Re: [firedrake] seg faults associated to stokes weak form details
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@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@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
On 24 Apr 2018, at 19:14, Ed Bueler <elbueler@alaska.edu> wrote:
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
This is 20859 commits after the 3.4.2 tag. It's from about three weeks ago. Dunno why the git describe our out is this.
The PETSc Team petsc-maint@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!
Aha, it's a python script, so just run firedrake-status, rather than try to source it. Thanks, Lawrence
Ed
On Mon, Apr 23, 2018 at 2:31 PM, Ed Bueler <elbueler@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 _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (2)
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Ed Bueler
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Lawrence Mitchell