August 2017 - firedrake - imperial.ac.uk

Normal to curved surface
by Dodwell, Timothy 25 Aug '17

25 Aug '17

Hi all, New to firedrake, I am building a test problem for a new PhD which is poro-elastic consolidation of a sphere, I want to apply a pressure boundary (Neumann) condition to a curved surface. I.e \int (\sigma \dot n) \dot v\; ds Where n is the normal vector to the surface ds. Is there a function normal() which returns it for me. A look a documentation doesn’t look promising! Cheers Tim Dr Tim Dodwell Senior Lecturer in Engineering Mathematics Rm 221 - Harrison Building College of Engineering, Mathematics & Physical Sciences University of Exeter Exeter Devon EX4 4PY mail: t.dodwell(at)exeter.ac.uk<http://exeter.ac.uk/> tel: +44 (0)1392 725899 mob: +44 (0)7745 622870 web: http://emps.exeter.ac.uk/engineering/staff/td336 Papers and Pre-prints: @Research-Gate<https://www.researchgate.net/profile/Timothy_Dodwell> Citations: @Google-Scholar<https://scholar.google.co.uk/citations?user=lPpjRfUAAAAJ&hl=en>

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FEniCS'18 Conference 21-23 March, University of Oxford
by Patrick Farrell 24 Aug '17

24 Aug '17

We're pleased to announce that registration and talk/poster abstract submission is now open for the FEniCS Conference 2018, 21-23 March 2018, at the University of Oxford. For further details please see https://fenicsproject.org/fenics18/ . We are very much looking forward to seeing you all in Oxford! Best regards, Patrick

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Using Intel's SDE and VTune for Firedrake/Python
by Justin Chang 24 Aug '17

24 Aug '17

Hi guys, I want to measure AI using the procedure described here on the NERSC website: http://www.nersc.gov/users/application-performance/measuring-arithmetic-int… Basically they obtain FLOPs from Intel's SDE and the bytes from VTune. And in their C code example, they inserted macros to indicate where to start and stop the measurements. Does anyone here know how to do something similar for Python-based programs? Or if there's a "hack" to allow me to insert these C macros into the firedrake code somewhere? Thanks, Justin

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Re: [firedrake] Can't terminate simulation
by Andrew McRae 14 Aug '17

14 Aug '17

For me, it's always been the case that Ctrl+C does nothing *while PETSc is doing a linear solve*... if GMRES isn't converging (so runs to the default ksp_max_it of 10,000), or if it takes a lot of iterations, this could certainly take a few minutes if it's a big system. The program would then be killed when leaving the linear solve. However, this was true before the Python 3 switch, and Anna's traceback looks a bit different... On 14 August 2017 at 10:30, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: > Sometimes “many times” can be 15-20 or even more, and it could take a few > minutes. I thought it would be better to report it just in case it can be > fixed. > > On 14 Aug 2017, at 10:23, Miklós Homolya <m.homolya14(a)imperial.ac.uk> > wrote: > > Just pressing Ctrl+C many times, that will terminate the process > eventually... > > On 14/08/17 09:59, Anna Kalogirou wrote: > > Dear all, > > This is a bit of a silly comment, but I have noticed that since the > upgrade to python3 I can’t terminate a simulation with ctrl+c. > > I get the following on the screen and the simulation continues to run: > > ^CTraceback (most recent call last): > File "libpetsc4py/libpetsc4py.pyx", line 858, in > libpetsc4py.MatMult_Python > File "/Users/dkc16gyu/firedrake/src/PyOP2/pyop2/petsc_base.py", line > 1008, in mult > x.comm.tompi4py().bcast(a) > File "PETSc/Comm.pyx", line 105, in petsc4py.PETSc.Comm.tompi4py > File "PETSc/petscmpi.pxi", line 50, in petsc4py.PETSc.mpi4py_Comm_New > File "<frozen importlib._bootstrap>", line 961, in _find_and_load > File "<frozen importlib._bootstrap>", line 946, in > _find_and_load_unlocked > File "<frozen importlib._bootstrap>", line 885, in _find_spec > File "<frozen importlib._bootstrap_external>", line 1157, in find_spec > File "<frozen importlib._bootstrap_external>", line 1129, in _get_spec > File "<frozen importlib._bootstrap_external>", line 1268, in find_spec > File "<frozen importlib._bootstrap_external>", line 59, in _path_join > KeyboardInterrupt > > The above exception was the direct cause of the following exception: > > SystemError: <built-in method insert of list object at 0x108236708> > returned a result with an error set > Exception ignored in: 'petsc4py.PETSc.traceback' > SystemError: <built-in method insert of list object at 0x108236708> > returned a result with an error set > > > Best wishes, > > Anna. > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

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Can't terminate simulation
by Anna Kalogirou 14 Aug '17

14 Aug '17

Dear all, This is a bit of a silly comment, but I have noticed that since the upgrade to python3 I can’t terminate a simulation with ctrl+c. I get the following on the screen and the simulation continues to run: ^CTraceback (most recent call last): File "libpetsc4py/libpetsc4py.pyx", line 858, in libpetsc4py.MatMult_Python File "/Users/dkc16gyu/firedrake/src/PyOP2/pyop2/petsc_base.py", line 1008, in mult x.comm.tompi4py().bcast(a) File "PETSc/Comm.pyx", line 105, in petsc4py.PETSc.Comm.tompi4py File "PETSc/petscmpi.pxi", line 50, in petsc4py.PETSc.mpi4py_Comm_New File "<frozen importlib._bootstrap>", line 961, in _find_and_load File "<frozen importlib._bootstrap>", line 946, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 885, in _find_spec File "<frozen importlib._bootstrap_external>", line 1157, in find_spec File "<frozen importlib._bootstrap_external>", line 1129, in _get_spec File "<frozen importlib._bootstrap_external>", line 1268, in find_spec File "<frozen importlib._bootstrap_external>", line 59, in _path_join KeyboardInterrupt The above exception was the direct cause of the following exception: SystemError: <built-in method insert of list object at 0x108236708> returned a result with an error set Exception ignored in: 'petsc4py.PETSc.traceback' SystemError: <built-in method insert of list object at 0x108236708> returned a result with an error set Best wishes, Anna.

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Re: [firedrake] broken install using python3
by David Ham 09 Aug '17

09 Aug '17

Hi Anna, I notice that your gcc and mpi are quite old. You probably want to run brew update brew upgrade to have more recent versions. Regards, David On Wed, 9 Aug 2017 at 10:06 Homolya, Miklós <m.homolya14(a)imperial.ac.uk> wrote: > Can you try to compile and run this program and see what happens? > > #include <stdio.h> > #include <mpi.h> > > main(int argc, char **argv) > { > int node; > > MPI_Init(&argc,&argv); > MPI_Comm_rank(MPI_COMM_WORLD, &node); > > printf("Hello World from Node %d\n",node); > > MPI_Finalize(); > } > > > For example, if the above code is saved as mpi_hello.c, then run > $ mpicc mpi_hello.c -o mpi_hello > $ ./mpi_hello > $ mpirun -n 3 ./mpi_hello > > > On 09/08/17 10:01, Anna Kalogirou wrote: > > Hi Miklos, > > I did run brew doctor already, fixed all the warnings and attempted the > installation again. Same error. > How do I fix the MPI C compiler then? > > Thanks, > > Anna. > > On 9 Aug 2017, at 09:58, Miklós Homolya <m.homolya14(a)imperial.ac.uk> > wrote: > > Hello Anna, > > > Apparently you MPI C compiler is not working. Are your brew packages > up-to-date, and is the output of "brew doctor" clean? > > > Regards, > > Miklos > > On 08/08/17 22:39, Anna Kalogirou wrote: > > Dear all, > > I have been trying to install firedrake on my other laptop but I get > errors at the petsc stage. Install log is attached. > > Thank you, > > Anna. > > > > > > On 31 Jul 2017, at 16:17, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > <a.kalogirou(a)leeds.ac.uk> wrote: > > > > Thanks Lawrence, the second installation attempt worked. > > > > Best, Anna. > > > > > >> On 31 Jul 2017, at 15:17, Lawrence Mitchell > <lawrence.mitchell(a)imperial.ac.uk> <lawrence.mitchell(a)imperial.ac.uk> > wrote: > >> > >> > >>> On 31 Jul 2017, at 14:07, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > <A.Kalogirou(a)leeds.ac.uk> wrote: > >>> > >>> I also have an issue with libspatialindex. Any ideas? > >>> > >> > >> 2017-07-31 13:49:27,832 DEBUG ssh: Could not resolve hostname > github.com: nodename nor servname provided, or not known > >> fatal: Could not read from remote repository. > >> > >> Please make sure you have the correct access rights > >> and the repository exists. > >> > >> 2017-07-31 13:49:27,833 WARNING Failed to clone libspatialindex using > ssh, falling back to https. > >> 2017-07-31 13:49:57,912 DEBUG fatal: unable to access ' > https://github.com/firedrakeproject/libspatialindex.git/': Could not > resolve host: github.com > >> > >> 2017-07-31 13:49:57,913 ERROR Failed to clone libspatialindex branch > master. > >> 2017-07-31 13:49:57,926 INFO > >> > >> > >> It looks like your internet connection or DNS fell over. Cloning the > libspatialindex repository failed. > >> > >> Lawrence > >> _______________________________________________ > >> firedrake mailing list > >> firedrake(a)imperial.ac.uk > >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- Dr David Ham Department of Mathematics Imperial College London

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broken install using python3
by Shipton, Jemma 09 Aug '17

09 Aug '17

Hi All, I have tried to run "python3 firedrake-install --install gusto" and almost succeeded. I've attached the log file... I had to interrupt a previous install but I just removed the directory and started again - not sure if that's the problem. Thanks! Jemma

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