April 2018 - firedrake - imperial.ac.uk

demo for printing and doing certain all-reduce operations smoothly in parallel?
by Ed Bueler 09 May '18

09 May '18

Dear Firedrake -- So far so good! However, I am not sure of certain best practices in parallel. Consider the following familiar Helmholtz example. I have added some printing fluff before and after: from firedrake import * mesh = UnitSquareMesh(10, 10) V = FunctionSpace(mesh, "CG", 1) u = TrialFunction(V) v = TestFunction(V) f = Function(V) x, y = SpatialCoordinate(mesh) print('setting up problem') f.interpolate((1+8*pi*pi)*cos(x*pi*2)*cos(y*pi*2)) a = (dot(grad(v), grad(u)) + v * u) * dx L = f * v * dx u = Function(V) solve(a == L, u, options_prefix='s', solver_parameters={'ksp_type': 'cg'}) f.interpolate(cos(x*pi*2)*cos(y*pi*2)) L2err = sqrt(assemble(dot(u - f, u - f) * dx)) umax = u.dat.data.max() print('L2 error norm = %g, max(u) = %g' % (L2err,umax)) Suppose we run first in serial and then on two processes: (firedrake) ~$ python3 helmholtz.py -s_ksp_converged_reason setting up problem Linear s_ solve converged due to CONVERGED_RTOL iterations 13 L2 error norm = 0.0625707, max(u) = 1.03139 (firedrake) ~$ mpiexec -n 2 python3 helmholtz.py -s_ksp_converged_reason Linear s_ solve converged due to CONVERGED_RTOL iterations 28 setting up problem L2 error norm = 0.0625707, max(u) = 0.803552 setting up problem L2 error norm = 0.0625707, max(u) = 1.03138 This reveals several issues: 1. Should I use "if COMM_WORLD.rank == 0:" to avoid printing n times? Or should I use a collective print like PetscPrintf()? If so where could I find a demo? (I'm familiar with the C API not petsc4py ...) 2. There is a flush issue if I only print on rank 0; the solver reports CONVERGED before the first print happens. How to flush or avoid the need to flush? 3. It looks like "assemble()" does a MPI_Allreduce() to get the right L2 error. Is that right? How to do this myself, for example for the solution maximum to appear on all ranks? (Probably a petsc4py call?) Is there a demo which shows how the firedrake developers prefer to do these things? Parallel best-practices, more or less. All the demos I can find seem to be serial w.r.t. the above niceties. The page https://www.firedrakeproject.org/parallelism.html addresses less-introductory parallelism issues in my opinion. I am not worried about the math either; I'm aware that the above difference in CG iterations has everything to do with the difference in default preconditioning. Thanks! Ed -- Ed Bueler Dept of Math and Stat and Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775-6660 301C Chapman

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Re: [firedrake] hello
by Lawrence Mitchell 26 Apr '18

26 Apr '18

(adding firedrake(a)imperial.ac.uk back to CC) On 26/04/18 12:01, Naceur Bouziani wrote: > Dear Lawrence > > yes I will do this and send you the output. Is it a file that I can > download to send or should I copy some thing in a file ? Please run the commands, and copy the output from your terminal, then include that output in what you send. Thanks, Lawrence > yours Naceur > > 2018-04-26 11:47 GMT+02:00 Lawrence Mitchell > <lawrence.mitchell(a)imperial.ac.uk > <mailto:lawrence.mitchell@imperial.ac.uk>>: > > Dear Naceur, > > On 26/04/18 08:53, Naceur Bouziani wrote: > > Lawrence the test fails at exodus > > > > [ 32%] > > tests/regression/test_exodus_mesh.py Makefile:60 : la recette pour la > > cible « test » a échouée > > make: *** [test] Erreur de segmentation (core dump créé) > > (firedrake) naceur@Sibelius:~/Bureau/PDE/firedrake/src/firedrake$ > > Hmm, this fails reading a mesh file in Exodus format. > > The segmentation fault is worrying. > > Can you run, in the same directory you run "make alltest" in: > > gdb --args python -c "from firedrake import Mesh; > print(Mesh('tests/meshes/brick.e').num_cells())" > > This will give you a GDB prompt: > > GNU gdb (Ubuntu 7.11.1-0ubuntu1~16.5) 7.11.1 > Copyright (C) 2016 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or later > <http://gnu.org/licenses/gpl.html <http://gnu.org/licenses/gpl.html>> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law. Type "show > copying" > and "show warranty" for details. > This GDB was configured as "x86_64-linux-gnu". > Type "show configuration" for configuration details. > For bug reporting instructions, please see: > <http://www.gnu.org/software/gdb/bugs/ > <http://www.gnu.org/software/gdb/bugs/>>. > Find the GDB manual and other documentation resources online at: > <http://www.gnu.org/software/gdb/documentation/ > <http://www.gnu.org/software/gdb/documentation/>>. > For help, type "help". > Type "apropos word" to search for commands related to "word"... > Reading symbols from python...(no debugging symbols found)...done. > (gdb) > > Type "run" at the prompt: > > (gdb) run > > I get something like: > > Starting program: /data/lmitche1/src/firedrake/bin/python -c from\ > firedrake\ import\ Mesh\;\ > print$Mesh\(\'tests/meshes/brick.e\'$.num_cells\) > [Thread debugging using libthread_db enabled] > Using host libthread_db library > "/lib/x86_64-linux-gnu/libthread_db.so.1". > [New Thread 0x7fffe640e700 (LWP 52433)] > 140 > [Thread 0x7fffe640e700 (LWP 52433) exited] > [Inferior 1 (process 52429) exited normally] > (gdb) > > But you will get a segmentation fault, once gdb has caught the error > type "backtrace" and send the results. > > Hopefully that will give some insight into where things are failing. > > Thanks, > > Lawrence > >

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Cannot install firedrake
by Mohammad Sarraf Joshaghani 26 Apr '18

26 Apr '18

Hello, I successfully installed firedrake but when I try to test the firedrake installation i get this error: (firedrake) [msarrafj@caml-lin Software]$ python -c "import firedrake" Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/firedrake/firedrake/__init__.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/firedrake/firedrake…>", line 32, in <module> from pyop2 import op2 # noqa: F401 File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/__init__.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/__init_…>", line 4, in <module> from pyop2.op2 import * # noqa File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/op2.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/op2.py>", line 42, in <module> from pyop2.base import i # noqa: F401 File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/base.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/base.py>", line 57, in <module> from pyop2.sparsity import build_sparsity ImportError: /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so: <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsit…:> undefined symbol: PetscMallocA Attached is the associated firedrake-install.log if it helps Thanks in advance for your help. Sincerely, Sarraf

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Re: [firedrake] it all makes sense
by Lawrence Mitchell 25 Apr '18

25 Apr '18

(reintroduced firedrake cc) On 25/04/18 19:06, Ed Bueler wrote: >> So possibly if you ran the installer when PETSC_DIR was unset, and >> then later happened to set it, you wouldn't have got this warning. > > This is sort of missing the point. You are assuming that my machine > is devoted to firedrake and it is not. > > Ed's behavior most of the time: Use PETSc with C. Keep petsc master > up to date. PETSC_DIR is set in my .bashrc. (And until recently: no > firedrake on machine.) Sure. > Ed installs firedrake: Yes it complains PETSC_DIR is set. I try > --honour-petsc-dir and it fails. (Presumably I had a petsc master > commit that was bad for petsc4py etc.) So I unset PETSC_DIR and get > successful installation. Things work that day. > > Ed turns on machine next day: Do "source firedrake/bin/activate". No > complaint that environment PETSC_DIR is different from one used in > firedrake install. Instead: bizarre seg faults ... because under the > hood the dynamic linking is to the wrong PETSc ?! ... Yes, I agree this is a bad failure mode. > So: Presumably activate should check PETSC_DIR against the one used > in the firedrake install? Warn if not equal? > > Not sure of the right way to do it, but some such check worthwhile? We can't do it in activate (because we don't control what's written to that script). However, I think we can do it on firedrake import. I do that here: https://github.com/firedrakeproject/firedrake/pull/1224 After this is merged (and you've done firedrake-update) you get an ImportError when importing firedrake in python if either: 1. PETSC_DIR is set, but you did not install with --honour-petsc-dir; 2. PETSC_DIR is not set, but you did install with --honour-petsc-dir. This should hopefully catch issues early, rather than late, and we can avoid this kind of dance in the future. Thanks, Lawrence

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it all makes sense
by Ed Bueler 25 Apr '18

25 Apr '18

Lawrence -- > > Petsc Development GIT revision: v3.4.2-20859-g7bfdb6492c GIT Date: 2018-04-03 16:04:52 -0500 > This is 20859 commits after the 3.4.2 tag. It's from about three weeks ago. > Dunno why the git describe our out [output?] is this. Odd, but I got it. Wasn't reading the whole string. > > > Can you post the output of firedrake-status? > > Both with the reinstalled firedrake, and the old, it crashes... > Aha, it's a python script, so just run firedrake-status, rather than try to source it. Got it. And firedrake-status tells me that PETSC_DIR is my own or "None" according to whether I do "unset PETSC_DIR" before running activate or not. Makes sense! > > I have now reinstalled firedrake with PETSC_DIR unset ... But if I run > > activate later it seems to use the value of PETSC_DIR at that time. > > I'll reiterate that firedrake runs with (basically) petsc master. However, > we had issues with changes not being made simultaneously in petsc > and petsc4py. Hence we maintain a fork with known good branch pointers > for both (and slepc and slepc4py). These are the "firedrake" branches > you can see at github.com/firedrakeproject/petsc etc... > firedrake-install clones and builds these packages. Understood. > If you have PETSC_DIR set then it complains (or it should). It does not complain. It probably should? Would have saved me confusion. Turns out my PETSC_DIR had almost the same master commit, but not quite .. thus truely weird seg faults when that petsc was silently linked. By the way, gdb --args python3 script.py works for me. In fact I tried it in my debugging earlier but the seg fault was so bad (... in PetscFinalize() or something ... can't reconstruct ...) that it did not help when I most needed it. > You can run with your prebuilt petsc: run the install with --honour-petsc-dir. > But we don't guarantee that you will get all the different bits matching. Actually now that I know it is v3.4.2 + 20,000 commits I'm good with firedrake's petsc choice! ;-) > > So it looks like I should do > > $ unset PETSC_DIR > > $ source firedrake/bin/activate > > every time I start firedrake? Is this the correct action if one has > > PETSC_DIR set? > I think so yes. It's possible that this env variable interferes with the library > that petsc4py loads, and if things have changed, maybe you get issues. firedrake-status confirms that "unset PETSC_DIR" action is really needed. Should this be documented in the firedrake install instructions? Maybe the fact that I already have PETSc on my machine is a special case ... but probably not that special. In any case, everything works now. It is even true that all the hiccups have clear explanations! Awesome! Also my Stokes solver works as expected. ;-) Ed -- Ed Bueler Dept of Math and Stat and Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775-6660 301C Chapman

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hello
by Naceur Bouziani 25 Apr '18

25 Apr '18

I did not succed to install firedrake too bad for me could you help me please ? here is what i get when runing make alltests the errors are at the end of this log (firedrake) naceur@kahina:~/Documents/firedrake/src/firedrake$ make alltest Building extension modules running build_ext cythoning firedrake/dmplex.pyx to firedrake/dmplex.c building 'firedrake.dmplex' extension creating build creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/firedrake mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc4py/include -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include -I/home/naceur/Documents/firedrake/include -I/usr/include/python3.5m -c firedrake/dmplex.c -o build/temp.linux-x86_64-3.5/firedrake/dmplex.o In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/dmplex.c:566: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscbag.h:4:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:5, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsys.h:255:0: warning: "__STDC_FORMAT_MACROS" redefined #define __STDC_FORMAT_MACROS /* required for using PRId64 from c++ */ ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/numpyconfig.h:4:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/npy_common.h:5, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:4, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/dmplex.c:566: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/_numpyconfig.h:31:0: note: this is the location of the previous definition #define __STDC_FORMAT_MACROS 1 ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_facet_numbering’: firedrake/dmplex.c:4524:229: warning: passing argument 3 of ‘DMPlexGetSupport’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_11 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm, (*__Pyx_BufPtrCContig1d(PetscInt *, __pyx_pybuffernd_facets.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_facets.diminfo[0].strides)), (&__pyx_v_cells))); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(0, 64, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:71:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_2closure_ordering’: firedrake/dmplex.c:5955:126: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, (__pyx_v_closure[(2 * __pyx_v_ci)]), (&__pyx_v_face_vertices))); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 190, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_20mark_entity_classes’: firedrake/dmplex.c:14346:115: warning: passing argument 4 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_8 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_point_sf->sf, NULL, (&__pyx_v_nleaves), (&__pyx_v_ilocal), NULL)); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 901, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_22get_entity_classes’: firedrake/dmplex.c:15262:90: warning: passing argument 2 of ‘ISGetIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_7 = __pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_class_is->iset, (&__pyx_v_indices))); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 975, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscvec.h:9:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscmat.h:6, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdm.h:6, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmda.h:4, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:13, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscis.h:52:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode ISGetIndices(IS,const PetscInt *[]); ^ firedrake/dmplex.c:15343:94: warning: passing argument 2 of ‘ISRestoreIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_7 = __pyx_f_9firedrake_6dmplex_CHKERR(ISRestoreIndices(__pyx_v_class_is->iset, (&__pyx_v_indices))); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 981, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscvec.h:9:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscmat.h:6, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdm.h:6, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmda.h:4, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:13, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscis.h:53:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode ISRestoreIndices(IS,const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_36get_cell_remote_ranks’: firedrake/dmplex.c:19792:122: warning: passing argument 4 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 1297, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c:19792:141: warning: passing argument 5 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 1297, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_get_edge_global_vertices’: firedrake/dmplex.c:20058:96: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, __pyx_v_facet, (&__pyx_v_vs))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 1334, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_get_communication_lists’: firedrake/dmplex.c:20732:97: warning: passing argument 3 of ‘DMPlexGetSupport’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_3 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm, __pyx_v_f, (&__pyx_v_support))); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 1437, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:71:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c:21213:126: warning: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types] qsort(__pyx_v_cfacets, ((__pyx_v_offsets[0])[(__pyx_v_nranks[0])]), (sizeof(struct __pyx_t_9firedrake_6dmplex_CommFacet)), (&__pyx_f_9firedrake_6dmplex_CommFacet_cmp)); ^ In file included from /usr/include/python3.5m/Python.h:34:0, from firedrake/dmplex.c:4: /usr/include/stdlib.h:764:13: note: expected ‘__compar_fn_t {aka int (*)(const void *, const void *)}’ but argument is of type ‘int (*)(void *, void *)’ extern void qsort (void *__base, size_t __nmemb, size_t __size, ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_plex_get_restricted_support’: firedrake/dmplex.c:21369:95: warning: passing argument 3 of ‘DMPlexGetSupport’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm, __pyx_v_f, (&__pyx_v_support))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 1557, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:71:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_traverse_cell_string’: firedrake/dmplex.c:21585:94: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, __pyx_v_c, (&__pyx_v_cone))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 1621, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c:21666:105: warning: passing argument 3 of ‘DMPlexGetConeOrientation’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetConeOrientation(__pyx_v_plex->dm, __pyx_v_c, (&__pyx_v_cone_orient))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 1630, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:67:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientation(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_40orientations_facet2cell’: firedrake/dmplex.c:24681:96: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, __pyx_v_c, (&__pyx_v_cone))); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 1998, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c:24690:107: warning: passing argument 3 of ‘DMPlexGetConeOrientation’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetConeOrientation(__pyx_v_plex->dm, __pyx_v_c, (&__pyx_v_cone_orient))); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 1999, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:67:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientation(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c:24893:100: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, __pyx_v_facet, (&__pyx_v_cone))); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 2055, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_42exchange_cell_orientations’: firedrake/dmplex.c:25444:123: warning: passing argument 4 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_10 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_10 == ((int)-1))) __PYX_ERR(0, 2101, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c:25444:142: warning: passing argument 5 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_10 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_10 == ((int)-1))) __PYX_ERR(0, 2101, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_46prune_sf’: firedrake/dmplex.c:26190:120: warning: passing argument 4 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 2161, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c:26190:139: warning: passing argument 5 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 2161, __pyx_L1_error) ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0, from firedrake/dmplex.c:568: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const PetscSFNode**); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_8get_cell_nodes.isra.79’: firedrake/dmplex.c:2282:82: warning: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1) ((type)((char*)buf + i0 * s0) + i1) ^ firedrake/dmplex.c:8816:21: note: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ was declared here __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents; ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_6create_section.isra.80’: firedrake/dmplex.c:8602:19: warning: ‘__pyx_v_ndof’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_7 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSectionSetDof(__pyx_v_section->sec, __pyx_v_p, __pyx_v_ndof)); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 472, __pyx_L1_error) ^ firedrake/dmplex.c:2282:82: warning: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1) ((type)((char*)buf + i0 * s0) + i1) ^ firedrake/dmplex.c:7858:21: note: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ was declared here __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents; ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_DMPlexGetAdjacency_Facet_Support’: firedrake/dmplex.c:27239:15: warning: ‘__pyx_v_point’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_1 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexRestoreTransitiveClosure(__pyx_v_dm, __pyx_v_point, PETSC_TRUE, (&__pyx_v_closureSize), (&__pyx_v_closure))); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 2317, __pyx_L1_error) ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_10get_facet_nodes.isra.78’: firedrake/dmplex.c:2282:82: warning: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1) ((type)((char*)buf + i0 * s0) + i1) ^ firedrake/dmplex.c:9771:21: note: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ was declared here __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents; ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_12boundary_nodes.isra.77’: firedrake/dmplex.c:10809:21: warning: ‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents; ^ firedrake/dmplex.c:10791:7: warning: ‘__pyx_v_layers’ may be used uninitialized in this function [-Wmaybe-uninitialized] int __pyx_v_layers; ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_traverse_cell_string’: firedrake/dmplex.c:21821:7: warning: ‘__pyx_v_support_size’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_locally_orient_quadrilateral_plex’: firedrake/dmplex.c:22177:12: warning: ‘__pyx_v_size’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (unlikely(!(__pyx_t_14 != 0))) { ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_38quadrilateral_facet_orientations.isra.59’: firedrake/dmplex.c:24163:7: warning: ‘__pyx_v_size’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (__pyx_t_49 = 0; __pyx_t_49 < __pyx_t_48; __pyx_t_49+=1) { ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/firedrake/dmplex.o -lpetsc -o /home/naceur/Documents/firedrake/src/firedrake/firedrake/ dmplex.cpython-35m-x86_64-linux-gnu.so -L/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib -Wl,-rpath,/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib -Wl,-rpath,/home/naceur/Documents/firedrake/lib cythoning firedrake/extrusion_numbering.pyx to firedrake/extrusion_numbering.c building 'firedrake.extrusion_numbering' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc4py/include -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include -I/home/naceur/Documents/firedrake/include -I/usr/include/python3.5m -c firedrake/extrusion_numbering.c -o build/temp.linux-x86_64-3.5/firedrake/extrusion_numbering.o In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/extrusion_numbering.c:567: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscbag.h:4:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:5, from firedrake/extrusion_numbering.c:569: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsys.h:255:0: warning: "__STDC_FORMAT_MACROS" redefined #define __STDC_FORMAT_MACROS /* required for using PRId64 from c++ */ ^ In file included from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/numpyconfig.h:4:0, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/npy_common.h:5, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:4, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/extrusion_numbering.c:567: /home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/_numpyconfig.h:31:0: note: this is the location of the previous definition #define __STDC_FORMAT_MACROS 1 ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/firedrake/extrusion_numbering.o -lpetsc -o /home/naceur/Documents/firedrake/src/firedrake/firedrake/ extrusion_numbering.cpython-35m-x86_64-linux-gnu.so -L/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib -Wl,-rpath,/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib -Wl,-rpath,/home/naceur/Documents/firedrake/lib cythoning firedrake/hdf5interface.pyx to firedrake/hdf5interface.c building 'firedrake.hdf5interface' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc4py/include -I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include -I/home/naceur/Documents/firedrake/include -I/usr/include/python3.5m -c firedrake/hdf5interface.c -o build/temp.linux-x86_64-3.5/firedrake/hdf5interface.o firedrake/hdf5interface.c:565:18: fatal error: hdf5.h: Aucun fichier ou dossier de ce type compilation terminated. warning: firedrake/dmplexinc.pxi:61:4: 'PetscSFNode' redeclared warning: firedrake/dmplex.pyx:1393:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1393:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1785:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1785:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1786:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1786:4: Buffer unpacking not optimized away. warning: firedrake/dmplexinc.pxi:61:4: 'PetscSFNode' redeclared error: command 'mpicc' failed with exit status 1 Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests ============================= test session starts ============================== platform linux -- Python 3.5.2, pytest-3.5.0, py-1.5.3, pluggy-0.6.0 rootdir: /home/naceur/Documents/firedrake/src/firedrake, inifile: setup.cfg collected 0 items / 1 errors ==================================== ERRORS ==================================== ______________________________ ERROR collecting _______________________________ ../../lib/python3.5/site-packages/_pytest/config.py:334: in _getconftestmodules return self._path2confmods[path] E KeyError: local('/home/naceur/Documents/firedrake/src/firedrake/tests/extrusion') During handling of the above exception, another exception occurred: ../../lib/python3.5/site-packages/_pytest/config.py:365: in _importconftest return self._conftestpath2mod[conftestpath] E KeyError: local('/home/naceur/Documents/firedrake/src/firedrake/tests/extrusion/conftest.py') During handling of the above exception, another exception occurred: ../../lib/python3.5/site-packages/_pytest/config.py:371: in _importconftest mod = conftestpath.pyimport() ../../lib/python3.5/site-packages/py/_path/local.py:668: in pyimport __import__(modname) <frozen importlib._bootstrap>:969: in _find_and_load ??? <frozen importlib._bootstrap>:958: in _find_and_load_unlocked ??? <frozen importlib._bootstrap>:664: in _load_unlocked ??? <frozen importlib._bootstrap>:634: in _load_backward_compatible ??? ../../lib/python3.5/site-packages/_pytest/assertion/rewrite.py:213: in load_module py.builtin.exec_(co, mod.__dict__) tests/extrusion/conftest.py:2: in <module> from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh firedrake/__init__.py:27: in <module> firedrake_configuration.setup_cache_dirs() firedrake_configuration/__init__.py:46: in setup_cache_dirs os.environ["PYOP2_CACHE_DIR"] = os.path.join(config["options"]["cache_dir"], "pyop2") E TypeError: 'NoneType' object is not subscriptable During handling of the above exception, another exception occurred: ../../lib/python3.5/site-packages/py/_path/common.py:377: in visit for x in Visitor(fil, rec, ignore, bf, sort).gen(self): ../../lib/python3.5/site-packages/py/_path/common.py:418: in gen dirs = self.optsort([p for p in entries ../../lib/python3.5/site-packages/py/_path/common.py:419: in <listcomp> if p.check(dir=1) and (rec is None or rec(p))]) ../../lib/python3.5/site-packages/_pytest/main.py:434: in _recurse ihook = self.gethookproxy(path) ../../lib/python3.5/site-packages/_pytest/main.py:338: in gethookproxy my_conftestmodules = pm._getconftestmodules(fspath) ../../lib/python3.5/site-packages/_pytest/config.py:348: in _getconftestmodules mod = self._importconftest(conftestpath) ../../lib/python3.5/site-packages/_pytest/config.py:376: in _importconftest raise ConftestImportFailure(conftestpath, sys.exc_info()) E _pytest.config.ConftestImportFailure: TypeError("'NoneType' object is not subscriptable",) E File "<frozen importlib._bootstrap>", line 969, in _find_and_load E File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked E File "<frozen importlib._bootstrap>", line 664, in _load_unlocked E File "<frozen importlib._bootstrap>", line 634, in _load_backward_compatible E File "/home/naceur/Documents/firedrake/lib/python3.5/site-packages/_pytest/assertion/rewrite.py", line 213, in load_module E py.builtin.exec_(co, mod.__dict__) E File "/home/naceur/Documents/firedrake/src/firedrake/tests/extrusion/conftest.py", line 2, in <module> E from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh E File "/home/naceur/Documents/firedrake/src/firedrake/firedrake/__init__.py", line 27, in <module> E firedrake_configuration.setup_cache_dirs() E File "/home/naceur/Documents/firedrake/src/firedrake/firedrake_configuration/__init__.py", line 46, in setup_cache_dirs E os.environ["PYOP2_CACHE_DIR"] = os.path.join(config["options"]["cache_dir"], "pyop2") !!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!! =========================== 1 error in 0.42 seconds ============================ Makefile:60 : la recette pour la cible « test » a échouée make: *** [test] Erreur 2 (firedrake) naceur@kahina:~/Documents/firedrake/src/firedrake$

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value of PETSC_DIR used by activate?
by Ed Bueler 24 Apr '18

24 Apr '18

It looks like I have found part of my confusion. I have now reinstalled firedrake with PETSC_DIR unset, so there is an old PETSc (i.e. 3.4.2) inside the firedrake directory. But if I run activate later it seems to use the value of PETSC_DIR at that time. This is my working explanation for why I get seg faults and why "gdb --args python3 MYSCRIPT.py" shows backtraces with the wrong PETSc (i.e. the 3.9 version I am using for other purposes). So it looks like I should do $ unset PETSC_DIR $ source firedrake/bin/activate every time I start firedrake? Is this the correct action if one has PETSC_DIR set? Ed -- Ed Bueler Dept of Math and Stat and Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775-6660 301C Chapman

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Re: [firedrake] seg faults associated to stokes weak form details
by Ed Bueler 24 Apr '18

24 Apr '18

Thanks Lawrence. > I tried. But all four versions work for me. > ... > If you built your own PETSc, can you say what commit you used? I was indeed using my own petsc. It was 3.8.4. When I reinstalled firedrake using "unset PYTHONPATH" and "unset PETSC_DIR" before running the firedrake-install script ... I think this is the right way to get firedrake to install its own PETSC ... then all four version worked. My concern with the working version is that firedrake chooses a petsc version from 2013 or so? I think 3.4.2 is that old ( http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/) (firedrake) ~/repos/mccarthy/stokes[master*]$ ./linflowstep.py -version -------------------------------------------------------------------------- Petsc Development GIT revision: v3.4.2-20859-g7bfdb6492c GIT Date: 2018-04-03 16:04:52 -0500 The PETSc Team petsc-maint(a)mcs.anl.gov http://www.mcs.anl.gov/petsc/ See docs/changes/index.html for recent updates. See docs/faq.html for problems. See docs/manualpages/index.html for help. Libraries linked from /home/ed/firedrake/lib/python3.6/site-packages/petsc/lib -------------------------------------------------------------------------- effective viscosity 1.46e+12 Pa s reading mesh from glacier.msh ... ... > Can you post the output of: > firedrake-status? Both with the reinstalled firedrake, and the old, it crashes; here is the reinstalled case: (firedrake) ~/repos/mccarthy/stokes[master*]$ source ~/firedrake/bin/firedrake-status __requires__: command not found bash: /home/ed/firedrake/bin/firedrake-status: line 4: syntax error near unexpected token `'pkg_resources'' bash: /home/ed/firedrake/bin/firedrake-status: line 4: `__import__('pkg_resources').require('firedrake==0.13.0+2004.gc8a194d9')' Thanks for your help! Ed On Mon, Apr 23, 2018 at 2:31 PM, Ed Bueler <elbueler(a)alaska.edu> wrote: > Dear Firedrake -- > > My smooth progress with this awesome tool has hit a first barrier. > > The attached linear stokes code works as is with the "VERSION 1" weak > form. Run simply as "python3 ./linflowstep.py". The attached mesh file is > read by default. > > But with "grad()" replaced by "epsilon()", as recommended in the UFL > manual*, which is VERSION 2, I get seg fault. Slight modifications do or > do not work according to mere value of the constant (see VERSION 3/4 ... > weird). > > Can you reproduce? Any ideas? > > I seek to use the strain rate tensor (= epsilon(u)) in a nonnewtonian > stokes job, but this is blocking. > > Thanks, > > Ed > > PS* https://media.readthedocs.org/pdf/fenics-ufl/stable/fenics-ufl.pdf > page 23 > > PPS Any advice for using a debugger on firedrake codes? I am used to > debugging PETSc C codes using gdb, but that is not working for me yet. > > > > -- > Ed Bueler > Dept of Math and Stat and Geophysical Institute > University of Alaska Fairbanks > Fairbanks, AK 99775-6660 > 301C Chapman > -- Ed Bueler Dept of Math and Stat and Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775-6660 301C Chapman

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Re: [firedrake] Poisson equation; homogeneous vs nonhomogeneous
by Lawrence Mitchell 24 Apr '18

24 Apr '18

[Re-adding firedrake(a)imperial.ac.uk to CC, please do keep the mailing list in the CC line so that others can see the response too. You'll likely get faster and/or more accurate help that way!] On 23/04/18 21:10, Eric M wrote: > revision: > I put gx in VGrad as well. My outputs are as expected. > Though it seems slightly strange to have what should be an exact > function (gx) interpolated to a discontinuous space. See below. > On Mon, Apr 23, 2018 at 2:51 PM, Eric M <eric.malitz(a)gmail.com > <mailto:eric.malitz@gmail.com>> wrote: > > Aha, there is a confusion here between what is a coefficient > in some finite element space, and what is a symbolic expression. > You start with u, which is a Function in some finite element > space. > Now grad(u)[0], or u.dx(0) (these actually produce the same > thing) are symbolic expressions. > If you want to look at the values, you first need to > interpolate (or project) the expression into a suitable finite > element space: > e.g, if u is in FunctionSpace(mesh, "CG", 2) > Then perhaps: > VGrad = FunctionSpace(mesh, "DG", 1) > gradu = project(grad(u), VGrad) > gradu.dat.data[:] ... > > > For an exact solution g, I have gx, it's derivative. I wish to > compare gx against the x derivative of a solution uk. I have: > > V = FunctionSpace(mesh, "Lagrange", 2) > Sigma = TensorFunctionSpace(mesh, "Lagrange", 2) > gx=Function(V) > gx.interpolate(x*exp((x**2+y**2)/2)) > > VGrad=FunctionSpace(mesh,"DG",1) > > (solve a problem, split uk from the mixed solution so uk is in V) > > gradu_x=project(grad(uk)[0],VGrad) > > But now gradu_x and gx are different lengths. I see why we would > use this VGrad. Does it make sense to do > VGrad=FunctionSpace(mesh,"Lagrange",2) instead? I suggested a DG space because in general the grad of some CG space is not continuous. But if you have some exact expression you can compare to, then you can compute norms directly: gx = x*exp((x**2 + y**2)/2) L2diff = norm(gx - grad(uk)[0]) Make sense? Cheers, Lawrence

2 1

seg faults associated to stokes weak form details
by Ed Bueler 24 Apr '18

24 Apr '18

Dear Firedrake -- My smooth progress with this awesome tool has hit a first barrier. The attached linear stokes code works as is with the "VERSION 1" weak form. Run simply as "python3 ./linflowstep.py". The attached mesh file is read by default. But with "grad()" replaced by "epsilon()", as recommended in the UFL manual*, which is VERSION 2, I get seg fault. Slight modifications do or do not work according to mere value of the constant (see VERSION 3/4 ... weird). Can you reproduce? Any ideas? I seek to use the strain rate tensor (= epsilon(u)) in a nonnewtonian stokes job, but this is blocking. Thanks, Ed PS* https://media.readthedocs.org/pdf/fenics-ufl/stable/fenics-ufl.pdf page 23 PPS Any advice for using a debugger on firedrake codes? I am used to debugging PETSc C codes using gdb, but that is not working for me yet. -- Ed Bueler Dept of Math and Stat and Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775-6660 301C Chapman

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