Sandbox Evaluation of Entries in PhysioNet/Computing in Cardiology Challenges

This page describes how entries in PhysioNet/CinC Challenges are evaluated and scored automatically. The method described below has been developed to support the 2017 Challenge.

This page also includes instructions for setting up a replica of the Challenge test environment, which may be useful for debugging Challenge entries.

For previous Challenge test environments, see the archived documentation:

Structure of a 2017 Challenge entry

A Challenge entry must be uploaded in the form of a zip archive (entry.zip) or a gzipped tar archive (entry.tar.gz.) The entry must contain all source code for your algorithm, as well as any data files required to run it (e.g., numerical models that are derived from the training databases.) In addition, the following files must be included in the top-level directory of the entry:

AUTHORS.txt
A text file listing the authors of the entry (individuals who contributed to the design or implementation of the algorithm), and their affiliations.
LICENSE.txt
A text file listing the terms for distribution. Official Challenge entries must be distributable under a license approved by the Open Source Initiative.
dependencies.txt (example)
A text file containing the names of additional packages that must be installed prior to compiling and running the entry. Lines beginning with ‘#’ are treated as comments. Each non-comment line must contain either the name of a package (e.g., python3), or the name of a package followed by ‘=’ and a version number (e.g., wfdb = 10.5.25~pre2-0~pn1.) The version number is required if the package comes from the Challenge repository.
setup.sh (example)
A shell script to be invoked by /bin/bash. This script is run once, during stage 1 (see below), to compile the entry.
next.sh (example)
A shell script to be invoked by /bin/bash. This script is run once for each record in the database, during stages 2 and 3. The name of the record is passed as the first command-line argument (‘$1’), and the script must write its result to answers.txt.
answers.txt (example)
A text file giving the expected output for each record in the “validation” set. During stage 2, this will be compared against the result of running next.sh.

An entry may also contain a file DRYRUN, which causes evaluation to stop after the end of stage 2.

Evaluation details

All of the processing needed to check, evaluate, and score challenge entries is performed on dedicated 64-bit Linux servers, under control of the supervisor script (evaluate). Each server runs several virtual machines (VMs) using qemu and kvm hardware virtualization.

Newly uploaded entries are initially placed into a queue. The oldest entry in the queue is loaded into an idle VM as soon as one is available, and stage 1 processing begins.

Stage 1 (prep): The entry is checked to be certain that it contains all of the components required by the rules of the challenge. If so, the packages specified by dependencies.txt are installed. Finally, the entry's setup.sh script is run. The evaluation ends if stage 1 does not succeed for any of these reasons:

If stage 1 ends early, the diagnostic output of setup.sh (its standard output and standard error output) is reported in the last case, or an appropriate error message is reported otherwise. If setup.sh exits successfully (with zero status), the entry is queued for stage 2 processing.

Stage 2 (quiz): The validation data set is copied into the VM. The entry's next.sh script is run for each record in this set. The evaluation ends if stage 2 does not succeed for any of these reasons:

If stage 2 ends early, the diagnostic output of next.sh (its standard output and standard error output) is reported in the first case, or an appropriate error message is reported otherwise. If all of the training set records are processed successfully, and all results match the expected results, and the entry does not include a DRYRUN file (which forces a premature exit after completion of stage 2), the entry is queued for stage 3 processing.

In order to be fair to all competitors, the limits on entry running time are measured in CPU instructions rather than in seconds (since the exact running time will depend on many factors that are impractical to control, such as hard disk access speeds.) On a GNU/Linux system, you can measure the number of instructions used by your program by running the command perf stat -e instructions:u ./next.sh A00001.

Stage 3 (exam): The test data set is copied into the VM. The entry's next.sh script is run once with each test record as input. Unlike stage 2, however, errors do not cause premature termination of stage 3, and next.sh's diagnostic output is not reported (to prevent leakage of information about the test data). The numbers of failures and timeouts, if any, are reported in lieu of detailed diagnostics. The results are collected and transmitted from the VM to the dedicated host for stage 4 processing.

Stage 4 (score): The collected results are compared with the Challenge's reference results to determine performance statistics and scores, which are reported to the user.

Replicating the Challenge test environment

In order to test your entry, it is not necessary to replicate the Challenge test hardware, but it may be helpful to compare it with your hardware to estimate your entry's run time. The dedicated Challenge servers have two quad-core 2.6 GHz AMD Opteron 6212 CPUs and 96 GB of RAM.

Each virtual machine is configured with a single-core amd64 CPU, 2 GB of RAM, a 2 GB read-write /home partition, and a 500 MB read-write /tmp partition. The root filesystem is an aufs filesystem with 5 GB of space for installing packages. A virtual CD-ROM drive and serial port are used for transferring data to and from the guest system. A virtual Ethernet interface is provided only when running MATLAB entries, and only allows connections to the designated MATLAB license server.

To replicate the Challenge test software environment available within the VMs, install 64-bit Debian 8 (jessie), then install these additional packages:

sudo apt-get install devscripts build-essential zip

(See the complete list of packages included in the base system as of Tuesday, 28 March 2017 at 21:26 CEST.)

In addition, enable the PhysioNet Challenge package repository:

sudo tee -a /etc/apt/sources.list <<EOF
deb http://physionet.org/physiotools/debian/ jessie-challenge-2017 main contrib non-free
deb-src http://physionet.org/physiotools/debian/ jessie-challenge-2017 main contrib non-free
EOF

gpg --recv-keys BDE026E5901D1BE2
gpg --export BDE026E5901D1BE2 | sudo apt-key add -
sudo apt-get update

You may install and use the test software environment on a spare computer if you wish, or in a VM using whatever VM technology you prefer on your favorite host OS. On the Challenge servers, we use qemu-kvm, hosted on Debian GNU/Linux.