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setup_personal.md

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Setup for Personal Machines

In general, when following these instructions make sure that you satisfy the following:

  1. Old configuration is backed up, i.e., ~/.spack moved out of the way
  2. Spack is not sourced anywhere in the shell start-up scripts
  3. Use a new clone to avoid configuration changes in the old checkout

Prerequisites

Building software on MacOS

To install end-user software on MacOS, please defer to brew.

Before starting, please install XCode and brew and make sure that there is a working Python on your machine, preferably from XCode or another stable source. It is recommended to rebuild a Spack-based Python for utmost independence and to minimize potential build problems for binary Python libraries.

If issues arise to find stdio.h correctly building software outside the Spack stack, e.g., neuron, issue the following command if using a POSIX shell:

$ export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)

Or set it in fish:

$ set -x SDKROOT (xcrun --sdk macosx --show-sdk-path)

Then install a Fortran compiler, which Spack will pick up and use in conjunction with Apple's CLang:

$ brew install gcc

Building software on Ubuntu

Ubuntu / Debian have a habit of being somewhat special, patching upstream projects in unexpected ways. Consider yourself warned to not rely on system packages and defer to Spack-installed ones when needed.

First, ensure that the essential packages to building stuff are installed:

$ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
$ sudo apt update
$ sudo apt install build-essential gcc-11 g++-11 gfortran-11

If Python 3 is not your default, tell Ubuntu to use a newer one, e.g., Python 3.8 by setting the default python:

$ sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.8 1

To check that we are using Python 3 as python:

$ sudo update-alternatives --config python
There is only one alternative in link group python
(providing /usr/bin/python): /usr/bin/python3.8. Nothing to configure.

Spack Setup

Now clone our version of Spack and find compilers and external packages:

$ git clone -c feature.manyFiles=true https://github.com/BlueBrain/spack.git
$ . spack/share/spack/setup-env.sh
$ spack compiler find
$ spack external find

Additional Configuration

Remove Flawed External Packages

Use the following commands to remove software that may be too customized to use reliably:

$ spack config rm packages:hdf5
$ spack config rm packages:openmpi
$ spack config rm packages:python
$ spack config rm packages:sqlite

Tuning on MacOS

Edit the resulting externals, removing any references to brew from the system, the latter two as they are unfit to be used as full dependencies with Spack:

$ spack config edit packages

With this minimal setup, Spack should operate independent of the system and the brew installation.

Tuning on Ubuntu

You may want to purge older GCCs from ~/.spack/linux/compilers.yaml if Spack implies older GCC by default.