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firedrakeproject / firedrake

Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)
https://firedrakeproject.org
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Install script hangs during petsc install on clean 15.10 VM #617

Closed dorugeber closed 9 years ago

dorugeber commented 9 years ago

Terminal output below, in three sections.

andrew@ubuntu:~$ curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 19358  100 19358    0     0  43535      0 --:--:-- --:--:-- --:--:-- 43599
andrew@ubuntu:~$ python firedrake-install
apt 1.0.10.2ubuntu1 for amd64 compiled on Oct  5 2015 15:55:05
Supported modules:
*Ver: Standard .deb
*Pkg:  Debian dpkg interface (Priority 30)
 Pkg:  Debian APT solver interface (Priority -1000)
 S.L: 'deb' Standard Debian binary tree
 S.L: 'deb-src' Standard Debian source tree
 Idx: Debian Source Index
 Idx: Debian Package Index
 Idx: Debian Translation Index
 Idx: Debian dpkg status 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.
dpkg-query: package 'python-dev' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package python-dev...missing.
dpkg-query: package 'git-core' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package git-core...missing.
dpkg-query: package 'mercurial' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package mercurial...missing.
dpkg-query: package 'python-pip' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package python-pip...missing.
dpkg-query: package 'libopenmpi-dev' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package libopenmpi-dev...missing.
dpkg-query: package 'openmpi-bin' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package openmpi-bin...missing.
dpkg-query: package 'libblas-dev' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package libblas-dev...missing.
dpkg-query: package 'liblapack-dev' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package liblapack-dev...missing.
dpkg-query: package 'gfortran' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package gfortran...missing.
dpkg-query: package 'cmake' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Checking for presence of package cmake...missing.
Installing missing packages: python-dev, git-core, mercurial, python-pip, libopenmpi-dev, openmpi-bin, libblas-dev, liblapack-dev, gfortran, cmake.
[sudo] password for andrew: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  autotools-dev cmake-data gfortran-5 git git-man javascript-common
  libblas-common libblas3 libcr0 liberror-perl libexpat1-dev libgfortran-5-dev
  libgfortran3 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev
  libibverbs1 libjs-excanvas libjsoncpp0v5 liblapack3 libltdl-dev libnuma-dev
  libopenmpi1.6 libpython-dev libpython2.7-dev libtool mercurial-common
  ocl-icd-libopencl1 openmpi-common python-colorama python-distlib
  python-ndg-httpsclient python-requests python-setuptools python-urllib3
  python-wheel python2.7-dev
Suggested packages:
  codeblocks eclipse ninja-build gfortran-multilib gfortran-doc
  gfortran-5-multilib gfortran-5-doc libgfortran3-dbg git-daemon-run
  git-daemon-sysvinit git-doc git-el git-email git-gui gitk gitweb git-arch
  git-cvs git-mediawiki git-svn apache2 lighttpd httpd blcr-dkms
  libhwloc-contrib-plugins libtool-doc autoconf automaken gcj-jdk qct kdiff3
  kdiff3-qt kompare meld tkcvs mgdiff python-mysqldb python-pygments
  opencl-icd openmpi-checkpoint python-setuptools-doc python-ntlm
Recommended packages:
  python-dev-all
The following NEW packages will be installed:
  autotools-dev cmake cmake-data gfortran gfortran-5 git git-core git-man
  javascript-common libblas-common libblas-dev libblas3 libcr0 liberror-perl
  libexpat1-dev libgfortran-5-dev libgfortran3 libhwloc-dev libhwloc-plugins
  libhwloc5 libibverbs-dev libibverbs1 libjs-excanvas libjsoncpp0v5
  liblapack-dev liblapack3 libltdl-dev libnuma-dev libopenmpi-dev
  libopenmpi1.6 libpython-dev libpython2.7-dev libtool mercurial
  mercurial-common ocl-icd-libopencl1 openmpi-bin openmpi-common
  python-colorama python-dev python-distlib python-ndg-httpsclient python-pip
  python-requests python-setuptools python-urllib3 python-wheel python2.7-dev
0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
Need to get 51.5 MB of archives.
After this operation, 156 MB of additional disk space will be used.
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Get:33 http://archive.ubuntu.com/ubuntu/ wily/universe python-colorama all 0.3.3-1 [21.4 kB]
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Get:37 http://archive.ubuntu.com/ubuntu/ wily/main python-ndg-httpsclient all 0.4.0-1 [24.9 kB]
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Get:39 http://archive.ubuntu.com/ubuntu/ wily/main python-requests all 2.7.0-3 [53.8 kB]
Get:40 http://archive.ubuntu.com/ubuntu/ wily/main python-setuptools all 18.4-1 [171 kB]
Get:41 http://archive.ubuntu.com/ubuntu/ wily/universe python-pip all 1.5.6-7ubuntu1 [99.5 kB]
Get:42 http://archive.ubuntu.com/ubuntu/ wily/universe python-wheel all 0.26.0-1 [46.4 kB]
Get:43 http://archive.ubuntu.com/ubuntu/ wily/main libnuma-dev amd64 2.0.10-1ubuntu6 [31.7 kB]
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Get:45 http://archive.ubuntu.com/ubuntu/ wily/main ocl-icd-libopencl1 amd64 2.2.7-2 [29.7 kB]
Get:46 http://archive.ubuntu.com/ubuntu/ wily/universe libhwloc-plugins amd64 1.11.0-1 [12.1 kB]
Get:47 http://archive.ubuntu.com/ubuntu/ wily/main libibverbs-dev amd64 1.1.8-1.1ubuntu1 [77.2 kB]
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Fetched 51.5 MB in 13s (3,762 kB/s)                                            
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
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Setting up libblas3 (1.2.20110419-10) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-10) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
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update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
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update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
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Setting up mercurial-common (3.4-1ubuntu2) ...
Setting up mercurial (3.4-1ubuntu2) ...

Creating config file /etc/mercurial/hgrc.d/hgext.rc with new version
Setting up libibverbs1 (1.1.8-1.1ubuntu1) ...
Setting up libopenmpi1.6 (1.6.5-11) ...
Setting up openmpi-common (1.6.5-11) ...
Setting up openmpi-bin (1.6.5-11) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up python-colorama (0.3.3-1) ...
Setting up python2.7-dev (2.7.10-4ubuntu1) ...
Setting up python-dev (2.7.9-1) ...
Setting up python-distlib (0.2.1-1) ...
Setting up python-ndg-httpsclient (0.4.0-1) ...
Setting up python-urllib3 (1.11-1) ...
Setting up python-requests (2.7.0-3) ...
Setting up python-setuptools (18.4-1) ...
Setting up python-pip (1.5.6-7ubuntu1) ...
Setting up python-wheel (0.26.0-1) ...
Setting up libnuma-dev:amd64 (2.0.10-1ubuntu6) ...
Setting up libhwloc-dev:amd64 (1.11.0-1) ...
Setting up ocl-icd-libopencl1:amd64 (2.2.7-2) ...
Setting up libhwloc-plugins (1.11.0-1) ...
Setting up libibverbs-dev (1.1.8-1.1ubuntu1) ...
Setting up libopenmpi-dev (1.6.5-11) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Processing triggers for libc-bin (2.21-0ubuntu4) ...
Installing virtualenv.
Downloading/unpacking virtualenv
  Downloading virtualenv-13.1.2-py2.py3-none-any.whl (1.7MB): 1.7MB downloaded
Installing collected packages: virtualenv
Successfully installed virtualenv
Cleaning up...
Virtual env installed. Please run firedrake-install again.
andrew@ubuntu:~$ python firedrake-install
apt 1.0.10.2ubuntu1 for amd64 compiled on Oct  5 2015 15:55:05
Supported modules:
*Ver: Standard .deb
*Pkg:  Debian dpkg interface (Priority 30)
 Pkg:  Debian APT solver interface (Priority -1000)
 S.L: 'deb' Standard Debian binary tree
 S.L: 'deb-src' Standard Debian source tree
 Idx: Debian Source Index
 Idx: Debian Package Index
 Idx: Debian Translation Index
 Idx: Debian dpkg status 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: python-dev
Status: install ok installed
Priority: optional
Section: python
Installed-Size: 45
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Multi-Arch: allowed
Source: python-defaults
Version: 2.7.9-1
Depends: python (= 2.7.9-1), libpython-dev (= 2.7.9-1), python2.7-dev (>= 2.7.9-1~)
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: 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: 1:2.5.0-1
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.
Original-Maintainer: Gerrit Pape <pape@smarden.org>
Homepage: http://git-scm.com/
Checking for presence of package git-core...installed.
Package: mercurial
Status: install ok installed
Priority: optional
Section: vcs
Installed-Size: 213
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Version: 3.4-1ubuntu2
Depends: libc6 (>= 2.14), python (<< 2.8), python (>= 2.7~), ucf (>= 2.0020), mercurial-common (= 3.4-1ubuntu2)
Recommends: openssh-client
Suggests: qct, kdiff3 | kdiff3-qt | kompare | meld | tkcvs | mgdiff
Breaks: hgsubversion (<< 1.8-1), hgview-common (<< 1.8.1), mercurial-git (<= 0.6.1-2), 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: http://mercurial.selenic.com/
Original-Maintainer: Python Applications Packaging Team <python-apps-team@lists.alioth.debian.org>
Checking for presence of package mercurial...installed.
Package: python-pip
Status: install ok installed
Priority: optional
Section: python
Installed-Size: 457
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: all
Version: 1.5.6-7ubuntu1
Depends: ca-certificates, python-colorama, python-distlib, python-html5lib, python-pkg-resources, python-requests, python-setuptools (>= 0.6c1), python-six, python, python:any (<< 2.8), python:any (>= 2.7.5-5~)
Recommends: build-essential, python-dev-all (>= 2.6), 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: http://www.pip-installer.org/
Original-Maintainer: Debian Python Modules Team <python-modules-team@lists.alioth.debian.org>
Checking for presence of package python-pip...installed.
Package: libopenmpi-dev
Status: install ok installed
Priority: extra
Section: libdevel
Installed-Size: 2879
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Source: openmpi
Version: 1.6.5-11
Depends: libc6 (>= 2.8), libopenmpi1.6 (= 1.6.5-11), openmpi-common (= 1.6.5-11), libibverbs-dev (>= 1.1.7), libhwloc-dev
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: Debian Open MPI Maintainers <pkg-openmpi-maintainers@lists.alioth.debian.org>
Homepage: http://www.open-mpi.org/
Checking for presence of package libopenmpi-dev...installed.
Package: openmpi-bin
Status: install ok installed
Priority: extra
Section: net
Installed-Size: 381
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Source: openmpi
Version: 1.6.5-11
Depends: libc6 (>= 2.8), libopenmpi1.6, openmpi-common (= 1.6.5-11)
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: Debian Open MPI Maintainers <pkg-openmpi-maintainers@lists.alioth.debian.org>
Homepage: http://www.open-mpi.org/
Checking for presence of package openmpi-bin...installed.
Package: libblas-dev
Status: install ok installed
Priority: optional
Section: libdevel
Installed-Size: 1251
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Source: blas
Version: 1.2.20110419-10
Provides: libblas.so
Depends: libblas3 (= 1.2.20110419-10)
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/blas/
Checking for presence of package libblas-dev...installed.
Package: liblapack-dev
Status: install ok installed
Priority: optional
Section: libdevel
Installed-Size: 10592
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Source: lapack
Version: 3.5.0-4
Provides: liblapack.so
Depends: liblapack3 (= 3.5.0-4), libblas-dev | libblas.so
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.
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: 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 (1.144ubuntu1)
Version: 4:5.2.1-3ubuntu1
Provides: fortran-compiler
Depends: cpp (>= 4:5.2.1-3ubuntu1), gcc (>= 4:5.2.1-3ubuntu1), gfortran-5 (>= 5.2.1-12~)
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: cmake
Status: install ok installed
Priority: optional
Section: devel
Installed-Size: 13822
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Multi-Arch: foreign
Version: 3.2.2-2ubuntu3
Depends: cmake-data (= 3.2.2-2ubuntu3), procps, libarchive13, libc6 (>= 2.15), libcurl3 (>= 7.16.2), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libjsoncpp0v5, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Pre-Depends: dpkg (>= 1.17.5~)
Recommends: gcc, make
Suggests: codeblocks, eclipse, ninja-build
Conffiles:
 /etc/bash_completion.d/cmake 89a2635a79da8cbc1c78dd7e50e56898
 /etc/bash_completion.d/cpack 8d65632f9a6c67527019978f17469d7d
 /etc/bash_completion.d/ctest 6d4ba44ad1a0f63e9a6415c6e4ff36bc
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: http://cmake.org/
Original-Maintainer: Modestas Vainius <modax@debian.org>
Checking for presence of package cmake...installed.
Creating firedrake virtualenv.
/home/andrew/firedrake/bin/pip install -U pip
Requirement already up-to-date: pip in ./firedrake/lib/python2.7/site-packages
Cloning firedrake
The authenticity of host 'github.com (192.30.252.129)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'github.com,192.30.252.129' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone firedrake using ssh, falling back to https.
Cloning into 'firedrake'...
remote: Counting objects: 12602, done.
remote: Compressing objects: 100% (156/156), done.
remote: Total 12602 (delta 106), reused 12 (delta 12), pack-reused 12434
Receiving objects: 100% (12602/12602), 11.54 MiB | 774.00 KiB/s, done.
Resolving deltas: 100% (8214/8214), done.
Checking connectivity... done.
Successfully cloned firedrake branch master.
Cloning the dependencies of firedrake
Cloning instant
The authenticity of host 'bitbucket.org (131.103.20.167)' can't be established.
RSA key fingerprint is SHA256:zzXQOXSRBEiUtuE8AikJYKwbHaxvSc0ojez9YXaGp1A.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'bitbucket.org,131.103.20.167' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone instant using ssh, falling back to https.
Cloning into 'instant'...
remote: Counting objects: 2893, done.
remote: Compressing objects: 100% (941/941), done.
remote: Total 2893 (delta 1970), reused 2580 (delta 1755)
Receiving objects: 100% (2893/2893), 533.96 KiB | 383.00 KiB/s, done.
Resolving deltas: 100% (1970/1970), done.
Checking connectivity... done.
Successfully cloned instant branch master.
Cloning ufl
Warning: Permanently added the RSA host key for IP address '131.103.20.168' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone ufl using ssh, falling back to https.
Cloning into 'ufl'...
remote: Counting objects: 18321, done.
remote: Compressing objects: 100% (4780/4780), done.
remote: Total 18321 (delta 14808), reused 16934 (delta 13511)
Receiving objects: 100% (18321/18321), 2.89 MiB | 674.00 KiB/s, done.
Resolving deltas: 100% (14808/14808), done.
Checking connectivity... done.
Successfully cloned ufl branch master.
Cloning fiat
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone fiat using ssh, falling back to https.
Cloning into 'fiat'...
remote: Counting objects: 2326, done.
remote: Compressing objects: 100% (1018/1018), done.
remote: Total 2326 (delta 1626), reused 1800 (delta 1268)
Receiving objects: 100% (2326/2326), 480.45 KiB | 407.00 KiB/s, done.
Resolving deltas: 100% (1626/1626), done.
Checking connectivity... done.
Successfully cloned fiat branch master.
Cloning ffc
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone ffc using ssh, falling back to https.
Cloning into 'ffc'...
remote: Counting objects: 33048, done.
remote: Compressing objects: 100% (7864/7864), done.
remote: Total 33048 (delta 24563), reused 32949 (delta 24496)
Receiving objects: 100% (33048/33048), 4.83 MiB | 595.00 KiB/s, done.
Resolving deltas: 100% (24563/24563), done.
Checking connectivity... done.
Successfully cloned ffc branch master.
Cloning PyOP2
Warning: Permanently added the RSA host key for IP address '192.30.252.128' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone PyOP2 using ssh, falling back to https.
Cloning into 'PyOP2'...
remote: Counting objects: 17282, done.
remote: Compressing objects: 100% (84/84), done.
remote: Total 17282 (delta 54), reused 0 (delta 0), pack-reused 17198
Receiving objects: 100% (17282/17282), 9.01 MiB | 766.00 KiB/s, done.
Resolving deltas: 100% (11572/11572), done.
Checking connectivity... done.
Successfully cloned PyOP2 branch master.
Cloning the dependencies of PyOP2
Cloning petsc
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone petsc using ssh, falling back to https.
Cloning into 'petsc'...
remote: Counting objects: 637500, done.
remote: Compressing objects: 100% (176541/176541), done.
remote: Total 637500 (delta 486125), reused 597445 (delta 458009)
Receiving objects: 100% (637500/637500), 117.43 MiB | 635.00 KiB/s, done.
Resolving deltas: 100% (486125/486125), done.
Checking connectivity... done.
Successfully cloned petsc branch firedrake.
Cloning petsc4py
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone petsc4py using ssh, falling back to https.
Cloning into 'petsc4py'...
remote: Counting objects: 9949, done.
remote: Compressing objects: 100% (2788/2788), done.
remote: Total 9949 (delta 7507), reused 9175 (delta 6904)
Receiving objects: 100% (9949/9949), 1.33 MiB | 618.00 KiB/s, done.
Resolving deltas: 100% (7507/7507), done.
Checking connectivity... done.
Successfully cloned petsc4py branch firedrake.
Cloning COFFEE
Warning: Permanently added the RSA host key for IP address '192.30.252.130' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone COFFEE using ssh, falling back to https.
Cloning into 'COFFEE'...
remote: Counting objects: 2874, done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 2874 (delta 0), reused 0 (delta 0), pack-reused 2870
Receiving objects: 100% (2874/2874), 885.35 KiB | 757.00 KiB/s, done.
Resolving deltas: 100% (2094/2094), done.
Checking connectivity... done.
Successfully cloned COFFEE branch master.
/home/andrew/firedrake/bin/pip install Cython>=0.22
Collecting Cython>=0.22
  Downloading Cython-0.23.4.tar.gz (1.6MB)
    100% |████████████████████████████████| 1.6MB 277kB/s 
Building wheels for collected packages: Cython
  Running setup.py bdist_wheel for Cython
  Stored in directory: /home/andrew/.cache/pip/wheels/54/26/ba/05c8576cfb4c49c315c618d4a7ffd4df636b3df1d521f53f2c
Successfully built Cython
Installing collected packages: Cython
Successfully installed Cython-0.23.4
Installing petsc/
/home/andrew/firedrake/bin/pip install --no-deps --ignore-installed petsc/
Processing ./petsc
Installing collected packages: petsc
  Running setup.py install for petsc

One hour later, it was still at this stage.

^CTraceback (most recent call last):
  File "firedrake-install", line 422, in <module>
    install("petsc/")
  File "firedrake-install", line 268, in install
    run_pip(["--ignore-installed", package])
  File "firedrake-install", line 249, in run_pip
    check_call(sudopip + args)
  File "firedrake-install", line 163, in check_call
    subprocess.check_call(arguments)
  File "/usr/lib/python2.7/subprocess.py", line 535, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib/python2.7/subprocess.py", line 1384, in wait
    pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
  File "/usr/lib/python2.7/subprocess.py", line 476, in _eintr_retry_call
    return func(*args)
KeyboardInterrupt
andrew@ubuntu:~$ Operation cancelled by user
^C
andrew@ubuntu:~$
dorugeber commented 9 years ago

Running python firedrake-install again fails at

...
Creating firedrake virtualenv.
/home/andrew/firedrake/bin/pip install -U pip
Requirement already up-to-date: pip in ./firedrake/lib/python2.7/site-packages
Traceback (most recent call last):
  File "firedrake-install", line 405, in <module>
    os.mkdir("src")
OSError: [Errno 17] File exists: 'src'
dham commented 9 years ago

Can you verify that petsc will pip install outside of the install script? Also, is it conceivable that Petsc just takes an hour to build on your machine?

dorugeber commented 9 years ago

Running pip install --no-deps --ignore-installed petsc/ from the ~/firedrake/src directory works (in under 5 minutes).

dorugeber commented 9 years ago 
(firedrake)andrew@ubuntu:~/firedrake/src$ pip install --no-deps --ignore-installed petsc/
Processing ./petsc
Installing collected packages: petsc
  Running setup.py install for petsc
Successfully installed petsc-3.7.0.dev0
dham commented 9 years ago

I'm mystified. That's exactly what the script does.

dorugeber commented 9 years ago

Will try that again from clean, in case my non-virtualenv petsc install messed things up.

dorugeber commented 9 years ago

I'll close this, because I believe you were right that "Petsc just takes [more than] an hour to build". It took the best part of an hour on my (faster) desktop... I didn't realise PETSc is set to install a bunch of packages by default, unless the appropriate flag is set.

Unfortunately the new install wasn't error-free, so I'll dump that in a new issue.