Linux tool enabling reproducible experiments (unpacker)
Project description
ReproZip is a tool aimed at scientists using Linux distributions, that simplifies the process of creating reproducible experiments from programs.
It uses the ptrace facilities of Linux to trace the processes and files that are part of the experiment and build a comprehensive provenance graph for the user to review.
Then, it can pack these files in a package to allow for easy reproducibility elsewhere, either by unpacking and running on a compatible machine or by creating a virtual machine through Vagrant.
http://vida-nyu.github.io/reprozip/
Quickstart
Packing
On the machine where the experiment is setup, install reprozip:
$ pip install reprozip
Then run your experiment under reprozip’s monitoring (simply prefix reprozip trace):
$ reprozip trace ./myexperiment -my --options inputs/somefile.csv other_file_here.bin
This leaves you with a .reprozip directory, in which you’ll find the config.yml configuration file. In it, you can edit the command-line and environment variables, and choose which files are to be packed.
If you are using one of the supported Linux distributions (currently Debian and Ubuntu), these files are organized by package, plus an other_files: section at the end. You can add or remove files, or choose not to include a package by changing packfiles: true to packfiles: false; this allows you to make a smaller packs, since reprounzip can get these files from the package manager easily (however versions might differ).
Once done editing .reprozip/config.yml, or if you left everything as-is, simply run the packer: (note that you should review the configuration to be sure not to include sensitive information)
$ reprozip pack my_experiment.rpz
Unpacking
$ pip install reprounzip # Installing the packages on the host machine $ reprounzip installpkgs my_experiment.rpz # Unpacking in a directory $ reprounzip directory my_experiment.rpz mydirectory $ mydirectory/script.sh # Building a chroot environment $ reprounzip chroot my_experiment.rpz mychroot $ sudo mychroot/script.sh # Building a virtual machine (requires Vagrant) $ pip install reprounzip-vagrant $ reprounzip vagrant --use-chroot my_experiment.rpz mytemplate $ cd mytemplate; vagrant up $ vagrant ssh vagrant@vm$ sh /vagrant/script.sh
Links and references
This package holds the unpacker components (and the ‘reprounzip’ command-line utility); see reprozip for the packer (which only works on Linux).
Github page: https://github.com/ViDA-NYU/reprozip
Bug tracker: https://github.com/ViDA-NYU/reprozip/issues
Contact us at reprozip-users@vgc.poly.edu
ReproZip is currently being developed at NYU. The team includes:
Fernando Chirigati
Rémi Rampin
Dennis Shasha
Juliana Freire
Publications:
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