- Status: planned, active, completed
- Start Date: DD/MM/YY
- End Date: DD/MM/YY
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Short description of the FedCloud Use Case.
Use case 1
Using VMs prepared with Gromacs and some other software to run MD simulations for educational purpose, possibly on multi-core VMs. These VMs are currently run on the SARA cloud for a computer practical of University courses, see here.
Use case 2
Validating and improving biomolecular NMR structures using VirtualCing (VCing), a Virtual Machine (VM) equipped with a complex suite of ~25 programs.
A presentation of the current deployment at the Dutch National HPC Cloud is available here, and recently a paper has been published here.
The cloud usage framework is based on a pilot job mechanism making use of the ToPoS tool. Therefore, such a framework would naturally allow for execution of VCing tasks across multiple cloud providers. Do notice that the framework is independent on the cloud access interface: it would work also with simple grid jobs, as far as the user-defined (or VO manager defined) VCing VM is available at the grid site e.g. in a SE (or in the VO software area mounted by the WNs) and the grid job is allowed to start the VM. Technical details about its current implementation are available here.
Furthermore, a live demonstration about the deployment and use of VCing on the WNoDeS testbed of the INFN-CNAF computing centre has been shown at the EGI TF 2012 held in September.
VCing OS is Ubuntu 11.04 i386, and its image size has been recently shrinked to 8.1 GB in compressed qcow2 kvm format (from a 20 GB raw image). A demo version of the VCing image has been recently uploaded in the EGI marketplace and is freely available for demonstration shows.
1. Here below are the steps carried out to make the VCing demo image work with the WNoDeS framework for the network and debian/ubuntu:
- modifying the file /etc/network/interfaces as follows:
auto lo iface lo inet loopback auto eth0 allow-hotplug eth0 iface eth0 inet dhcp auto eth1 allow-hotplug eth1 iface eth1 inet dhcp
- deleting /etc/udev/rules.d/70-persistent-net.rules file
- removing the hostaname in the file /etc/hostname
Other Cloud frameworks of course can have their own contextualisation recipes.
2. From any machine having the Topos library add the tokens to the Topos server VCing demo area https://topos.grid.sara.nl/4.1/pools/vCingDemo
$ ./topos createTokensFromLinesInFile vCingDemo demo_token_list.txt
For testing purpose you can also try with one token by adding manually from the Topos web interface e.g. the following line:
refineEntryNrg 1iy6 9 http://nmr.cmbi.ru.nl/NRG-CING/data firstname.lastname@example.org:/mnt/data/D/NMR_REDO . . BY_CH23_BY_ENTRY CING 0 auto 0 0 1
3. You can start now as many as possible VCing instances on the federated cloud. Job payloads will be retrieved automatically by the VCing from the Topos server pool until all the tokens are processed. For demo show purposes you can check live the token list here and see that they get first locked and then disappear when processed. A graphical example of the final result can be shown by clicking here.
4. Output data are copied at the end of the processing from VCing to the NMR server nmr.cmbi.ru.nl hosted at CMBI:
- ssh traffic must be allowed from the VCing instance to the NMR server
- the cloud subnet address must be included in the /etc/firewall.conf of the NMR server
- a post-processing script does untar the zipped data output and makes it accessible through web e.g. from here
- File 1
- File 2