OK, now it is not finding some libraries: In file included from /usr/include/spatialindex/SpatialIndex.h:30:0, from /usr/include/spatialindex/capi/sidx_config.h:56, from /usr/include/spatialindex/capi/sidx_api.h:34, from firedrake/spatialindex.c:245: /usr/include/spatialindex/tools/Tools.h:59:20: fatal error: iostream: No such file or directory #include <iostream> ^ compilation terminated. error: command 'mpicc' failed with exit status 1 all the best --cjc On 25 June 2016 at 15:41, Homolya, Miklós <m.homolya14@imperial.ac.uk> wrote:
I have seen such problems already, so it might be systematic, but I'm not sure what are the exact circumstances that trigger this problem.
Try:
make clean all
in the Firedrake source directory. ------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Colin Cotter <colin.cotter@imperial.ac.uk> *Sent:* 25 June 2016 14:54:41 *To:* firedrake *Subject:* [firedrake] missing 'comm'
Dear Firedrakers, Upon calling
mesh = IcosahedralSphereMesh(1.0,3,2)
I get an error,
Traceback (most recent call last): File "dcmip_3-1_linear_advection_triangle_bdfm1.py", line 31, in <module> extrusion_type="radial") File "<decorator-gen-274>", line 2, in ExtrudedMesh File "/home/cjc1/firedrake-dev/firedrake/src/PyOP2/pyop2/profiling.py", line 59, in wrapper return f(*args, **kwargs) File "/home/cjc1/firedrake-dev/firedrake/src/firedrake/firedrake/mesh.py", line 1232, in ExtrudedMesh mesh.init() File "/home/cjc1/firedrake-dev/firedrake/src/firedrake/firedrake/mesh.py", line 831, in init self._callback(self) File "/home/cjc1/firedrake-dev/firedrake/src/firedrake/firedrake/mesh.py", line 1165, in callback self.topology.init() File "<decorator-gen-272>", line 2, in init File "/home/cjc1/firedrake-dev/firedrake/src/PyOP2/pyop2/profiling.py", line 59, in wrapper return f(*args, **kwargs) File "/home/cjc1/firedrake-dev/firedrake/src/firedrake/firedrake/mesh.py", line 407, in init self._callback(self) File "/home/cjc1/firedrake-dev/firedrake/src/firedrake/firedrake/mesh.py", line 375, in callback dmplex.mark_entity_classes(self._plex) File "firedrake/dmplex.pyx", line 632, in firedrake.dmplex.mark_entity_classes (firedrake/dmplex.c:9423) AttributeError: 'module' object has no attribute 'comm'
Is this another petsc4py issue?
cheers --cjc
-- http://www.imperial.ac.uk/people/colin.cotter
www.cambridge.org/9781107663916
-- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916
Hi FDs, (i) The upwind example is odd in that the real boundaries are treated in a special way rather than setting the outside value in the same numerical flux as anywhere else; my question is how this can be fixed? So no special terms at the in- and outflow, just specify the outside velocity used. This is imo the proper DG way not was is done now. (ii) Attached my attempt to do a time dependent advection with Crank Nicolson, which works but does not yet give the right answer, in part due to (i). [I don't understand why I have to make my theta variable that a constant but other wise it did not work.] Any suggestions, corrections, also on other silly things done by me? Next step is to extend to system with 3 equations; hence the few extra but unused variables. Thanks, from midnight Seoul in old style Korean guesthouse. Onno ________________________________
Hello Onno, I just tried running your code but see that I can't because I don't have the rectmesh.msh. Might you be able to send that so we can see exactly what you see? Francis P.S. I would also be curious to see the gmsh file that generated the msh file if possible. ------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 ________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Onno Bokhove [O.Bokhove@leeds.ac.uk] Sent: Saturday, June 25, 2016 11:05 AM To: firedrake Subject: [firedrake] upwind example remark; extension to CN in time Hi FDs, (i) The upwind example is odd in that the real boundaries are treated in a special way rather than setting the outside value in the same numerical flux as anywhere else; my question is how this can be fixed? So no special terms at the in- and outflow, just specify the outside velocity used. This is imo the proper DG way not was is done now. (ii) Attached my attempt to do a time dependent advection with Crank Nicolson, which works but does not yet give the right answer, in part due to (i). [I don't understand why I have to make my theta variable that a constant but other wise it did not work.] Any suggestions, corrections, also on other silly things done by me? Next step is to extend to system with 3 equations; hence the few extra but unused variables. Thanks, from midnight Seoul in old style Korean guesthouse. Onno ________________________________
participants (3)
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Colin Cotter
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Francis Poulin
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Onno Bokhove