >>>>>>>>>>>>>>> Kostas >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Sun, May 16, 2021 at 10:07 AM Tetsuo Koyama < >>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Dear Kostas >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I am looking inside the source code. >>>>>>>>>>>>>>>> > if (generic_expressions.size()) {...} >>>>>>>>>>>>>>>> Sorry it looks complex for me. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> FYI. I found that MPI process 1 and 2 is different in the >>>>>>>>>>>>>>>> following line. >>>>>>>>>>>>>>>> > if (iter.finished(crit)) { >>>>>>>>>>>>>>>> This is in the "Newton_with_step_control" function in >>>>>>>>>>>>>>>> getfem_model_solvers.h. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> "crit" is calculated by rit = res / approx_eln and res and >>>>>>>>>>>>>>>> approx_eln is ... >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> $ mpirun -n 1 python demo_parallel_laplacian.py >>>>>>>>>>>>>>>> res=1.31449e-11 >>>>>>>>>>>>>>>> approx_eln=6.10757 >>>>>>>>>>>>>>>> crit=2.15222e-12 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> $ mpirun -n 2 python demo_parallel_laplacian.py >>>>>>>>>>>>>>>> res=6.02926 >>>>>>>>>>>>>>>> approx_eln=12.2151 >>>>>>>>>>>>>>>> crit=0.493588 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> res=0.135744 >>>>>>>>>>>>>>>> approx_eln=12.2151 >>>>>>>>>>>>>>>> crit=0.0111128 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I am now trying to understand what is the correct residual >>>>>>>>>>>>>>>> value of Newton(-Raphson) algorithm. >>>>>>>>>>>>>>>> I will be glad if you have an opinion. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best Regards Tetsuo >>>>>>>>>>>>>>>> 2021年5月11日(火) 19:28 Tetsuo Koyama <[email protected]>: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Dear Kostas >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > The relevant code is in the void model::assembly >>>>>>>>>>>>>>>>> function in getfem_models.cc. The relevant code assembling >>>>>>>>>>>>>>>>> the term you add >>>>>>>>>>>>>>>>> with md.add_nonlinear_term(..) must be executed inside the if >>>>>>>>>>>>>>>>> condition >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > if (generic_expressions.size()) {...} >>>>>>>>>>>>>>>>> > You can have a look there and ask for further help if it >>>>>>>>>>>>>>>>> looks too complex. You should also check if the test works >>>>>>>>>>>>>>>>> when you run it >>>>>>>>>>>>>>>>> with md.add_nonlinear_term but setting the number of MPI >>>>>>>>>>>>>>>>> processes to one. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks. I will check it. And the following command >>>>>>>>>>>>>>>>> completed successfully.. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> $ mpirun -n 1 python demo_parallel_laplacian.py >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> So all we have to check is compare -n 1 with -n2 . >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best regards Tetsuo >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 2021年5月11日(火) 18:44 Konstantinos Poulios < >>>>>>>>>>>>>>>>> [email protected]>: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Dear Tetsuo, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The relevant code is in the void model::assembly function >>>>>>>>>>>>>>>>>> in getfem_models.cc. The relevant code assembling the term >>>>>>>>>>>>>>>>>> you add with >>>>>>>>>>>>>>>>>> md.add_nonlinear_term(..) must be executed inside the if >>>>>>>>>>>>>>>>>> condition >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> if (generic_expressions.size()) {...} >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> You can have a look there and ask for further help if it >>>>>>>>>>>>>>>>>> looks too complex. You should also check if the test works >>>>>>>>>>>>>>>>>> when you run it >>>>>>>>>>>>>>>>>> with md.add_nonlinear_term but setting the number of MPI >>>>>>>>>>>>>>>>>> processes to one. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> BR >>>>>>>>>>>>>>>>>> Kostas >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, May 11, 2021 at 10:44 AM Tetsuo Koyama < >>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Dear Kostas >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you for your reply. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > Interesting. In order to isolate the issue, can you >>>>>>>>>>>>>>>>>>> also check with >>>>>>>>>>>>>>>>>>> > md.add_linear_term(..) >>>>>>>>>>>>>>>>>>> > ? >>>>>>>>>>>>>>>>>>> It ends when using md.add_linear_term(..). >>>>>>>>>>>>>>>>>>> It seems that it is a problem of >>>>>>>>>>>>>>>>>>> md.add_nonlinear_term(..). >>>>>>>>>>>>>>>>>>> Is there a point which I can check? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best regards Tetsuo. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 2021年5月11日(火) 17:19 Konstantinos Poulios < >>>>>>>>>>>>>>>>>>> [email protected]>: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Dear Tetsuo, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Interesting. In order to isolate the issue, can you >>>>>>>>>>>>>>>>>>>> also check with >>>>>>>>>>>>>>>>>>>> md.add_linear_term(..) >>>>>>>>>>>>>>>>>>>> ? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best regards >>>>>>>>>>>>>>>>>>>> Kostas >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Tue, May 11, 2021 at 12:22 AM Tetsuo Koyama < >>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Dear GetFEM community >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I am running MPI Parallelization of GetFEM.The running >>>>>>>>>>>>>>>>>>>>> command is >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> $ git clone >>>>>>>>>>>>>>>>>>>>> https://git.savannah.nongnu.org/git/getfem.git >>>>>>>>>>>>>>>>>>>>> $ cd getfem >>>>>>>>>>>>>>>>>>>>> $ bash autogen.sh >>>>>>>>>>>>>>>>>>>>> $ ./configure --with-pic --enable-paralevel=2 >>>>>>>>>>>>>>>>>>>>> $ make >>>>>>>>>>>>>>>>>>>>> $ make install >>>>>>>>>>>>>>>>>>>>> $ mpirun -n 2 python demo_parallel_laplacian.py >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The python script ends correctly. But when I changed >>>>>>>>>>>>>>>>>>>>> the following linear term to nonlinear term the script >>>>>>>>>>>>>>>>>>>>> did not end. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -md.add_Laplacian_brick(mim, 'u') >>>>>>>>>>>>>>>>>>>>> +md.add_nonlinear_term(mim, "Grad_u.Grad_Test_u") >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Do you know the reason? >>>>>>>>>>>>>>>>>>>>> Best regards Tetsuo >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>
