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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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
Hi Tom, On 01/11/16 14:20, T. M. Bendall wrote:
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?
I think this is nothing specific to firedrake-install. But rather that creating the virtualenv is failing. Let's try: $ which virtualenv $ virtualenv testing And see what happens... If that fails, it looks like in the past you installed virtualenv locally, can you pip uninstall it? # Repeat this fixed-point iteration until convergence is achieved $ pip uninstall virtualenv And then try running $ hash -r $ which virtualenv $ virtualenv testing2 If that works, you can blow away the testing/testing2 directories, and firedrake-install should get past this initial failure. Lawrence
Hi Lawrence, Thanks very much for your help. I now tried reinstalling and it failed again, coming up against this: 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 924, in create_environment site_packages=site_packages, clear=clear, symlink=symlink)) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 1129, in install_python copyfile(join(stdlib_dir, fn), join(lib_dir, fn), symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 352, in copyfile copyfileordir(src, dest, symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 327, in copyfileordir shutil.copytree(src, dest, symlink) File "/usr/lib/python2.7/shutil.py", line 177, in copytree os.makedirs(dst) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 17] File exists: '/home/tmb15/src/firedrake/lib/python2.7/lib-dynload' On 01/11/16 14:31, Lawrence Mitchell wrote:
Hi Tom,
On 01/11/16 14:20, T. M. Bendall wrote:
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? I think this is nothing specific to firedrake-install. But rather that creating the virtualenv is failing.
Let's try:
$ which virtualenv $ virtualenv testing
And see what happens...
If that fails, it looks like in the past you installed virtualenv locally, can you pip uninstall it?
# Repeat this fixed-point iteration until convergence is achieved $ pip uninstall virtualenv
And then try running
$ hash -r $ which virtualenv $ virtualenv testing2
If that works, you can blow away the testing/testing2 directories, and firedrake-install should get past this initial failure.
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 01/11/16 14:52, T. M. Bendall wrote:
Hi Lawrence,
Thanks very much for your help. I now tried reinstalling and it failed again, coming up against this:
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 924, in create_environment site_packages=site_packages, clear=clear, symlink=symlink)) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 1129, in install_python copyfile(join(stdlib_dir, fn), join(lib_dir, fn), symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 352, in copyfile copyfileordir(src, dest, symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 327, in copyfileordir shutil.copytree(src, dest, symlink) File "/usr/lib/python2.7/shutil.py", line 177, in copytree os.makedirs(dst) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 17] File exists: '/home/tmb15/src/firedrake/lib/python2.7/lib-dynload'
If you don't care about any existing "firedrake" virtualenv in /home/tmb15/src/firedrake, please remove that entire directory tree. I assume you are running firedrake-install from /home/tmb15/src. If you do care, move it out the way, and then do firedrake-install. Lawrence
Dear Lawrence, Again, thanks for your help. That seemed to work, although I have come up against another error deep inside the installation. Sorry the error message is so long, I'm not sure exactly what the most useful bit would be... Installing firedrake/ /home/tmb15/src/firedrake/bin/pip install --no-deps --ignore-installed firedrake/ Processing ./firedrake Installing collected packages: firedrake Running setup.py install for firedrake ... error Complete output from command /home/tmb15/src/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-3AwIsU-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-XNmbta-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/tmb15/src/firedrake/include/site/python2.7/firedrake: running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/firedrake copying firedrake/output.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/halo.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/optimizer.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/version.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/ufl_expr.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/assembly_cache.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/extrusion_utils.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/plot.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/expression.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/pointeval_utils.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/exceptions.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/linear_solver.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/utility_meshes.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/parameters.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/matrix.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/constant.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/_version.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/interpolation.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/pointquery_utils.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/norms.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/petsc.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/projection.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/variational_solver.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/assemble.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/functionspace.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/functionspaceimpl.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/bcs.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/mesh.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/nullspace.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/logging.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/__init__.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/formmanipulation.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/tsfc_interface.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/assemble_expressions.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/function.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/solving.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/utils.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/checkpointing.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/parloops.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/solving_utils.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/functionspacedata.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/dmhooks.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/vector.py -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/citations.py -> build/lib.linux-x86_64-2.7/firedrake creating build/lib.linux-x86_64-2.7/firedrake/mg copying firedrake/mg/interface.py -> build/lib.linux-x86_64-2.7/firedrake/mg copying firedrake/mg/mesh.py -> build/lib.linux-x86_64-2.7/firedrake/mg copying firedrake/mg/__init__.py -> build/lib.linux-x86_64-2.7/firedrake/mg copying firedrake/mg/utils.py -> build/lib.linux-x86_64-2.7/firedrake/mg copying firedrake/mg/ufl_utils.py -> build/lib.linux-x86_64-2.7/firedrake/mg creating build/lib.linux-x86_64-2.7/firedrake/slope_limiter copying firedrake/slope_limiter/limiter.py -> build/lib.linux-x86_64-2.7/firedrake/slope_limiter copying firedrake/slope_limiter/vertex_based_limiter.py -> build/lib.linux-x86_64-2.7/firedrake/slope_limiter copying firedrake/slope_limiter/__init__.py -> build/lib.linux-x86_64-2.7/firedrake/slope_limiter creating build/lib.linux-x86_64-2.7/firedrake/matrix_free copying firedrake/matrix_free/operators.py -> build/lib.linux-x86_64-2.7/firedrake/matrix_free copying firedrake/matrix_free/__init__.py -> build/lib.linux-x86_64-2.7/firedrake/matrix_free copying firedrake/matrix_free/preconditioners.py -> build/lib.linux-x86_64-2.7/firedrake/matrix_free creating build/lib.linux-x86_64-2.7/firedrake_configuration copying firedrake_configuration/__init__.py -> build/lib.linux-x86_64-2.7/firedrake_configuration copying firedrake/firedrake_geometry.h -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/evaluate.h -> build/lib.linux-x86_64-2.7/firedrake copying firedrake/locate.c -> build/lib.linux-x86_64-2.7/firedrake creating build/lib.linux-x86_64-2.7/firedrake/icons copying firedrake/icons/play.png -> build/lib.linux-x86_64-2.7/firedrake/icons copying firedrake/icons/plus.png -> build/lib.linux-x86_64-2.7/firedrake/icons copying firedrake/icons/minus.png -> build/lib.linux-x86_64-2.7/firedrake/icons UPDATING build/lib.linux-x86_64-2.7/firedrake/_version.py set build/lib.linux-x86_64-2.7/firedrake/_version.py to '0.13.0+752.g812a6f4' running build_ext cythoning firedrake/dmplex.pyx to firedrake/dmplex.c warning: firedrake/dmplex.pyx:1197:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1197:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1589:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1589:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1590:4: Buffer unpacking not optimized away. warning: firedrake/dmplex.pyx:1590:4: Buffer unpacking not optimized away. building 'firedrake.dmplex' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/firedrake mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc4py/include -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include -I/usr/include/python2.7 -c firedrake/dmplex.c -o build/temp.linux-x86_64-2.7/firedrake/dmplex.o In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/dmplex.c:406: /home/tmb15/src/firedrake/local/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 /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscbag.h:4:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:5, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsys.h:241:0: warning: "__STDC_FORMAT_MACROS" redefined #define __STDC_FORMAT_MACROS /* required for using PRId64 from c++ */ ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/numpyconfig.h:4:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h:5, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/dmplex.c:406: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/_numpyconfig.h:30:0: note: this is the location of the previous definition #define __STDC_FORMAT_MACROS 1 ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:270:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode DMAddBoundary(DM, DMBoundaryConditionType, const char[], const char[], PetscInt, PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt *, void *); ^ /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:272:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode DMGetBoundary(DM, PetscInt, DMBoundaryConditionType *, const char **, const char **, PetscInt *, PetscInt *, const PetscInt **, void (**)(), PetscInt *, const PetscInt **, void **); ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:21:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:273:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode PetscDSAddBoundary(PetscDS, DMBoundaryConditionType, const char[], const char[], PetscInt, PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt *, void *); ^ /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:275:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode PetscDSGetBoundary(PetscDS, PetscInt, DMBoundaryConditionType *, const char **, const char **, PetscInt *, PetscInt *, const PetscInt **, void (**)(), PetscInt *, const PetscInt **, void **); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_facet_numbering’: firedrake/dmplex.c:3940:243: warning: passing argument 3 of ‘DMPlexGetSupport’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_12 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm, (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_facets.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_facets.diminfo[0].strides)), (&__pyx_v_cells))); if (unlikely(__pyx_t_12 == -1)) __PYX_ERR(0, 57, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:66:29: 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:5385:126: 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 == -1)) __PYX_ERR(0, 183, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29: 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_14mark_entity_classes’: firedrake/dmplex.c:9833:128: warning: passing argument 4 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_point_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 629, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c:9833:147: warning: passing argument 5 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_point_sf->sf, (&__pyx_v_nroots), (&__pyx_v_nleaves), (&__pyx_v_ilocal), (&__pyx_v_iremote))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 629, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c:9949:85: warning: passing argument 2 of ‘ISGetIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_cell_is->iset, (&__pyx_v_cells))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 644, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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:10237:85: warning: passing argument 2 of ‘ISGetIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_cell_is->iset, (&__pyx_v_cells))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 680, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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:10558:86: warning: passing argument 2 of ‘ISGetIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_facet_is->iset, (&__pyx_v_facets))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 709, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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: In function ‘__pyx_pf_9firedrake_6dmplex_16get_entity_classes’: firedrake/dmplex.c:11507:90: warning: passing argument 2 of ‘ISGetIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_8 = __pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_class_is->iset, (&__pyx_v_indices))); if (unlikely(__pyx_t_8 == -1)) __PYX_ERR(0, 789, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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:11586:94: warning: passing argument 2 of ‘ISRestoreIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_8 = __pyx_f_9firedrake_6dmplex_CHKERR(ISRestoreIndices(__pyx_v_class_is->iset, (&__pyx_v_indices))); if (unlikely(__pyx_t_8 == -1)) __PYX_ERR(0, 795, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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_26plex_renumbering’: firedrake/dmplex.c:15026:88: warning: passing argument 2 of ‘ISGetIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_facet_is->iset, (&__pyx_v_facets))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 1063, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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:15104:92: warning: passing argument 2 of ‘ISRestoreIndices’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_9 = __pyx_f_9firedrake_6dmplex_CHKERR(ISRestoreIndices(__pyx_v_facet_is->iset, (&__pyx_v_facets))); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 1070, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/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_28get_cell_remote_ranks’: firedrake/dmplex.c:15485:123: 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 == -1)) __PYX_ERR(0, 1101, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c:15485:142: 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 == -1)) __PYX_ERR(0, 1101, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_get_edge_global_vertices’: firedrake/dmplex.c:15751:96: 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 == -1)) __PYX_ERR(0, 1138, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29: 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:16430:97: 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 == -1)) __PYX_ERR(0, 1241, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:66:29: 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:16906:126: 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/python2.7/Python.h:42:0, 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:17060:95: 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 == -1)) __PYX_ERR(0, 1361, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:66:29: 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:17274:94: 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 == -1)) __PYX_ERR(0, 1425, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29: 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:17355:105: 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 == -1)) __PYX_ERR(0, 1434, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:62:29: 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_32orientations_facet2cell’: firedrake/dmplex.c:20346:97: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_10 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, __pyx_v_c, (&__pyx_v_cone))); if (unlikely(__pyx_t_10 == -1)) __PYX_ERR(0, 1802, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29: 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:20355:108: warning: passing argument 3 of ‘DMPlexGetConeOrientation’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_10 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetConeOrientation(__pyx_v_plex->dm, __pyx_v_c, (&__pyx_v_cone_orient))); if (unlikely(__pyx_t_10 == -1)) __PYX_ERR(0, 1803, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:62:29: 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:20558:101: warning: passing argument 3 of ‘DMPlexGetCone’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_10 = __pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm, __pyx_v_facet, (&__pyx_v_cone))); if (unlikely(__pyx_t_10 == -1)) __PYX_ERR(0, 1859, __pyx_L1_error) ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0, from firedrake/dmplex.c:408: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29: 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_34exchange_cell_orientations’: firedrake/dmplex.c:20885:122: warning: passing argument 4 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_5 = __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_5 == -1)) __PYX_ERR(0, 1897, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c:20885:141: warning: passing argument 5 of ‘PetscSFGetGraph’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_5 = __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_5 == -1)) __PYX_ERR(0, 1897, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_38prune_sf’: firedrake/dmplex.c:21596:120: 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 == -1)) __PYX_ERR(0, 1957, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscInt ** {aka const int **}’ but argument is of type ‘PetscInt ** {aka int **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c:21596:139: 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 == -1)) __PYX_ERR(0, 1957, __pyx_L1_error) ^ In file included from firedrake/dmplex.c:416:0: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29: note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’ PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote); ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_traverse_cell_string’: firedrake/dmplex.c:17508:7: warning: ‘__pyx_v_support_size’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { ^ firedrake/dmplex.c: In function ‘__pyx_f_9firedrake_6dmplex_locally_orient_quadrilateral_plex’: firedrake/dmplex.c:17869:12: 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_30quadrilateral_facet_orientations.isra.33’: firedrake/dmplex.c:19827:7: warning: ‘__pyx_v_size’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (__pyx_t_48 = 0; __pyx_t_48 < __pyx_t_6; __pyx_t_48+=1) { ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/firedrake/dmplex.o -lpetsc -o build/lib.linux-x86_64-2.7/firedrake/dmplex.so -L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/lib cythoning firedrake/hdf5interface.pyx to firedrake/hdf5interface.c building 'firedrake.hdf5interface' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc4py/include -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include -I/usr/include/python2.7 -c firedrake/hdf5interface.c -o build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12, from firedrake/hdf5interface.c:403: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:270:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode DMAddBoundary(DM, DMBoundaryConditionType, const char[], const char[], PetscInt, PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt *, void *); ^ /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:272:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode DMGetBoundary(DM, PetscInt, DMBoundaryConditionType *, const char **, const char **, PetscInt *, PetscInt *, const PetscInt **, void (**)(), PetscInt *, const PetscInt **, void **); ^ In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:21:0, from firedrake/hdf5interface.c:403: /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:273:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode PetscDSAddBoundary(PetscDS, DMBoundaryConditionType, const char[], const char[], PetscInt, PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt *, void *); ^ /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:275:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] PETSC_EXTERN PetscErrorCode PetscDSGetBoundary(PetscDS, PetscInt, DMBoundaryConditionType *, const char **, const char **, PetscInt *, PetscInt *, const PetscInt **, void (**)(), PetscInt *, const PetscInt **, void **); ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o -lpetsc -o build/lib.linux-x86_64-2.7/firedrake/hdf5interface.so -L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/lib cythoning firedrake/spatialindex.pyx to firedrake/spatialindex.c building 'firedrake.spatialindex' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include -I/home/tmb15/src/firedrake/include -I/usr/include/python2.7 -c firedrake/spatialindex.c -o build/temp.linux-x86_64-2.7/firedrake/spatialindex.o In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/spatialindex.c:406: /home/tmb15/src/firedrake/local/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 /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:409: /usr/include/spatialindex/tools/Tools.h:59:20: fatal error: iostream: No such file or directory compilation terminated. error: command 'mpicc' failed with exit status 1 ---------------------------------------- Command "/home/tmb15/src/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-3AwIsU-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-XNmbta-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/tmb15/src/firedrake/include/site/python2.7/firedrake" failed with error code 1 in /tmp/pip-3AwIsU-build/ Traceback (most recent call last): File "firedrake-install", line 702, in <module> install(p+"/") File "firedrake-install", line 431, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 294, in run_pip_install check_call(pipinstall + args) File "firedrake-install", line 181, in check_call subprocess.check_call(arguments) File "/usr/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/tmb15/src/firedrake/bin/pip', 'install', '--no-deps', '--ignore-installed', 'firedrake/']' returned non-zero exit status 1 On 01/11/16 14:56, Lawrence Mitchell wrote:
On 01/11/16 14:52, T. M. Bendall wrote:
Hi Lawrence,
Thanks very much for your help. I now tried reinstalling and it failed again, coming up against this:
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 924, in create_environment site_packages=site_packages, clear=clear, symlink=symlink)) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 1129, in install_python copyfile(join(stdlib_dir, fn), join(lib_dir, fn), symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 352, in copyfile copyfileordir(src, dest, symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 327, in copyfileordir shutil.copytree(src, dest, symlink) File "/usr/lib/python2.7/shutil.py", line 177, in copytree os.makedirs(dst) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 17] File exists: '/home/tmb15/src/firedrake/lib/python2.7/lib-dynload' If you don't care about any existing "firedrake" virtualenv in /home/tmb15/src/firedrake, please remove that entire directory tree. I assume you are running firedrake-install from /home/tmb15/src.
If you do care, move it out the way, and then do firedrake-install.
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 01/11/16 15:41, T. M. Bendall wrote:
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o -lpetsc -o build/lib.linux-x86_64-2.7/firedrake/hdf5interface.so -L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/lib cythoning firedrake/spatialindex.pyx to firedrake/spatialindex.c building 'firedrake.spatialindex' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include -I/home/tmb15/src/firedrake/include -I/usr/include/python2.7 -c firedrake/spatialindex.c -o build/temp.linux-x86_64-2.7/firedrake/spatialindex.o In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/spatialindex.c:406:
/home/tmb15/src/firedrake/local/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 /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:409: /usr/include/spatialindex/tools/Tools.h:59:20: fatal error: iostream: No such file or directory compilation terminated. error: command 'mpicc' failed with exit status 1
This is the problem. The version of spatialindex shipped with ubuntu has a broken C API. We include our own, but you appear to be picking up the system version. Does it work if you do "apt-get remove libspatialindex-dev"? Lawrence
Dear Lawrence, I'm afraid I'm still having problems, so that doesn't seem to have fixed it. The error looks the same (I've attached the install log) Tom On 01/11/16 17:32, Lawrence Mitchell wrote:
On 01/11/16 15:41, T. M. Bendall wrote:
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o -lpetsc -o build/lib.linux-x86_64-2.7/firedrake/hdf5interface.so -L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/lib cythoning firedrake/spatialindex.pyx to firedrake/spatialindex.c building 'firedrake.spatialindex' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include -I/home/tmb15/src/firedrake/include -I/usr/include/python2.7 -c firedrake/spatialindex.c -o build/temp.linux-x86_64-2.7/firedrake/spatialindex.o In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/spatialindex.c:406:
/home/tmb15/src/firedrake/local/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 /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:409: /usr/include/spatialindex/tools/Tools.h:59:20: fatal error: iostream: No such file or directory compilation terminated. error: command 'mpicc' failed with exit status 1
This is the problem. The version of spatialindex shipped with ubuntu has a broken C API. We include our own, but you appear to be picking up the system version.
Does it work if you do "apt-get remove libspatialindex-dev"?
Lawrence
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On 02/11/16 10:46, T. M. Bendall wrote:
Dear Lawrence,
I'm afraid I'm still having problems, so that doesn't seem to have fixed it. The error looks the same (I've attached the install log)
Aha, the problem is that your firedrake-install script is very old (from before March this year). Can you try pulling a new version following the instructions on the website? Cheers, Lawrence
It seems I hadn't deleted the old install script when tried that before... This has solved it, thank you so much. Tom On 02/11/16 10:50, Lawrence Mitchell wrote:
On 02/11/16 10:46, T. M. Bendall wrote:
Dear Lawrence,
I'm afraid I'm still having problems, so that doesn't seem to have fixed it. The error looks the same (I've attached the install log) Aha, the problem is that your firedrake-install script is very old (from before March this year). Can you try pulling a new version following the instructions on the website?
Cheers,
Lawrence
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Lawrence Mitchell
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T. M. Bendall