- firedrake - imperial.ac.uk

Locally installed FFC not found on ARCHER
by Eike Mueller 30 Jan '15

30 Jan '15

Dear firedrakers, I need to install my own version of FFC, since the one already installed in /work/y07/y07/fdrake appears not to be compatible with the firedrake version I use: RuntimeError: Incompatible Firedrake version 0.12.0 and FFC version unknown. So I installed FFC locally and added it to PYTHONPATH: /work/n02/n02/eike//git_workspace//firedrake-helmholtzsolver/source:/work/n02/n02/eike//git_workspace//firedrake-bench:/work/n02/n02/eike//git_workspace//pybench:/work/n02/n02/eike//git_workspace//firedrake:/work/n02/n02/eike//git_workspace//PyOP2:/work/n02/n02/eike//git_workspace//petsc4py/cray-gnu-shared/lib/python2.7/site-packages/:/work/n02/n02/eike//git_workspace//COFFEE/build/lib:/work/n02/n02/eike//git_workspace//ffc/build/lib.linux-x86_64-2.7/:/work/n02/n02/eike//Library:/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages:/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages:/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages:/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages:/work/y07/y07/fdrake/instant/lib/python2.7/site-packages:/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages:/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages:/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages:/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib/pyth on2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7:/usr/local/packages/cse/bolt/0.6/modules However, in python, the /work/y07/y07/fdrake version comes *first*, so it always picked up when I import ffc and I keep getting the error message above: eike@eslogin008 $ python Python 2.7.6 |Anaconda 1.9.2 (64-bit)| (default, Jan 17 2014, 10:13:17) [GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import sys >>> print sys.path ['', '/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.4.0_-py2.7-linux-x86_64.egg', '/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages/decorator-3.4.0-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/GridDataFormats-0.2.4-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/extasy.coco-0.1-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/MDAnalysis-0.8.1-py2.7-linux-x86_64.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/GridDataFormats-0.2.4-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/apache_libcloud-0.15.1-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg', '/work/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source', '/work/n02/n02/eike/git_workspace/firedrake-bench', '/work/n02/n02/eike/git_workspace/pybench', '/work/n02/n02/eike/git_workspace/firedrake', '/work/n02/n02/eike/git_workspace/PyOP2', '/work/n02/n02/eike/git_workspace/petsc4py/cray-gnu-shared/lib/python2.7/site-packages', '/work/n02/n02/eike/git_workspace/COFFEE/build/lib', '/work/n02/n02/eike/git_workspace/ffc/build/lib.linux-x86_64-2.7', '/work/n02/n02/eike/Library', '/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages', '/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages', '/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages', '/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages', '/work/y07/y07/fdrake/instant/lib/python2.7/site-packages', '/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages', '/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages', '/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages', '/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib/python2.7/site-packages', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7', '/usr/local/packages/cse/bolt/0.6/modules', '/work/y07/y07/cse/anaconda/1.9.2/lib/python27.zip', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/plat-linux2', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-tk', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-old', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-dynload', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/PIL'] Any idea what is going on here? I can of course remove the unwanted FFC path, but there must be a more obvious solution. Thanks a lot, Eike

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Re: [firedrake] Locally installed FFC not found on ARCHER
by David Ham 29 Jan '15

29 Jan '15

Can we change the way FFC uses setuptools so this doesn't happen? I mean the easy_install faff doesn't occur for all python packages, right? On 29 January 2015 at 11:43, Rathgeber, Florian < florian.rathgeber(a)imperial.ac.uk> wrote: > Eike, I have fixed this, so you should be able to remove your hack. > > For reference: the problem is the following file: > /work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/easy-install.pth > > This file is (re)created *every time* the FFC installation is updated > since FFC uses the setuptools egg installation. Due to a setuptools > "feature" all the eggs contained in this file are *prepended* to > sys.path and end up *before* anything in PYTHONPATH and there is > *nothing* you can do to prevent this. The only fix is to edit this .pth > file and remove or comment the offending lines (first and last). > > What we might be able to do is not actually install FFC but point the > module at the source try and build the extension modules in place. > Thoughts? > > On 29/01/15 11:25, Eike Mueller wrote: > > Hi Lawrence, > > > > ok, adding > > > > import sys > > > sys.path.remove('/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.4.0_-py2.7-linux-x86_64.egg') > > > > > > at the top of firedrake/__init__.py seems to fix it for me. > > > > Thanks, > > > > Eike > > > > > > On 29/01/15 10:37, Lawrence Mitchell wrote: > > On 29/01/15 10:23, Eike Mueller wrote: > >>>> Dear firedrakers, > >>>> > >>>> I need to install my own version of FFC, since the one already > >>>> installed in /work/y07/y07/fdrake appears not to be compatible with > >>>> the firedrake version I use: > >>>> > >>>> RuntimeError: Incompatible Firedrake version 0.12.0 and FFC > >>>> version unknown. > >>>> > >>>> So I installed FFC locally and added it to PYTHONPATH: > >>>> > >>>> > /work/n02/n02/eike//git_workspace//firedrake-helmholtzsolver/source:/work/n02/n02/eike//git_workspace//firedrake-bench:/work/n02/n02/eike//git_workspace//pybench:/work/n02/n02/eike//git_workspace//firedrake:/work/n02/n02/eike//git_workspace//PyOP2:/work/n02/n02/eike//git_workspace//petsc4py/cray-gnu-shared/lib/python2.7/site-packages/:/work/n02/n02/eike//git_workspace//COFFEE/build/lib:/work/n02/n02/eike//git_workspace//ffc/build/lib.linux-x86_64-2.7/:/work/n02/n02/eike//Library:/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages:/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages:/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages:/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages:/work/y07/y07/fdrake/instant/lib/python2.7/site-packages:/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages:/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages:/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages:/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib > /p > >>>> > >> y > > th > >>>> > >>>> > >>>> > on2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7:/usr/local/packages/cse/bolt/0.6/modules > >>>> > >>>> > >>>> > >>>> > >>>> However, in python, the /work/y07/y07/fdrake version comes *first*, > >>>> so it always picked up when I import ffc and I keep getting the > >>>> error message above: > > > > This looks like the standard easy_install disaster. I never know how > > to fix this unfortunately. > > > > Lawrence > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] Locally installed FFC not found on ARCHER
by David Ham 29 Jan '15

29 Jan '15

> > > On 29 January 2015 at 11:51, Rathgeber, Florian < florian.rathgeber(a)imperial.ac.uk> wrote: > On another note: I *really* don't have time to continue maintaining the > fdrake modules on ARCHER and appreciate if someone else (Michael? > Lawrence?) could take on this task. I also don't have time to sort out > this current issue, sorry about that. > > I totally understand. This is in a very literal sense not your job. We will explicitly reallocate this task. David > Florian > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] Locally installed FFC not found on ARCHER
by Andrew McRae 29 Jan '15

29 Jan '15

Why are we installing FFC in the first place? Is it just because there are some C files (which we don't use) that need compiling? On 29 Jan 2015 11:43, "Rathgeber, Florian" <florian.rathgeber(a)imperial.ac.uk> wrote: > Eike, I have fixed this, so you should be able to remove your hack. > > For reference: the problem is the following file: > /work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/easy-install.pth > > This file is (re)created *every time* the FFC installation is updated > since FFC uses the setuptools egg installation. Due to a setuptools > "feature" all the eggs contained in this file are *prepended* to > sys.path and end up *before* anything in PYTHONPATH and there is > *nothing* you can do to prevent this. The only fix is to edit this .pth > file and remove or comment the offending lines (first and last). > > What we might be able to do is not actually install FFC but point the > module at the source try and build the extension modules in place. > Thoughts? > > On 29/01/15 11:25, Eike Mueller wrote: > > Hi Lawrence, > > > > ok, adding > > > > import sys > > > sys.path.remove('/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.4.0_-py2.7-linux-x86_64.egg') > > > > > > at the top of firedrake/__init__.py seems to fix it for me. > > > > Thanks, > > > > Eike > > > > > > On 29/01/15 10:37, Lawrence Mitchell wrote: > > On 29/01/15 10:23, Eike Mueller wrote: > >>>> Dear firedrakers, > >>>> > >>>> I need to install my own version of FFC, since the one already > >>>> installed in /work/y07/y07/fdrake appears not to be compatible with > >>>> the firedrake version I use: > >>>> > >>>> RuntimeError: Incompatible Firedrake version 0.12.0 and FFC > >>>> version unknown. > >>>> > >>>> So I installed FFC locally and added it to PYTHONPATH: > >>>> > >>>> > /work/n02/n02/eike//git_workspace//firedrake-helmholtzsolver/source:/work/n02/n02/eike//git_workspace//firedrake-bench:/work/n02/n02/eike//git_workspace//pybench:/work/n02/n02/eike//git_workspace//firedrake:/work/n02/n02/eike//git_workspace//PyOP2:/work/n02/n02/eike//git_workspace//petsc4py/cray-gnu-shared/lib/python2.7/site-packages/:/work/n02/n02/eike//git_workspace//COFFEE/build/lib:/work/n02/n02/eike//git_workspace//ffc/build/lib.linux-x86_64-2.7/:/work/n02/n02/eike//Library:/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages:/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages:/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages:/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages:/work/y07/y07/fdrake/instant/lib/python2.7/site-packages:/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages:/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages:/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages:/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib > /p > >>>> > >> y > > th > >>>> > >>>> > >>>> > on2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7:/usr/local/packages/cse/bolt/0.6/modules > >>>> > >>>> > >>>> > >>>> > >>>> However, in python, the /work/y07/y07/fdrake version comes *first*, > >>>> so it always picked up when I import ffc and I keep getting the > >>>> error message above: > > > > This looks like the standard easy_install disaster. I never know how > > to fix this unfortunately. > > > > Lawrence > >

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Fwd: Re: [PRISM] PRISM Research Data and Software Management
by Lawrence Mitchell 29 Jan '15

29 Jan '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Imperial firedrakers, for those of you not on the PRISM list, note there is a talk on research data management *today* at 11am in Aeronautics (see below for more info). You may wish to come along. Cheers, Lawrence - -------- Forwarded Message -------- Subject: Re: [PRISM] PRISM Research Data and Software Management Date: Wed, 28 Jan 2015 12:44:32 +0000 From: Chris Cantwell <c.cantwell(a)imperial.ac.uk> Organization: Imperial College London To: prism(a)imperial.ac.uk Dear all, Just to reminder you, we have the PRISM RDM meeting tomorrow at 11am in RH266 (Aeronautics). Cheers, Chris On 18/01/15 20:06, Chris Cantwell wrote: > Dear all, > > Due to the coincidental scheduling of a College-wide RDM review > meeting in this slot, the PRISM RDM micro-workshop has been pushed > back to allow us to hear about the outcome of this meeting. The new > time is: > > *Thursday 29th January, 11am - 1pm* > > The room remains the same. > > Cheers, Chris > > > On 09/01/15 17:05, Chris Cantwell wrote: >> Dear all, >> >> The next PRISM technical seminar will be an micro-workshop on >> research data and software management. >> >> Time: Wednesday 28th January, 2-4pm Place: Roderic Hill >> RH266 (Aeronautics) >> >> There will be a talk from Christian Jacobs on research data >> management using PyRDM and Gerard Gorman will provide a brief >> update on the College's current thinking. There will also be time >> for discussion as to how the PRISM partners can best capitalise >> on this topic. >> >> Cheers, Chris >> >> > - -- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell _______________________________________________ prism mailing list prism(a)imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/prism -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJUygNlAAoJECOc1kQ8PEYvSiAIAMUp7VFAEkylIyGqny96r9Ms DMrFsLUZSOHw3Br0RwQrEzfTziZ+kDTwPSotsE+vV24m7n7ecT3wjd6sRB3jVc4E Yc1BFDXeZEXMRdKATgjTvvfLQwcmEm4v05Z0MzPG/E9DE8kWvQUdIELXPH7YbGdr oW902HGbIxHzS7qcuL6oXisXenZdBcnh9kRCLgNwlRt0Ph4h0MKSqCrd6K/M0n3E 7UeiPUAf4nu5FzG0SNIFtXcv7Tc4PHKgE+kEZ8TgsIYhnUXn+MDMLZCMb2OUfriC ZTRHURc9cehEBznUhUnoPhi3wpcmGeTLkkCckJ6TKPXm/oHXa0cjV3DUveL7QIg= =Z9rP -----END PGP SIGNATURE-----

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petsc4py installation on ARCHER: directory lib/petsc-conf not found
by Eike Mueller 28 Jan '15

28 Jan '15

Dear firedrakers, I'm trying to update my firedrake installation on ARCHER, and I came across an issue with petsc4py. I'm using the dmplex-1d-refinement branch of PETSc (latest version from mapdes), which I can build without problems. When I then try to install petsc4py (branch firedrake, also from mapdes) I get: eike@eslogin006 $ python setup.py install --prefix=`pwd`/$PETSC_ARCH running install running build running build_src running build_py running build_ext error: /work/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/lib/petsc-conf/variables: No such file or directory This directory is not created during the PETSc installation, so it's odd that petsc4py is looking for it. There seem to have been some recent changes to the configuration, see e.g. here: commit 76e91a3c243d089c5102cc8e68a0881b5d48a885 Author: Barry Smith <bsmith(a)mcs.anl.gov> Date: Tue Jan 13 10:11:20 2015 -0600 location of PETSc configuration files was changed to lib/petsc-conf from the previous directory conf I rolled back to petsc4py commit 99a07fb395949e1c03fb0af8954d784f5c3b18fe, but if I try to build then I get the error message below. I suspect that the dmplex-1d-refinement PETSc branch is missing the relevant changes in the master? Should I use a different PETSc branch? Thanks a lot, Eike eike@eslogin006 $ git log -1 commit 99a07fb395949e1c03fb0af8954d784f5c3b18fe Merge: bcfcbe4 02ee487 Author: Lisandro Dalcin <dalcinl(a)gmail.com> Date: Tue Jan 13 17:46:49 2015 +0300 Merge branch 'maint' eike@eslogin006 $ python setup.py install --prefix=`pwd`/$PETSC_ARCH running install running build running build_src running build_py running build_ext PETSC_DIR: /work/n02/n02/eike/git_workspace/petsc PETSC_ARCH: cray-gnu-shared version: 3.5.2 development scalar-type: real precision: double language: CONLY compiler: cc linker: cc building 'PETSc' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/cray-gnu-shared creating build/temp.linux-x86_64-2.7/cray-gnu-shared/src cc -pthread -fPIC -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/work/n02/n02/eike/git_workspace/petsc -I/fs2/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/include -I/work/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/include -I/work/n02/n02/eike/git_workspace/petsc/include -Isrc/include -I/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include -I/work/y07/y07/cse/anaconda/1.9.2/include/python2.7 -c src/PETSc.c -o build/temp.linux-x86_64-2.7/cray-gnu-shared/src/PETSc.o In file included from /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0, from /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/include/petsc4py/numpy.h:11, from src/petsc4py.PETSc.c:240, from src/PETSc.c:3: /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/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 src/PETSc.c:3:0: src/petsc4py.PETSc.c: In function '__pyx_pf_8petsc4py_5PETSc_4SNES_56hasNPC': src/petsc4py.PETSc.c:150802:3: warning: implicit declaration of function 'SNESHasNPC' [-Wimplicit-function-declaration] __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_CHKERR(SNESHasNPC(__pyx_v_self->snes, (&__pyx_v_has_npc))); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[35]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ src/petsc4py.PETSc.c: In function '__pyx_pf_8petsc4py_5PETSc_4SNES_188getCompositeNumber': src/petsc4py.PETSc.c:159512:3: warning: implicit declaration of function 'SNESCompositeGetNumber' [-Wimplicit-function-declaration] __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_CHKERR(SNESCompositeGetNumber(__pyx_v_self->snes, (&__pyx_v_cn))); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[35]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ src/petsc4py.PETSc.c: In function '__pyx_pf_8petsc4py_5PETSc_6DMPlex_120distributeOverlap': src/petsc4py.PETSc.c:211458:47: warning: passing argument 3 of 'DMPlexDistributeOverlap' from incompatible pointer type __pyx_t_3 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, __pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:236, from src/PETSc.c:3: /work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: note: expected 'ISLocalToGlobalMapping' but argument is of type 'struct _p_PetscSF **' PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, ISLocalToGlobalMapping, PetscSF *, DM *); ^ In file included from src/PETSc.c:3:0: src/petsc4py.PETSc.c:211458:47: warning: passing argument 4 of 'DMPlexDistributeOverlap' from incompatible pointer type __pyx_t_3 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, __pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:236, from src/PETSc.c:3: /work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: note: expected 'struct _p_PetscSF **' but argument is of type 'struct _p_DM **' PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, ISLocalToGlobalMapping, PetscSF *, DM *); ^ In file included from src/PETSc.c:3:0: src/petsc4py.PETSc.c:211458:47: error: too few arguments to function 'DMPlexDistributeOverlap' __pyx_t_3 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, __pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:236, from src/PETSc.c:3: /work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: note: declared here PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, ISLocalToGlobalMapping, PetscSF *, DM *); ^ error: command 'cc' failed with exit status 1

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Question on mixed solves: RHS is not defined in product function space
by Eike Mueller 22 Jan '15

22 Jan '15

Dear firedrakers, assume I want to do the following solve of a mixed system: V1 = FunctionSpace(mesh, 'RT', 1) V2 = FunctionSpace(mesh, 'DG', 0) W = V1 * V2 lmbda = 1 u, p = TrialFunctions(W) v, q = TestFunctions(W) f = Function(V1) g = Function(V2) a = (p*q - q*div(u) + lmbda*inner(v, u) + div(v)*p)*dx L = (dot(u,f)+p*g)*dx u = Function(W) solve(a == L, u, solver_parameters=...) But now I take out the line L = (dot(u,f)+p*g)*dx and assume that somewhere I calculate instead: L1 = dot(TestFunction(V1),f)*dx L2 = TestFunction(V2)*g*dx L1 and L2 taken together contain the same information as L, but I can’t write L=L1+L2, because L1 and L2 were not defined using the mixed function spaces (assume that I calculated L1 and L2 somewhere else in the code, and I only use the mixed function spaces in this subroutine). So given L1 and L2, how can I build L, which can be used in the solve? What I currently do is this: m_u = dot(TestFunction(V1),TrialFunction(V1))*dx m_p = TestFunction(V2)*TrialFunction(V2)*dx f_u = Function(V1) f_p = Function(V2) solve(m_u=L1,f_u) solve(m_p=L2,f_p) L = (dot(u,f_u)+p*f_g)*dx which I believe does the right thing, but it involves mass solves. Is there a better way? Can I copy the data over directly? Thanks a lot, Eike -- Dr Eike Hermann Mueller Research Associate (PostDoc) Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 5803 e.mueller(a)bath.ac.uk http://people.bath.ac.uk/em459/

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Meetings this term
by Lawrence Mitchell 15 Jan '15

15 Jan '15

Dear all, we need to set a time for our meetings this term. Last term, 4pm on Tuesdays worked well. Does it still work well? Lawrence

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Re: [firedrake] PyOP2 code generation and C interface
by David Ham 14 Jan '15

14 Jan '15

Yes indeed. In fact Coffee is a better indicator of how you should do code generation, and Pymbolic (by Andreas Klöckner) is better still. On 13 January 2015 at 19:02, Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk> wrote: > > > On 13 Jan 2015, at 18:45, Eike Mueller <e.mueller(a)bath.ac.uk> wrote: > > > > thanks, yes, that's what I was looking for, I will have a look at the > code. I'm asking because our new PhD student, who will work on code > generation for Molecular Dynamics, started this week. So I wanted to get > some ideas as to what you are doing. > > Note, fwiw, that we don't hold up the pyop2 code generation as a paragon > of good programming practice. If you're looking for examples of excellent > code gen, we can probably point to better ones. > > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] PyOP2 code generation and C interface
by David Ham 13 Jan '15

13 Jan '15

Hi Eike, Two important questions there. I think the argument for using ctypes rather than swig is that ctypes is automatic and robust. Swig seems to involve more manual intervention and complexity. The code generation happens in two places. The user kernel is either already a C string or (more usually) is a Coffee AST. The Coffee AST has the built-in ability to generate the C code for that part. However I suspect you are more interested in where the code generation for the wrapper code happens. This happens in host.JITModule.compile . It uses a wrapper template from sequential.JITModule (sequential.JITModule is a subclass of host.JITModule). Is that what you were after? Cheers, David On 12 January 2015 at 22:46, Eike Mueller <e.mueller(a)bath.ac.uk> wrote: > Dear firedrakers, > > am I right in saying that PyOP2 (and firedrake) uses ctypes to access > the methods in the compiled C-libraries? Why did you use ctypes (and not > swig, for example)? I.e. you generate c source files, compile them into .so > libraries and then call that code through ctypes? Which files should I look > at to understand how this works for a simple example (say a parloop)? > compilation.py seems to load a .so library, but where is all the code > generation? > > Thanks, > > Eike > > -- > > Dr Eike Hermann Mueller > Research Associate (PostDoc) > > Department of Mathematical Sciences > University of Bath > Bath BA2 7AY, United Kingdom > > +44 1225 38 5633 <+44%201225%2038%205633> > e.mueller(a)bath.ac.uk > <http://people.bath.ac.uk/em459/>http://people.bath.ac.uk/em459/ > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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