ReproZip is a general tool for Linux distributions that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.
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README.rst

ReproZip

Note
This is the very first version of ReproZip. The newest one is available at https://www.reprozip.org/

ReproZip is a general tool for Linux distributions that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science. It tracks operating system calls and creates a package that contains all the binaries, files and dependencies required to run a given command on the author's computational environment E. ReproZip also generates a workflow specification for the experiment, which can be used to help reviewers to explore and verify the experiment. A reviewer can extract the files and workflow on another environment E' (e.g., the reviewer's desktop), without interfering with any program or dependency already installed on E'.

Limitations:

  • Environments E and E' need to have similar hardware architecture and Linux kernel.
  • An experiment cannot be reproduced if its executables and scripts use hard-coded absolute paths.
  • Repeatability of non-deterministic processes is not guaranteed.

Publications:

The source code is available on GitHub:

git clone https://github.com/fchirigati/reprozip.git
cd reprozip
python setup.py install

For more information, to report bugs and to give some feedback, contact Fernando Chirigati at fchirigati [at] nyu [dot] edu.

How To Install ReproZip

For installation instructions, please refer to INSTALL.txt.

How To Use ReproZip

Packing

Suppose your experiment is executed by the following command line:

./experiment input_file.txt -i 150 -o output_file.txt

First, issue the following command:

reprozip --pack -e -c "./experiment input_file.txt -i 150 -o output_file.txt"

This will allow ReproZip to transparently gather all the necessary information. Argument -e means that the experiment should be executed prior to the creation of the package -- in case you have already executed it before with ReproZip, ReproZip may gather information stored in MongoDB rather than executing the experiment again.

This step will create a configuration file, named rep.config, in your working directory. Use it to exclude files that you do not want to be packed. You may also use Unix wildcards to exclude them (at the end of the configuration file, under [exclude]).

Next, use the following command (in the same working directory) to finally pack the experiment:

reprozip --pack -g --name my_experiment

This command will create a package (my_experiment.tar.gz) in your working directory.

For more information about available ReproZip arguments, please use:

reprozip --help

Unpacking

Unpacking is quite simple. Just use:

reprozip --exp my_experiment.tar.gz

This will unpack the experiment in a directory named my_experiment in the current working directory. To extract the experiment in another directory, just use the argument --wdir with the desired path.

Reproducing the Experiment

To reproduce the experiment, just use:

./my_experiment/rep.exec

Using VisTrails for Reproducibility

Alternatively, you can use the VisTrails workflow to reproduce, vary and explore the results. You can skip steps 1, 2 and 3 if you had VisTrails already installed when unpacking the experiment.

  1. Download VisTrails at http://www.vistrails.org/index.php/Downloads and install it;
  2. Create a directory named CLTools under $HOME/.vistrails;
  3. Copy the clt file under my_experiment/vistrails/cltools to $HOME/.vistrails/CLTools;
  4. Open VisTrails, and go to File -- Import -- Workflow...;
  5. Choose the xml file under my_experiment/vistrails;
  6. Play with the workflow!

For more information about VisTrails, please visit http://www.vistrails.org

Using ReproZip with Virtual Machines

One of the limitations of ReproZip is that the original environment E and the environment E' where the experiment will be reproduced need to be compatible, i.e., they need to have a similar hardware architecture and Linux kernel. Of course, this is not often the case. In these situations, you may create a virtual machine with an environment similar to E, use ReproZip to unpack your experiment in the virtual machine, and send this virtual machine to whoever wants to reproduce your experiment. Voila! ReproZip just made it easier for you to port your experiment to a virtual machine!

Information about MongoDB

Schema of Database

The schema used to store the provenance data is the same one - with a few additions - used by the Burrito System (http://www.pgbovine.net/burrito.html), developed by Philip Guo. The data about the processes of an experiment is stored under a database named reprozip_db, and a collection named process_trace. The schema is the following:

{
    "_id" : *unique id of document*,
    "pid" : *process id*,
    "ppid" : *id of parent process*,
    "creation_time" : *creation time of process*,
    "exit_time" : *exit time of process*,
    "uid" : *user id*,
    "other_uids" : *other user ids*,
    "phases" : *list of the phases of the process*,
    "most_recent_event_timestamp" : *the time of the most recent event in the process*,
    "exit_code" : *exit code of the process*,
    "exited" : *a boolean that indicates whether the process has exited*
}

A phase of a process has the following schema:

{
    "start_time" : *start time of the phase*,
    "name" : *name of program executed*,
    "execve_filename" : *filename of program executed*,
    "execve_argv" : *command line arguments*,
    "execve_pwd" : *working directory*,
    "execve_env" : *environment variables*,
    "files_read" : *list of files that were read*,
    "files_written" : *list of files that were written*,
    "files_renamed" : *list of files that were renamed*,
    "symlinks" : *list of symbolic links, together with their corresponding targets*,
    "directories" : *list of accessed directories*
}

You may use this schema information to query the process data in MongoDB, in case you find it useful. The configuration parameters to start the MongoDB server can be found at $HOME/.reprozip/config.

Configuration Parameters

ReproZip uses MongoDB in the packing step to keep information about packed experiments. There is no option to use ReproZip in the packing step without MongoDB.

In case you already have MongoDB installed, you may find it useful to change the default settings of the mongod instance that ReproZip initiates at the beginning of the packing step (note that ReproZip kills this instance at the end of its execution), so that it reflects your installation. ReproZip creates its own database to include all the data, so you do not need to worry about it overriding your data.

The default settings can be found at ReproZip's configuration file ($HOME/.reprozip/config). The parameters are:

  • on: indicates whether ReproZip should create its own mongod instance; set it to False in case you want to use a mongod instance that is already running;
  • port: specifies the port for the mongod to listen for client connections;
  • dbpath: specifies a directory for the mongod instance to store its data;
  • logpath: specifies a path for the log file;
  • quiet: indicates whether MongoDB should limit the amount of output; setting it to True keeps the output significantly smaller;
  • journaling: indicates whether journaling is enabled; the default is False.

ReproZip Team

  • Fernando Chirigati - contact him at fchirigati [at] nyu [dot] edu to report bugs, give feedback and make suggestions about ReproZip
  • Dennis Shasha
  • Juliana Freire

Acknowledgements

  • Jesse Lingeman
  • Lis Custodio
  • Tiago Etiene
  • Sinesio Pesco
  • Claudio Silva
  • VisTrails team