This document will walk you through compiling your own scientific python distribution from source,
without sudo, on a linux machine. The core numpy and scipy libraries will be linked against
Intel MKL for maximum performance.
This procedure has been tested with Rocks Cluster Linux 6.0 (Mamba) and CentOS 6.3.
| import numpy as np | |
| import scipy.special | |
| from scipy.misc import logsumexp | |
| def invpsi(y): | |
| """ | |
| Inverse digamma (psi) function. The digamma function is the | |
| derivative of the log gamma function. | |
| """ | |
| # Adapted from matlab code in PMTK (https://code.google.com/p/pmtk3), copyright |
| Sourcing python-remove-tests-dir-hook | |
| Sourcing python-catch-conflicts-hook.sh | |
| Sourcing python-remove-bin-bytecode-hook.sh | |
| Sourcing setuptools-build-hook | |
| Using setuptoolsBuildPhase | |
| Using setuptoolsShellHook | |
| Sourcing pip-install-hook | |
| Using pipInstallPhase | |
| Sourcing python-imports-check-hook.sh | |
| Using pythonImportsCheckPhase |
| @nix { "action": "setPhase", "phase": "unpackPhase" } | |
| unpacking sources | |
| unpacking source archive /nix/store/wwlnj2kmyrrcw1r1s3n51p6nia59xb2p-source | |
| source root is source | |
| @nix { "action": "setPhase", "phase": "patchPhase" } | |
| patching sources | |
| @nix { "action": "setPhase", "phase": "autoreconfPhase" } | |
| autoreconfPhase | |
| autoreconf: export WARNINGS= | |
| autoreconf: Entering directory '.' |
| Sourcing python-remove-tests-dir-hook | |
| Sourcing python-catch-conflicts-hook.sh | |
| Sourcing python-remove-bin-bytecode-hook.sh | |
| Sourcing setuptools-build-hook | |
| Using setuptoolsBuildPhase | |
| Using setuptoolsShellHook | |
| Sourcing pip-install-hook | |
| Using pipInstallPhase | |
| Sourcing python-imports-check-hook.sh | |
| Using pythonImportsCheckPhase |
| @nix { "action": "setPhase", "phase": "unpackPhase" } | |
| unpacking sources | |
| unpacking source archive /nix/store/nzdrhpb4s4zl8kk86fv45i3aflb9brkz-source | |
| source root is source | |
| @nix { "action": "setPhase", "phase": "patchPhase" } | |
| patching sources | |
| @nix { "action": "setPhase", "phase": "configurePhase" } | |
| configuring | |
| no configure script, doing nothing | |
| @nix { "action": "setPhase", "phase": "buildPhase" } |
| @nix { "action": "setPhase", "phase": "unpackPhase" } | |
| unpacking sources | |
| unpacking source archive /nix/store/bfpn2d2jylawzm1pm51can52i9crcjqc-source | |
| source root is source | |
| @nix { "action": "setPhase", "phase": "patchPhase" } | |
| patching sources | |
| @nix { "action": "setPhase", "phase": "autoreconfPhase" } | |
| autoreconfPhase | |
| autoreconf: export WARNINGS= | |
| autoreconf: Entering directory '.' |
| Sourcing python-remove-tests-dir-hook | |
| Sourcing python-catch-conflicts-hook.sh | |
| Sourcing python-remove-bin-bytecode-hook.sh | |
| Sourcing setuptools-build-hook | |
| Using setuptoolsBuildPhase | |
| Using setuptoolsShellHook | |
| Sourcing pip-install-hook | |
| Using pipInstallPhase | |
| Sourcing python-imports-check-hook.sh | |
| Using pythonImportsCheckPhase |
| @nix { "action": "setPhase", "phase": "unpackPhase" } | |
| unpacking sources | |
| unpacking source archive /nix/store/q6s0c0srva5h5jhn8pj1p8fjn8va05vk-source | |
| source root is source | |
| @nix { "action": "setPhase", "phase": "patchPhase" } | |
| patching sources | |
| @nix { "action": "setPhase", "phase": "configurePhase" } | |
| configuring | |
| @nix { "action": "setPhase", "phase": "buildPhase" } | |
| building |
| @nix { "action": "setPhase", "phase": "unpackPhase" } | |
| unpacking sources | |
| unpacking source archive /nix/store/q6s0c0srva5h5jhn8pj1p8fjn8va05vk-source | |
| source root is source | |
| @nix { "action": "setPhase", "phase": "patchPhase" } | |
| patching sources | |
| @nix { "action": "setPhase", "phase": "configurePhase" } | |
| configuring | |
| @nix { "action": "setPhase", "phase": "buildPhase" } | |
| building |