11-14 April 2011
Radisson Blu Hotel Lietuva, Vilnius
Europe/Vilnius timezone

Workflow processing with gLite L&B: medical imaging case study

11 Apr 2011, 09:00
Radisson Blu Hotel Lietuva, Vilnius

Radisson Blu Hotel Lietuva, Vilnius

Konstitucijos pr. 20 LT - 09308 Vilnius, Lithuania
Poster Poster Posters


Aleš Křenek (CESNET)


We developed extensions to the L&B service which allow tracking execution of a
generic workflow, described in terms of UML activity diagram/XMI document. The
workflow can consist of nodes representing both jobs run on the grid and user
actions. The implementation is fully neutral wrt. the actual engine
responsible for execution of the workflow; according to the L&B design, L&B is
responsible for tracking the execution, not its run, it is not yet another
workflow engine.

The development was done on demand of the medical imaging group, fulfilling its
immediate needs. However, we keep the design of the middleware layer to be
reasonably generic and we plan to offer it to cover other similar requirements.

The implementation is being tested on NGI CZ resources.


The gLite Logging and Bookkeeping service (L&B) was designed to track user jobs
on the grid. The tracking is decoupled from the services that are responsible
for the actual job execution (WMS and CE in particular). Besides simple jobs
L&B supports WMS DAGs (directed acyclic graphs) and job collections.

In this work we extend the set to more generic workflows which may contain,
besides automatically executed jobs, also user actions. We demonstrate
feasibility of the extensions on a specific usecase in the medical imaging
application area.

Description of the work

First, the L&B is extended to store a template of the user's workflow. The
template is a UML activity diagram, expressed in terms of XMI document, having
uniquely identified nodes (executed actions) and edges (dependencies).

When a workflow instance is ready to be run, it is registered in L&B, bound to a
specific template there, and assigned a unique job (workflow) identifier.

Workflow nodes are instantiated by individual jobs which declare themselves
that they belong to a particular workflow id, and they implement its specific
node. Technically this is done by a new L&B event which is logged upon the job
submission. The necessary information, id of the workflow node in particular,
is extracted from the job description (Torque submit file or gLite JDL) where
it must be provided by the user. For actions taken by the user, the
information is provided explicitly, typically in a single call to an L&B API
wrapper which tells L&B "I've done this".

On the other hand, queries to L&B are used to find out which actual jobs
represent nodes of a workflow instance and what is their state (not started
yet, running, done, essentially). Moreover, the L&B state computation logic is
extended to understand the workflow definition and to be able to identify
"pending" workflow nodes, i.e. their prerequisites are satisfied but the nodes
have not been instantiated yet.

Finally, through the standard L&B user tags, both the whole workflow and its
nodes can be annotated, and the annotations used to narrow down further

By design, L&B does not replace a workflow engine, which is left with the
responsibility to start runnable jobs, deal with eventual job failures etc.
However, similarly to gLite WMS, the workflow engine can rely on the
information retrieved from L&B. In the usecase described bellow trivial job
dependencies are handled by the Torque batch system, while the user-assisted
operations are based on L&B information fully.


The described development was driven by the demand of the group providing the
recognised collection of pathology images http://atlases.muni.cz. The workflow
starts with acquiring a gigapixel-sized raw image from a microscope. The image
is split up into approx. 30,000 tiles which are processed individually (colour
correction, sharping etc.) as parallel jobs. Then the tiles are composed back
into a huge image. After this phase the user's expert assessment is required
to provide further parameters of additional colour corrections, cropping, and
geometric transformation. Those operations are applied on the huge image, and
it can be repeated several times with different parameter settings eventually.
Besides the intentional tuning some of the operations may fail and require
re-run with different parameters. Finally, the image is tiled again and scaled
down for presentation at the web site.

The group runs the image processing workflows on NGI CZ resources. Recently
they extended their equipment, they are able to produce significantly higher
number of raw images so that their production starts overlapping with the
processing, and the entire process becomes difficult to manage manually. This
was the primary motivation, the L&B, which tracks the users jobs anyway, gets
extended to become the user's experiment "logbook" replacing tedious and error
prone manual work. In the current prototype the user is given a graphical tool
which queries L&B and displays currently active workflows, highlighting those
where user action is required. The actiond themselves are done with the original
tools then. Even this loose integration improves the user's work significantly
because of fully offloading the need to keep track of dozens of active

On the other hand, the extensions to L&B were designed in a reasonably generic
way so that those should be reusable in other application scenarios as well.

Primary authors

Aleš Křenek (CESNET) David Veselý (Masaryk University) Lukáš Hejtmánek (Masaryk University)

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