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INRIA Paris/Rocquencourt Conda Packages Documentation Release 1.0.0 INRIA Paris/Rocquencourt Conda packages Documentation Release 1.0.0 David Froger Jun 05, 2017 Contents 1 User documentation 3 1.1 Getting started..............................................3 1.2 Package listing..............................................4 1.3 Package details..............................................9 1.4 Linking with packages.......................................... 10 2 Packager documentation 13 2.1 External links............................................... 13 2.2 build.sh guidelines............................................. 13 2.3 Vagrant boxes.............................................. 16 2.4 Package testing.............................................. 17 2.5 Documenting............................................... 17 3 Contact 19 i ii INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 The INRIA Paris-Rocquencourt SED Conda channel aims at easily distributing scientific softwares and libraries using the Conda package manager. Supported platforms are GNU/Linux 64 bits (old system like CentOS 5 are not supported) and OSX from 10.7 to 10.11. Windows is not supported yet (no plan to support it for now). Root privileges are not required, except for installing compilers in the system. Conda recipes are available. Contents 1 INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 2 Contents CHAPTER 1 User documentation Getting started Prerequisites on GNU/Linux Install gcc, g++, and gfortran. For example, using apt-get: sudo apt-get install gcc g++ gfortran or using yum: yum install gcc-c++ gcc-gfortran Prerequisites on OSX Install Xcode Command Line Tools. Download gfortran (select the gfortran-X.X-bin.tar.gz package) from HPC Mac OS X, and install it: sudo tar xvzf gfortran-X.X-bin.tar.gz -C / Conda installation Download the Conda installer, and install conda: On GNU/Linux 64 bits: wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh bash Miniconda-latest-Linux-x86_64.sh or, on OSX: 3 INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 curl -O https://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh bash Miniconda-latest-MacOSX-x86_64.sh You will be asked for a place to install miniconda. Either choose the default $HOME/miniconda or a custom place, for example /local/<user>/miniconda. At the end of the installation, you will be asked for modifying your Bash configuration file (~/.bashrc on GNU/Linux, or ~/.bash_profile on OSX): answer yes. To take this modification into account, either open a new terminal, or update the one you are using with: source ~/.bashrc # on GNU/Linux source ~/.bash_profile # on OSX Note: the Conda cheat sheet is a usefull ressource to get started with Conda, (managing environments for example is worth to learn). Installing packages Install a package provided by the The INRIA Paris-Rocquencourt SED Conda channel , for example: conda install -c inria-pro-sed petsc Your may also want to add the inria-pro-sed Conda channel to your configuration (this modify your ~/.condarc): conda config --add channels inria-pro-sed in order to omit the -c option: conda install petsc Package listing Linear algebra libraries Available libraries are: 4 Chapter 1. User documentation INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 Pack- Description Links age METIS Serial Graph Partitioning and Fill-reducing Matrix Ordering recipe, pack- ages Mumps A parallel sparse direct solver recipe, pack- ages Open Open MPI: A high performance message passing library recipe, MPI pack- ages ParMETIS ParMETIS is an MPI-based parallel library that implements a variety of algorithms for recipe, partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of pack- sparse matrices. ages PETSc PETSc: Portable, Extensible Toolkit for Scientific Computation recipe, pack- ages ScaLA- ScaLAPACK is a library of high-performance linear algebra routines for parallel recipe, PACK distributed memory machines. pack- ages Su- SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric recipe, perLU_DISTsystems of linear equations on high performance machines. pack- ages Eigen Eigen is a C++ template library for linear algebra. recipe, pack- ages Note: • Open MPI is build with C, C++ and Fortran API. Relationships between main libraries are (blue indicate package provided by continuum.io). 1.2. Package listing 5 INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 PETSc SuperLU_DIST Mumps ScaLAPACK ParMETIS OpenBLAS OpenMPI METIS dolfin boost qt vtk Eigen3 ffc ply OpenMPI ufl fiat instant six sympy numpy SWIG CMake 6 Chapter 1. User documentation INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 Image processing libraries (not yet available) Pack- Description Links age Open- OpenMVS (Multi-View Stereo) is a library for computer-vision scientists and recipe, MVS especially targeted to the Multi-View Stereo reconstruction community. packages Open- “open Multiple View Geometry” is a library for computer-vision scientists and recipe, MVG especially targeted to the Multiple View Geometry community. packages GLFW GLFW is an Open Source, multi-platform library for creating windows with OpenGL recipe, package contexts and receiving input and events. OpenExifOpenExif is an object-oriented library for accessing Exif formatted JPEG image files. recipe, package OSI Osi (Open Solver Interface) provides an abstract base class to a generic linear recipe, package programming (LP) solver, along with derived classes for specific solvers. CLP Clp (Coin-or linear programming) is an open-source linear programming solver recipe, package written in C++. Mesa Mesa is an open-source implementation of the OpenGL specification - a system for recipe not rendering interactive 3D graphics. available, package OpenMVS OpenMVG GLFW OpenEXIF CLP OSI Mesa Software engineering tools Available tools: 1.2. Package listing 7 INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 Package Description Links buildbot- Buildbot is an open-source framework for automating software build, test, and recipe, master release processes. packages buildbot- Buildbot is an open-source framework for automating software build, test, and recipe, slave release processes. packages klink A Simple and Clean Sphinx Docs Theme recipe, packages nbtools Tools for managing IPython notebooks recipe, packages Relationships between main libraries are (blue indicate package provided by continuum.io). Buildbot Master python2.7 Twisted Jinja2 dateutil SQLAlchemy Migrate SQLAlchemy Decorator Tempita nbtools Python Jinja2 IPython Notebook matplotlib nose ghdiff chardet File format libraries Available libraries: 8 Chapter 1. User documentation INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 Pack- Description Links age GetPot Powerful Input File and Command Line Parser recipe, packages h5utils h5utils is a set of utilities for visualization and conversion of scientific data in the free, recipe, portable HDF5 format. packages HDF5 HDF5 is a data model, library, and file format for storing and managing data. recipe, packages LM5 Reads and writes mesh files (.mesh) or physical solution files (.sol) recipe, packages yaml- A YAML parser and emitter in C++ recipe, cpp packages Note: • HDF5 is build with C and C++ API. Python bindings Available Python bindings are: Pack- Description Links age h5py The h5py package is a Pythonic interface to the HDF5 binary data format. recipe, packages mpi4py This package provides Python bindings for the Message Passing Interface (MPI) recipe, standard. packages petsc4py PETSc for Python recipe, packages Package details Integer and real types Numerical algebra libraries make use of 32 bits index integers and 64 bits floating point numbers. Note: OpenBLAS is provided by continuum analytics. The package openblas-0.2.14-3 contains the file in- clude/openblas_config.h. This file does not defined OPENBLAS_USE64BITINT, so blasint is a int (32 bits). C++ standard library on OSX On OSX, two implementations of the C++ standard library are available: • The GNU implementation: libstdc++.dylib • The Clang implementation: libc++.dylib The ABI of these two libraries are incompatibles. All packages in the INRIA Paris-Rocquencourt SED Conda channel are built with the Clang implementation. 1.3. Package details 9 INRIA Paris/Rocquencourt Conda packages Documentation, Release 1.0.0 Note: A Python script (for example), may import a C++ extension linked with libc++.dylib and another C++ exten- sion linked with libstdc++.dylib without problems, as long as the two extensions do not directly exchange C++ data structures. glibc and gcc versions Packages are build on Centos 6.6, using glibc version 2.12, and gcc version 4.4.7. As a consequence, packages will work on all GNU/Linux distribution providing glibc version 2.12 or greater. Taken from distrowatch, here are some examples: distribution glibc gcc centos 5.11 2.5 4.1.2 centos 6.6 2.12 4.4.7 centos 7.0 2.17 4.8.3 ubuntu 12.04 2.15 4.6.3 ubuntu 14.04 2.19 4.8.2 debian 7 2.13 4.7.2 fedora 17 2.15 4.7.0 suse 12.1 2.12.1 4.6.2 Instead of using the system gcc, we may in the future use the gcc conda package, which provide a recent gcc version, linked with an old glibc version. But currently (5 October, 2015), gcc Conda package (4.8.5-3, in asmeurer channel), has too much problems: • https://groups.google.com/a/continuum.io/forum/#!search/froger/conda/Lb_Vnz6O85s/20dsvlvlBwAJ • https://github.com/conda/conda-recipes/issues/435 • https://github.com/conda/conda-recipes/issues/431
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