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Welcome to the RADICAL-Cybertools Tutorial!
RADICAL-Cybertools provide interoperable access to compute and data resources, support task-level parallelism and support “custom workflows” that are very common and prevalent in usage. There are three tutorials: the first is on RADICAL-Pilot, the second on RepEx and the third on EnMD-Toolkit.
In turn, each RADICAL-Cybertools tutorial will have three parts:
- The first is the ability to work through previously created and existing user guide so as to develop a basic understanding of the tools and how these tools can help Molecular Science problems,
- The second will be to use specific examples created for the purpose of the workshop; these will be based upon the user guide but will require the participants to “scale” onto real supercomputers,
- Open ended exercises that will allow the participants to apply the tools and techniques learnt to their own scientific problems.
The first part of each workshop will be performed on laptop/local resources. However, in order to appreciate the power of the tools, the second and third part will be performed on systems that are capable of supporting multiple simulations concurrently.
Here is the schedule for Workshop 5.
Here is a link to a pre-workshop survey
Here is a [link to a post-workshop survey] (https://docs.google.com/a/santcroos.net/forms/d/1ZymVxwHnqD5gY2uqCLeHmnW-klnZ83M10RmSyYJepa8/viewform)
Part I: Introduction to RADICAL-Cybertools
- Slides Lecture Slides
- A. A brief overview of RADICAL-Pilot
- User Guide
- B. Exercises using RADICAL-Pilot
- C. Open Exercises using RADICAL-Pilot
Using the XSEDE endpoint
We will use
workflow.iu.xsede.org as access point to the XSEDE supercomputers (Stampede and Comet). The exercises will guide you in detail through the installation and configuration of RADICAL-Pilot -- but the quick procedure is:
- login to
workflow.iu.xsede.org, use you XSEDE Portal account username/password
- run the following commands
# source /opt/tutorials/radical-tutorial/rp-tut.sh # virtualenv --system-site-packages $HOME/ve # source $HOME/ve/bin/activate # pip install radical.pilot # radicalpilot-version # cd $HOME/ve/share/radical.pilot/examples/
The following URLs correspond to the main project websites. It may be helpful to visit these websites after the tutorial is over, for your reference.
- RADICAL-EnMD : http://github.com/radical-cybertools/radical.ensemblemd
- RADICAL-RepEx : https://github.com/radical-cybertools/radical.repex
- RADICAL-Pilot : http://github.com/radical-cybertools/radical.pilot
- RADICAL-SAGA : http://github.com/radical-cybertools/saga-python
- RADICAL-UTILS : http://github.com/radical-cybertools/radical.utils
- ExTASY : http://github.com/radical-cybertools/ExTASY