November 2016 - firedrake - imperial.ac.uk

New firedrake-status command
by David Ham 02 Nov '16

02 Nov '16

Dear Firedrakers, I'm happy to announce a new convenience feature in Firedrake. As of current master, the firedrake-status shell command is available. Typing firedrake-status will print out: * Your current configuration (ie the contents of firedrake_configuration.get_config()) * The current branch and commit of all the Firedrake components. * The value of some critical environment variables. This is useful for working out what state your Firedrake install is in - particularly for checking that you're using the right set of branches. Additionally, running: firedrake-status --log will produce a more verbose set of similar configuration information. This will be very helpful for us in helping you debug configuration and installation issues. Regards, David

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Problem with NonlinearVariationalProblem
by T. M. Bendall 02 Nov '16

02 Nov '16

Dear Firedrakers, Having updated Firedrake I'm having trouble running old code that previously worked. In particular one of the variational solvers isn't working. The code is: Q_initialprob = NonlinearVariationalProblem(Functional, z, bcs = bc1, nest=False) Q_initialsolve = NonlinearVariationalSolver(Q_initialprob, solver_parameters={ 'ksp_type':'gmres', 'pc_type':'lu', 'pc_factor_mat_solver_package': 'mumps' }) And my error message: Traceback (most recent call last): File "src/experiment_stochastic_QG.py", line 32, in <module> main() File "src/experiment_stochastic_QG.py", line 22, in main conserving_stochastic_QG_scheme(k, m) File "/home/tmb15/src/stochastic-gfd/stochastic_QG_paper/src/energy_conserving_stochastic_QG_model.py", line 374, in conserving_stochastic_QG_scheme nest=False) TypeError: __init__() got an unexpected keyword argument 'nest' (firedrake) tmb15@tom-Latitude-E5450:~/src/stochastic-gfd/stochastic_QG_paper$ gedit src/energy_conserving_stochastic_QG_model.py & I don't really know what I'm doing, but I tried just removing "nest = False", and got this error message: Traceback (most recent call last): File "src/experiment_stochastic_QG.py", line 32, in <module> main() File "src/experiment_stochastic_QG.py", line 22, in main conserving_stochastic_QG_scheme(k, m) File "/home/tmb15/src/stochastic-gfd/stochastic_QG_paper/src/energy_conserving_stochastic_QG_model.py", line 384, in conserving_stochastic_QG_scheme Q_initialsolve.solve() File "/home/tmb15/src/firedrake/src/firedrake/firedrake/variational_solver.py", line 192, in solve self.snes.solve(None, v) File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:171835) petsc4py.PETSc.Error: error code 56 [0] SNESSolve() line 4128 in /tmp/pip-Tvwyv5-build/src/snes/interface/snes.c [0] SNESSolve_NEWTONLS() line 230 in /tmp/pip-Tvwyv5-build/src/snes/impls/ls/ls.c [0] KSPSolve() line 620 in /tmp/pip-Tvwyv5-build/src/ksp/ksp/interface/itfunc.c [0] KSPSetUp() line 393 in /tmp/pip-Tvwyv5-build/src/ksp/ksp/interface/itfunc.c [0] PCSetUp() line 968 in /tmp/pip-Tvwyv5-build/src/ksp/pc/interface/precon.c [0] PCSetUp_LU() line 92 in /tmp/pip-Tvwyv5-build/src/ksp/pc/impls/factor/lu/lu.c [0] MatGetOrdering() line 260 in /tmp/pip-Tvwyv5-build/src/mat/order/sorder.c [0] MatGetOrdering_ND() line 19 in /tmp/pip-Tvwyv5-build/src/mat/order/spnd.c [0] No support for this operation for this object type [0] Cannot get rows for matrix type nest Any idea what I should do? Thanks, Tom

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Problems with Firedrake having updated Ubuntu
by T. M. Bendall 02 Nov '16

02 Nov '16

Dear Firedrakers, Last week I made the terrible decision to update the version of Ubuntu on my computer, and amongst other problems I found that Firedrake was no longer working. I tried updating it, but the update kept on failing and I am now trying to reinstall. However this is failing (error message below). Does anyone have any idea how I can fix this? Best, Tom apt 1.2.12 (amd64) Supported modules: *Ver: Standard .deb *Pkg: Debian dpkg interface (Priority 30) Pkg: Debian APT solver interface (Priority -1000) S.L: 'deb' Debian binary tree S.L: 'deb-src' Debian source tree Idx: Debian Source Index Idx: Debian Package Index Idx: Debian Translation Index Idx: Debian dpkg status file Idx: Debian deb file Idx: Debian dsc file Idx: Debian control file Idx: EDSP scenario file Package: build-essential Status: install ok installed Priority: optional Section: devel Installed-Size: 20 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Version: 12.1ubuntu2 Depends: libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11) Description: Informational list of build-essential packages If you do not plan to build Debian packages, you don't need this package. Starting with dpkg (>= 1.14.18) this package is required for building Debian packages. . This package contains an informational list of packages which are considered essential for building Debian packages. This package also depends on the packages on that list, to make it easy to have the build-essential packages installed. . If you have this package installed, you only need to install whatever a package specifies as its build-time dependencies to build the package. Conversely, if you are determining what your package needs to build-depend on, you can always leave out the packages this package depends on. . This package is NOT the definition of what packages are build-essential; the real definition is in the Debian Policy Manual. This package contains merely an informational list, which is all most people need. However, if this package and the manual disagree, the manual is correct. Original-Maintainer: Matthias Klose <doko(a)debian.org> Checking for presence of package build-essential...installed. Package: cmake Status: install ok installed Priority: optional Section: devel Installed-Size: 14215 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Multi-Arch: foreign Version: 3.5.1-1ubuntu3 Depends: cmake-data (= 3.5.1-1ubuntu3), procps, libarchive13, libc6 (>= 2.15), libcurl3 (>= 7.16.2), libexpat1 (>= 2.0.1), libgcc1 (>= 1:3.0), libjsoncpp1, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3) Pre-Depends: dpkg (>= 1.17.5~) Recommends: gcc, make Suggests: codeblocks, eclipse, ninja-build Description: cross-platform, open-source make system CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. CMake is quite sophisticated: it is possible to support complex environments requiring system configuration, pre-processor generation, code generation, and template instantiation. . CMake was developed by Kitware as part of the NLM Insight Segmentation and Registration Toolkit project. The ASCI VIEWS project also provided support in the context of their parallel computation environment. Other sponsors include the Insight, VTK, and VXL open source software communities. Homepage: https://cmake.org/ Original-Maintainer: Debian CMake Team <pkg-cmake-team(a)lists.alioth.debian.org> Checking for presence of package cmake...installed. Package: gfortran Status: install ok installed Priority: optional Section: devel Installed-Size: 15 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Source: gcc-defaults (1.150ubuntu1) Version: 4:5.3.1-1ubuntu1 Provides: fortran-compiler, gfortran-mod-14 Depends: cpp (>= 4:5.3.1-1ubuntu1), gcc (>= 4:5.3.1-1ubuntu1), gfortran-5 (>= 5.3.1-3~) Suggests: gfortran-multilib, gfortran-doc Description: GNU Fortran 95 compiler This is the GNU Fortran 95 compiler, which compiles Fortran 95 on platforms supported by the gcc compiler. It uses the gcc backend to generate optimized code. . This is a dependency package providing the default GNU Fortran 95 compiler. Original-Maintainer: Debian GCC Maintainers <debian-gcc(a)lists.debian.org> Checking for presence of package gfortran...installed. Package: git-core Status: install ok installed Priority: optional Section: vcs Installed-Size: 8 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: all Multi-Arch: foreign Source: git Version: 1:2.7.4-0ubuntu1 Depends: git (>> 1:1.7.0.2) Description: fast, scalable, distributed revision control system (obsolete) Git is popular version control system designed to handle very large projects with speed and efficiency; it is used for many high profile open source projects, most notably the Linux kernel. . Git falls in the category of distributed source code management tools. Every Git working directory is a full-fledged repository with full revision tracking capabilities, not dependent on network access or a central server. . This is a transitional dummy package. The 'git-core' package has been renamed to 'git', which has been installed automatically. This git-core package is now obsolete, and can safely be removed from the system if no other package depends on it. Homepage: https://git-scm.com/ Original-Maintainer: Gerrit Pape <pape(a)smarden.org> Checking for presence of package git-core...installed. Package: libblas-dev Status: install ok installed Priority: optional Section: libdevel Installed-Size: 1063 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Source: lapack Version: 3.6.0-2ubuntu2 Provides: libblas.so Depends: libblas3 (= 3.6.0-2ubuntu2), gfortran Suggests: liblapack-doc-man, liblapack-doc Description: Basic Linear Algebra Subroutines 3, static library This package is a binary incompatible upgrade to the blas-dev package. Several minor changes to the C interface have been incorporated. . BLAS (Basic Linear Algebra Subroutines) is a set of efficient routines for most of the basic vector and matrix operations. They are widely used as the basis for other high quality linear algebra software, for example lapack and linpack. This implementation is the Fortran 77 reference implementation found at netlib. . This package contains a static version of the library. Original-Maintainer: Debian Science Team <debian-science-maintainers(a)lists.alioth.debian.org> Homepage: http://www.netlib.org/lapack/ Checking for presence of package libblas-dev...installed. Package: liblapack-dev Status: install ok installed Priority: optional Section: libdevel Installed-Size: 10696 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Source: lapack Version: 3.6.0-2ubuntu2 Provides: liblapack.so Depends: liblapack3 (= 3.6.0-2ubuntu2), libblas-dev | libblas.so Suggests: liblapack-doc-man, liblapack-doc Description: Library of linear algebra routines 3 - static version LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scientific community. . This package contains a static version of the library. Original-Maintainer: Debian Science Team <debian-science-maintainers(a)lists.alioth.debian.org> Homepage: http://www.netlib.org/lapack/ Checking for presence of package liblapack-dev...installed. Package: libopenmpi-dev Status: install ok installed Priority: extra Section: libdevel Installed-Size: 4212 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Source: openmpi Version: 1.10.2-8ubuntu1 Depends: libc6 (>= 2.8), libopenmpi1.10 (= 1.10.2-8ubuntu1), openmpi-common (= 1.10.2-8ubuntu1), libibverbs-dev (>= 1.1.7), libhwloc-dev Suggests: opennmpi-doc Conflicts: libopenmpi-dev, openmpi-bin (<= 1.2.4-0), openmpi-dev Description: high performance message passing library -- header files Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers. . This package contains the header files and compiler wrappers which are needed to compile and link programs against libopenmpi. Original-Maintainer: Alastair McKinstry <mckinstry(a)debian.org> Homepage: http://www.open-mpi.org/ Checking for presence of package libopenmpi-dev...installed. Package: libspatialindex-dev Status: install ok installed Priority: optional Section: libdevel Installed-Size: 2221 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Multi-Arch: same Source: spatialindex Version: 1.8.5-3 Depends: libspatialindex4v5 (= 1.8.5-3), libspatialindex-c4v5 (= 1.8.5-3) Recommends: pkg-config Description: General framework for developing spatial indices - development files Spatialindex is a C++ library that provides a framework for developing spatial indices. Currently it defines generic interfaces, provides simple main memory and disk based storage managers and a robust implementation of an R*-tree, an MVR-tree and a TPR-tree. . This package contains the development files to build third parties programs. Original-Maintainer: Debian GIS Project <pkg-grass-devel(a)lists.alioth.debian.org> Homepage: http://libspatialindex.github.io/ Checking for presence of package libspatialindex-dev...installed. Package: mercurial Status: install ok installed Priority: optional Section: vcs Installed-Size: 182 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Version: 3.7.3-1ubuntu1 Depends: libc6 (>= 2.14), python (<< 2.8), python (>= 2.7~), ucf (>= 2.0020), mercurial-common (= 3.7.3-1ubuntu1) Recommends: openssh-client Suggests: qct, kdiff3 | kdiff3-qt | kompare | meld | tkcvs | mgdiff Breaks: hgsubversion (<< 1.8.3-2), hgview-common (<< 1.8.1), mercurial-crecord (<= 0.20140626-1), mercurial-git (<< 0.8.3-1), qct (<< 1.7-2~) Description: easy-to-use, scalable distributed version control system Mercurial is a fast, lightweight Source Control Management system designed for efficient handling of very large distributed projects. . Its features include: * O(1) delta-compressed file storage and retrieval scheme * Complete cross-indexing of files and changesets for efficient exploration of project history * Robust SHA1-based integrity checking and append-only storage model * Decentralized development model with arbitrary merging between trees * High-speed HTTP-based network merge protocol * Easy-to-use command-line interface * Integrated stand-alone web interface * Small Python codebase . This package contains the architecture dependent files. Homepage: https://www.mercurial-scm.org/ Original-Maintainer: Python Applications Packaging Team <python-apps-team(a)lists.alioth.debian.org> Checking for presence of package mercurial...installed. Package: openmpi-bin Status: install ok installed Priority: extra Section: net Installed-Size: 410 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Source: openmpi Version: 1.10.2-8ubuntu1 Depends: libc6 (>= 2.8), libopenmpi1.10, openmpi-common (= 1.10.2-8ubuntu1) Suggests: gfortran, openmpi-checkpoint Conflicts: openmpi-bin Conffiles: /etc/openmpi/openmpi-default-hostfile 4d7d71ebdeff9befad1c1077fcede06f /etc/openmpi/openmpi-mca-params.conf a580b08b8d721deffd5d003d57d6f61d /etc/openmpi/openmpi-totalview.tcl 9fb9ef7e46e3f47b6e60c5e7b55f66cc Description: high performance message passing library -- binaries Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers and computer science researchers. . Features: * Full MPI-2 standards conformance * Thread safety and concurrency * Dynamic process spawning * High performance on all platforms * Reliable and fast job management * Network and process fault tolerance * Support network heterogeneity * Single library supports all networks * Run-time instrumentation * Many job schedulers supported * Internationalized error messages * Component-based design, documented APIs . This package contains the Open MPI utility programs. Original-Maintainer: Alastair McKinstry <mckinstry(a)debian.org> Homepage: http://www.open-mpi.org/ Checking for presence of package openmpi-bin...installed. Package: python-dev Status: install ok installed Priority: optional Section: python Installed-Size: 18 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: amd64 Multi-Arch: allowed Source: python-defaults Version: 2.7.11-1 Depends: python (= 2.7.11-1), libpython-dev (= 2.7.11-1), python2.7-dev (>= 2.7.11-1~) Description: header files and a static library for Python (default) Header files, a static library and development tools for building Python modules, extending the Python interpreter or embedding Python in applications. . This package is a dependency package, which depends on Debian's default Python version (currently v2.7). Original-Maintainer: Matthias Klose <doko(a)debian.org> Homepage: http://www.python.org/ Checking for presence of package python-dev...installed. Package: python-pip Status: install ok installed Priority: optional Section: python Installed-Size: 620 Maintainer: Ubuntu Developers <ubuntu-devel-discuss(a)lists.ubuntu.com> Architecture: all Version: 8.1.1-2ubuntu0.2 Depends: ca-certificates, python-pip-whl (= 8.1.1-2ubuntu0.2), python:any (<< 2.8), python:any (>= 2.7.5-5~) Recommends: build-essential, python-all-dev (>= 2.6), python-setuptools, python-wheel Description: alternative Python package installer pip is a replacement for easy_install, and is intended to be an improved Python package installer. It integrates with virtualenv, doesn't do partial installs, can save package state for replaying, can install from non-egg sources, and can install from version control repositories. Homepage: https://pip.pypa.io/en/stable/ Original-Maintainer: Debian Python Modules Team <python-modules-team(a)lists.alioth.debian.org> Checking for presence of package python-pip...installed. Creating firedrake virtualenv. Traceback (most recent call last): File "firedrake-install", line 668, in <module> virtualenv.create_environment("firedrake", site_packages=False) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 1004, in create_environment install_wheel(to_install, py_executable, search_dirs) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 969, in install_wheel 'PIP_NO_INDEX': '1' File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 910, in call_subprocess % (cmd_desc, proc.returncode)) OSError: Command /home/tmb15/src/firedrake/bin/python -c "import sys, pip; sys...d\"] + sys.argv[1:]))" setuptools pip wheel failed with error code 1

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Spectral basis
by David Ham 01 Nov '16

01 Nov '16

Hi James, cc everyone, In response to your question on slack earlier, it depends a little what you want. If you want spectral elements, as in high order finite elements, then the element tabulator FIAT supports them for intervals now, though they need some plumbing into UFL since there don't seem to be the right aliases set up at that level. >From that you can get high order elements on quadrilaterals using the tensor element functionality, although you won't get very good performance in assembly because we don't yet support the sum factorisation algorithm which is required to do that. Miklos is currently working on making that go. If you want triangles then life is somewhat more complicated and you'd need to do significantly more work in FIAT. We could talk about that. If you actually want to make a spectral model (i.e. one mega-high order element) then Firedrake may well not be the right tool, and we should talk about what you really need. Regards, David

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Re: [firedrake] gamg message
by Colin Cotter 01 Nov '16

01 Nov '16

Yes, I just reproduced it on my workstation picking up from a cleanly completed job. cheers --cjc On 1 November 2016 at 09:29, Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk> wrote: > > > On 01/11/16 08:44, Colin Cotter wrote: > > Dear all, > > What does this message mean: > > > No idea. Do you have a simple to reproduce test case? E.g., does it > happen on systems other than archer? > > Lawrence > > > petsc4py.PETSc.Error: error code 77 > > [147] SNESSolve() line 4060 in > > /home2/y07/y07/fdrake/petsc/src/snes/interface/snes.c > > [147] SNESSolve_KSPONLY() line 40 in > > /home2/y07/y07/fdrake/petsc/src/snes/impls/ksponly/ksponly.c > > [147] KSPSolve() line 659 in > > /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itfunc.c > > [147] KSPSolve_GMRES() line 239 in > > /home2/y07/y07/fdrake/petsc/src/ksp/ksp/impls/gmres/gmres.c > > [147] KSPInitialResidual() line 69 in > > /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itres.c > > [147] KSP_PCApply() line 245 in > > /home2/y07/y07/fdrake/petsc/include/petsc/private/kspimpl.h > > [147] PCApply() line 482 in > > /home2/y07/y07/fdrake/petsc/src/ksp/pc/interface/precon.c > > [147] PCApply_FieldSplit_Schur() line 921 in > > /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c > > [147] KSPSolve() line 602 in > > /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itfunc.c > > [147] KSPSetUp() line 393 in > > /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itfunc.c > > [147] PCSetUp() line 968 in > > /home2/y07/y07/fdrake/petsc/src/ksp/pc/interface/precon.c > > [147] PCSetUp_GAMG() line 526 in > > /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/gamg/gamg.c > > [147] PCGAMGCoarsen_AGG() line 1001 in > > /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/gamg/agg.c > > [147] smoothAggs() line 333 in > > /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/gamg/agg.c > > [147] Petsc has generated inconsistent data > > [147] !(matA_1 && !matA_1->compressedrow.use) > > > > I received it when trying to restart a parallel job from a checkpoint > > on Archer. > > > > cheers > > --cjc > > > > -- > > http://www.imperial.ac.uk/people/colin.cotter > > > > www.cambridge.org/9781107663916 <http://www.cambridge.org/9781107663916> > > > > > > > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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gamg message
by Colin Cotter 01 Nov '16

01 Nov '16

Dear all, What does this message mean: petsc4py.PETSc.Error: error code 77 [147] SNESSolve() line 4060 in /home2/y07/y07/fdrake/petsc/src/snes/interface/snes.c [147] SNESSolve_KSPONLY() line 40 in /home2/y07/y07/fdrake/petsc/src/snes/impls/ksponly/ksponly.c [147] KSPSolve() line 659 in /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itfunc.c [147] KSPSolve_GMRES() line 239 in /home2/y07/y07/fdrake/petsc/src/ksp/ksp/impls/gmres/gmres.c [147] KSPInitialResidual() line 69 in /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itres.c [147] KSP_PCApply() line 245 in /home2/y07/y07/fdrake/petsc/include/petsc/private/kspimpl.h [147] PCApply() line 482 in /home2/y07/y07/fdrake/petsc/src/ksp/pc/interface/precon.c [147] PCApply_FieldSplit_Schur() line 921 in /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c [147] KSPSolve() line 602 in /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itfunc.c [147] KSPSetUp() line 393 in /home2/y07/y07/fdrake/petsc/src/ksp/ksp/interface/itfunc.c [147] PCSetUp() line 968 in /home2/y07/y07/fdrake/petsc/src/ksp/pc/interface/precon.c [147] PCSetUp_GAMG() line 526 in /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/gamg/gamg.c [147] PCGAMGCoarsen_AGG() line 1001 in /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/gamg/agg.c [147] smoothAggs() line 333 in /home2/y07/y07/fdrake/petsc/src/ksp/pc/impls/gamg/agg.c [147] Petsc has generated inconsistent data [147] !(matA_1 && !matA_1->compressedrow.use) I received it when trying to restart a parallel job from a checkpoint on Archer. cheers --cjc -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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(no subject)
by Dave Culley 01 Nov '16

01 Nov '16

Hello all, I did a firedrake-update - which worked fine then a firedrake-clean but dmplex seems to throw an error Traceback (most recent call last): File "/home/lcs/Programs/firedrake/bin/firedrake-clean", line 3, in <module> from firedrake.tsfc_interface import clear_cache, TSFCKernel File "/home/lcs/Programs/firedrake/src/firedrake/firedrake/__init__.py", line 29, in <module> from firedrake.assemble import * File "/home/lcs/Programs/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module> from firedrake import assemble_expressions File "/home/lcs/Programs/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 18, in <module> from firedrake import function File "/home/lcs/Programs/firedrake/src/firedrake/firedrake/function.py", line 10, in <module> from firedrake import functionspaceimpl File "/home/lcs/Programs/firedrake/src/firedrake/firedrake/functionspaceimpl.py", line 16, in <module> from firedrake.functionspacedata import get_shared_data File "/home/lcs/Programs/firedrake/src/firedrake/firedrake/functionspacedata.py", line 30, in <module> from firedrake import dmplex as dm_mod ImportError: cannot import name dmplex importing firedrake throws the same error. What was my misstep? Thanks Dave

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